Mycobacterium microti, a member of the Mycobacterium tuberculosis complex, was originally described as the cause of tuberculosis in wild rodents. However, in the last few years, an increasing number of cases have been reported in wildlife (wild boars and badgers) and livestock (goat and cattle) in the frame of bovine tuberculosis (bTB) surveillance program, demonstrating the risk of interference with bTB diagnosis in France. In 2019, we detected four cattle infected with M.microti, from three different herds in three different distant regions. For all these cases, ante-mortem diagnosis by the skin test ) was positive. Confirmation of M.microti infection was based on molecular tests, i.e., specific real-time PCR and spoligotyping. These results highlight a non-negligible risk of interference in the bTB diagnosis system and raise concern about the reliability of diagnostic tests used for bTB surveillance. The use of highly specific tests, like the interferon gamma test (IFN-γ) employed in France or new synthetic specific tuberculins for skin testing could alternatively be used to accurately identify M.bovis (or Mycobacterium caprae) infection at ante-mortem examination. At post-mortem diagnosis, the use of specific molecular tools should be considered to accurately distinguish pathogens within the MTBC and to avoid misleading bTB diagnosis. Mycobacterium bovis is a transmissible notifiable disease whose prevalence in cattle herds in Europe has been increasing despite long lasting and costly control campaigns. In France—declared officially bTB free in 2001 by the EU—M. bovis infection is recurrent at a regional level in cattle and wildlife. The surveillance system in France is based on ante-mortem screening  and Interferon gamma test (IFN-γ)) in cattle [Bovine tuberculosis (bTB) mainly caused by M. bovis infection in badgers, wild boars and deer through a combination of passive and active surveillance protocols adapted to the estimated risk level in each area of the country.Since 2010, France has also implemented a surveillance system in wildlife called Sylvatub [Mycobacterium microti, a member of the Mycobacterium tuberculosis complex (MTBC), is the causative agent of tuberculosis in voles. However, infection by this bacterium was described in a large number of other animal species [M. microti infection cases was identified in France through Sylvatub [M. microti was also identified in farmed animals, i.e., a goat [ species . RecentlSylvatub , highligSylvatub . Moreove, a goat  and a co, a goat .M. microti infection in four cattle detected successively between December 2018 and July 2019 during bTB surveillance in three regions in France with different bTB epidemiological contexts . Bovine and avian purified protein derivative (PPD) were injected intradermally and separately in the mid-cervical region, after the measurement of skin-fold thickness at day 0 . In France, bovine and avian PPD are used at a concentration of 25,000 international units (IU)/mL. The 72 h skin-fold thickness at the avian PPD injection (A3) and bovine PPD (B3) injection site were measured. Differences of skin-fold thickness at injection points were interpreted according to Animals were examined because they presented non-negative skin test results and were slaughtered for diagnostic purposes. Tracheobronchial (TB), retropharyngeal (RP), mediastinal (MD) and mesenteric (MS) lymph nodes were sampled on each animal and submitted to the diagnostic tests implemented in France.M. bovis. Two to 5 g of sampled tissues were crushed with a 4% sulfuric acid solution to decontaminate the tissue. After 10 min, the acid was neutralized by adding a 6% sodium hydroxide solution. After decontamination, the supernatant was seeded on two different solid media: Löwenstein-Jensen and Coletsos. All seeded media were incubated at 37 °C +/- 3 °C for three months and examined every two weeks. Any isolated mycobacterial strain is submitted to the NRL for further characterization.Briefly, histopathology was based on Hematoxylin-Eosine and Ziehl Neelsen staining. Bacterial culture is performed following the protocol established by the French National Reference Laboratory (NRL) (NF U 47–104) for isolation of ®  on Bio-PLex 200/Luminex 200® were used to differentiate M. microti vs M. bovis infections. The presence or absence of the 43 spacer sequences contained in the DR locus is represented in a binary code of 43 entries. Spoligotypes are named according to an agreed international convention (www.mbovis.org) [DNA extraction was performed after mechanical lysis using an LSI MagVetTM Universal Isolation Kit  with a KingFisherTM Flex automate , following the manufacturer’s instructions. The LSI VetMAXTM MTBC Real-Time PCR kit , which targets IS6110  was usedM. microti spoligotype SB0118.In December 2018, in Côte d’Or , a beef cattle organic herd  of 128 cows was tested by SICCT. This herd has been bTB free since its establishment. Three cows had positive results, and 6 other cows of the same heifer lot gave doubtful results . All then = 48), the number of incident outbreaks has been decreasing every year. The spatial distribution of the outbreaks shows a decrease in the extent of the endemic area between 2015 and 2017. The number of incident outbreaks detected decreased during these three years in Côte-d’Or  [In this region, skin testing is performed annually. Since 2010, the year of the highest number of incident outbreaks in the department , 68 cattle from a bTB free since its establishment, were tested to the SICCT test. A four-year-old Limousine was doubtful (DB − DA = 3 mm and DB = 3.5 mm). No VL was detected at slaughterhouse inspection. A positive first line PCR result was obtained on the MD lymph node. Further characterization confirmed M. bovis outbreaks in the last years [This case is located in a “reinforced prophylaxis zone” (RPZ) established for the 2017–2018 prophylactic campaign. Risk areas are identified based on the outbreaks observed in cattle and wildlife, and are subject to reinforced annual screening [M. microti spoligotype SB0112 was confirmed by the NRL.In July 2019, in Ariège , a third case was identified during bTB prophylaxis. This cow belonging to a bTB free since its establishment, gave positive results at the SICCT (DB − DA = 9 mm and DB = 15 mm). The cow was a 5-year-old Gasconne. No VL were observed at slaughterhouse inspection. A positive first-line PCR result was obtained on RP and TB lymph nodes. M. microti infection in wildlife [M. microti cases have also been identified in cats, dogs and llamas [In this department, the rhythm of skin testing prophylaxis is triennial. The number of outbreaks identified in this department has been decreasing between 2010 (nine outbreaks) and 2015 (three outbreaks). No outbreak was detected between 2016 and 2018, and there were only two in 2019. However, this department is a hotspot of wildlife ,11. Inded llamas .The main results on these three cases are summed up in M. microti infection in cattle highlight a non-negligible risk of interference in the TB diagnosis system. M. microti has previously been isolated in skin test reactor cattle in the UK [M. microti infection in a goat and in a cow in a region of the Alps Mountains [M. microti infection in cattle may not be as rare as previously thought. All cattle were infected by M. microti presenting the same genotype circulating in the region and identified in wildlife: SB0118 in Nouvelle Aquitaine, and Burgundy, SB0112 in Occitanie [These consecutive cases of n the UK . In Franountains ,6, demonccitanie ,11.M. microti, and already currently used in the IFN-γ test employed in France [M. bovis (or Mycobacterium caprae) infection vs M. microti infection at ante-mortem examination as they are mainly based on the BCG and M. microti absence of ESAT6 and CFP10 antigens [These results raise concern about the reliability of diagnostic tests used for bTB surveillance. The use of highly specific ante-mortem tests based on specific antigens such as ESAT6 and CFP10, which are absent in n France , could bantigens .M. microti bacilli was quite important. The Ct values we observed in PCR, i.e., 27–34, are very similar to those found in M. bovis infected animals and confirmed by bacteriology in our lab. This corresponds roughly to 104–102 CFU/g of infected tissue . Besides, the immunological response observed at skin testing were important, which could be a response to the bacillus proliferation as if real infection were taking place in the animal. Without molecular diagnosis, as almost systematically for M. microti infections, this bacillus could not have been detected and identified [M. microti are those found in the same regions beforehand, highlighting the strong clonality of this MTBC member which is the same phenomenon that we also observe for M. bovis in France [Even though no visible lesions were detected for these cases, the load of entified ,15,16,17n France .M. microti exposition and infection remains unknown. It could either be by direct contact of infected rodents in the barns or by indirect contact through consumption of contaminated cattle pastures, food or water sources.The source of cattle M. bovis and by M. microti are exclusive individually ,


The HANPP was 80 g C/m2/yr, which represented 51% of the potential net primary production (NPPpot), and the HANPP efficiency was 70% in this region. (2) The areas with high HANPP values mainly occurred in northern Xinjiang and northwest of the Tianshan Mountains, while areas with low HANPP values mainly occurred in southern Xinjiang and southwest of the Tianshan Mountains. (3) Interannual variations in HANPP and NPPpot were significantly positively correlated (P<0.01). Interannual variations in HANPP efficiency and grazing intensity were negatively correlated (P<0.01). These results can help identify the complex impacts of human activities on grassland ecosystems and provide basic data for grassland management.The human appropriation of net primary production (HANPP) was developed to estimate the intensity of human activities in natural ecosystems, which is still unclear in the Xinjiang grasslands. Using the Biome-Biogeochemical Cycle (Biome-BGC) grazing model in combination with field data, we assessed the HANPP and explored its spatiotemporal patterns in the Xinjiang grasslands. Our results showed that (1) the HANPP increased from 38 g C/m Humans have extensively altered global ecosystems ,2. ComplThe HANPP indicator framework has been applied within empirical studies at various spatial and temporal scales. Global estimates of the HANPP have shown an increasing correlation with socioeconomic development, with a global HANPP of 25–30% calculated over the last several decades ,12–14. SXinjiang is located in Northwest China, an arid region with widely distributed grassland ecosystems. The grassland area accounts for 34% of the total land area in Xinjiang, and grazing is the main anthropogenic activity in the local grasslands. Due to the arid climate, the grassland ecosystem in Xinjiang is extremely fragile and generally more sensitive to human activity . In addipot) and total actual net primary production (NPPact) in grazed grassland; then, HANPP can be estimated. We focused on three objectives: (1) analyze the interannual variations in the HANPP, (2) explore the spatial patterns of the HANPP, and (3) reveal the relationships between the subcomponents of the NPP and grazing intensity in the Xinjiang grasslands from 1979 to 2012.In this study, the HANPP in the Xinjiang grasslands was estimated using the Biome-Biogeochemical Cycle (Biome-BGC) grazing model in combination with large amounts of field data. This model can effectively estimate total potential net primary production ) is the carbon consumed by domestic animals (NPP harvest) [e is the grazing efficiency of the domestic livestock (ha/d per sheep unit) which means grazing area in one day per sheep unit, Sr is the grazing intensity (sheep/ha); Cleaf is the C in the leaf biomass (g C/m2); (Cleaf)U is the residual aboveground Cleaf that is unavailable to domestic livestock (g C/m2); and Dx is the consumption rate of the domestic livestock based on satiation (g C/(d.sheep)). According to Luo et al. [leaf)U is 6.75 g C/m2 [x is 2.4 kg C/(d.sheep). In this study, HANPP is calculated based on Haberl et al. [act is the total NPP in grazed conditions (g C/m2) and NPPpot is the total NPP in ungrazed conditions (g C/m2) (Dr = 0). In this study, according to the HANPP efficiency definition by Fetzel et al. [Where C'harvest) .Dr=GeSro et al. , the gra5 g C/m2 ,34, and l et al. , the HANA high HANPP efficiency indicates a high ratio of consumption by domestic livestock to the total HANPP and the bulk of the appropriated biomass that enters the socioecological system .In this study, the required data included the model input data and validated data. The model input data included grazing data, meteorological data, and other auxiliary data. The model-validated data included the observed NPP data. Grasslands in Xinjiang are public spaces open to everyone; therefore, special permission was not required for access.http://www.fao.org/docrep/010/a1259e/a1259e00.htm) by converting the raster data to ASCII text using the R program. To ensure a high degree of data precision, these grazing data were corrected in accordance with the statistics from the Xinjiang yearbook [http://www.chinaforage.com/standard/zaixuliang.htm). We converted all livestock into sheep units according to these standards.Grazing data at the regional scale were derived from the Food and Agriculture Organization of the United Nations (FAO) (yearbook . These ghttp://westdc.westgis.ac.cn/data/7a35329c-c53f-4267-aa07-e0037d913a-21) by converting NetCDF data to ASCII text using the R program. These data sets can be used for ecological modeling. The meteorological data at the model validation points were obtained through actual observations.The meteorological data included the daily maximum and minimum air temperatures, daily average air temperature, humidity, incident solar radiation, precipitation and day length. These data at the regional scale were derived from the China Meteorological Forcing Data set (https://www.worldclim.org). The soil data included sand/silt/clay percentages and the effective soil depth. These data were derived from the Harmonized World Soil Database (HWSD) (http://westdc.westgis.ac.cn/data/611f7d50-b419-4d14-b4dd-4a944b141-175). The soil and elevation data at the model validation points were obtained through field investigations.In this study, C3 grass (the default in the model) was used to determine the ecophysiological parameters, and some key parameters, including the yearday to start new growth, yearday to end litterfall, new fine root C:new leaf C and average specific leaf area of the canopy, were corrected according to previous studies in the Xinjiang grasslands ,32. The The model validation data were collected from both field observations and previous publications by Han et al. . There w2 = 0.94) and ungrazed (R2 = 0.87) conditions  in the Xinjiang grasslands. The HANPP increased from 38 g C/m2/yr in 1979 to 88 g C/m2/yr in 2012, with an average annual increase of 1.47%. From 1979 to 2005, with increased grazing intensity, the HANPP fluctuated but increased from 38 to 126 g C/m2/yr, with an average annual increase of 3.26 g C/m2/yr. A similar trend was observed for Dr, which increased slowly from 1979 to 2005. From 2005 to 2010, the grazing intensity decreased remarkably, and the HANPP noticeably decreased, with an average annual decrease of 3.50 g C/m2. In general, with the increase in grazing intensity, the difference between NPPpot and NPPact increased.pot in the Xinjiang grasslands from 1979 to 2012. The HANPP efficiency showed frequent fluctuations and an average annual decrease of 0.74% from 1979 to 2012. In general, Dr was the major contributor to the HANPP in the Xinjiang grasslands from 1979 to 2012. HANPP%NPPpot generally showed an increase from 25% to 60%, and the average annual increase was 1.03% from 1979 to 2012. From 1979 to 2005, the changes in HANPP efficiency and HANPP%NPPpot generally showed opposite trends with the increase in grazing intensity.2/yr, which accounted for 51% of the NPPpot in the Xinjiang grasslands.pot from 1979 to 2012 was 0.591 (P<0.01); both correlations were significant according to Pearson's correlation analysis. The correlation coefficient of the interannual variations in the HANPP and HANPP efficiency was -0.655 (P<0.01), indicating a significant negative correlation according to Pearson's correlation analysis. The NPPact and HANPP efficiency were both negatively correlated with grazing intensity, and the correlation coefficients were -0.395 and -0.212, respectively  and grazing management in the Xinjiang grasslands. The high HANPP values mainly occurred in northern Xinjiang and northwest of the Tianshan Mountains due to the high grazing intensity and good plant growth in these regions. Low HANPP values mainly occurred in southern Xinjiang and southwest of the Tianshan Mountains due to low grazing intensity and poor plant growth. Negative HANPP values occurred in some regions, indicating that moderate grazing promoted plant growth in these regions. This research provides a better understanding of the spatiotemporal patterns of the HANPP in the Xinjiang grasslands and offers a more detailed and reliable theoretical reference to formulate reasonable grazing management in different regions.The Biome-BGC grazing model was used in combination with field data to estimate the HANPP and explore its spatiotemporal patterns in the Xinjiang grasslands. Our results showed that HANPP generally increased from 1979 to 2012 due to increased grazing intensity in the Xinjiang grasslands. The HANPP was 80 g C/m


In this work, the processes of photodissociation of some diatomic molecular ions are investigated. The partial photodissociation cross-sections for the individual rovibrational states of the diatomic molecular ions, which involves alkali metals, as well as corresponding data on molecular species and molecular state characterizations, are calculated. Also, the average cross-section and the corresponding spectral absorption rate coefficients for those small molecules are presented in tabulated form as a function of wavelengths and temperatures. The presented results can be of interest for laboratory plasmas as well as for the research of chemistry of different stellar objects with various astrophysical plasmas. Advances in the research of ultra-low-temperature gases have prompted a new interest in alkali–dimer cations . Recent NaH+ in , Li2+ an Na2+ in  and for in [+ in . These dFrom ,9,10 andMost alkali hydride ionic and neutral molecules are very useful in understanding the formation and the evolution of the Molecular Universe . Even thM and M is an atom whose ionization potential is less than the corresponding value for atom X. In this paper, we will focus on the investigation of photodestruction of the following species: We determine theoretically calculated partial photodissociation cross-sections for the individual rovibrational states of the diatomic molecular ions Also, the average cross-section and the corresponding spectral absorption rate coefficients for the photodissociation of the mentioned molecular ions are obtained for a wide region of wavelengths and temperatures. The presented results here are ready for further use with a particular emphasis on the applications for astro-plasma research and low-temperature laboratory plasma research ,25,26,27The paper is structured as follows. In The partial photodissociation cross-sections for the individual rovibrational states of the diatomic molecular ions which involve alkali metals are calculated. Also, the average cross-section and the corresponding spectral absorption rate coefficients for those small molecules T, which are relevant for modeling laboratory [In boratory  and astrboratory ,11,28. TThe obvious qualitative difference in the photodissociation cross-section behavior shown in The behavior of molecular-ion photodissociation rate coefficient Equation , is grapTo prepare easier and more satisfying usage of calculated data in modeling as well as in explanation of experimental results in laboratories, we give a simple fitting formula for the photodissociation rate coefficients as a second-degree polynomial (logarithmic) based on a least-square method:In Also, we give table in online material with the data of the selected fits of the Equation  to the pThe calculated rate coefficient see  for the es of Io ,31. One The additional examples i.e., the figures for the moderate-density and high-density models of Io’s atmosphere can be found in https://www.ivoa.net/documents) compatible format [We prepared data in Virtual Observatory (VO)  fThe rate coefficients and cross-sections are acquired using a quantum mechanical method where the photodissociation process is treated as outcome of radiative transitions between the ground and the first excited adiabatic electronic state of the molecular-ion . The trJ and v, are given in accordance with [In accordance with the dipole approximation the partial cross-sections nce with ,47 by exgiven in . Figure In the general case mean thermal photodissociation cross-section can be expressed as in ,48 by thσ=∑Jed as in ,47.Using Equation  the photK=σ, NThis enables further calculation of the spectral absorption coefficients during the process of applying an atmosphere model with the given plasma parameters or e.g., plasma composition in laboratory investigation. The bound-free absorption process  i.e., pree e.g., ). It canEquation  and the Equation . Corresp=σNM+=KNWe have calculated the average cross-section for the photodissociation processes and the corresponding spectral rate coefficient of the diatomic molecular ions


Low grade gliomas are the most frequent brain tumors in children and encompass a spectrum of histologic entities which are currently assigned World Health Organisation grades I and II. They differ substantially from their adult counterparts in both their underlying genetic alterations and in the infrequency with which they transform to higher grade tumors. Nonetheless, children with low grade glioma are a therapeutic challenge due to the heterogeneity in their clinical behavior – in particular, those with incomplete surgical resection often suffer repeat progressions with resultant morbidity and, in some cases, mortality. The identification of up-regulation of the RAS–mitogen-activated protein kinase (RAS/MAPK) pathway as a near universal feature of these tumors has led to the development of targeted therapeutics aimed at improving responses while mitigating patient morbidity. Here, we review how molecular information can help to further define the entities which fall under the umbrella of pediatric-type low-grade glioma. In doing so we discuss the specific molecular drivers of pediatric low grade glioma and how to effectively test for them, review the newest therapeutic agents and their utility in treating this disease, and propose a risk-based stratification system that considers both clinical and molecular parameters to aid clinicians in making treatment decisions. OfManagement of pLGG is intimately related to surgical resection, and complete resection remains the most favorable predictor of patient outcome . Often, In the last decade, significant molecular data has emerged to suggest that pLGG near universally up-regulate the RAS-mitogen-activated protein kinase (RAS/MAPK) pathway , 229. ThpLGG form a heterogeneous group of neoplasms that encompass tumors of primarily glial histology, including astrocytic and/or oligodendroglial, and tumors of mixed neuronal-glial morphology. These tumors are considered grades I and II according to the current WHO classification where they are distinguished from high grade glioma on the basis of specific morphologic features or, in the case of diffuse glioma, based on the absence of necrosis, mitoses and microvascular proliferation , 199. HiIn many cases the different histologic entities are readily distinguished, however cases of overlapping morphology are well documented. These include, for example, reports of histological overlap between pleomorphic xanthoastrocytoma and ganglioglioma , 62, 208IDH1 mutations, in addition to 1p/19q co-deletion for the latter. Tumors with the morphology of oligodendroglioma or diffuse astrocytoma in the pediatric age group often do not have IDH1 mutations and/or 1p/19q co-deletion and are therefore considered oligodendroglioma, NEC or, of even greater concern, diffuse astrocytoma, IDH-wildtype. The latter raising concern for molecular glioblastoma (GBM). Both of these diagnoses may lead to conventional adult diffuse glioma treatments involving cytotoxic chemotherapy and radiation, particularly in the adolescent and young adult age group. However, in IDH1 wild-type cases, pediatric oligodendrogliomas most frequently harbor alterations in FGFR1 including TKD-duplications or SNVs or BRAF p.V600E  or BRAF p.V600E. IDH1 wild-type diffuse astrocytoma most frequently harbor BRAF p.V600E mutations, accounting for ~40% of cases  is the most common inheritable tumor predisposition syndrome worldwide and is associated with a wide range of clinical manifestations including skin pigmentation abnormalities, learning disabilities, seizures, and vasculopathies , 19. NF1ator RAS , 89, 177ator RAS , 218. NFator RAS , 159. Hoator RAS .TP53, CDKN2A and ATRX. Therefore, obtaining a biopsy from, at minimum, patients deemed higher risk, may prove valuable in identifying patients that require refined and/or novel treatments and distinguishing them from NF1-HGG, particularly in adults.Despite their benign course, NF1-pLGG arising in younger children (<2 years) and/or outside of the optic pathway are recognized as being at a higher risk of progression and/or death . HistoriBRAF gene , trametinib (NCT03363217), cobimetinib (NCT02639546), and binimetinib (NCT02285439) are at various stages of clinical testing. For selumetinib, both phase I and II trials have been completed [For pLGG that are not suitable for type I BRAF inhibitors  for treatment of malignant glioma harboring FGFR-TACC fusions [Due to its functional importance and frequent implications in cancer, multiple small molecular inhibitors of  fusions  and seve fusions . ResultsALK, ROS1 and NTRK are relatively rare in pLGG. Conveniently, alterations in these genes are common in adult malignancies including lung and colorectal cancer and as such, targeted agents with federal approval have already been developed and tested. These include Crizotinib (NCT00939770) [Alterations in 0939770) , ceritin0939770) , and cab0939770) , as well0939770) , and lar0939770) , 194, th0939770) . In pedi0939770) , 53, 120The importance of molecular testing in tumor diagnostics is increasingly recognised and became formalised for brain tumors in the most recent WHO classification . As we gKIAA1549-BRAF fusion, and arising in a child between 3-12 years would typically be viewed as low risk and a "watch and wait" strategy may be employed, followed by less aggressive therapies if the tumor were to progress. In contrast, a tumor in an unfavorable location or highly disseminated with high risk molecular features will require close clinical follow-up and a more aggressive therapeutic approach  aims to match actionable mutations to 9 investigational therapies, providing a glimpse into the future of pLGG treatment. In this context it is important to be aware of which methods are available to be used that are not reliant on expensive NGS-based technologies, and here we provide a testing pipeline to aid in testing decisions. Importantly, molecular stratification is only one factor influencing the behavior of pLGG. Other factors such as age, tumor location, and histopathology are required to inform a comprehensive approach to prognostication and treatment of pLGG. We therefore propose a pLGG risk classification schema that utilizes the breadth of clinical and molecular information available to best equip clinicians as we transition to this new era of pLGG classification and treatment.


Musculoskeletal conditions are managed within primary care, but patients can be referred to secondary care if a specialist opinion is required. The ever-increasing demand for health care resources emphasizes the need to streamline care pathways with the ultimate aim of ensuring that patients receive timely and optimal care. Information contained in referral letters underpins the referral decision-making process but is yet to be explored systematically for the purposes of treatment prioritization for musculoskeletal conditions.This study aims to explore the feasibility of using natural language processing and machine learning to automate the triage of patients with musculoskeletal conditions by analyzing information from referral letters. Specifically, we aim to determine whether referral letters can be automatically assorted into latent topics that are clinically relevant, that is, considered relevant when prescribing treatments. Here, clinical relevance is assessed by posing 2 research questions. Can latent topics be used to automatically predict treatment? Can clinicians interpret latent topics as cohorts of patients who share common characteristics or experiences such as medical history, demographics, and possible treatments?We used latent Dirichlet allocation to model each referral letter as a finite mixture over an underlying set of topics and model each topic as an infinite mixture over an underlying set of topic probabilities. The topic model was evaluated in the context of automating patient triage. Given a set of treatment outcomes, a binary classifier was trained for each outcome using previously extracted topics as the input features of the machine learning algorithm. In addition, a qualitative evaluation was performed to assess the human interpretability of topics.The prediction accuracy of binary classifiers outperformed the stratified random classifier by a large margin, indicating that topic modeling could be used to predict the treatment, thus effectively supporting patient triage. The qualitative evaluation confirmed the high clinical interpretability of the topic model.The results established the feasibility of using natural language processing and machine learning to automate triage of patients with knee or hip pain by analyzing information from their referral letters. Currently, a pathway recommended for musculoskeletal conditions such as knee or hip pain consists of their management within primary care followed by referral to a multiprofessional assessment and treatment clinic if a specialist opinion is required . The agiIndeed, NLP has repeatedly demonstrated its feasibility to extract clinical variables from clinical narratives, making them available for large-scale analysis down the stream . Traditiunknown unknowns, such as patient safety unknown ut safety , and 50/t safety .The research gaps identified in this overview of related work are as follows. Despite finding various clinical applications, LDA is yet to be used to support triage. The biggest challenge for these applications to become widely adopted in clinical practice is the perception of interpretability. However, few studies have specifically evaluated the interpretability of the LDA outputs from a clinician's perspective. Clinical terminologies have been combined with the LDA to improve interpretability, but the resources used to support such functionality do not include the Unified Medical Language System (UMLS), which offers a unique opportunity to abstract clinical concepts into higher categories of knowledge. Finally, for the topics to be easily distinguishable , their number needs to reflect the latent themes and patterns present in a given data set. However, none of the considered approaches provided a strategy to infer the value of this hyperparameter from the data. In this study, we addressed these four gaps.First, we applied the LDA to a corpus of referral letters and used topics as features to automatically classify each letter against a list of potential treatments. This can then be used to automate patient triage, that is, assort them into priority groups according to their medical needs. Second, we proposed a novel method for evaluating the interpretability of topics. Third, we used the UMLS to incorporate the interpretation of clinical concepts at different levels of abstraction into the LDA. Finally, we systematically fine-tuned the number of topics using a measure of topic coherence.Data collection was originally described in the study by Button et al . In summThe care pathway is illustrated in Patients were recruited from one Local Health Board, an administrative unit within the National Health Service in Wales, which supports a population of around 445,000 people. A total of 634 participants were recruited between August 2016 and January 2017, and their referral letters were collected. The follow-up data collection was completed in June 2018. This included recording of any treatments performed. A subset of 576 patients with complete data, including the original referral letter and the corresponding treatments, was used in this study. The distribution of their treatments is given in The main research question addressed in this study is as follows: Can triaging patients (into cohorts) based on their referral letters be semiautomated? To that end, we designed a system that can support referral decision making . A corpuThe linguistic preprocessing and normalization module originally developed to support cohort selection from hospital discharge summaries was adapted for this study . In addiphysiotherapy theme in referral letters, ultimately resulting in the words “Jane” and “Doe” emerging as the topic descriptors. Not only are these words not informative of the topic but they also cannot be generalized to other data sets where these names do not exist, or they refer to different persons, thus rendering the model either inapplicable or inaccurate. To prevent a topic model from overfitting to personal names, they are replaced by a generic representative. For this purpose, we originally considered existing named entity recognition libraries  to r to rphysies . Linking synonyms gives the model a better chance of capturing the semantics of underlying topics. Linguistic preprocessing implements lexical normalization, where both formal and informal abbreviations are translated to a standard vocabulary. For instance, “TKR” and “physio” would be translated to “total knee replacement” and “physiotherapy,” respectively. However, the problem of term variation may still persist. Examples from our corpus are many: “tear” versus “rupture,” “painkiller” versus “analgesic,” “oedema” versus “swelling,” “patella” versus “kneecap,” etc. The UMLS , which ipainkillers/C0002771 stronger than paracetamol.She struggles to take any analgesics/C0002771.He is opposed to regular oedema/C0013604 and bursitis.His recent magnetic resonance imaging shows swelling/C0013604 of the knee joint.There is a little bit of tear/C3203359 of the medial meniscus.The magnetic resonance imaging showed a complex rupture/C3203359.She has had a likely anterior cruciate ligament n-gram language model [n being fixed to 2 and 3. Examples from our corpus , “ligament” , “condyle”  or indeed a “joint line” . Similarly, it remains unclear which anatomical entity is affected by “tenderness.” To alleviate this problem, topic modeling approaches often use an ge model , with n r corpus  illustraiability ,28.McMurray test/C3669149.I could not reproduce pain with McMurray and Ege testing/C3669149.She does however experience pain on total knee replacement/C0086511 as his pain has increased.He would be keen to consider a knee arthroplasty/C0086511.She is relatively young for consideration of knee prosthesis/C0086511.She has poor mobility following a few revisions of a right bilateral knee pain/C2220048 for a number of years.He is a 67-year-old male who has had pain in both knees/C2220048 with regular effusions.She has persistent medial joint line tenderness/C0576135.She has crepitus in his left knee with tender medial joint line/C0576135.No swelling of the knee but tender across his medial joint line/C0576135.He had an effusion present and was tenderness along the joint line medially/C0576135.On examination there was daily  or recreational activity (DORA)), we can observe common themes emerging focusing on age, fitness, and injury: young, physically active patients with a sports-related injury. These factors play an important role in recommending the most appropriate treatments. Their association with the given semantic type means that it could be a useful topic descriptor. For example, a clinician can reasonably assume that the given topic refers to a cohort of young, fit patients with a sports-related injury. Semantic type markups can be processed by topic modeling software similar to any other tokens in the corpus and, therefore, can be used as potential topic descriptors.MetaMap, a highly configurable dictionary lookup software, can be used to discover the UMLS concepts in the text . We usedrugby/DORA [This 22 year old was tackled in gby/DORA  and sustskiing/DORA last year felt something pop in her knee.She is a delightful 27 year old female who when football/DORA, which he is now unable to do.He is normally quite active and enjoys badminton/DORA, which is something that he does.It first started about an hour after playing sport/DORA but has been unable to recently.He was previously very active and was involved in ice hockey/DORA player.He is a keen basketball/DORA.Thank you for seeing this man who two years ago injured his right knee playing netball/DORA injury.She is a very athletic female, and back in 2013 had a golf/DORA worsens it.It was not caused by trauma, but playing tennis/DORA on a weekly basis.Patient is normally very fit and active playing To implement our topic modeling approach, we used the LDA method, which discovers latent topics in a corpus of documents based on a Bayesian statistical modeling approach . This apn-grams into the BOW representation. As described earlier, we opted to use tokens that represent markups of concepts and semantic types as an alternative to n-grams with added benefits of normalizing lexical and syntactic variation associated with biomedical terms. We ran experiments with different combinations of features, as described in We used an open-source implementation of the LDA algorithm included in the Gensim library . Each doThe performance of machine learning models depends not only on the parameters whose values the model learns during the training phase  but also on the values of hyperparameters , which are fixed before the training begins. The predictive performance of different topic modeling algorithms was found to vary substantially in practice. However, when the hyperparameters were optimized, these differences diminished significantly . One of Perplexity, a measure of how well a probabilistic model predicts a sample, is commonly used to evaluate topic models. It is calculated as the inverse of the geometric mean per-word likelihood, with lower values indicating better models . A heuriResults section. As In general, perplexity was found not to be well correlated with the human rating of topic interpretability . AlternaRecent studies have shown that optimizing a model for perplexity may not yield human interpretable topics . This liIn the first approach, 2 words are said to be collocated if they co-occur more often than would be expected by chance. In corpus linguistics, collocation is measured by estimating relevant probabilities from a corpus of text documents, which can be either the original corpus used to learn the topic model or a reference corpus such as Wikipedia. Probabilities are estimated using Boolean documents. The number of documents in which the word (or a pair of words) occurs is divided by the total number of documents. Neither the number of occurrences within a document nor the distances between words are taken into account; hence, the name Boolean. A virtual document can be defined as a paragraph, sentence, or text window, which, by being smaller parts of the whole document, indirectly account for the distances between words.These probabilities are used to calculate pair-wise word coherence measures such as pointwise mutual information (PMI) , normaliP, against the probability that they would co-occur under the assumption of their independence, P(wi)P(jw). Higher values indicate a stronger association between the 2 words. NPMI follows the same logic, but it also imposes a fixed upper bound of 1 to indicate perfect association by normalizing PMI using the joint probability of 2 words. This makes its interpretation more intuitive while also reducing the bias toward less frequently occurring words. Both measures are symmetric, which is not a property of human word associations. By basing LCP on a simple conditional probability P(iw | jw), it adds direction to measuring the association of 2 words.PMI compares the probability of 2 words co-occurring, n words:Topic coherence is calculated by averaging the pair-wise word coherence across its , and LCP are commonly referred to as CUCI (or CPMI) [CNPMI [CUMass [iw as a vector whose j-th coordinate corresponds to C. On the basis of the distributional hypothesis, which states that words with similar distributions have similar meanings, we can use cosine similarity between the corresponding vectors to estimate the similarity between 2 words:Topic coherence measures based on PMI, NPMIor CPMI) , CNPMI [) [CNPMI , and CUM [CUMass , respectn words [Topic coherence can now be calculated by averaging the contextual similarity across its n words :CV [CNPMI but differs from Ccos in a way in which it aggregates the similarity values. Instead of pair-wise comparison, each word is compared with the set of top-ranked words whose context vectors have been summed up.In a comparative analysis, the best correlation with human topic coherence ratings was achieved with CV , a topicCUCI [CNPMI [CUMass [CV [The Gensim library , which wCUCI , CNPMI [I [CNPMI , CUMass  [CUMass , and CV Mass [CV . Table 4The extrinsic evaluation assesses the performance of a topic model in the context of a predefined task. In an envisaged scenario, topic modeling could be used to semiautomate patient triage by using topics to predict the most appropriate treatments . Our datAs a result of topic modeling, each referral letter was mapped to a topic distribution vector. Each coordinate contained a score that the letter received against the corresponding topic. Effectively, the corpus was transformed into a document-topic matrix. We trained a binary classifier for each treatment using the document-topic matrix. It takes a topic distribution vector of a referral letter as input and outputs a yes or no decision for the corresponding treatment.k-nearest neighbor algorithm with k=5 in a quest to reduce overfitting. The cross-validation results are shown in We used 10-fold cross-validation to measure its prediction accuracy A=(TP+TN)/N, which was calculated using true positives (TP), true negatives (TN), and the total number (N). Cross-validation experiments were performed for each data set described in Not surprisingly, the worst results were achieved on discharge and review appointment. One would intuitively expect that these outcomes would be the least homogeneous with respect to topic distribution. In other words, any musculoskeletal patient would eventually be either discharged or reviewed, regardless of their condition. The best results were achieved for the 2 most imbalanced treatment outcomes, Nutritionist and Any other referral, with only 15 and 16 positive instances, respectively, out of a total of 576, where overfitting the majority class was most likely to have occurred. The accuracy of predicting the remaining treatment outcomes outperformed the stratified random classifier by a large margin, indicating that topic modeling could be used to support patient triage . On averQualitative evaluation is de facto the gold standard for measuring the interpretability of a topic model. However, involving human raters makes such an evaluation expensive to implement in practice. For that reason, we singled out a topic model with the highest coherence  and clasTo measure the interpretability of topics, we designed experiments using a novel protocol illustrated in In the second phase, both clinicians gained access to the other one's choice of a topic's description. They were then asked to independently estimate the similarity of the 2 descriptions on a 6-point Likert scale: −3 (very dissimilar), −2 (moderately dissimilar), −1 (slightly dissimilar), 1 (slightly similar), 2 (moderately similar), and 3 (very similar). The average similarity was used to estimate the interpretability of topics under the hypothesis that high similarity implies high interpretability and vice versa. The responses to the 2 questionnaires are presented in The average confidence was found to be 3.00 and 2.00 between the two annotators. The average similarity was found to be 2.00 for both annotators. One participant was consistently more confident than the other, but they were mostly not more than one Likert point apart. The biggest discrepancy between the 2 Likert points was found for topics T8 and T11. When cross-referenced against the topic similarity scores, most dissimilar descriptions were observed. Overall, the participants' perception of topic similarity was consistent, with one Likert point difference throughout.To generalize these findings, we calculated the interannotator agreement for both confidence and similarity . For thiThis study explored the feasibility of using NLP and machine learning to automate triage of patients with musculoskeletal conditions by analyzing information from referral letters. Specifically, we determined that LDA can automatically assort referral letters into topics that are clinically relevant. In other words, latent topics provide information that is considered relevant when prescribing treatments.First, our experiments confirmed that latent topics could be used to automatically predict an appropriate treatment. A supervised classifier based on latent topics as its sole feature consistently outperformed the baseline method. Further improvements in the performance of such classifiers stand to be gained by incorporating other types of features that can be obtained from the patients' electronic health records, for example, demographics, body mass index, and imaging reports. However, this was beyond the scope of this study, which was concerned only with establishing the clinical relevance of automatically extracted latent topics. On their own, these topics proved to be sufficiently discriminative features for treatment recommendations based on machine learning.Second, our experiments confirmed that latent topics could be interpreted by clinicians as cohorts of patients who share common characteristics or experiences such as medical history, demographics, and possible treatments. Specifically, the words associated with each topic by the LDA algorithm proved to be sufficiently descriptive to enable clinical specialists to interpret the topic's underlying semantics.The first set of experiments established the clinical relevance of latent topics from a machine perspective: a treatment can be recommended automatically for an individual patient. The second set of experiments established the clinical relevance of latent topics from a human perspective: a treatment can be recommended by a clinician for an automatically identified cohort of patients. Both treatment recommendation scenarios support the hypothesis that topic modeling can support patient triage. Automating this process can be used to address areas where bottlenecks exist. Efficient referral to appropriate services such as analgesia or diagnostics not only improves patient experience and health outcomes but also reduces queuing arising from nonurgent demand, thus minimizing the delays for those with urgent care needs.Our approach used information contained in referral letters to underpin the referral decision-making process. Successful automation of this process has the potential to streamline care pathways and ensure that patients receive timely and optimal care. In clinical applications such as patient triage, interpretability is the key to build trust for all stakeholders, clinicians, and patients alike. Our approach to qualitative evaluation sets a precedent in measuring the interpretability of automated outputs, which is emerging as the next big challenge for clinical NLP. The unsupervised aspect of the proposed approach avoids the need for data annotation and, therefore, can be readily deployed to tackle other bottlenecks along the musculoskeletal pathway. For example, imaging and pathology reports can be processed in the same way to automatically redirect patients to the most appropriate services.


Neisseria gonorrhoeae.It is unclear how important bystander selection is in the genesis of antimicrobial resistance (AMR) in We assessed bystander selection in a novel way. Mixed-effects linear regression was used to assess if country-level prevalence of gonococcal AMR in 30 European countries predicts homologous AMR in other bacteria. The data used was from the European Antimicrobial Resistance Surveillance Network.E. coli , Acinetobacter spp.  and Pseudomonas aeruginosa  but not Klebsiella pneumoniae. Azithromycin resistance in N. gonorrhoeae was positively associated with macrolide resistance in Streptococcus pneumoniae . No association was found for cephalosporins.The prevalence of gonococcal ciprofloxacin resistance was found to be positively associated with AMR prevalence in Gonococcal AMR is linked to that in other bacteria. This finding is likely explained by high antimicrobial consumption in affected populations and provides additional motivation for strengthening antimicrobial stewardship programs. Neisseria gonorrhoeae has developed antimicrobial resistance (AMR) to every major class of antimicrobials used to treat it [N. gonorrhoeae is vital to prevent the future emergence of AMR. Initially, it was thought that the major AMR determinant was exposure to antibiotics used to treat gonorrhoea [N. gonorrhoeae is asymptomatic for much or most of the time it circulates in a population means that antibiotics used for other indications needed to be considered (bystander selection) [Mycoplasma genitalium genital infections may drive AMR in N. gonorrhoeae, little direct evidence to support this notion has been published [Treponema pallidum, the bacterium responsible for syphilis, was strongly associated with population-level consumption of macrolides [treat it , 2. Thertreat it . Understnorrhoea –6. The alection) . Since glection) . While aublished . One stucrolides . Other scrolides . Understcrolides .Fig. 1CN. gonorrhoeae, with some studies finding no association [N. gonorrhoeae where travel has been shown to have played a vital role in the spread of AMR [Ecological studies have reached different conclusions regarding the association between general antimicrobial consumption and the emergence of AMR in ociation  and otheociation , 13, 14.ociation . For exaociation . Exposurociation . This prd of AMR . The prod of AMR –20. The These limitations motivated the current study where we approach the problem via a novel methodology. In addition to assessing the traditional association between antimicrobial consumption and gonococcal AMR, we analyze the association between gonococcal AMR and homologous AMR in other pathobionts. The hypothesis we test is that gonococcal AMR is associated with AMR in these pathobionts Fig. . FindingEscherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter spp., Pseudomonas aeruginosa, Enterococcus faecalis, Enterococcus faecium, Staphylococcus aureus), with the exception of Greece which did not report data on S. pneumoniae. Only data from invasive  isolates are included in EARS-Net. This is done to limit biases that may emerge if isolates from all anatomical sites were included. Further details can be found in the EARS-Net reporting protocol [https://www.ecdc.europa.eu/en/surveillance-atlas-infectious-diseasesThe AMR data was taken from the European Centre for Disease Prevention and Control (ECDC) Surveillance Atlas which reports resistance prevalence estimates from the European Antimicrobial Resistance Surveillance Network (EARS-Net) - the EU’s main surveillance system for AMR in bacteria that cause serious infections. All 28 EU Member States and two EEA countries (Iceland and Norway) participate in EARS-Net. The countries provide data for all eight species under surveillance . The following minimum inhibitory concentration (MIC) breakpoints were used to define gonococcal antimicrobial resistance: Azithromycin: > 0.5 mg/L, Cefixime: > 0.12 mg/L, Ceftriaxone: > 0.12 mg/L, Ciprofloxacin: > 0.06 mg/L [The ECDC Surveillance Atlas reports gonococcal AMR for ciprofloxacin (a fluoroquinolone), azithromycin (a macrolide), cefixime and ceftriaxone (both Extended Spectrum (ES) cephalosporins) by country and year for 30 countries from 1997 to 2018. Since our hypothesis tested homologous class bystander selection, we limited our analysis to the 5 bacterial species that reported AMR for fluoroquinolones, macrolides or ESCephalosporins  were used as a measure of national general population-level antimicrobial drug consumption , 26. ESAN. gonorrhoeae and each of the other bacterial species. The following mixed effects linear model was used:For each antibiotic class, mixed effects linear regression was used to assess the association between the prevalence of AMR in N.gonorrhoeae_resistance-to-X in year Y and country C) ~ (Species-Z_resistance-to-X in year Y and country C) + (random intercept for country C) + intercept + error, where species-Z is one of E. coli, K. pneumoniae, S. pneumoniae, Acinetobacter spp. or P. aeruginosa, and X could be fluoroquinolones, macrolides or ESCephalosporins. ~  + (random intercept for country C) + intercept + error.P-value of < 0.05 was regarded as significant.The statistical analyses were performed in Stata 16.0. A This analysis involved ecological analyses of public access data and thus no Ethics approval was necessary.There were large variations (up to 300-fold) in the consumption of cephalosporins, fluoroquinolones and macrolides between countries Table . The medE. coli and K. pneumoniae. The prevalence of fluoroquinolone resistance in N. gonorrhoeae declined over time.For each of the bacterial species, the prevalence of AMR varied considerably between countries Table . There wE. coli , Acinetobacter spp.  and P. aeruginosa  but not K. pneumoniae , Acinetobacter spp. , N. gonorrhoeae  and K. pneumoniae  but not P. aeruginosa , but not N. gonorrhoeae was associated with macrolide consumption  consumption and prevalence of antimicrobial resistance to fluoroquinolones in Neisseria gonorrhoeae (Ng) and Escherichia coli (Ec) in 30 European countries. Figure S2. Macrolide consumption and prevalence of antimicrobial resistance to azithromycin in Neisseria gonorrhoeae (Ng) and macrolides in Streptococcus pneumoniae (Sp) in 30 European countries.


Mycobacterium bovis and is characterized by the development of granulomatous lesions in the lymph nodes, lungs and other tissues. It poses serious public health impacts and food security challenges to the agricultural sector in terms of dairy and meat productions. In Ethiopia, BTB has been considered as a priority disease because of its high prevalence in urban and peri-urban dairy farms. However, there has not been any national control program in the country. Thus, in order to initiate BTB control program in the country, information on control options is needed to tailor the best option for the Ethiopian situation. The objective of this study was to identify, evaluate and rank various BTB control options in Ethiopia using a multi-criteria decision analysis based on preference ranking organization method for enrichment evaluations (PROMETHEE) approach while accounting for the stakeholders' preferences. Control options were evaluated under two scenarios: with (scenario 1) and without (scenario 2) bacillus Calmette–Guérin (BCG) vaccination. Nine potential control options were identified that include combinations of three control options (1) test and slaughter with or without government support, (2) test and segregation, and (3) BCG vaccination. Under scenario 1, BCG vaccination, BCG vaccination and test and slaughter with partial compensation by government, and BCG vaccination and test and slaughter with full compensation by government were the top three ranked control options. Under scenario 2, test and slaughter with full compensation by government was the preferred control option, followed by test and segregation supported by test and slaughter with full government compensation, and test and slaughter with half compensation by government. Irrespective of the variability in the weighting by the stakeholders, the sensitivity analysis showed the robustness of the ranking method. In conclusion, the study demonstrated that BCG vaccination, and test and slaughter with full compensation by government were the two most preferred control options under scenarios 1 and 2, respectively. National level discussions were strongly recommended for further concretization and implementation of these control measures.Bovine tuberculosis (BTB) is a zoonotic bacterial infection caused by  M. bovis, a member of the Mycobacterium tuberculosis complex  from various pertinent organizations in Ethiopia were invited. Out of the 15 stakeholders invited, 10 of them agreed to participate in the MCDA process  software 1.4 was used to perform pair-wise comparisons of the performance of control options using the preferences of the stakeholders to compute the overall outranking scores .Based on the scores, the identified control options were listed from the most to the least preferred option. For ranking of the control options and visual display of the analysis results, the Geometrical analysis for interactive aid (GAIA) with two dimension (U-V) views and PROMETHEE table were used. The action profiles of the control options were performed for the top ranked control options to evaluate their relative performance on each criterion. The GAIA and sensitivity analysis were performed for scenario 1. GAIA walking weights were run to conduct sensitivity analysis to see the effect of weighing the evaluation criteria by stakeholders on the group ranking when the weights of the criterion were changed and to assess the robustness of the results.From the 10 stakeholders participate in the MCDA process (S1–S10), nine were from the government organization and one stakeholder represented an association of privately owned dairy farmers . The staAll stakeholders generated a specific weighting scheme based on their perceived relative importance of each criterion as defined for the intended decision-making process. For this, each stakeholder was provided 100 points, and was asked to distribute the points to all specified criteria. The weighting of the stakeholders varied among the clusters and within the cluster criteria. Three stakeholders  gave the highest weight for the economic criteria, while the other seven stakeholders gave the highest weight to the epidemiologic cluster: reduction of BTB prevalence. The social ethics cluster and criteria generally received the least weight by all stakeholders . Under sTo the best of our knowledge this is the first study to identify, evaluate and rank different BTB control options using MCDA tool based on the stakeholders' opinions and preferences in Ethiopia. Despite high prevalence of the disease in dairy cattle in the country, currently there is no BTB control and /or eradication program. The participation of stakeholders to achieve the purpose and use of participatory approaches such as MCDA are helpful to identify and evaluate BTB control options. In the present study, we generated the desired data from stakeholders who represented organizations with direct responsibilities or had specific interests in BTB prevention and control in Ethiopia.In addition to identifying, evaluating and ranking of BTB control options, the stakeholders also identified various pre-requisite measures such as legal framework for the implementation and allied issues as an integral part of a control program prior to its application. Similarly, these measures were identified and their implications on the future prevention and control of BTB in Ethiopia were mentioned as daunting tasks by Dibaba et al. . In agreM. bovis infected animals from BCG-vaccinated animals   . The expVA role) . HoweverAccording to the stakeholders, BCG vaccination poorly reduces the prevalence of BTB in cattle. This is likely influenced by the role of BCG in sensitizing cattle to respond to the conventional BTB diagnostic test, combined with the low level of protection of BCG vaccine in cattle compared to its relative effectiveness in humans . To overThe second and the third control options involve prior application of BCG vaccination to reduce the number of positive cattle followed by test and slaughter with half and full compensation by the government, respectively. In high income countries, test and slaughter is the most preferred and a widely applied approach to control and eventually eradicate BTB, since the prevalence is low , 7, 10. Alternatively, as revealed by the present study, applying BCG vaccination to reduce the prevalence and progression of BTB and subsequent integration with other control options such as test and slaughter, could be a novel approach for Ethiopia which can also be adopted by other low and middle income countries where BTB is endemic and implementation of test and slaughter policy is practically challenging. To that end, the availability and accessibility of commercial BCG vaccine is critically needed. In addition, mutual understanding, acceptability and cooperation between dairy cattle owners and the government are profoundly needed particularly regarding cost recovery scheme for the implementation of the approach.Under scenario 2 (which did not consider BCG vaccination as a feasible option), test and slaughter with full compensation by the government ranked the number one preferred control option. Indeed, this could be the most preferred and acceptable option for the cattle owner from the perespective of relatively practical applicability and lower socio-economic impacts. However, this might not be acceptable to the government, as it would be too costly vis-a-vis to other priorities of the government . BesidesM. bovis is killed at pasteurization temperature and holding time  and third (test and slaughter with cost sharing) options, would be the preferred options in developing countries. There are compelling evidences that test and segregation method significantly reduced the incidence of BTB , 31. Theing time . Use of n = 10) of the stakeholders gave the highest weight to the epidemiologic criterion  in evaluating the identified control options, while the social ethics criteria generally received the least weight. The epidemiologic criterion is practically important for the control and eradication of BTB. For instance, the application of test and slaughter policy is challenged mainly due to economic and animal welfare reasons, and this impact is lower when the prevalence of BTB is low . Third, it is necessary to critically evaluate the outcomes of the control program in the selected areas and then extend the best practices to scale up the program to other regions of the country. Finally, conducting persistent surveillance and monitoring of the status of BTB across the country will be needed to develop a national database that would help in periodic evaluation of the effectiveness of the control measures put in place and taking timely corrective actions as needed. An effective and safe BCG vaccine for use in cattle is critical for this approach.In conclusion, the study used an MCDA tool in identifying and evaluating BTB control options in Ethiopia. According to the stakeholders' preferences, calf vaccination and test and slaughter with full cost compensation by government are the best control options under a scenario that included BCG vaccination and a scenario with no BCG vaccination, respectively. Moreover, the study showed that integrating calf BCG vaccination with other potential control options, in minimizing the number of test positive cattle thereby decreasing the cost of compensation for culled/slaughtered cattle and maintain animal welfare as the most suitable BTB control option in Ethiopia that can also be used by other countries, especially low income countries.The original contributions generated for the study are included in the article/supplementary materials, further inquiries can be directed to the corresponding author/s.FG, GEA, KM, TB, MM, and GA designed the study. FG, SL, TT, ZA, BU, and GA collected and summarized the data during multi-criteria decision process. FG analyzed the data. FG wrote the manuscript. FG, GEA, KM, TB, TT, MM, RS, SL, ZA, BU, and GA critically revised and edited the manuscript and approved its submission.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


The identification of a relationship between neural activation changes with compensatory molecular phenotypes at the synaptic level paves the way for future work to understand the limits of brain reorganization of functional networks in neurological disorders.The association between molecular and functional brain plasticities in health and disease remains an outstanding research challenge. Functional up-regulation of postsynaptic D2 receptors has been documented in PD while its significance at the neural activity level has never been identified. Here we provide a link between synaptic plasticity at the molecular level and reorganization of brain activity patterns. We combined molecular imaging of dopamine D 2 receptors has been documented while its significance at the neural activity level has never been identified. We investigated cortico-subcortical plasticity in PD using the oculomotor system as a model to study reorganization of dopaminergic networks. This model is ideal because this system reorganizes due to frontal-to-parietal shifts in blood oxygen level–dependent (BOLD) activity. We tested the prediction that functional activation plasticity is associated with postsynaptic dopaminergic modifications by combining positron emission tomography/functional magnetic resonance imaging to investigate striatal postsynaptic reorganization of dopamine D2 receptors (using 11C-raclopride) and neural activation in PD. We used covariance (connectivity) statistics at molecular and functional levels to probe striato-cortical reorganization in PD in on/off medication states to show that functional and molecular forms of reorganization are related. D2 binding across regions defined by prosaccades showed increased molecular connectivity between both caudate/putamen and hyperactive parietal eye fields in PD in contrast with frontal eye fields in controls, in line with the shift model. Concerning antisaccades, parietal-striatal connectivity dominated in again in PD, unlike frontal regions. Concerning molecular–BOLD covariance, a striking sign reversal was observed: PD patients showed negative frontal-putamen functional–molecular associations, consistent with the reorganization shift, in contrast with the positive correlations observed in controls. Follow-up analysis in off-medication PD patients confirmed the negative BOLD–molecular correlation. These results provide a link among BOLD responses, striato-cortical synaptic reorganization, and neural plasticity in PD.The link between synaptic plasticity and reorganization of brain activity in health and disease remains a scientific challenge. We examined this question in Parkinson’s disease (PD) where functional up-regulation of postsynaptic D Parkinson’s disease (PD) is a neurodegenerative disorder, triggered by selective loss of dopaminergic neurons in the pars compacta of the substantia nigra and is characterized by hypokinesia, tremor, rigidity, and postural instability .2 receptors in the basal ganglia (BG) remains a mystery. Such mechanisms are probably best explored at a network level using covariance statistics-based approaches for positron emission tomography (PET) data  studies. Execution of PSs elicits activation of the FEF, supplementary eye field (SEF), and PEF, while ASs trigger additional activation of the dorsolateral prefrontal cortex and anterior cingulate gyrus , 10. PD 1 and D2 receptors subtypes are found in infragranular layers where layer-V FEF neurons project to the SC (2 receptor modulation in FEF is more effective when eye movements are performed to the stimulus (PSs)  .2 type receptor radioligand 11C-raclopride, which is well suited to measure synaptic D2 receptors in PD  in the BG with the density of receptors in areas involved in saccades (FEF and PEF) and, second, the link between DVR in the BG with the blood oxygen level–dependent (BOLD) signal (translated as activation β-weights) of regions involved in saccade execution (FEF and PEF), while performing PS or AS tasks. Furthermore, we investigated whether the same patterns could be identified off medication to rule out these effects being simply explained by medication.We used unimodal and multimodal covariance statistics to explore the relationship between saccade-related fMRI activity and DSI Appendix, Table S1) were recruited from the movement disorder clinic at Coimbra University Hospital Centre from April 2015 to December 2018. Seven patients  were asked to interrupt their dopaminergic medication , at least, 12 h before the fMRI experiment  with no history of neurological, psychiatric, or visual disorder were recruited from our volunteers’ database.All participants went through cognitive evaluation . Exclusion criteria included cognitive deterioration , moderate to severe depression (GDS > 21), other types of Parkinsonism and/or inability to perform the oculomotor task inside the fMRI scanner . Afterward, a blank screen was shown for 1 s, and the trial was completed.PS and AS runs included 64 trials each. Although random, the presentation of the target was organized in six blocks of horizontal saccades interleaved with six blocks of vertical saccades. Each run began with a 30 s extra period of fixation, and blocks ended with a 16.5 s of fixation to ensure recovery of the hemodynamic response .During the PS run, the participants had to perform a saccade toward the blue target and in the opposite direction in the AS run.The duration of the fixation cross as well as target positioning was random and counterbalanced.3, matrix size = 256 × 256, and field of view 256 mm).Imaging data were collected on a 3.0 T scanner MAGNETOM Trio  using a 12-channel head coil . Anatomical volumes were acquired first using a high resolution T1-weighted MPRAGE (magnetization prepared rapid gradient echo) . The slices covered the whole brain and were oriented according to a parallel plan regarding the line that passes by anterior and posterior commissures.Functional scans were obtained using a two-dimensional gradient-echo echo-planar imaging sequence  . Standard preprocessing included slice-time correction, realignment, unwarping, anatomical coregistration, segmentation, normalization to the Montreal Neurological Institute (MNI) template, and smoothing with a Gaussian kernel with a full width at half maximum (FWHM) of 6 mm.The regressors were defined based on the onset and duration of each movement direction . The regressor called “baseline” represents the time intervals between regressors during which no event occurred. The hemodynamic response was modeled using a canonical response function .11C-raclopride uptake in these structures.To test the main questions of this paper, focused on oculomotor circuitry, a region of interest (ROI)-based approach was performed. The selected ROIs for this study were the left and right FEFs (in Brodmann’s Area [BA] 6/8) , 25, 26,P value between 1 × 10−6 and 0.01 with no extended voxels). First level contrasts were computed by setting the regressor of interest to 1 to identify regions responding to horizontal and vertical saccades. Next, per subject, we overlapped the clusters that activated in horizontal and vertical paradigms. Then, we extracted the center of mass of that overlapped region (or peak voxel within the expected BA). The final ROI was defined as a spherical volume with radius of 6 mm. When the intersection was null, we used a mean group ROI-based imputation.The FEF or PEF ROIs were identified for each subject from functional imaging data: First level contrasts were calculated, and the activated ROIs localized in areas compatible with BA 6/8 or BA 39/40 were segmented ; per ROI and per subject, we extracted the β-weights from fMRI data for each contrast as well as the mean value of the DVR using PET molecular imaging data (see sections 2.2.5 and 2.2.6).11C-raclopride acquisitions were performed in the same scanner (Philips PET/CT Gemini GXL) preceded by a low-dose brain CT acquisition for attenuation correction. Acquisitions were dynamic, lasted for 90 min (30 frames: 4 × 15 s + 4 × 30 s + 3 × 60 s + 2 × 120 s + 5 × 240 s+ 12 × 300 s), and started immediately after the intravenous bolus injection of ∼555 MBq of 11C-raclopride. These were reconstructed using the LOR RAMLA algorithm (Philips PET/CT Gemini GXL) with attenuation and scatter correction. An isotropic voxel size of 2 mm was defined.All SI Appendix, Fig. S1 depicts the D2 receptor DVR average map in healthy participants.2 type receptors available have higher DVR than regions with low density of dopamine D2 type receptors available. DVR are computed by fitting the following equation to the data extracted from the dynamic PET image . ET image :∫0tTargewhere  the DVR . DVR andIn order to overlap FEF and PEF ROIs found using fMRI with PET data to further extract respective DVR values, for each participant, the DVR image (voxelwise DVR) was first rigidly registered with the correspondent MRI-T1 image. Then, the MRI-T1 image was spatially normalized to the MNI space using the DARTEL algorithm implemented in the SPM12, and the geometric transformation found was applied to the DVR image. After this process, the voxelwise DVR of all participants was defined in the MNI space in the same way as the fMRI activation maps. Finally, all normalized DVR images were smoothed with a Gaussian kernel of 12 mm FWHM. Both caudate and putamen were segmented manually using images in the native space.The individual ROIs from FEFs (right and left) and PEFs (right and left) found functionally from fMRI data analysis and, thus, that derived from PS and AS experiments and the manually segmented ROIs of caudate and putamen were used as masks over the spatially normalized DVR images. Using the 3D Slicer Software, the mean DVR for each region and for each subject was extracted for further statistical analysis.R values were also performed. The statistical analysis was performed using IBMSPSS vs. 24.The main goal of this study was to infer about covariance statistics. Such functional connectivity patterns were assessed by calculating the Pearson correlations coefficient between molecular imaging and neural activity and whether they were distinct in PD. To answer our first goal, we investigated unimodal “molecular connectivity” by correlating the mean binding sites from caudate and putamen with the mean binding sites of the right and left FEFs or PEFs. Subsequently, we analyzed multimodal molecular–BOLD activity functional connectivity for the mean binding sites of the caudate or putamen with the BOLD signal represented as β-activation weights from left and right FEFs or PEFs. Direct group comparisons of regression (β) slopes and of differences between The main goals of this paper were to study unimodal (molecular [DVR]–molecular) and multimodal  covariance statistics  patterns in PD across oculomotor regions and the BG. Our main aim was to link the density of receptors in the BG with the saccade evoked BOLD signal in oculomotor regions FEF and PEF. Based on the literature, DVR differences between groups were not expected, which was confirmed in our data set. No previous studies addressed covariance statistics.First, we analyzed the link between DVRs of the caudate and the putamen and DVRs in left or right FEFs/PEFs for the control group and PD groups.R = 0.701, P = 0.035; R = 0.718, P = 0.030, respectively). Between group slope comparisons showed a significant difference . In the PD group, we found a positive and significant correlation between both the caudate and the putamen and the right PEF   .In PS-defined ROIs, we found a positive and significant correlation between both the caudate and the putamen and the left FEF in the control group (ctively) . In otheR = 0.604, P = 0.022; right PEF vs. caudate: R = 0.579, P = 0.030; left PEF vs. putamen: R = 0.597, P = 0.024; right PEF vs. putamen: R = 0.691, P = 0.006) .In AS-defined areas, positive and significant correlations were found between both the caudate and the putamen and the PEF in the PD group (left PEF vs. caudate: = 0.006) . ConcernIn this section, we focused on molecular (DVR)–BOLD activation correlations .R = 0.699, P = 0.036). In the PD group, we found surprising reversals in polarity of the correlation patterns. Accordingly, we found a negative and significant correlation between the DVR in the putamen and the BOLD signal in the left  and right FEF  while performing vertical PS. t19 = 4.37, P = 0.0003; putamen—right FEF t19 = 2.64, P = 0.016). Group comparisons between R coefficients (after Fisher to Z conversion) also showed significant differences .Concerning PS-related areas, we found a positive and significant correlation between the DVR in the putamen and the BOLD signal in the left FEF during vertical PS in the control group  and the DVR in the putamen and the BOLD signal in the left FEF during horizontal PS . SI Appendix, Fig. S2 shows the results concerning the PD on- and off-medication groups for the left FEF.As a follow-up analysis, we investigated a potential medication effect. Concerning PS-related areas, for the off-medication PD group, a negative and significant regression was seen between the DVR in the caudate and the BOLD signal in the left FEF during vertical PS  and multimodal  functional correlations (connectivity) patterns. fMRI activation studies in PD have consistently shown activation shifts 11, , 30, 31,When investigating a molecular correlate in PS-related FEF and PEF regions, we found that, while in controls the DVR (binding sites availability) correlated positively between the FEF and the BG, in PD patients, such positive correlation was seen between the BG and the PEF and was absent for FEF. The latter finding suggests favored positive PEF-putamen coupling in PD.FEF is considered the primary gaze center, providing top-down information to the afferent region PEF to coordinate visual attention , 32, 33.Thus, the shift from frontal to parietal networks is accompanied by molecular changes as indexed by covariance statistics as markers of synaptic plasticity.2 receptors signaling in the primate frontal cortex whereby D2 receptor stimulation affects motor activity tuning only when eye movements are performed to the stimulus  or by a reduction in extracellular dopamine (the extracellular dopamine reduced by the dopaminergic degeneration can no longer compete for the D2 receptor binding with 11C-raclopride). We do believe that the second alternative is more unlikely because extracellular dopamine depends on medication, and our effects did show not to depend on medication. Moreover, the link between synaptic dopamine status and reorganization of brain activity patterns as established by PET and fMRI measurements in the same participants would still hold true. Finally, we found striking reversals in regression slopes irrespective of differences in offset levels, which renders the second alternative also unlikely.To the authors’ best knowledge, no study had performed such uni- and multimodal approaches, providing such a link between molecular and functional reorganization in PD. DVR modifications can be caused by an increase in the number of DDespite the inherent limitations of PET/CT in terms of temporal resolution, the use of covariance metrics has been demonstrated in this regard to be a promising approach .2 receptor binding and reorganization of the saccadic cortical network reflects parietostriatal rerouting in response to a progressive frontostriatal dopamine deficit. This paves the way for future work to understand the limits of brain reorganization of functional networks in neurological disorders.In sum, we found a tight link between functional activation and synaptic changes at the molecular level, reflecting network reorganization in PD. The association between DSupplementary File


Kaposi sarcoma (KS) is an AIDS-defining angioproliferative malignancy associated with high morbidity and mortality. Most KS patients in regions with high incidence such as sub-Saharan Africa present late with advanced stage disease. Admitted KS patients have high mortality rates. Factors associated with mortality of admitted KS patients are poorly defined.We conducted a retrospective file review to ascertain reasons for admission and identify factors associated with mortality of admitted HIV-associated (epidemic) KS patients in Zambia. Baseline study variables were collected, and patients were retrospectively followed from admission to time of discharge or death.P = 0.02), fever , and sepsis . Baseline hemoglobin levels  and baseline platelet counts  were significantly lower in mortalities vs discharges. Baseline white cell counts were higher in mortalities vs discharges , and HIV-1 viral loads at the time of admission were higher in mortalities vs discharges . However, only sepsis (or signs and symptoms of sepsis) were independently associated with mortality after controlling for confounders.Mortality rate for admitted epidemic KS patients was high at 20%. The most common reasons for admission included advanced KS disease, severe anemia, respiratory tract infections, and sepsis. The majority (48%) of admitted patients had advanced clinical stage with visceral involvement on admission. Clinical predictors of mortality on univariate analysis included visceral KS [odds ratio (OR) = 13.74; 95% confidence interval (95% CI) = 1.68–113; In conclusion, common reasons for admission of epidemic KS patients include advanced disease, severe anemia, respiratory tract infections, and signs and symptoms of sepsis. Signs and symptoms of sepsis are independent predictors of mortality in these patients. KSHV seroprevalence is high in sub-Saharan Africa, and hence the high prevalence of KS in this region. KS commonly not only affects the skin, but can also affect other parts of the body, including the gastrointestinal tract, respiratory tract, lymph nodes, and conjunctiva of the eyes.Kaposi sarcoma (KS) is an angioproliferative spindle cell tumor of endothelial origin. Classic KS mainly affects elderly men of Eastern European descent. Endemic KS, also known as African cutaneous KS, is more common in sub-Saharan Africa among HIV-seronegative individuals. Iatrogenic KS mainly affects patients on immunosuppressive drugs such as those undergoing organ transplants. Epidemic or AIDS-Associated KS is seen in HIV-infected individuals, is a WHO HIV stage 4 disease, is the most common type of KS worldwide, and has a rapidly progressive disease course.There are 4 main subtypes of KS. These include classic, endemic, iatrogenic, and epidemic KS. However, despite combination antiretroviral therapy, epidemic KS is still highly prevalent with high mortality rates world-wide, and especially in sub-Saharan Africa. Between 2008 and 2013, the University Teaching Hospital (UTH) in Zambia recorded at least 726 incident KS cases, majority of which were HIV-associated.The introduction of antiretroviral therapy (ART) has led to a reduced incidence and improved survival of epidemic KS globally.[5] About 10% to 20% of patients present with advanced disseminated disease and/or complications such as anemia, and are admitted to the inpatient medical wards. Several factors including stage of KS at presentation, ART status, and CD4 counts have been reported to predict outcomes of KS patients. In addition, recurrence rates of chemotherapy-treated epidemic KS patients are high.Unlike other forms of KS, AIDS-associated KS has a rapidly progressing disease course, and may disseminate in a short period of time to involve the viscera, including lungs and gastrointestinal tract. KS remains one of the most common AIDS-related malignancies in Zambia, with numerous admissions to our hospitals. KS patients make up about 70% of all dermatological admissions at UTH. There is paucity of data regarding the factors affecting outcomes of admitted epidemic KS patients. Most previous studies have focused on outcomes of epidemic KS in general, and not specifically on the admitted population of epidemic KS patients. Therefore, this study aimed at determining reasons for admission, and identifying clinical and laboratory parameters that predict mortality or discharge of admitted epidemic KS patients.2A retrospective file review of a series of HIV-associated/epidemic KS patients admitted in the period from April 2019 to November 2019 was carried out. We reviewed medical records of adult epidemic KS patients aged 18 years and older, who were admitted to the medical wards of the Adult hospital of the University Teaching Hospitals (UTH) in Lusaka, Zambia.We used printed data collection forms to obtain information from patient files. The information was later entered into an excel spreadsheet and then exported to STATA for analysis. The clinical and sociodemographic information collected included age, gender, previous hospital admissions, smoking, alcohol use, ART status, adherence to ART, duration on ART, other comorbidities , duration of KS, KS clinical stage, history of receiving chemotherapy, fever, palor, jaundice, weight loss, treatment given during admission . We also collected laboratory parameters, including full blood count, liver function test, renal function test, HIV viral loads, CD4 counts, and histopathology staging.The main objective of the study was to identify reasons for admission and factors associated with outcomes  of admitted adult epidemic KS patients at UTH. Ethical approvals for a waiver of consent were obtained from the University of Zambia Biomedical Research Ethics Committee, and the National Health Research Authority. Obtaining informed consent from the actual participants was not possible, as this was a retrospective study and study participants were not available to give consent, as they were either discharged or had died.P values < .25 on univariate logistic regression and predictors known to be associated with the outcome regardless of P values, were included on the multivariate logistic regression model. Among the highly correlated variables, only one was included in the multivariable model. The prediction of our model for outcome was determined by the AUC-ROC curve. The Hosmer–Lameshow goodness of fit test was used to determine how well our model fit the data. We also used the logistic regression model to test for interactions between variables that may possibly modify the observed effect.All data were analyzed using STATA version 15 . Baseline characteristics were analyzed using summary and descriptive statistics. Continuous variables are presented as median and interquartile range, while dichotomous or categorical variables are presented as percentages. The Mann–Whitney test was used for group comparisons of continuous variables. Univariate logistic regression was used to determine the association between the dichotomous outcome and the categorical and continuous predictors. Multivariate logistic regression was used to control for confounders. Predictors with 3We collected and analyzed information of 54 epidemic KS patients admitted in the period from April 2019 to April 2020. Among these, 43 (80%) were discharged, while 11 (20%) were mortalities. Baseline characteristics of the study participants, by outcome, are summarized in Table The most common reason for admission for discharged patients was advanced/disseminated KS followed by severe anemia, and the most common reason for admission for individuals who died was severe anemia followed by sepsis Fig. . Other rKS clinical staging at presentation was different between the discharged patients and mortalities. Among the discharged patients, 14% presented with localized cutaneous KS, 49% had disseminated cutaneous KS, while 37% had advanced KS . Among the mortalities, 9% had disseminated cutaneous disease on admission, while 91% had advanced KS.On univariate logistic regression, the factors significantly associated with mortality included history of previous hospital admissions, presence of visceral KS, fever, and an admission diagnosis of sepsis. In addition, hospital interventions including oxygen therapy, intravenous antibiotics, and blood transfusion were significantly associated with mortality Table .We also collected and compared results of routine laboratory tests done on admission. Individuals who died had statistically significantly low hemoglobin levels and low platelet counts as compared to individuals who were discharged. Those who died also had statistically significantly high white blood cell counts and median HIV viral load as compared to those who were discharged Table .P = .96). In addition, there was no multicollinearity of the variables in the model, with a mean variance inflation factor of 1.36 .We built a multivariate logistic regression model with variables that were statistically significant on univariate logistic regression and the laboratory parameters that were significantly associated with the outcome on univariate analysis. After adjusting for age, gender, hemoglobin levels, platelet count, and creatinine, sepsis remained a significant independent predictor of mortality Table . The mulP = .30), and between blood transfusion and anemia (P = .69) were not statistically significant.Testing for interactions between sepsis and intravenous antibiotics  of AIDS-associated KS patients presented with advanced disease and had high mortality rates. Fever is a common sign of sepsis; thus, most of our patients who were diagnosed with sepsis also had fever.Clinical predictors of mortality on univariate logistic regression included visceral KS, fever, and sepsis. Advanced KS presents as multiple disseminated KS lesions with or without massive lymphedema and often accompanied with visceral involvement. When KS involves the viscera, commonly lungs and gastrointestinal tract, patients often have systemic life-threatening complications requiring admission and intensive care. Hence, the prognosis for advanced KS is usually poor.Medical interventions, including blood transfusion, oxygen, and intravenous antibiotics, were also associated with death on univariate logistic regression. As most of the patients who died were very ill, with advanced KS disease on admission, they were more likely to be commenced on these medical interventions. Therefore, these treatments were only predictors of mortality in the sense that they were likely to be initiated in very ill KS patients who had advanced disease. The severe anemia in the individuals who died may be a result of the more advanced HIV disease and advanced KS. Thrombocytopenia has previously been reported in KS patients and supposedly results from platelet sequestration in the abnormal KS tumor vessels.,16 Therefore, advanced disease with numerous KS lesions possibly explains why individuals who died had lower platelet counts. At the time of admission, patients who eventually died also had higher white cell counts above the upper limit of normal. Our findings are consistent with previous studies that have reported high white cell and neutrophil counts to be associated with a poor prognosis in the form of death or KS disease progression.,18 Higher white cell counts may reflect a higher degree of chronic inflammation or may be a sign of sepsis in individuals who died. HIV viral load was 500-fold higher at baseline in individuals who eventually died than individuals who were discharged. HIV viral load is a marker of HIV disease control. In addition, poor control of HIV infection predisposes to KS development and progression. In our study cohort, individuals who died had a history of poor compliance to ART compared to those who were discharged from hospital. This may have contributed to the advanced disease presentation, high HIV viral load, and poor outcome. However, CD4 counts were not predictive of mortality.Several laboratory parameters, including low hemoglobin, low platelets, high white cell counts, and high HIV-1 viral loads, were also significantly associated with mortality. Anemia is a risk factor for HIV infection, and has previously been associated with shorter survival in HIV-infected patients. Unfortunately, blood cultures were not done to confirm the diagnosis of sepsis in our patients due to unavailability of resources. It is possible that the signs and symptoms of sepsis were due to a phenomenon called Kaposi sarcoma inflammatory cytokine response (KICS). KICS is common in severely ill KS patients, mimics severe sepsis, is associated with high Interleukin 6 (IL-6) production, associated with high KSHV viral loads, and is also associated with a high mortality rate.–24 It is more probable that our patients had KICS and not sepsis. This is because empirical intravenous broad-spectrum antibiotics that are known to be effective in septic HIV individuals in our setting were administered in our patients with signs of sepsis; however, these antibiotics had no effect and even seemed to be associated with poor outcomes. Furthermore, there was no interaction between treatment with intravenous antibiotics and a diagnosis of sepsis. Prospective cohort studies and more extensive laboratory testing need to be conducted to address this issue.After controlling for other predictors of mortality, only sepsis (or signs and symptoms of sepsis) was independently associated with mortality. Sepsis is common in immunosuppressed HIV patients. It has been previously identified as a major cause of admission and mortality in HIV patients.5We could not definitely differentiate sepsis vs KICS because blood cultures, KSHV viral loads, and IL-6 levels were not assessed during admission. A prospective cohort study would be required to definitively address this. In addition, the sample size was not powered enough to determine statistical differences in marginally significant variables including hemoglobin levels and creatinine on multivariate regression.6Advanced disease with visceral involvement, severe anemia, and symptoms and signs of sepsis were among the most common reasons for admission of epidemic KS patients. Several factors, including advanced KS clinical stage, sepsis, low hemoglobin, low platelet count, high white cell count, and high HIV viral load, were associated with mortality. However, only signs and symptoms of sepsis were independent predictors of mortality for admitted KS patients.Conceptualization: Owen Ngalamika.Data curation: Faheema Vally, Wencilaus Margret Pious Selvaraj.Formal analysis: Owen Ngalamika.Funding acquisition: Owen Ngalamika.Investigation: Faheema Vally.Methodology: Faheema Vally, Owen Ngalamika.Resources: Faheema Vally, Owen Ngalamika.Supervision: Owen Ngalamika.Validation: Wencilaus Margret Pious Selvaraj, Owen Ngalamika.Writing – original draft: Faheema Vally.Writing – review & editing: Faheema Vally, Wencilaus Margret Pious Selvaraj, Owen Ngalamika.


Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS) are two imprinting disorders associated with opposite molecular alterations in the 11p15.5 imprinting centres. Their clinical diagnosis is confirmed by molecular testing in 50–70% of patients. The authors from different reference centres for BWS and SRS have identified single patients with unexpected and even contradictory molecular findings in respect to the clinical diagnosis. These patients clinically do not fit the characteristic phenotypes of SRS or BWS, but illustrate their clinical heterogeneity. Thus, comprehensive molecular testing is essential for accurate diagnosis and appropriate management, to avoid premature clinical diagnosis and anxiety for the families. However, in BWS 50% of cases show loss of maternal allele methylation of imprinting centre 2 (IC2 or KCNQ1OT1:TSS-DMR). Sequence variants in et al., To identify the major molecular changes, first-line testing for BWS and SRS is recommended to include DNA methylation analysis of IC1 and IC2 , the initial clinical suspicion of BWS based on some key features according to the recent consensus guidelines  in the presence of an 11p15 molecular anomaly is within the BWSp. ILO is sufficient to prompt BWS testing  ascertainment bias for referrals meeting specific clinical criteria; (b) the relative likelihood of imprinting disturbance restricting rather than enhancing growth; (c) mosaic LOM in different tissues, with the critical imprinting disturbance eluding detection in the tissue analysed mutations in patients with unspecific phenotypes. As these examples show, the application of clinical scoring systems and the clinical evaluation can be a major prerequisite for a more directed diagnostic testing strategy, but some patients might be missed if the decision about molecular testing is strictly based on fulfilment of clinical criteria. We want to emphasize that in patients with inconclusive clinical features the communication of a clinical diagnosis should be delayed until molecular confirmation is available because a premature diagnosis might cause anxiety to the families.The discrepancy between clinical and molecular features of BWS and SRS is an infrequent occurrence. Though objective numbers are lacking, these cases probably represent ⩽1% of diagnostic referrals. Prompt, sensitive and comprehensive molecular testing is essential for accurate diagnosis, appropriate management and genetic counselling, for these as for all imprinting disorders.