Patients who develop an active tuberculosis infection during tumor necrosis factor (TNF) inhibitor treatment typically discontinue TNF inhibitor and receive standard anti-tuberculosis treatment. However, there is currently insufficient information on patient outcomes following resumption of TNF inhibitor treatment during ongoing anti- tuberculosis treatment. Our study was designed to investigate the safety of resuming TNF inhibitors in ankylosing spondylitis (AS) patients who developed tuberculosis as a complication of the use of TNF inhibitors.Through the nationwide registry of the Korean Society of Spondyloarthritis Research, 3929 AS patients who were prescribed TNF inhibitors were recruited between June 2003 and June 2014 at fourteen referral hospitals. Clinical information was analyzed about the patients who experienced tuberculosis after exposure to TNF inhibitors. The clinical features of resumers and non-resumers of TNF inhibitors were compared and the outcomes of tuberculosis were surveyed individually.Fifty-six AS patients were treated for tuberculosis associated with TNF inhibitors. Among them, 23 patients resumed TNF inhibitors, and these patients were found to be exposed to TNF inhibitors for a longer period of time and experienced more frequent disease flare-up after discontinuation of TNF inhibitors compared with those who did not resume. Fifteen patients resumed TNF inhibitors during anti-tuberculosis treatment (early resumers) and 8 after completion of anti-tuberculosis treatment (late resumers). Median time to resuming TNF inhibitor from tuberculosis was 3.3 and 9.0 months in the early and late resumers, respectively. Tuberculosis was treated successfully in all resumers and did not relapse in any of them during follow-up .Instances of tuberculosis were treated successfully in our AS patients, even when given concomitantly with TNF inhibitors. We suggest that early resumption of TNF inhibitors in AS patients could be safe under effective coverage of tuberculosis. Tuberculosis is a serious complication associated with tumor necrosis factor (TNF) blockade therapy –3. Risk When active tuberculosis occurs in patients with AS on TNF inhibitors, a full course of anti-tuberculosis therapy and withdrawal of the biologics is generally recommended , 10, 11.Although novel approaches are under investigation, treatment options are limited, particularly in non-steroidal anti-inflammatory drug (NSAID)-refractory AS . The excTherefore, in order to critically evaluate strategy of resuming TNF inhibitors after tuberculosis treatment, we sought to assess the safety of resuming TNF inhibitors concomitantly with or after completing anti-tuberculosis chemotherapy based on a present nationwide study in an intermediate tuberculosis burden area.AS patients who had been treated with TNF inhibitors in 14 referral hospitals between June 2003 and June 2014 were recruited in the registry of the Korean Society of Spondyloarthritis Research (KSSR). All patients met the 1984 modified New York criteria for AS . The hisThis multi-site study protocol was approved by the institutional review boards from all participating sites including Eulji General Hospital, Inha University School of Medicine, Catholic University of Daegu School of Medicine, Gachon University Gil Hospital, Hanyang University Guri Hospital, Ajou University Hospital, Keimyung University Dongsan Medical Center, Chungnam National University Hospital, Kyung Hee University Hospital at Gangdong, Pusan National University Hospital, Kyung Hee University Medical center, Seoul National University Hospital, Hanyang University Hospital for Rheumatic Disease and Asan Medical Center. Each review boards waived the requirement for the investigator to obtain a signed consent form for all subjects as the research presents no more than minimal risk of harm to subjects. The review boards found that the only record linking the subject and the research would be the consent document and the waiver or alteration of normal consent procedures will not adversely affect the rights and welfare of the subjects. All patient records/information were anonymized.Mycobacterium tuberculosis infection; a positive acid-fast bacillus (AFB) culture, a positive Mycobacterium tuberculosis polymerase chain reaction, and the presence of caseating granulomas on tissue specimens. Patients were also diagnosed as having active tuberculosis if high clinical suspicion was supported by radiographic evidence or high adenosine deaminase levels in adequate specimens together with clinical improvement upon anti-tuberculosis treatment.Active tuberculosis was diagnosed based on microbiological or pathological evidence of In cases in which a patient was treated with two or more TNF inhibitors, the last TNF inhibitor used before the onset of tuberculosis was regarded as the causative agent. Follow-up was censored at the most recent follow-up or death, whichever came first.TNF inhibitor treatment was stopped if active tuberculosis diagnosed unless a therapeutic benefit from continuation of TNF inhibitor treatment was expected. All patients were treated with adequate anti-tuberculosis treatment. Briefly, first-line agents  were applied for 6 months in pulmonary tuberculosis and for 9–12 months in extrapulmonary tuberculosis. TNF inhibitors were resumed at physician’s discretion, mostly when clinically indicated in patients experiencing a flare-up of AS activity with worsened pain or immobility, usually after checking anti-tuberculosis drug sensitivity. Researchers reported the AS disease activity at the close time after suspension of TNF inhibitor as being improved, stable or being worsened grounded on patients’ medical records. Selection of a specific TNF inhibitor was at the discretion of each attending physician. To detect a recurrence of tuberculosis, our patients were observed for active tuberculosis infection during routine clinical practice if they contacted patients with active tuberculosis or showed symptoms and signs suspicious of active tuberculosis. The outcome of tuberculosis was surveyed in the patients who resumed TNF inhibitors if they failed initial tuberculosis treatment or had been hospitalized.The characteristics of resumers and non-resumers of TNF inhibitors after initiation of anti-tuberculosis treatment were compared. Resumers were further separated into two subgroups: early resumers (who resumed TNF inhibitors during anti-tuberculosis treatment) and late resumers (who resumed TNF inhibitor after completion of anti-tuberculosis treatment).Data are expressed as medians , and differences were analyzed using the Chi-squared test and Student’s t-test or the Mann-Whitney U test (for continuous variables) as appropriate. All statistical analyses were performed using SPSS 19.0 for Windows .As shown in Among patients with active tuberculosis (n = 56), fourteen patients (25.0%) had extrapulmonary and twenty (35.7%) had disseminated tuberculosis. Interestingly, 2/3 of patients (67.9%) experienced tuberculosis infection after 1-yr exposure of TNF inhibitors and 1/4 of patients (26.8%) had been treated for LTBI before initiation of TNF inhibitor. These findings suggest the possibility of new tuberculosis outweighing reactivation of LTBI.Anti-tuberculosis chemotherapy was started on the basis of clinical (n = 18), microbiological (n = 36) or pathological (n = 2) findings. Of these 56 AS patients, 23 resumed TNF inhibitors after initiating the anti-tuberculosis treatment (15 patients during anti-tuberculosis treatment and 8 after completion of anti-tuberculosis treatment).P = 0.03). Otherwise baseline features were not different between the groups, including LTBI and history of cured tuberculosis before anti-TNF treatment.Baseline demographics of the AS patients who resumed TNF inhibitors or did not resume after active tuberculosis are compared in P < 0.001). Non-resumers were treated more often with glucocorticosteroid, NSAIDs and DMARDs instead of TNF inhibitor. Paradoxical response after discontinuation of etanercept was reported from a patient in non-resumer group. Sudden onset of pleural effusion after 2 months of discontinuation of etanercept while receiving proper tuberculosis chemotherapy was noted in that patient, eventually, the diagnosis of paradoxical response following discontinuation of TNF inhibitor was made.All resumers, except 1 who had stable disease and 1 with unavailable data, reported to have worsened AS disease activity while 15 patients among non-resumers had worsened disease activity, with 13 stable and 4 improved disease activity during suspension of TNF inhibitor. Resumers experienced disease flares from patients’ perspective more frequently than non-resumers  restarted TNF inhibitor after completion of anti-tuberculosis treatment while 15 patients (early resumers) restarted during anti-tuberculosis treatment (median duration 9.0 (IQR 7.4–12.6) vs. 3.3 (2.9–4.7) months) . BaselinPatients who develop active tuberculosis following TNF inhibitor use typically discontinue TNF inhibitor use as soon as possible, and reuse of TNF inhibitors has been opposed because of concerns about recurrence of tuberculosis. However, unlike the situation with RA, there are few options for controlling AS disease activity. Here, we found favorable long term outcomes of active tuberculosis in AS patients when they resumed TNF inhibitors. Furthermore, the outcomes were not different in patients who resumed TNF inhibitors before completion of anti-tuberculosis treatment or after completion.et al. reported 10 cases of tuberculosis during TNF inhibitor treatment in 437 AS patients from a single center. Five patients among them restarted anti TNF treatment after a mean of 14 months of tuberculosis diagnosis without relapse within those months or the following period [There have been few studies of the outcome and safety of re-administration of TNF inhibitors in AS patients who were infected with tuberculosis due to their previous use –22. One g period . In FranMycobacterium tuberculosis while taking anti-TNF treatment were not worse than those of community-acquired tuberculosis, despite the higher frequency of the extra-pulmonary type in the TNF inhibitor-associated tuberculosis [Mycobacterium tuberculosis transit from a dormant into a replicating state [Limitations of guidelines on continuation or recommencement of TNF inhibitor after tuberculosis infection stem from lack of published studies attempting to examine the issue. The guidelines of the British Thoracic Society address continuation of TNF inhibitor if clinically indicated and if patients are under appropriate tuberculosis treatment . The belrculosis . Additiorculosis . TNF inhng state . Moreoveng state . Both thIn our registry, the most frequently resumed TNF inhibitor was etanercept, a recombinant protein of soluble TNF receptor, which has been considered having lesser risk of tuberculosis compared to monoclonal antibodies . In the In our registry, two thirds of patients with active tuberculosis showed negative screening results for LTBI prior to starting TNF inhibitor and it took longer time (25.7 mon) to develop tuberculosis than previous reports in which presented active tuberculosis shortly after induction of TNF inhibitor consistent with reactivation of LTBI , 23. TheSeveral limitations on the study could be addressed. First, the follow-up period after resuming TNF inhibitors may not have been enough. However, it was nearly as long as the exposure to TNF inhibitors leading up to the tuberculosis infection. Second, resuming protocols were not standardized. Physicians decided when to resume considering patients’ symptom and signs as well as their comorbidities. Accordingly, data on AS disease activity at the close time after TNF suspension were to track patient’s perspectives and classified with applying neither Bath Ankylosing Spondylitis Disease Activity Index nor Ankylosing Spondylitis Disease Activity Score. Third, patient information was collected in a retrospective manner. Nevertheless, the current study has strength in the data collected as it is from real practice in an intermediate tuberculosis burden area and involves larger numbers than those evaluated in previous reports. Moreover, the data composition is of multicenter registry covering patients treated in secondary or tertiary hospitals nationwide.Ultimately, our nationwide study supports the view that TNF inhibitors can be resumed early in AS patients once active tuberculosis is under control. Sensitivity to the anti-tuberculosis drug should then be confirmed, and drug compliance and the formation of cavities, which are factors associated with treatment failure , should S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.


Bothrops moojeni venom  inhibits TNF directly by promoting its degradation. This inhibition was demonstrated by both in vitro and in vivo assays, using known TLR ligands. These findings are supported by molecular docking results, which reveal interaction between BmooMP-alpha-I and TNF. The major cluster of interaction between BmooMP-alpha-I and TNF was confirmed by the structural alignment presenting Ligand Root Mean Square Deviation LRMS = 1.05 Å and Interactive Root Mean Square Deviation IRMS = 1.01 Å, this result being compatible with an accurate complex. Additionally, we demonstrated that the effect of this metalloprotease on TNF is independent of cell cytotoxicity and it does not affect other TLR-triggered cytokines, such as IL-12. Together, these results indicate that this zinc metalloprotease is a potential tool to be further investigated for the treatment of inflammatory disorders involving TNF deregulation.Tumor necrosis factor (TNF) is a major cytokine in inflammatory processes and its deregulation plays a pivotal role in several diseases. Here, we report that a zinc metalloprotease extracted from  TNF is a classical pro-inflammatory cytokine involved in the modulation of acute inflammatory responses and host defense mechanisms . HoweverMetalloproteases are enzymes characterized by presenting a catalytic zinc ion in its active site . Snake vThe SVMPs are divided into three main classes according to their domain organization: SVMPs of the class PI contain only the metalloprotease domain in the mature protein, including the canonical zinc-binding motif HEXXHXXGXXH followed by a Met-turn motif. The class PII is comprised of enzymes containing a disintegrin domain following the metalloprotease domain. Class PIII SVMPs contain the metalloprotease domain, the disintegrin-like (Dis-like) domain and a cysteine-rich domain (Cys-rich). Post-translational processing of precursors of some PIII metalloproteinases results in the release of the Dis-like and Cys-rich domains (DC fragment) ,11. AddiB. moojeni snake venom is a fibrin(ogen)olytic and non-hemorrhagic zinc metalloprotease of the class PI SVMPs with a molecular mass of 24.5 kDa [BmooMP-alpha-I isolated from 24.5 kDa ,13. This24.5 kDa .Previous study of the crystal structure of BmooMP-alpha-I showed that the enzyme presents a catalytic zinc ion displaying an unusual octahedral coordination, which includes three canonical histidines . From thStudies of BmooMP-alpha-I to date have focused only on its fibrin(ogen)olytic and non-hemorrhagic activity. The major aim of the present study was to investigate whether this metalloprotease could modulate TNF inflammatory properties, considering that the precursor form of this cytokine is targeted by TACE, another metalloprotease from the same class .Bothrops snakes is proteolysis, which is responsible for the main clinical manifestations of bothropic acidents [Venoms secreted by snakes constitute a complex mixture of molecules with various biological activities directed to different targets . This isacidents .B. moojeni, a significant amount if compared with other fibrin(ogen)olytic enzymes isolated from similar preparations [In the present study BmooMP-alpha-I was isolated from crude venom by using combined chromatographic protocols. Ion exchange chromatography on DEAE-Sephacel column resulted in the separation of five protein fractions, (peaks E1–E5) A. Fractiarations ,15,16,17Next, 1D and 2D electrophoretic analysis was carried out of the B1 fraction under non-reducing conditions. 1D SDS-PAGE confirmed BmooMP-alpha-I as a monomer, with apparent molecular mass of 23 kDa D. The BmThe effect of BmooMP-alpha-I fraction was assessed for TNF production by BMDMs stimulated with known TLR ligands. Treatment of BMDMs with BmooMP-alpha-I reduced significantly the TNF detection in LPS-primed macrophages for all enzyme concentrations that were tested A. In conTo further confirm the inhibitory effect of the BmooMP-alpha-I metalloproteasee on TNF, we examined the effect of this enzyme in a model of LPS-induced sepsis in mice, as it was already known that death caused by septic shock is crucially dependent on TNF production . It was 2EDTA ) It was observed that the levels of TNF decreased by 53.4% after incubation with the pure metalloprotease. In addition, the level of TNF was restored by 80% in the presence of NA2EDTA ). As demonstrated in 2EDTA, a chelating agent used to remove bivalent ions, which completely eliminates the biological activity of SVMPs [In order to verify whether TNF was directly cleaved by BmooMP-alpha-I, additional experiments were performed. First, the effect of this metalloprotease was determined on degradation of TNF or IL-12 by ELISA. Levels of TNF were determined under different conditions, as TNF and IL-12 standard cytokines or antibodies against them (capture antibodies) were incubated with the following preparations: pure protein ; BmooMP-alpha-I inactivated with NA NA2EDTA A. In con NA2EDTA B. As conof SVMPs . Furtherof SVMPs ,23.Agkistrodon acutus snake, which showed a protective role in sepsis by promoting proteolysis of fibrin and TNF, accompanied by a decrease of the plasmatic concentration of this cytokine [To confirm the proteolysis of TNF by metalloprotease BmooMP-alpha-I and to assess whether this effect could present a dose-dependent fashion, additional 1D SDS-PAGE and Western blotting experiments were carried out. The 1D SDS-PAGE with silver stained gel showed that 12 μg/mL of BmooMP-alpha-I was active against TNF and caused a degradation of this substrate, which could be evidenced by the fading of its chains, as demonstrated by the electrophoretic profile of the reaction A. The cocytokine ,25. The cytokine .α–I_rmsd < 1.5 Å), intermediate (1.5 Å < Cα–I _rmsd ≤ 2.2 Å), and hard (Cα–I _rmsd > 2.2 Å) [To explore the mechanism of the protein-protein interaction, docking analyses of BmooMP-alpha-I protein (3GBO) and TNF (2TNF) were performed using the available protein structures (PDB), followed by structural alignment in the Swiss PDB Viewer. The major cluster of interaction between BmooMP-alpha-I and TNF was confirmed by the structural alignment that presented LRMS = 1.05 Å and IRMS = 1.01 Å . This re> 2.2 Å) ,29,30. NIn order to evaluate the stability of the potential interactions, an electrostatic analysis was carried out. The interaction between the BmooMP-alpha-I and TNF complex occurs among the following residues, respectively: Glu33-Arg32, Val171-Gln31; Ala49-Asn39; Arg28-Glu89, Arg43-Asp53; Arg43-Glu127; Arg43-Asp53; Arg43-Glu127; Val35-Asn39; Ala49-Asn39; Gln133-Gln31; Gly40-Asp42; His32-Tyr87; His32-Val91; Tyr42-Asn39; Ala49-Ser86; Val35-Tyr87 . This ann = 98%) were located in allowed regions  was determined, which is consistent with a favorable model of interaction (G-factor > −0.5)  B. ConcerN-terminal residues) and lower domain , which is consistent with other metzincins, such as adamalysin-II [The platform CLUSPRO has been generally used for docking analysis, as in actin-actin interaction . This dolysin-II . This aclysin-II . In thislysin-II . It is iBothropos jararaca possess propensity for the amino acid arginine in the position 1, although a difference exists in the residue preferred at position 6 and 6′, conferring certain specificity for the class of metalloproteases [Studies of homology among sequences cleaved by metalloproteases utilizing bioinformatics have been developed once the classes of proteases possess homology on their preferential cleavage sites. For instance, a study pointed out that A and PA-BJ metalloproteases from roteases . The preroteases , corroboroteases . In thisroteases ,41. Anotroteases ,43. It iroteases . Thus, BB. moojeni which we found able to hydrolyze TNF. In the literature a high degree of homology among snake venom metalloproteases (SVMPs), metalloproteases from mammalian extracellular matrix (MMPs), and the metalloproteases from disintegrin family (ADAMs), have been described. These families of enzymes are able to degrade subtracts from different sources. In this context, MMPs can cleave cytokines and chemokines, even though the existence of components from the extracellular matrix [start” or “stop” signaling during an inflammatory response [It is important to emphasize that the metalloprotease BmooMP-alpha-I is a fibrin(ogen)olytic non-hemorrhagic SVMP that is naturally produced by r matrix . Concernr matrix . These sresponse . Thus, aresponse .In summary, the results described in the present study shed light for future investigations concerning the clinical applications of the zinc metalloprotease BmooMP-alpha-I, since it was demonstrated that this enzyme is able to promote significant proteolysis of TNF. The next step will be to confirm the TNF sequence that is cleaved by this metalloprotease. Therefore, future studies are necessary to determine whether this enzyme could induce protection in experimental models in vivo, particularly those involving TNF as a critical mediator of inflammatory diseases, in order to verify its potential protective role, as well as the existence of possible side effects from its therapeutic use.Male C57BL/6 mice (18–22 g) were housed in temperature-controlled rooms and received water and food ad libitum until enrolled in experimental conditions. These studies were approved by the Experimental Animals Committee of Universidade Federal de Uberlândia  in accordance with the procedures established by the University Federation for Animal Welfare.B. moojeni venom was purchased from Bioagents Serpentarium . BmooMP-alpha-I was isolated and its purity and biological activity assessed as previously published [Desiccated ublished ,13, withublished .w/v) in acetic acid:methanol:water  solution. The relative molecular mass of the purified enzyme was estimated by Kodak 1D image analysis software . BmooMP-alpha-I was also submitted to 2D electrophoresis, by taking120 μg of samples solubilized in 125 μL of isoelectric focalization (IEF) solution  and resolved into IEF capillary gel for 12 h, followed by 12% SDS-PAGE.Samples of the BmooMP-alpha-I were boiled for 3 min in the presence of sample buffer and resolved in 1D SDS-PAGE at 12%, as previously described [5 macrophages/well were maintained in 96-well plates in triplicates, for 24 h, in RPMI 1640 medium , supplemented with 10% fetal calf serum , at standard mammalian cell culture conditions (37 °C and 5% CO2). BMDMs were then primed with known TLR agonists  for 3 h. Next, BmooMP-alpha-I preparations were added at concentrations of 12 µg/mL, 6 µg/mL or 3 µg/mL and the plates were incubated for an additional 24 h. Supernatants were collected and stored at −80 °C until assayed for cytokine production. As negative controls, cells were incubated with medium only, while positive controls consisted of cells incubated with TLR agonists. Cell viability rates were determined by MTT assay, as previously described [To determine the effect of BmooMP-alpha-I in the TNF molecule, it was used an in vitro model based on bone marrow derived macrophages (BMDM) priming with known Toll-like receptor (TLR) agonists, as previously described . Suspensescribed .Escherichia coli  was injected intraperitoneally (i.p.) in mice to induce acute systemic TNF, following a model for induction of endotoxic shock, as published elsewhere [n = 10/group) were pre-treated i.p. with PBS (control) or BmooMP-alpha-I (50 μg), 60 min prior to LPS stimulation (100 µg/mouse). Blood samples were collected from the retro-orbital plexus after 90 min of LPS challenge and serum samples were obtained by centrifugation , and stored at −80 °C until assayed for cytokine measurement.Lipopolysaccharide (LPS) from lsewhere . BrieflyTNF levels were determined in supernatants from cell cultures and serum samples using a commercial ELISA kit, following the manufacturer’s instructions . In addition, IL-12p40 production was also assessed in these samples, using an appropriate kit . The cytokine concentrations in the samples were calculated by comparison with standard curves of the respective murine recombinant cytokine.2EDTA or BmooMP-alpha-I incubated for 2 h at 37 °C with specific polyclonal antibodies (pAb) were included in each assay, as additional controls. In parallel, anti-TNF antibody samples were also submitted to the same conditions, to ensure assay specificity. After incubation, the samples were submitted for detection of TNF by sandwich ELISA (ELISA kit R & D Systems).To determine whether BmooMP-alpha-I was able to inhibit TNF detection, mouse recombinant protein  was pre-incubated with BmooMP-alpha-I (12 μg) or medium alone, as negative controls. Samples of BmooMP-alpha-I inactivated by 10 mM NADifferent BmooMP-alpha-I masses  were mixed with rTNF (0.7 ng) in PBS pH 7.2 and incubated at 37 °C for 45 min. Negative controls consisted of metalloprotease masses incubated with sterile PBS only. After incubation, each sample was analyzed by 1D SDS-PAGE (18%), as previously described . Gels weTNF proteolysis was further assessed by Western blotting. For this purpose, samples of rTNF (1.4 ng) were incubated with BmooMP-alpha-I (24 μg) or sterile PBS at 37 °C for 45 min. After incubation, the samples were electrotransferred to nitrocellulose membranes, as described . BlottedG factor > −0.5. Drugscore PPI 2.2 [The X-ray crystallography or nuclear magnetic resonance (NMR) of the primary sequence was searched in the RCSB Protein Data Bank . Both Bm PPI 2.2  was asse PPI 2.2  was emplp < 0.05 were considered significant and the results are representatives from at least three independent experiments.Statistical analysis of data concerning cytokine concentrations was performed using dedicated software , using One-way ANOVA or Two-way ANOVA, followed by post-test comparisons. Values of


Hydrocephalus is an under-recognized presentation of progressive supranuclear palsy (PSP) and dementia with Lewy bodies (DLB).We describe four normal pressure hydrocephalus (NPH)-like presentations of pathology-proven PSP (n = 3) and DLB (n = 1) and review the literature on the hydrocephalic presentation of these atypical parkinsonisms.Despite the presence of ventriculomegaly disproportionate to the extent of parenchymal atrophy, all patients demonstrated early postural impairment and/or oculomotor abnormalities that encouraged a diagnostic revision. Hallucinations were the only early atypical manifestation of the hydrocephalic DLB presentation.and PSP) actually represent the hydrocephalic presentation of selected neurodegenerative disorders.Early postural impairment, falls, oculomotor impairment, and/or hallucinations are inconsistent with the diagnosis of NPH and suggest PSP or DLB as the underlying NPH mimic. We postulate that previously reported cases of “dual” pathology  contains supplementary material, which is available to authorized users. Of the 12 patients who underwent VPS placement, definite gait improvement was present in only 6 by one year and just 4 after 3 years, one third of the original VPS-treated cohort. Remarkably, pathology available in 5 patients in the VPS-treated cohort revealed the presence of neurodegenerative disorders, progressive supranuclear palsy (PSP) and dementia with Lewy bodies (DLB), each accounting for a case.Hydrocephalus as an imaging finding is commonly interpreted as potentially representing normal pressure hydrocephalus (NPH) largely because of the favorable therapeutic implications . Howeverlacement . Betweensustained response to VPS placement is paramount to justifying this invasive procedure. We examined four patients referred to us for suspected NPH but whose pathology demonstrated PSP and DLB. The preliminary diagnosis of NPH in these patients was based on the interpretation of imaging features, namely the presence of hydrocephalus judged disproportionate to the extent of surrounding parenchymal atrophy. While a careful neurological examination suggested further NPH work up was unwarranted in three patients, cerebrospinal fluid diversion in one (case 4) supported this diagnosis by yielding subjective benefits in gait and urinary function. In addition to early impairment postural reflexes, other clinical red flags against NPH emerged between 12 and 24 months. We suggest that PSP and DLB, as previously reported for Alzheimer disease (AD), is capable of generating a neuroimaging profile suggestive of communicating hydrocephalus, with ventriculomegaly disproportionate to the extent of parenchymal atrophy, prompting a diagnostic consideration for NPH and potentially misdirecting treatment toward cerebrospinal fluid diversion.Because of the large volume of NPH referrals to tertiary care centers, predicting a Four consecutive patients referred to our center for suspected NPH for whom brain autopsy was obtained were identified in our center from the years 2007–2012. After evaluation in our center, VPS placement was discouraged for the first three patients but pursued in the fourth to no avail. Written informed consent was obtained from all patients for the publication of patient-related data and videotapes.This 68-year-old woman developed balance impairment followed by falls, mostly forward, urinary incontinence, and intermittently slurred speech over a 2-year period. Head CT demonstrated mild to moderate hydrocephalus Figure A, promptThis 79-year-old man developed difficulty with “complex” leg movements, such as those required when walking across a railroad or stepping on a train wagon. Brain MRI obtained within one year was interpreted as mild hydrocephalus Figure B, promptThis 73-year-old man initially exhibited falls, visual hallucinations, irritability and combative behavior. Within two months he was unable to ambulate independently and had noticeable memory loss. Brain MRI taken at 3 months from symptom onset demonstrated moderate ventriculomegaly without overt atrophy in the apical cuts, suggesting the diagnosis of NPH Figure C. HoweveThis 72-year-old man with progressive gait and balance impairment underwent a brain MRI, which upon presence of hydrocephalus, hyperdynamic fluid signal in the third ventricle, and entrapped sulci in several cortical areas Figure D prompteThere are two major shortcomings in the appraisal of NPH as an entity, namely the absence of clinical and pathological biomarkers and the reliance on short-term response to drainage for its definition , which oBesides early impairment of postural reflexes, our patients had early cognitive impairment, either predating or occurring concurrently with gait impairment. Cognitive impairment is a regrettable component of the “classic” NPH triad. Of the 8 cognitively impaired VPS-treated patients in the Mayo Clinic series, only 1 continued to benefit at 3 years . SimilarA major pitfall of the interpretation of these data is to assume that these patients had “co-occurrence” of AD and NPH , 6, rathPSP appears to be the most common etiology of suspected NPH with a parkinsonian phenotype Table . It was Our cases and the review of the literature highlight several key clinically relevant messages: 1) early cognitive impairment is the most important “cognitive red flag” of the NPH triad and predicts an alternative diagnosis; 2) early impairment of postural reflexes, with or without falls, is the most common “motor red flag” of the NPH triad, and should suggest PSP or DLB; 3) visual hallucinations are a strong clinical biomarker of synucleinopathies  and theiIn sum, hydrocephalus in the setting of postural impairment and/or oculomotor abnormalities most probably represents PSP or DLB. Hallucinations may be the only early manifestation of the hydrocephalic presentation of DLB. An initial promising response to VPS placement does not exclude the possibility of an underlying neurodegenerative disease. Furthermore, a fully formed “classic” triad of gait impairment, urinary incontinence, and cognitive impairment appears to be more common in conditions other than NPH. The accumulating evidence suggests that early postural impairment, falls, oculomotor impairment, or hallucinations are inconsistent with the diagnosis of NPH regardless of ventricular size. Recognition of the hydrocephalic presentation of PSP and DLB can avoid unnecessary and potentially harmful shunting procedures.Additional file 1: Video S1: Patient 1 shows growling dysarthria, restriction of upgaze with supranuclear vertical gaze palsy, appendicular dystonia with dysmetria, wide-based, short-stride gait with erect posture, mild retrocollis, and impaired postural reflexes. (MP4 11 MB)Additional file 2: Video S2: Patient 2 demonstrates upgaze restriction with nystagmus but no square-wave jerks or slow saccades. There was marked gait impairment with wide base support and retropulsion on pull test. (MP4 17 MB)Additional file 3: Video S3: Patient 3 shows marked retrocollis, severe dysarthria and ophthalmoplegia. Patient is videotaped over the course of a “bad spell”, in hindsight interpreted as part of his DLB-associated cognitive fluctuations. (MP4 13 MB)Additional file 4: Video S4: Patient 4 shows a wide based, unsteady gait. Disappearance of corrective saccades to the optokinetic strip was the early clue as to his subtle saccadic impairment, and predated a later development of supranuclear vertical gaze palsy. (MP4 13 MB)Authors’ original file for figure 1Authors’ original file for figure 2Below are the links to the authors’ original submitted files for images.


Renal replacement therapy (RRT) is necessary for the survival of patients with end-stage renal disease (ESRD) both prior to kidney transplantation or in patients where kidney transplantation is not available. Peritoneal dialysis (PD) and hemodialysis (HD) are lifesaving RRTs for more than 2 million patients with ESRD worldwide . As the In this special issue of BMRI, we present a number of articles prepared in part  with a support from the EuTRiPD initiative. These are both original research papers and review papers that (i) analyze basic aspects of peritoneal cell biology using in vitro methods, (ii) mimic clinical situations in relevant PD models in rodents, and (iii) describe the outcomes of clinical studies using new biomarkers or new interventions.In the following papers, firstly studies apply in vitro models to investigate the senescence-associated proteome in mesothelial cells, the effect of differently sterilized PD fluids on mesothelial stress responses, and the contribution of mesothelial-to-mesenchymal transition to peritoneal fibroblast expansion. Secondly with respect to papers in rodent PD models a new mouse uremic model is presented, the effect of rapamycin in a mouse model is shown, and moreover clear indications are described in protective effect of paricalcitol in a PD model and another PD-fibrosis-like model. Thirdly clinical material was used in studies showing the importance of, respectively, HA, microRNA, osmolarity of fluid, and tenascin-C levels reflecting peritoneal patient status. Finally underutilization of PD is discussed as originating from less education and referral pattern and moreover it is discussed that new biomarkers in PD could contribute significantly to making choices for the future as shown by EuTRiPD. The editors feel that all these papers give a good overview of the state of art in addressing all aspects of PD.Robert H. J. BeelenDonald J. FraserPeter RutherfordJanusz Witowski


Chemotherapy can cause cachexia, which is manifested by weight loss, inflammation and muscle atrophy. However, the mechanisms of tumor and chemotherapy on skeletal muscle proteolysis, remained unclear. In this report, we demonstrated that tumor-induced myostatin in turn induced TNF-α, thus activating calcium-dependent and proteasomal protein degradation. Chemotherapy activated myostatin-mediated proteolysis and muscle atrophy by elevating IL-6. In tumor-bearing mice under chemotherapy, supplementation with fish oil and selenium prevented a rise in IL-6, TNF-α and myostatin and muscle atrophy. The findings presented here allow us to better understand the molecular basis of cancer cachexia and potentiate nutrition supplementation in future cancer chemotherapy. Real-time qPCR primers were designed using the Primer3 webware; electrophoresis was performed to verify DNA products. Reactions were run on the Bio-Rad iCycler iQ system in the presence of the Sybr-Green PCR mix . The comparative threshold cycle  method w2, 1 mM dithiothreitol (DTT), and 5 μL of a protease inhibitor cocktail (Sigma)). Proteins (20 μg/lane) were separated on a 12.5% polyacrylamide gel (a precast SDS gel (Bio-Rad)) and then transferred to a polyvinylidene difluoride membrane . Proteins were determined using antibodies against mouse IL-6 , TNF , Myostatin , MAFbX , MuRF 1 , Cathepsina L , Calpain , p-IκB-α  and FOXO1 . The antibodies then were stripped off the membrane and re-probed with a specific antibody against β-actin . The intensity was quantified using the Fotodyne Image analysis System  and the TotalLab software .Proteins from tumors were extracted with a buffer solution , rabbit anti-mouse MuRF-1  and FITC-conjugates rabbit anti-mouse MAFbx . The secondary antibody was the FITC-conjugates goat anti-rabbit IgG .Data were expressed as means ± SD. Statistical significance was determined by one-way ANOVA followed by Bonferroni's multiple comparison test (Prism Graph Pad). Differences were considered statistically significant when P<0.05.


Despite the increasing popularity of the theory of change (ToC) approach, little is known about the extent to which ToC has been used in the design and evaluation of public health interventions. This review aims to determine how ToCs have been developed and used in the development and evaluation of public health interventions globally.We searched for papers reporting the use of “theory of change” in the development or evaluation of public health interventions in databases of peer-reviewed journal articles such as Scopus, Pubmed, PsychInfo, grey literature databases, Google and websites of development funders. We included papers of any date, language or study design. Both abstracts and full text papers were double screened. Data were extracted and narratively and quantitatively summarised.A total of 62 papers were included in the review. Forty-nine (79 %) described the development of ToC, 18 (29 %) described the use of ToC in the development of the intervention and 49 (79 %) described the use of ToC in the evaluation of the intervention. Although a large number of papers were included in the review, their descriptions of the ToC development and use in intervention design and evaluation lacked detail.The use of the ToC approach is widespread in the public health literature. Clear reporting of the ToC process and outputs is important to strengthen the body of literature on practical application of ToC in order to develop our understanding of the benefits and advantages of using ToC. We also propose a checklist for reporting on the use of ToC to ensure transparent reporting and recommend that our checklist is used and refined by authors reporting the ToC approach.The online version of this article (doi:10.1186/s13012-016-0422-6) contains supplementary material, which is available to authorized users. Most public health interventions are inherently complex, with multiple interacting components, delivered at multiple levels. This complexity makes them difficult to evaluate using traditional experimental designs. Public health interventions often rely on ongoing quality improvement based on the implementation experience. Therefore, they may not reach the level of stability required to conduct evaluations such as randomised controlled trials (RCTs) . Some reTheory-driven evaluation is a collection of evaluation methods which emphasise the importance of understanding how and why a programme works in order to evaluate it , 5. By plong-term outcome and then maps the required process of change and the short- and medium-term outcomes required to achieve this [assumptions about what needs to be in place for the ToC to occur are made explicit as well as the contextual factors which influence the ToC. Additional elements of a ToC can include beneficiaries, research evidence supporting the ToC, actors in the context, sphere of influence, strategic choices and interventions, timelines and indicators [ToC was developed by Weiss and others  within teve this . During dicators . These edicators .The ToC is usually developed in consultation with stakeholders through workshops or interviews although the participation of stakeholders can vary substantially in practice . For exaToC is distinct from sociological or psychological theories which describe why change occurs although these may be used to inform the ToC . For exaToC differs from other theory-driven approaches to evaluation despite similar origins. For example, although logic models outline the inputs, processes, outputs and outcomes of a programme in a similar manner to ToC, they can be rigid and do not make explicit the causal pathways through which change happens in the way that ToC does . SimilarToC has been used widely in the development sector for programme development and evaluation by funders such as the UK’s Department for International Development, Comic Relief, Grand Challenges Canada and the Gates Foundation , 19. HowThe lack of a systematic review means that there is no clear idea of how the ToC has been used and reported in the peer-reviewed and grey literature in relation to public health interventions. Given the increasing popularity of the ToC approach, understanding how it is has been used and described previously allows future users of the approach to learn from the work of others and build upon it. It also helps to move towards a more consistent way of using the ToC approach.How are ToCs for public health interventions developed and refined? development of an intervention; implementation of the intervention; development of indicators for measurement; evaluation of the intervention, including statistical approaches; and conceptualisation/evaluation of the influence of context.How is the ToC approach used in theIn this review, we sought to review both peer-reviewed and grey literature to determine how ToCs have been developed and used in the development and evaluation of public health interventions globally. Specifically, we sought to answer the following questions:The authors developed a protocol for this review which was agreed prior to the commencement of the study. This is available in Web Additional file The inclusion and exclusion criteria are listed in Table We required papers to specifically mention that they used “theory of change” and excluded those who did not for the following reasons. Firstly, as described above, there are a range of overlapping definitions for ToC and other programme evaluation methods. Given the often minimal amount of detail provided about the programme theory in papers, and especially in abstracts, it would be difficult to enforce a standard criteria for ToC against which papers could be evaluated for inclusion. Secondly, piloting the initial broad search strategy  returned more than 20,000 hits in only three databases. By refining the criteria to specify ToC by name, we were able to thoroughly explore literature which explicitly self-identified using ToC.As the focus of this review was on public health interventions, we excluded papers in which the long-term outcome of the ToC was a change within an individual rather than change in the population. For example, a ToC describing how cognitive behavioural therapy may impact on an individual’s cognitive processes and behaviour would be a change within the individual. However, if the focus of the ToC was on how a cognitive behavioural therapy intervention impacted the prevalence of depression would be change in the population. We excluded reviews and methodological or advocacy papers unless they included an example of how a ToC was developed or how ToC was used in the design, evaluation and/or implementation of a public health intervention. We did not limit the inclusion by date, language, study design or type of publication.The database searches were conducted between the 16th November and the 4th December 2013 by EB. The main search term used was “theory of change”. Where the database allowed, we limited this to health or healthcare and to humans. We searched databases of peer-reviewed journal articles . An example of a search string used for PyschInfo was “theory of change” AND . We also searched grey literature databases  and the first 50 pages of a Google search. The websites of Comic Relief, DFID, Grand Challenges Canada, The Bill and Melinda Gates Foundation, HIVOS, World Vision, the Robert Wood Johnson foundation, Actknowledge and the Theory of Change Community were also searched. In addition, we contacted experts in the field and sent requests for papers to two existing global mailing lists for evaluators: MandENEWS and Pelican.Following the search of databases of peer-reviewed journal articles, the titles and abstracts of the search results from peer-reviewed papers were exported into Endnote  where duFollowing the grey literature search as described above, all potentially relevant results were saved into Evernote . These wAny differences between authors’ opinions were resolved via discussion throughout the review process.The data from the papers were extracted by the first author (EB) onto a data extraction form. This included information on authors, publication dates, the type of interventions and outcomes, the development of ToC, the use of ToC in the design, implementation and evaluation of the intervention and the influence of context. The data collection form also included key principles of theory-driven evaluation proposed by Coryn et al. . These iDescriptive statistics were calculated using STATA 13 . The papIn total, 566 abstracts were screened, resulting in 200 full text peer-reviewed articles which were assessed for eligibility. An additional 65 records were identified from the grey literature search and screened for eligibility. A total of 62 papers were included , 26–82. The publication dates of the papers range between 1999 and 2013, with a steady increase in papers over time  of the papers developed their ToCs prospectively and 19.4 % (n = 12) retrospectively. The remainder either developed their ToC during project replanning (n = 3.5 %) or did not specify when they developed their ToC .Forty-nine papers (79 %) included some information on the ToC development process. Forty-three percent , diagrams  or both . In one case, a table was used. Table The resultant ToCs were described using narrative summaries n = 15, 3.1 %, diaEighteen papers (29 %) described the use of ToC in the development of a public health intervention. The majority of these reported that they used the ToC as a framework for the intervention , 43, 70 Forty-nine papers (79 %) describe the use of ToC in the evaluation of the intervention. This includes the development of indicators, the overall evaluation design and data analysis.The development of indicators used in the ToC was described in 28 papers. The indicators were often developed from the short-, medium- or long-term outcomes described in the ToC , 81, 84.The majority of papers (62.9 %) reported formulating their evaluation questions around the ToC. However, the papers varied in the amount of detail they provided on this process. A common description was that the ToC was used to provide a framework for the evaluation , 81, 82.The data collection and analysis methods used varied greatly across papers. Data collected for the evaluation included routinely collected data , 44, cusFew papers explicitly explored the influence of context of the intervention in relation to ToC. Although some ToCs mentioned context, particularly those with a realist evaluation focus, there was little description of how context affected the interpretation of the evaluation. There were some exceptions , 64, 72.Few papers reported on the identification of breakdowns and side effects, effectiveness or efficacy and causal explanation as described by Coryn et al. . Only foIn this systematic review, we provide an overview of how ToCs have been developed and used to develop and evaluate public health interventions. As expected, there is variation in how ToCs are developed and used in evaluation although the papers report very little detail about the ToC process.We have shown that the ToC approach has been in use since at least 1999 with 62 papers found in peer-reviewed journals and grey literature. This was significantly more than expected, given that Coryn et al.  found onIn this review, many papers provided little detail in relation to the process of ToC development and how the ToC was used to design the intervention or conduct the evaluation. For example, Bonner  describeIn contrast, other papers provided extensive detail on the ToC development process. For example, Hernandez and Hodges  describeA range of methods were used to develop ToCs. The methods ranged from participatory methods which encourage stakeholder participation and ownership of the ToC such as workshops and working groups, to more evaluator focused approaches such as programme observation and review of programme documentation. Although the reason for the choice of methods was rarely made explicit by the authors, these methods were presumably chosen based on the purpose, depth and level of stakeholder buy-in the ToC required. For example, the examples of the development of systems of care for children and adolescents with mental and behavioural disorders viewed stakeholder participation as very important and therefore held a series of workshops with multiple stakeholders from different government departments, service providers, families and service users , 50, 61.The lack of detail in most of the examples in this review makes it difficult to assess the thoroughness of ToC development. In many cases, the ToC seems to have been developed superficially and then used in a cursory way during evaluation. Similarly, where diagrams or narrative summaries of ToCs are presented in the papers, very little detail is included. Most authors present the long-term outcomes, sequence of change, beneficiaries and context. However, very few make their assumptions explicit although Vogel identifies these as a core part of ToC . Where Tn = 2). Given the popularity of ToC as a monitoring and evaluation tool by international development agencies such as the Department for International Development, UK, [A surprising finding of the review was the paucity of papers that describe the use of ToC for use during the implementation of the intervention (ent, UK, , we had ToC theorists such as Connell and Kubisch  emphasisMost papers failed to explicitly discuss the results of the ToC in relation to unexpected outcomes, direction of causation and mediation of effects. This is similar to the conclusions drawn by Coryn et al. who report that programme theory was not used in any meaningful way to develop evaluation questions or plan and conduct and interpret the analysis .It is interesting to note that no studies used ToC alongside RCTs as a method to unpack the programme theory underpinning the intervention. As we have noted previously, ToC holds much potential for this as RCTs alone are no longer considered adequate for the evaluation of complex health interventions .Detailed reporting of the ToC process is particularly important as definitions of ToC differ considerably . Many paTwo limitations to this review are the lack of double data extraction and the inability to effectively measure the quality of the included papers. We did extract data on a checklist of ToC components proposed by Vogel  and prinWe suggest that authors planning to report on ToC to guide the development or evaluation of public health interventions provide more detail on the ToC process to readers. In particular, it is important to make the ToC used explicit and this is usually easier in diagrammatic form. Complex ToCs can be simplified in a summary diagram with detailed ToCs provided as web appendices. This will help the reader to understand the authors’ expected pathways of change and judge their validity. In addition, it is imperative that authors describe in detail how the ToC was developed and used. This is particularly important as there is no single way to develop or use a ToC. Making the process explicit helps readers judge the credibility of the ToC and strengthen the literature in this field.We have therefore developed a checklist based on this review and the work of Coryn et al.  and VogeThe ToC approach is widespread in the public health literature. Clear reporting of the ToC process and outputs is important to improve to allow the readers a thorough understanding of the work and allows them to judge the validity of the approach. We recommend that our proposed checklist is used and refined by authors reporting the ToC approach.


To promote research activities in a particular research area, it is important to efficiently identify current research trends, advances, and issues in that area. Although review papers in the research area can suffice for this purpose in general, researchers are not necessarily able to obtain these papers from research aspects of their interests at the time they are required. Therefore, the utilization of the citation contexts of papers in a research area has been considered as another approach. However, there are few search services to retrieve citation contexts in the life sciences domain; furthermore, efficiently obtaining citation contexts is becoming difficult due to the large volume and rapid growth of life sciences papers.Here, we introduce the Colil (Comments on Literature in Literature) database to store citation contexts in the life sciences domain. By using the Resource Description Framework (RDF) and a newly compiled vocabulary, we built the Colil database and made it available through the SPARQL endpoint. In addition, we developed a web-based search service called Colil that searches for a cited paper in the Colil database and then returns a list of citation contexts for it along with papers relevant to it based on co-citations. The citation contexts in the Colil database were extracted from full-text papers of the PubMed Central Open Access Subset (PMC-OAS), which includes 545,147 papers indexed in PubMed. These papers are distributed across 3,171 journals and cite 5,136,741 unique papers that correspond to approximately 25 % of total PubMed entries.By utilizing Colil, researchers can easily refer to a set of citation contexts and relevant papers based on co-citations for a target paper. Colil helps researchers to comprehend life sciences papers in a research area more efficiently and makes their biological research more efficient.The online version of this article (doi:10.1186/s13326-015-0037-x) contains supplementary material, which is available to authorized users. The ability to efficiently identify current research trends, advances, and issues in a research area is highly important to researchers to promote their research activities. For example, in cases of international collaborative research, researchers often need to read relevant papers and summarize the current knowledge about the research area beyond their own research fields . AlthougIn life sciences papers, citations are widely used and typically consist of two parts: a) a list of references found at the end of the citing paper that provides full bibliographic information for each source; and b) reference markers located in the text that are linked to the references . The texTo make better use of citation data, we built the Colil database as Linked Open Data (LOD) by using the Resource Description Framework (RDF). RDF is a promising technology for describing, publishing, and linking life sciences data on the Web . In addiOur contribution is to provide LOD that include citation contexts in the life sciences domain. We provide three types of services that relate to the Colil database: a legacy web search interface (Colil), a SPARQL endpoint, and an ftp site to download dump files in RDF. The data needed for the Colil database have been extracted from open access papers deposited in the PubMed Central Open Access Subset (PMC-OAS) , which ii.e., by PubMed ID or keywords). If a user initiates a search by typing a PubMed ID into the upper text box In the cited paper area, Colil displays bibliographic information about the hit cited paper. This includes the title, authors, journal, year, volume, issue, and PubMed ID, and the title is anchor text that links to the corresponding PubMed page.Cited paper area (the upper right)In the citation context area, there is a list of the citation contexts for the hit cited paper. Colil highlights the reference markers, which are delimited by > > and < < in the citation contexts. Each row also includes the paper’s title and the section title of the citing paper. Furthermore, there are links to the corresponding pages at Colil, PubMed, and PMC. Rows in the list can be sorted in ascending or descending order for one of the following factors: PubMed ID, paper title, and section title. The list shows 20, 40, 60, or 100 results per page depending on the search condition. If the user clicks the anchor text for “Show query” on the upper side of the list, Colil shows the corresponding SPARQL query to obtain the result from our SPARQL endpoint.Citation context area (the lower right)In the relevant paper area, there is a list of the relevant papers that are co-cited with the hit cited paper. Each row also includes a relevance score, the titles of relevant papers linking to the corresponding Colil page, and a link to the corresponding PubMed page. The relevance score is equal to the number of citing papers Fig. . Rows inRelevant paper area (the lower left)Colil searches for a cited paper in the Colil database and then returns a list of the citation contexts for it and its relevant papers based on co-citations. Users can choose a search method , miRecords (2013), and miRTarBase (2013), which host the largest collection of manually curated experimental data;The experimentally validated miRNA-target interactions information have been documented in various databases, such as TarBase, MiRecords, miRWalk, miRTarBase, and miRNAMAP;TarBase and miRTarBase document the experimentally-verified information on miRNA-target interactions along with their validation methods such as reporter genes, qPCR, western blotting, microarrays, proteomics, sequencing, and degradome sequencing data;http://www.bioconductor.org/);For each miRNA, candidate targets have been inferred using data from six different databases  using the RmiR package from R Bioconductor  by using databases that collect manually curated miRNA–gene interactions with an experimental support. For this purpose, the researcher needs to identify current trends and issues concerning the databases. To obtain this information, by using Colil, the researcher can search for papers relevant to the databases and utilize the citation contexts for the papers. The researcher initiates a search for papers by typing keywords “database miRNA target interactions manually curated experimental support”. As the result of the PubMed search , Colil returns four papers, and three of them are original papers of widely-used databases such as TarBase, miRecords, and miRTarBase. Then, the researcher retrieves the corresponding citation contexts for the papers from Colil [see Additional file In addition to Colil, we also provide a SPARQL endpoint that makes it possible for those users who develop their own applications to retrieve data in the Colil database. In practice, Colil retrieves and uses data from the Colil SPARQL endpoint. For instance, Table ftp://ftp.ncbi.nlm.nih.gov/pub/pmc. In March 2014, there were 713,029 papers. From these PMC-OAS papers, we then selected 670,497 papers that are indexed in PubMed; this was so that we could provide users with the PubMed search function to look up papers. Finally, of these 670,497 papers, we selected 545,147 that cited at least one PubMed-indexed paper.We downloaded PMC-OAS papers, which are downloadable as XML files from the NCBI  FTP site at Obtaining full-text paperse.g., 1–6) or separated by a delimiter . We therefore built a parser for the different formats and types of reference markers. We used PubMed-indexed citations only.We parsed the XML files to extract references and reference markers. These components are easily identifiable because the files contain XML tags such as ref and xref. We then matched each bibliographic information component to its corresponding reference marker(s). Different journals utilize different formats for reference markers, and some reference markers are grouped together within a pair of parentheses; these multiple reference markers are concatenated by a connector , and the cocitationWith property, which has characteristics of symmetry, links the cited paper to the relevant paper. The RelevantBibliographicResource is used to describe the co-citation, which is between co-cited papers and has a relevance score using the RelevantScore property. The hasRelevantBibliographicResourceOf property links the cited paper to the co-citation, and the hasRelevantPaperId property links the co-citation to the relevant paper. The PubMed class and the Authors property are used to describe the bibliographic metadata and its authors, respectively. The pmcid property is used to describe PMC IDs, which are identifiers of papers in PMC.The Developing a newly compiled vocabularycolil:ReferencePaper and the colil:CitationPaper classes, respectively. We used the bibo:cites property to link the citing paper to the cited paper. We used the doco:contains property to represent a section in a document such as Introduction or Methods. Each section has a title and citation contexts, which are represented as the dcterms:title and the doco:contains properties, respectively. The citation context is represented as the colil:Context class, and the text is represented as the rdf:value property. We use the colil:mentions property to link the citation context to the cited paper.We built the Colil database by using COLILO. Figure colil:RelevantPaper class is used to represent the relevant paper, which is co-cited with another paper by other papers. We used the colil:cocitationWith property to link the cited paper to the relevant paper. To represent a relevance score between the cited paper and relevant paper, we provided the co-citation, which is represented as the colil:RelevantBibliographicResource class. The co-citation includes the relevance score, which is represented as the colil:RelevantScore property. The colil:hasRelevantBibliographicResourceOf property links the cited paper to the co-citation, and the colil:hasRelevantPaperId property links the co-citation to the relevant paper.Figure colil:pmcid and bibo:doi properties, respectively. The rdfs:seeAlso property is used to link external resources such as PMC, Biotea, DOI system, and TogoWS. Bibliographic metadata are represented as the colil:PubMed class by using the rdfs:seeAlso property. We used the togows:pmid, colil:Authors, togows:ti, and togows:so properties to represent the bibliographic metadata of PubMed IDs, authors, title, and sources.Figure Building the Colil databaseFigure Over the past 10 years, the number of PubMed-indexed papers published each year in PMC-OAS has grown, with the most recent years showing an exponential growth Fig. . We obtaConversely, 5,136,741 PubMed-indexed papers have been cited by at least one PMC-OAS paper; the cited papers correspond to approximately one-quarter of the entire PubMed entries and are distributed across 11,588 journals. Table We found 27,832,062 co-citations in cited papers. To calculate the chances of a given paper having a co-cited paper in a different relevance score range, we classified 11 cases of co-citations according to their relevance scores   as the tAs another use case, we envisage that Colil will help researchers to write citation contexts. In citation contexts, researchers must clarify the relationships between their paper and the papers cited within their paper . HoweverDue to the limited number of citing papers in the Colil database, there are cases where Colil is not able to provide enough citation contexts for a target paper. For example, papers cited in five or fewer citation contexts account for approximately 76 % of all the cited papers in the Colil database. One of the factors causing this issue is that the number of PubMed-indexed papers in PMC-OAS only corresponds to approximately 4 % of total PubMed entries at present; however, we expect that this situation will gradually improve because open access publications are gaining popularity and becoming the norm . Figure In contrast, there were 11,086 papers that were cited in 100 or more citation contexts. Although Colil may provide users with enough information and perspectives for these papers, it can be time consuming to find appropriate citation contexts for references. To alleviate this issue, we are considering providing users with a function to narrow down citation contexts according to their purposes. In previous studies, Amjad et al.  and TeufAs far as we know, Microsoft Academic Search (MAS) developed by Microsoft Research is the only search service to provide citation contexts in the life sciences domain except for Colil . MAS is A citation context can be defined as sentences that comment on the work of a citing paper. Based on our preliminary survey of citation contexts, we defined a citation context as a sentence that contains a reference marker, except when the reference marker is located at the end of the sentence. We call a sentence that contains a reference marker an “explicit citing sentence” . In thisThe Colil database includes citations, citation contexts, and co-citations extracted from full-text papers of PMC-OAS. To help users to utilize the database in their respective research environments, we provide three types of services: a Colil search service, a SPARQL endpoint, and an ftp site. Colil can facilitate finding a set of citation contexts and relevant papers based on co-citations for a target paper. This should help researchers to comprehend life sciences papers in a research area more efficiently and make their biological research more efficient..ftp://ftp.dbcls.jp/colil. COLILO is freely available under a Creative Commons Zero License at http://purl.jp/bio/10/colil/ontology/201303. Colil is available for public access at http://colil.dbcls.jp/browse/papers/.The Colil database is available under a Creative Commons Attribution 2.1 Japan License and can be downloaded at


To describe parental experiences of providing skin-to-skin care (SSC) to their newborn infants.SSC care for newborn infants has been reported to have positive physiological and psychological benefits to the infants and their parents. No systematic review regarding parental experiences has been identified.In this first part of a meta-study, the findings of a systematic literature review on parental experience of SSC care are presented.Four databases were searched, without year or language limitations, up until December 2013. Manual searches were performed in reference lists and in a bibliography of the topic.After a quality-appraisal process, data from the original articles were extracted and analysed using qualitative content analysis.The systematic and manual searches led to the inclusion of 29 original qualitative papers from nine countries, reporting experiences from 401 mothers and 94 fathers. Two themes that characterized the provision of SSC emerged: a restoring experience and an energy-draining experience.This review has added scientific and systematic knowledge about parental experiences of providing SSC. Further research about fathers’ experiences is recommended. Skin-to-skin care (SSC) started as kangaroo mother care (KMC) in a Colombian hospital in the late 1970s as a way to avoid cross-infections caused by a shortage of incubators in neonatal units, which forced preterm and low-birth weight infants to share incubators with each other. Another aim of KMC was to facilitate contact between mothers and their newborn babies, thus preventing infant abandonment and humanizing neonatal care  to shorter periods during the day  , Mesh-terms (PubMed) and key words from some relevant manually identified articles, the search-terms Kangaroo, Kangaroo Care, Skin-to-skin, Parents, Parental attitudes, Parental behaviour, Infant care, Mother, Father and Parent–child relations were used in different combinations. The searches were performed in March 2009. Since the initial searches revealed extensive published research on this topic from Latin-America, further database searches were performed in SciElo and LILACS, two databases specialized in Latin-American research. To ensure actuality, the literature searches were repeated in June 2010 and in November 2013, using the same methodology .Manual searches were also performed in a bibliography compiled by Susan Ludington , in reference lists and based on personal knowledge.Together the systematic searches resulted in 328 original papers of which 24 were duplicates. The manual search added a further 16 articles to be appraised for possible inclusion. Thus, the first set of articles for title and abstract review comprised 320 papers.As it was not possible to restrict the search to qualitative papers, the titles, and when available, the abstracts were scrutinized by each of the authors individually in order to identify papers that met the inclusion criteria. A large number of papers used quantitative methodology or focused on other aspects of newborn care, such as experiences of the neonatal intensive care unit (NICU) environment or breastfeeding, and were thus excluded from further analysis.Sixty-eight of the 320 papers were retained for the intended full text review. However, two of them could not be retrieved in full text, leaving 66 for further evaluation.The authors read and appraised the full text of the 66 articles and compared their decisions pertaining to inclusion/exclusion. Each paper was scrutinized by 2–3 researchers in Sweden and Brazil  and, in one case, by a Japanese researcher (one article in Japanese).All papers considered for inclusion were appraised by means of the Primary Research Appraisal Form presented by Paterson et al. . This ton=401) while 94 fathers where included.As a result of the quality appraisal, 26 papers were excluded due to methodological reasons  or for being beyond the scope of this review. Finally, an additional 11 papers were excluded because of flaws in the description of aims or analyses or because it was impossible to distinguish parental experiences from other findings . Most ofData related to parental experiences were retrieved from quotations in the original papers, as well as from the findings sections in these papers. All relevant data were extracted and copied into a “Citations and findings extract template,” which in the further process was regarded as the primary data for analysis.The meta-data analysis synthesizes data from the text of the included literature. The same data analysis techniques that can be used in primary research are also applicable to meta-data-analysis  was described as emanating from SSC  of this meta-research study. The use of nVivo8 facilitated the analysis phase by providing a good overview of the data, thus enabling the process of identifying patterns (Another possible limitation is that three of the original papers included report the experiences from delivery care settings while the rest reflect experiences from neonatal or KMC-settings. It was judged as best to include those three articles as they met the inclusion criteria in the searches. The findings from these papers do not render any exclusive categories; they just add some nuances in the overall identified pattern.This qualitative literature review has added scientific and systematic knowledge about parental experiences of providing SSC to their newborn infant. It constitutes a valuable complement to previous meta-analyses on physiological and psychosocial outcomes on mothers and infants, and it offers a more detailed picture than the previous meta-analyses on the topic. From an evidence-based perspective, this systematic review shows that mothers and fathers who provide SSC can experience the SSC as restorative, as well as energy-draining. However, as the mothers’ experiences previously have dominated research of the parental experiences of SSC, studies about the fathers’ experiences of providing SSC should be undertaken, in various geographical and cultural settings. Such knowledge could lead to a better understanding of the fathers’ situation within neonatal care.


Case control analysis of the RV144 phase III vaccine trial demonstrated that plasma IgG binding antibodies specific to scaffolded proteins expressing the first and second variable regions (V1V2) of HIV envelope protein gp120 containing the α4β7 binding motif correlated inversely with risk of infection. Subsequently antibodies to the V3 region were also shown to correlate with protection. The integrin receptor α4β7 was shown to interact with the LDI/V motif on V2 loop but recent studies suggest that additional regions of V2 loop could interact with the α4β7. Thus, there may be several regions on the V2 and possibly V3 loops that may be involved in this binding. Using a cell line, that constitutively expressed α4β7 receptors but lacked CD4, we examined the contribution of V2 and V3 loops and the ability of V2 peptide-, V2 integrin-, V3-specific monoclonal antibodies (mAbs), and purified IgG from RV144 vaccinees to block the V2/V3-α4β7 interaction.The gut mucosal homing integrin receptor α4β7 present on activated CD4We demonstrate that α4β7 on RPMI8866 cells bound specifically to its natural ligand mucosal addressin cell adhesion molecule-1 (MAdCAM-1) as well as to cyclic-V2 and cyclic-V3 peptides. This binding was inhibited by anti-α4β7-specific monoclonal antibody (mAb) ACT-1, mAbs specific to either V2 or V3 loops, and by purified primary virions or infectious molecular clones expressing envelopes from acute or chronic subtypes A, C, and CRF01_AE viruses. Plasma from HIV-1 infected Thai individuals as well as purified IgG from uninfected RV144 vaccinees inhibited (0–50%) the binding of V2 and V3 peptides to α4β7.Our results indicate that in addition to the tripeptide LDI/V motif, other regions of the V2 and V3 loops of gp120 were involved in binding to α4β7 receptors and this interaction was blocked by anti-V2 peptide, anti-V2 integrin, and anti-V3 antibodies. The ability of purified IgG from some of the uninfected RV144 vaccinees to inhibit α4β7 raises the hypothesis that anti-V2 and anti-V3 antibodies may play a role in blocking the gp120-α4β7 interaction after vaccination and thus prevent HIV-1 acquisition. The HIV field has expended great efforts to determine the mechanism(s) of protection observed in the HIV-1 RV144 phase III clinical trial. Immune correlate analysis and subsequent secondary analysis showed that antibodies against the HIV-1 Env gp120 V1V2 region correlated inversely with the risk of infection . This re4β7 integrin on lymphocytes binds to its cognate ligand MAdCAM-1 expressed on endothelial cells leading to the adhesion, extravasation, and homing of these lymphocytes to the gut tissues. The importance of the gut homing receptor α4β7 was further highlighted by the findings that it can also serve as a receptor for HIV-1 and SIV transmission leading to the up-regulation of LFA-1 and spread of HIV-1 from cell-to-cell through virological synapses  with chimeric transgenes encoding for HLA-DR*0401 [HLA-DRA/HLA-DRB1*0401] fused to the I-Ed MHC- II molecule)  that aftnfection . It has nfection . A stronnfection . The abosmission .4β7 has been thought to be through a conserved tripeptide motif LDI(V) present at the tip of V2 loop of HIV-1 gp120 , C (C-6980v0c22) [GenBank:HM215344], A(851891); Chronic CRF01_AE (CM235.2) [AF259954.1], C (ET02220LucR) [U46016]) [96-well plates were coated with MAdCAM-1 as described above. RPMI8866 cells (2 X 10U46016]) –32 or wi® was used as a nonspecific antibody control. Synagis® was incubated for 45 minutes with either MAdCAM-1 or with RPMI8866 cells and then placed in the assay system. The remainder of the assay was similar to that described above. Significance was determined by paired Student’s t test.Viruses were tested in triplicate in two independent experiments. In additional experiments, mannose, HIV-1 p24, and ovalbumin (0.2–10 μg/ml) were used in the competition assay as nonspecific protein controls (data in 6/ml) were incubated with V2-specific mAbs , V2i mAbs , V3 specific mAbs  or with a non-V2-specific mAb CH54 (5–50μg/ml), plasma from HIV-1 uninfected or naturally infected individuals (WRAIR protocol #1617), or with purified IgG (WRAIR Protocol #900) (10 μg/ml) from RV144 pre and post-vaccinated (6 month) individuals for 45 minutes at 37°C before being added in triplicate to the peptide coated plates for 1 hour at 37°C. The rest of assay is similar to that described in detail above. CH58, CH59, and CH54 are human monoclonal antibodies isolated from RV144 vaccinees [Streptavidin-coated plates were incubated with biotinylated cyclic V2 TH023 peptide (5 μg/ml in bicarbonate buffer as described above) for 1 hour at 37°C. RPMI8866 cells  or presence of mAb ACT-1 (open circles) were added to the wells, washed, and the binding of α4β7 on RPMI8866 cells to MAdCAM-1 was detected by the fluorescence of the added AlamarBlueIn order to demonstrate that HIV-1 envelope protein on the surface of virions is capable of binding α4β7 and thus inhibiting the binding of α4β7 to MAdCAM-1, varying amounts (based on p24 concentrations) of purified primary viruses including subtype B , subtype CRF01_AE 92TH023; , full-leIt has been previously reported that the binding of α4β7 integrin receptor to HIV-1 envelope protein is through the V2 region . Using oSimilar experiments were performed with biotinylated cyclic V3 peptides derived from subtypes CRF01_AE (TH023), B (MN), and acute subtype C (C06980v0c22) viruses. V3 peptides bound α4β7 integrin on RPMI8866 cells , which cThe schematic for the peptide competition assay is shown in In the RV144 immune correlates study, the vaccine-induced responses targeted multiple binding epitopes in the mid region of the V2 loop aa 169–184) that contained the integrin-binding motif LDI/V, which is also the motif present in MAdCAM-1. The vaccine-induced responses were associated with a decreased proportion of infecting viruses carrying residue K169 and an increased proportion of infecting viruses carrying I181 . Therefo9–184 tha®, a mAb against Respiratory Syncytial Virus (RSV) was added to MAdCAM-1 coated plates followed by the addition of RPMI8866 cells , which does not bind to the V2 or V3 region. These 3 mAbs were isolated from RV144 vaccinees . In addi66 cells  or RPMI8cells (®  and thenHuman V3-specific mAbs (2219 and 2557) were incubated with either cyclic V3 TH023  or V3 MNPlasma samples from Thai blood donors uninfected or infected with CRF01_AE virus were studied to determine if plasma from uninfected or naturally infected individuals could inhibit α4β7 on RMPI8866 cells from binding to either cyclic V2-TH023 or V2-MN peptides. Plasma samples from 10 volunteers (diluted 1:200) were individually incubated with either cyclic V2-TH023 or V2-MN peptide-coated plates, washed, and followed by the addition of RPMI8866 cells . The inhNext we studied the ability of purified IgG from 10 uninfected RV144 vaccinees, pre (visit 1) and week 26 , to inhibit α4β7 integrin binding to cyclic V2 TH023 and MN peptides . Two difThe α4β7 integrin receptor on the surface of T cells has been shown to interact with the V2 loop through the LDI/V motif . CryoEM In vivo studies in rhesus macaques have demonstrated that targeting α4β7 by administering an anti-α4β7 monoclonal antibody during acute infection reduces mucosal transmission of SIV mac251 [The RV144 immune correlates study has directed the focus of the HIV-1 field to the V1V2 and V3 regions of HIV-1 envelope protein gp120 . HoweverV mac251 .in vitro assay that utilizes primary CD4+ T cells [Both in vitro and SIV transmission /infection studies have their own limitations. In the host mucosa, the virus has to be captured from a relatively small inoculum in a short period of time and the initial interactions between the viral envelope, CD4, and α4β7 might be crucial. The current  T cells  for the  T cells . Theoret T cells . Several T cells , 42, 47 In the RV144 Phase III trial, the majority of the antibody responses to the V2 region were directed against the mid-region of the V2 loop, which included the LDI/V motif . HoweverSurprisingly, both MN and TH023 V3 peptides strongly inhibited (80%) the binding of MAdCAM-1 to α4β7 receptors. The inhibition was specific as the interaction could be blocked by ACT-1. The MN and TH023 V3 peptide sequences vary considerably between each other and their respective V2 sequences, thus providing additional support that besides the LDI motif, other regions in V2 and V3 are important for the α4β7-V2/V3 interaction. The binding could be due to charged amino acids and/or discontinuous epitopes in the highly dynamic V2/V3 loop regions. The direct intramolecular interaction between V2 and V3 loops stabilized by sulfated tyrosines within the V2 loop is further supported by biological and structural studies , 49. Fur4β7 binding has been demonstrated with a panel of V2-specific mouse mAbs whose epitopes overlap the integrin-binding site [Inhibition of αing site . The RV1ing site . In our Recently Mayr et al  and UpadAnti-V3 antibodies are present in the sera of virtually all individuals infected with HIV-1 , 55. Sev+ T cells as well as cell lines stably expressing α4β7. The binding as well as the infectivity of α4β7-activated CD4+ T cells was decreased in the presence of anti- α4β7 antibodies [Based on neutralization data, it is believed that V1V2 and V3 epitopes are not readily accessible on the envelope spikes , 61. Rectibodies . Of the tibodies , 41, whiThe two primary subtype B viruses, SF162 and TH023, that were able to inhibit α4β7-binding in our study are predicted to have a coiled structure and an α-helix in the 166–169 region of V2 while JRFL and US-1 that did not inhibit do not have a predicted coiled structure or α-helix. JRFL and US-1 are predicted to have a broken α-helix structure and a β-turn structure, respectively. This specific amino acid region of V2 contains both the sieve mutation at position 169  and a crDuring the course of HIV-1 infection, binding antibodies to various regions of the envelope protein are induced. Our studies indicate that plasma from chronic HIV-1 infected individuals contain antibodies directed against the V2 region that inhibit the binding of α4β7 to the V2 peptides to varying degrees. Interestingly, purified IgG from RV144 vaccinees also inhibited the binding of α4β7 to V2 TH023 and MN peptides, demonstrating that vaccination can induce these types of antibodies.Besides the known LDI motif, our study demonstrates previously unidentified regions in HIV-1 V2 and V3 loops that are important in α4β7 binding. As has been previously suggested, a combination of structure and charge within V2 may be the critical features modulating the effect of the α4β7-gp120 interaction. V2- and V3-specific binding mAbs were able to block the α4β7 binding. Epitopes involved in binding to the α4β7 region were accessible on PBMC produced primary infectious viruses and on acute infectious molecular clone viruses. From these data, we hypothesize that early induction of V2 specific antibodies targeting the α4β7 region as a result of vaccination can play a role in viral acquisition. Understanding the interaction of V2 and V3 regions of HIV-1 envelope with α4β7 will contribute to the selection and design of immunogens that can induce antibodies to these regions with protective functions.S1 Data(FCS)Click here for additional data file.S2 Data(FCS)Click here for additional data file.S3 Data(FCS)Click here for additional data file.S4 Data(FCS)Click here for additional data file.S5 Data(FCS)Click here for additional data file.S6 Data(FCS)Click here for additional data file.S7 Data(FCS)Click here for additional data file.S8 Data(FCS)Click here for additional data file.S9 Data(FCS)Click here for additional data file.S10 Data(FCS)Click here for additional data file.