In this paper I introduce computational techniques to extend qualitative analysis into the study of large textual datasets. I demonstrate these techniques by using probabilistic topic modeling to analyze a broad sample of 14,952 documents published in major American newspapers from 1980 through 2012. I show how computational data mining techniques can identify and evaluate the significance of qualitatively distinct subjects of discussion across a wide range of public discourse. I also show how examining large textual datasets with computational methods can overcome methodological limitations of conventional qualitative methods, such as how to measure the impact of particular cases on broader discourse, how to validate substantive inferences from small samples of textual data, and how to determine if identified cases are part of a consistent temporal pattern. Conventional qualitative methods for analyzing text are valuable, but they are also labor-intensive and do not scale well beyond small textual samples. Close reading and manual content coding, for example, are increasingly inadequate for examining the large textual datasets that are emerging as archives of books, newspapers, journal articles, and media transcripts assume digital form. In this paper I address this pressing methodological problem by demonstrating how computational methods can extend the reach of qualitative analysis into large textual datasets.As an illustrative exercise I analyze demarcation between science and non-science in public discourse. Such demarcation is conventionally analyzed through close readings or qualitative coding of small textual datasets generated during specific cases of scientific controversy, for example dozens of personal letters Through this exercise I demonstrate how computational data mining techniques can identify, and evaluate the significance of, qualitative information in large textual datasets. I also advance qualitative methodology by introducing computational techniques for measuring the impact of particular cases on broader discourse, validating substantive inferences from case studies, and determining if identified cases recur as part of a consistent temporal pattern.For this exercise I constructed a large textual dataset from newspapers, which provide the “master forum” for public discourse The search results were reviewed for technical validity, and approximately 2% of retrieved documents were excluded from the final dataset on technical grounds. Examples of technical exclusions include documents containing fewer than 200 characters, documents accidentally retrieved through systematic false positive matches (e.g. “U.N. scientific” rather than “unscientific”), documents that were not archived in a usable format , and documents that were duplicated in the archive. The resulting master dataset contained 14,952 documents. Metadata for each document included date of publication and original source.Analyzing thousands of documents using conventional qualitative coding techniques is practically impossible. I employ computational methods for topic discovery to move beyond this limitation. Computational topic modeling methods have been used successfully to answer questions that might otherwise be addressed by qualitative coding methods, such as which areas of science are growing or shrinking reproductive genetics and the other topic is focused on immunology. LDA estimates the probability that “viral” will be associated with “viral allograft antigen lupus” (immunology), the probability that the topic (immunology) will show up in any document, and the exact mixture of the resulting topics for each document in the corpus . The result resembles qualitative human classification of subject matter, but is generated probabilistically through computation I apply a probabilistic topic modeling technique called Latent Dirichlet Allocation (hereafter LDA) Because topic modeling is probabilistic, selecting an appropriate topic model involves a variety of tradeoffs and judgments by the human researcher. It is conventional to generate a range of candidate topic models, then use several qualitative and quantitative validation techniques to select the model that is the best fit for the specific research question All candidate topic solutions were subjected to a validation process consisting of three phases. In the initial validation phase, I reviewed the top 50 terms generated for each topic in each model to determine intelligibility. The basic test was whether or not I could summarize each topic in a brief label, such as “religion” or “presidential politics.” I also flagged probable “junk topics” such as overly-broad topics consisting of common adjectives or general terms dfr-analysis GitHub archive at https://github.com/agoldst/dfr-analysis.) In ambiguous cases that had been flagged as suspicious in the first phase of validation, these quantitative features provided additional information for rejecting topics that were overly broad or internally incoherent. At this phase topic solutions of 40 and 50 topics were rejected, primarily based on having too many topics that initially appeared coherent but on further review proved either to combine different subjects into single topics or to divide an identifiable subject across multiple topics.In the second validation phase I used quantitative diagnostic data from MALLET to verify or reject initial qualitative analysis of topics. In additional to conventional output of topic model data, MALLET provided diagnostic information such as topic-specific distribution over words relative to corpus distribution In the third validation phase I incorporated qualitative domain knowledge to “predict” various features of the remaining model and verify that these occurred as expected. I compared the relative distribution of topics over documents to verify that topics that might be expected to occur together more often in documents (e.g. topics focused on dining and cooking) had more similar distributions to each other than to topics that domain knowledge would suggest are unrelated (e.g. topics focused on cooking and space). I also charted the distribution over time for selected topics to verify that higher prominence in the corpus coincided with known events that should affect such distribution. For example, a topic that appears to be about presidential politics should be more prominent in presidential election years.The 45 topic solution emerged from the validation process as the best tradeoff between specificity of topics and significance of topics that still retained analytical interpretability. However, like any topic modeling solution, this solution still included some topics that were incoherent, not substantive, or very infrequently occurring television. After validation, 33 substantive topics emerged from within the 45 topic solution. Substantive topics are topics with word and phrase content that is focused on identifiable subjects of public discussion. For example, a topic containing words such as “show tv news television shows radio channel nbc series viewer” is probably focused on television. For each substantive topic I assigned a concise label to indicate the subject on which that topic's words and phrases are focused. I note these substantive topic labels in the remainder of the paper by using italics, for example educationliteraturescientific researchpublic policyevolutionstem cell researchracereligioncourtslegislationdisease riskconservationhealth caresexspaceclimate changeAfter assigning topic labels, I noted which topics in the model were focused on subjects that had already been identified in qualitative case studies of demarcation. In evolution), “Harvard Plans Center to Grow Stem Cells” (stem cell research), “Race Has No Basic Biologic Reality” (race), “Humans May Double the Risk of Heat Waves” (climate change), “Scandals Point to Weakness in Review Process” (scientific research), and “Vitamin C: Is Anyone Right On Dose?” (disease risk). Illustrative examples of demarcation language from documents with high proportions of these topics include:At the document level, typical documents with high proportions of these topics have titles such as “Intelligent Design: Ruling Bans Discussion of Concept” (evolution)“... intelligent design ‘is a religious view, a mere re-labeling of creationism, and not a scientific theory’” (stem cell research)“It is very troubling to see a major public policy decision about medical research made from an unscientific point of view.” (race)“... differentiating species into biologically defined ‘races’ has proven meaningless and unscientific as a way of explaining variation, whether in intelligence or other traits.” (climate change)“‘Modeling is not science,’ said Ebell...” (scientific research)“Thus, to many critics, peer review is a pseudo-scientific name given to an editorial process not unlike that common to many forms of journalism.” (disease risk)“'He had the best of intentions, but he did not have the science to support his hypothesis, Dr. Levine said.” , “Ready, Set, Goo: Gooey Butter Cake is a St. Louis Classic” (cooking), “Bachmann Wins Iowa Straw Poll, Bests 8 GOP Contenders” , “Ten Things to Know for Friday's Championship” (amateur sports), “Pakistan's Constitution Avenue” (war), and “Morris Graves – ‘Instruments for a New Navigation’” (style). Illustrative examples of demarcation language from documents with high proportions of these topics include:At the document level, typical documents with high proportions of these topics have titles such as “Consciousness in the Microchips” “At the same time Penrose resists turning over the perplexing problems of consciousness to mysticism or other non-scientific explanations.” (cooking)“‘Dangerously good!’ wrote one tester in our decidedly nonscientific tasting.” “The straw poll, staged in a day-long, county-fairlike environment in Ames, Iowa, is an important if unscientific barometer.” (amateur sports)“After our highly unscientific analysis, we're giving a slight nod to Eden Prairie.” (war)“The Pakistani president vowed to reform those madrasas, or Islamic schools, that teach only the Koran, and not science, math and literature.” (style)“Their whimsical mix of pseudoscience and philosophical pretensions, their ungainly position between sculpture and painting, doesn't work well.” (In addition to identifying qualitatively distinct topics in a large textual dataset, computational methods provide the necessary information to evaluate the significance of topics that the model identifies. From a topic modeling perspective, there are two basic ways to think about the significance of a topic. The first is to consider how commonly a topic occurs in the corpus as a whole, relative to other topics. If a reader encounters demarcation language, what subjects are they more likely to be reading about?polling and business are more likely in the corpus, while topics such as foreign trade and cooking are less likely in the corpus. The interpretation would be that someone encountering an article containing demarcation language is more likely to be reading about cultural history, polling and education, and less likely to be reading about evolution, stem cell research, or climate change.As The second way to think about significance is to consider how likely it is that a topic is significant when it occurs in a document. This version is more useful for understanding the significance of a topic at the document level rather than the level of the entire corpus. If a person encounters a topic in an article from the corpus, is it usually the main topic in the article, or is it usually a minor part of the article?evolution is less significant in the overall corpus (see pro sports and amateur sports, as well as climate change and space. A reranking in the opposite direction occurs for public policy, scientific research, and polling, which are more significant in the overall corpus but rarely occur as the main topic in a document. Topics such as race and presidential politics remain relatively less significant or more significant, respectively, regardless of which measure of significance is used.As rpus see , when itComputational methods overcome three key limitations that case studies using small datasets encounter. First, close readings and qualitative coding approaches offer no general way of evaluating whether case studies are important or not, as small samples of textual data lack visibility to broader patterns in the public sphere. Computational methods enable analysis of much larger samples that provide the comparison data necessary to evaluate the impact of particular cases on public discourse more broadly.evolution in the demarcation corpus over time. Many qualitative case studies have examined demarcation in public controversies over evolution, particularly in curricular challenges that result in legal battles between parents, activists, and local school boards McLean v. Arkansas in 1982, and Kitzmiller v. Dover in 2005 For example, evolution more or less significant to public discourse than demarcation activity around around some other topic? Looking at thousands of documents provides the information to answer this question. As a comparison example, race in the demarcation corpus over time. Like evolution, many qualitative case studies have examined demarcation in public controversies over race, particularly in legal battles over federal regulation of research subjects evolution, race not only is relatively low in prominence, but has changed very little over time.But is demarcation activity around evolution and race in this exercise is instructive because it provides a different set of information than analysis of small textual samples on either subject can provide. Close readings and qualitative coding of selected texts related to demarcation activity around race might well point to similar strategies, features, and arguments as demarcation activity around evolution. But looking at patterns in thousands of documents reveals that activity in one case successfully constituted a large part of public demarcation discourse, while activity in another case constituted only a small part of public demarcation discourse. By providing such comparison data, computational analysis of a large textual dataset places questions about particular cases or events in broader context.The comparison between Second, and similarly, looking at thousands of documents using computational methods provides the comparison data necessary to evaluate the external validity of broader inferences drawn from close readings or qualitative coding of small samples. Take, for example, the potential use of evidence from qualitative case studies around evolution to support broader claims about the relationship between religion and science. Case studies of particular instances of controversy find consistently that such challenges have a clear religious component religion and evolution over time. As religion is not very prominent in the demarcation corpus, and it has remained not very prominent for over thirty years, while evolution has varied in prominence in response to specific instances of demarcation activity. In the context of the large textual dataset in this exercise, the involvement of religion in public disputes around evolution appears to be exceptional.But are these instances of demarcation activity involving religion exceptional or normal? presidential politics in the demarcation corpus over time. Third, small textual samples are limited in their ability to determine whether or not particular cases are part of a consistent temporal pattern rather than unique or unusual. As an example, presidential politics confined to a unique event such as the Reagan landslide, or does it recur periodically? A case study of selected documents from public discourse on the 1980 election might be able to identify the demarcation activity. But it would be unable to determine whether or not the event was unique, or to what extent it recurred in later years. presidential politics, looking at thousands of documents shows that such demarcation occurs in a regular temporal pattern and can even be anticipated in future presidential election years.But is demarcation activity around Computational analysis of large textual datasets using topic modeling offers a productive way to expand qualitative research beyond the limitations of small datasets. Topic discovery does not replace close reading or qualitative coding. But, as this exercise shows, looking at thousands of documents across a broad range of subjects offers insights that are simply not available from approaches that rely on a narrow range or small set of textual data.Computational analysis of large datasets using topic modeling also expands the scope of qualitative research by locating qualitative case studies within a broader context. Such information can be used to evaluate and compare the importance of specific case studies, to validate inferences that are drawn from qualitative analysis of small textual samples, and to determine whether specific cases are part of a consistent temporal pattern. For scholars, these additional capabilities are crucial for placing qualitative findings in the context of broader theoretical and empirical problems.For all of its benefits, topic modeling of large datasets involves three important limitations. First, this approach does not address questions about who is using this language. In the demarcation example, who is making these distinctions, and why? Second, this approach does not address the target of language use. In the demarcation example, is the target of demarcation a person, an idea, or a set of activities? Third, this approach does not address why one form of language rather than another might be deployed. In the demarcation example, why use “anti-science” rather than “pseudoscience,” “non-science,” or “unscientific” in making distinctions?Such questions cannot be addressed only with topic modeling. Future research should employ more conventional qualitative methods to pursue these lines of inquiry. But topic modeling generatively extends the reach of qualitative analysis beyond its current limits, and points to productive new directions for exploration.


EHP. Environ HealthPerspect 123(4):A78; http://dx.doi.org/10.1289/ehp.1509968Schroeder JC, Booker SM. 2015. New developments at Published online 1 April 2015EHP.In the original version of this editorial Shaun Halloran’s previous employer wasincorrectly stated as the American Society of Chemical Engineers. Mr. Halloran wasemployed by the American Society of Civil Engineers before coming toEHP regrets the error.


Nanofibers are one-dimensional nanomaterial in fiber form with diameter less than 1 µm and an aspect ratio (length/diameter) larger than 100:1. Among the different types of nanoparticle-loaded nanofiber systems, nanofibers loaded with magnetic nanoparticles have gained much attention from biomedical scientists due to a synergistic effect obtained from the unique properties of both the nanofibers and magnetic nanoparticles. These magnetic nanoparticle-encapsulated or -embedded nanofiber systems can be used not only for imaging purposes but also for therapy. In this review, we focused on recent advances in nanofibers loaded with magnetic nanoparticles, their biomedical applications, and future trends in the application of these nanofibers. Nanofibers are fibers with diameters less than 1000 nm ,3,4,5. TIn the ES process, polymer nanofibers are produced by applying a strong electric field between a grounded target and the polymer solution. The polymer solution is fed with the use of a syringe pump through a metallic needle (spinneret) at a constant and controllable rate. The collector plate acts as the counter electrode on which the fibers are collected as a non-woven mesh or membrane. The process conditions and properties of the polymer solution influence the diameter of polymer nanofibers, which range from 10 to 1000 nm. The key advantage of producing polymer nanofibers with extremely small diameters is their large surface-to-mass ratio, high porosity, and superior mechanical performance ,9. MoreoSpinning polymer blends to create composite nanofibers allows for further tunability of nanofibers that can fulfill specific industrial requirements in terms of their material properties, thereby increasing their potential applications. Most recently, investigations have targeted the inclusion of other nanoscale structures within the nanofibers to produce structures with added functionality. For example, silver nanoparticles have been included in synthetic polymer nanofibers to produce a highly antimicrobial material . In anot3O4 nanoparticles in the nanofibers has been performed in both water and organic solvents, as well as sodium citrate and oleic acid, although the complete dispersion of Fe3O4 nanoparticles was not achieved due to these incompatible interfaces [Owing to the advantageous features of nanofibers and magnetic nanoparticles (MNPs), many researchers have incorporated MNPs into biodegradable nanofibers to produce paramagnetic nanofiber scaffolds. To prepare these composite nanofibers, one of the most commonly used techniques is the mixing of dry inorganic powder with a polymeric solution followed by ES, although the nanocomposites formed are not stable and tended to agglomerate. To overcome this problem, various surface treatments have been used including salinization, polymer coating, and grafting. In addition to this type of surface coating, dispersion of Feterfaces .3, was mixed with cellulose acetate (CA) or polyacrylonitrile (PAN) solution. The ES process was then followed by photo-reduction to form the silver NPs within the nanofibers formed. Chemical precursors of other metals were also used to obtain other types of hybrid nanofibers. For example, the chemical precursor of Pd was used to make poly(acrylonitrile-co-acrylic acid) (PAN-co-PAA)/Pd by ES [The addition of inorganic components to the polymer system facilitates the preparation of nanofibers with specific functionalities. A recent patent described an approach for preparing hybrid nanofibers by adding nanoparticles into the polymers . In thisPd by ES . In a sePd by ES . Other tPd by ES . Table 1et al. reported a new method for preparing aligned fibrous arrays of composite magnetic nanofibers by ES [Yang rs by ES . As show2, TiO2, and Al2O3 [Recent studies have demonstrated the possibility of obtaining composite nanofibers by ES of ceramics and biopolymers. Hydroxyapatite (HA), a major component of bone, is a widely used bioceramic. Hybrid E-spun nanofibers containing HA as a bone regeneration implant material revealed high mechanical strength and good biocompatibility . Observand Al2O3 .Polymer nanofibers loaded with Au, Ag, Pt, or Pd nanoparticles can be produced by ES with the addition of metal salt solutions as precursors. The diameters of the nanoparticles were in the range of 5 to 15 nm. These nanofibers have also been reported to have highly effective catalytic properties.MNPs are prepared via basic inorganic chemistry methods. Specifically, MNPs are prepared with magnetite, maghemite or iron alloys as the core magnetic material. MNPs can be prepared either by a single-step or a multi-step procedure, each of which has its advantages and disadvantages. There is no universal technique available for MNP synthesis. Commonly used methods for MNP synthesis will be briefly discussed in the following section.3O4), two stoichiometric solutions containing Fe2+ and Fe3+ ions are mixed with a base [3O4 (magnetite) to Fe2O3 (maghemite), which might impair advantageous properties of Fe3O4 (magnetite) in its application as a contrast agent in magnetic resonance imaging (MRI). It has been shown that in the spinel structure of magnetite, cationic vacancies are in the octahedral positions, which result in a lower net spontaneous magnetization [et al. found that Fe3O4 magnetite provided stronger proton relaxivities in MRI than Fe2O3 maghemite [2, which leads to a reduction of the particle sizes. However, it is not easy to perform both precipitation and the addition of protective coating materials to the magnetic particles because maintaining the pH is laborious.One simple chemical method available for the preparation of MNPs is the precipitation method. It was developed to use aqueous solutions of iron (II or III) ions. Precipitation of MNPs can be accomplished using one of two methods: wet precipitation or co-precipitation. The wet precipitation method was developed first for MNPs preparation . In the h a base . This cotization . In partaghemite . As the aghemite . One widMicelle formation is a classic process in surfactant chemistry . Normal Thermal decomposition is a popular method used in industry to synthesize MNPs because it does not use organic solvents . The use4 and LiAlH4, are used to prepare MNPs through the reduction of magnetic or non-magnetic metal oxides to magnetic metal oxides. NaBH4 is the most commonly used reductant because it is soluble in both methanol and water [Strong reducing agents, such as NaBHnd water ,58,59,60The development of MNP-functionalized nanofibers has attracted interest due to their potential use in scientific and industrial applications. The most widely used method for the preparation of MNP-loaded nanofibers is ES.et al. [et al. [co-glycolide) (PLGA) nanofibers using ES. The size and morphology of magnetically-functionalized E-spun nanofibers can be controlled by changing the polymer concentration. Singh et al. reported the development of magnetic nanofibrous scaffolds composed of PCL and MNPs for bone regeneration [wt % and subsequently E-spun into nonwoven nanofibrous webs. It was demonstrated that the fiber diameter was dependent on the MNPs added which in turn changes the electrical conductivity and viscosity of the solution. Other studies [l-lactic acid) (PLLA) and polyurethane to make electrospun nanofibers. Furthermore, Fan et al. [2O3 nano-composite fibers by suspending the Fe2O3 nanoparticles in PAN/DMF solution, followed by ES. The addition of MNPs to the precursor solution for the preparation of magnetic nanofibers can be beneficial because the spatial distribution of MNPs can be confined within the range of 200–500 nm in a one-dimensional structure  [The first documented use of electro-hydrodynamics to modify the shape of a liquid meniscus under the influence of an electric field was reported by William Gilbert in the late 16th century . In partet al.  was the et al. ,67. The et al. ,69. As set al. , as wellet al. . Luong-V [et al.  preparedneration . In this studies ,75,76,77n et al.  preparedrection) ; howeverrection) .Nanofibers functionalized with MNPs have gained attention because of their potential applications , includiBone regeneration by tissue engineering is very important for bone defects resulting from tumor resection, trauma, and skeletal abnormalities. Even though many kinds of scaffolds used for tissue engineering for bone repair have been investigated ,94, the et al. prepared a novel nanofibrous scaffold composed of maghemite super-paramagnetic MNPs, hydroxyapatite, and PLA [Using the ES technique, Meng  and PLA . The nanet al. [The resulting nanofiber webs became more hydrophilic with improved mechanical properties due to the addition of MNPs into the PCL scaffold. The addition of MNPs resulted in magnetic properties of the nanofibrous scaffolds, typical for weak ferromagnetic or super-paramagnetic materials, as well as increased hydrophilicity, accelerated scaffold degradation, and apatite-forming ability. When osteoblast cells were cultured on the MNP-loaded nanofibers versus on pure PCL nanofibers, initial cell adhesion and penetration increased. Furthermore, rats implanted with MNP-loaded PCL nanofibers showed significantly better bone regeneration with minimal adverse reactions. Singh et al.  incorporAnother study  reportedHydroxyapatite (HA), used extensively for bone regeneration, has also been applied as a scaffold. In one study , MNPs weHyperthermia-based cancer therapy using MNPs has recently gained wide interest; However, the application of free MNPs has several limitations due to low solubility, poor cancer targeting, and leakage of MNPs from the tumor location. Therefore, current strategy involves MNP-loaded electrospun nanofibers for localized hyperthermia-based tumor treatment.In a recent study, 50-nm iron oxide nanoparticles (IONPs) were loaded into polystyrene (PS) electrospun nanofibers to allow for repeated heating by applying an alternating magnetic field (AMF) with minimum IONP leakage. IONP-loaded PS nanofibers were made by spontaneous ES of IONPs after dispersing of IONPs in a PS solution containing a mixture of tetrahydrofuran and dimethylformamide (1:3 volume ratio) to form uniform nanoscale electrospun fibers. Most of the human SKOV-3 ovarian cancer cells attached to IONP-loaded PS nanofiber mats through applying an AMF were dead as a result of the cancer hyperthermia effect .2+/Fe3+ solution and co-precipitation of MNPs by ammonium hydroxide. However, there were not many differences in the morphologies and in vitro hyperthermic effects in Caco-2 cells between the nanofibers made by the two different methods; although, cross-linking of the MNP-loaded chitosan nanofibers with gluteraldehyde during ES was performed. Similarly, in another study [et al. loaded MNPs into thermoplastic poly (PET) nanofibers [In another study , electroer study , cross-lnofibers . MNP-loaet al. manipulated target cells in a scaffold using physical means, such as magnetic force [in vivo and convert extracellular mechanical stress to intracellular chemical cues [Tissue engineering is the substitution of any human organ or tissue with artificial functional materials using a combination of biology, medicine, and engineering. Recently, Preslar ic force . Nanofibic force , becauseic force ,94. In acal cues .In this review, magnetically functionalized E-spun nanofibers have been discussed from the standpoint of biomedical applications, including scaffolds, regenerative medicine, and cancer therapy. These fibers combine inherent characteristics of standard E-spun nanofibers, such as high porosity, high surface-area-to-volume ratio, flexibility, and ease of fiber production, with unique and advantageous magnetic properties.in vitro osteogenesis and tissue compatibility and the ability to regenerate bone in vivo due to their increased hydrophilicity, accelerated degradation, ability to form apatites, and enhanced mechanical properties by magnetic force, suggesting that they can be used as a new class of bone regenerative materials. In addition, electrospun nanofiber mats with a conformal coating on the surface of the mats may be used as an ideal wound-dressing material because they are antibacterial, nontoxic, non-antigenic, permeable for gaseous exchange, resistant to shearing forces (due to their elasticity), and are highly water-absorbent. However, the use of highly engineered electrospun nanofiber mats tailored for wound healing in the clinic requires further study. Furthermore, nanofiber systems may be used in the future as an alternative approach to gastro-retentive drug delivery systems for enhanced bioavailability and the controlled release of drugs because they provide prolonged contact time with the gastric mucosa, controlled release of the drug, and good stability.In the future, magnetic E-spun nanofibers will likely be used as a functionalized scaffold in tissue engineering because MNP-loaded nanofiber scaffolds have


The eating disorders (EDs), anorexia nervosa (AN), and bulimia nervosa (BN) are severe psychiatric disorders of unknown etiology. EDs usually begin during adolescence and occur most commonly in females  or excessive food intake , which may interact with dopamine circuits that are vulnerable to the effects of high or low food intake. Another important factor in triggering dopamine system alterations is puberty. Estrogen has a variety effects on eating behavior via neurotransmitter function and may play an important role in ED risk .The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Objective. To compare the image quality of coronary computed tomography angiography (CCTA) acquired under two conditions: 75% fixed as the acquisition window center (Group 75%) and the diagnostic phase for calcium scoring scan as the center . Methods. 320-row cardiac CT with a minimal acquisition window (scanned using “Target CTA” mode) was performed on 81 patients. In Group 75% (n = 40), CS was obtained and reconstructed at 75% and the center of the CCTA acquisition window was set at 75%. In Group CS (n = 41), CS was obtained at 75% and the diagnostic phase showing minimal artifacts was applied as the center of the CCTA acquisition window. Image quality was evaluated using a four-point scale (4-excellent) and the mean scores were compared between groups. Results. The CCTA scan diagnostic phase occurred significantly earlier in CS . The mean Group CS image quality score (3.58 ± 0.63) was also higher than that for Group 75% . Conclusions. The image quality of CCTA in Target CTA mode was significantly better when the center of acquisition window is adjusted using CS. Adult coronary computed tomography angiography (CCTA) usually begins with a noncontrast electrocardiogram-gated chest CT called a “calcium scoring (CS) scan” performed after scout scans. CS is used to determine the range of the CCTA scan and to calculate an Agatston score, the counterpart to the calcium score which is obtained using electron beam CT . BecauseSecond generation 320-row CT scanners with a rotation speed of 275 ms can scan the whole heart in one rotation, using a minimal acquisition window . This scan mode can be applied for evaluating cases with a heart rate lower than approximately 75 beats per minute (bpm). With Target CTA scans, the center of the acquisition window is set to any integral percentage, and X-ray exposure is limited to only the minimum duration needed to reconstruct the images. Although the acquisition window is set using only one integral, such as 75%, the scan has a short reconstruction window and the diagnostic phase  can be searched for within the acquisition window. As an example, use of a Target CTA scan of 75% in a patient with an RR interval of 1000 ms results in an acquisition window of 689–811 ms, with the center of the acquisition window at 750 ms and the width of reconstruction window at 122 ms . These phase types are searched using “PhaseNavi” cardiac-phase search software , which automatically searches for the phase that produces the lowest average SD value for all voxels in the volume. However, the results of automated phase searching do not always correspond with the diagnostic phase. Also, the most static phase needs to be visually searched using the same software, if the coronary arteries contain motion artifacts at the point identified by the automated phase search. Compared with other methods, Target CTA is reported to produce low-dose scans together with noninferiority in image quality .CS has been scanned using a 75% Target CTA mode for patients with a heart rate (HR) ≤ 75 bpm, and at 40% for those with an HR > 75 bpm. During the CS Target CTA scan, the reconstruction phase was fixed to 75%, and it was not possible for PhaseNavi software to adjust the reconstruction phase. However, a recent software upgrade  allows for the adjustment of CS scan reconstruction window. We hypothesized that the CS diagnostic phase correlates with that of CCTA and that the image quality of CCTA would improve with adjustment of the center of the CCTA acquisition window using the CS diagnostic phase as compared to using a fixed percentage value.Therefore the aim of this study was to determine potential correlation between CS and CCTA scan diagnostic phases and to compare the CCTA image quality with the use of 75% (Group 75%) versus the CS diagnostic phase (Group CS) as the center of the acquisition window.This study which was conducted at a single research center was approved by the local ethics committee. Because of this study's retrospective design, the requirement for informed consent prior to study participation was waived.The Target CTA scan was applied to the patients with sinus rhythm and an HR ≤ 75 bpm. For patients with arrhythmias, a different acquisition program had to be applied in order to run an arrhythmia exclusion program. Thus patients with sinus rhythm and an HR ≤ 75 bpm were included in our study.n = 13); single beat scan with long acquisition window because of heart rate fluctuation (n = 17); multiple heart beat acquisition (n = 23); wide-volume scanning performed to evaluate bypass grafts or aorta (n = 16); ventricular evaluation prior to catheter ablation (n = 3); or irregular protocol for evaluation of complex cardiac anomaly (n = 9). The final study group included 81 patients  who were scanned because of known or suspected coronary artery disease with chest pain and/or dyspnea, or abnormal electrocardiogram, echocardiogram, or treadmill results.We retrospectively reviewed the records of 162 consecutive patients who underwent CCTA between October 2013 and February 2014. In December 2013, we started to adjust the center of the CCTA acquisition window for Target CTA using the CS diagnostic phase. Single volume Target CTA mode scanning was not used for 81 patients because of the following reasons: nonsinus rhythm (κ = 0.014 mSv × mGy−1 × cm−1)  ± 61 ms}. The correlation between the CS and CCTA scan diagnostic phases was calculated using Spearman's correlation coefficient analysis.The minimal acquisition window scans (Target CTA mode) for October 2013 were reviewed  and were compared using Fisher's exact test or the chi-squared test. Statistical significance was accepted when p < 0.05.All statistical analyses were performed using JMP software . Quantitative variables were expressed as the mean ± standard deviation and group differences were tested by Student's p = 0.02, R2 = 0.113).There was no group difference in patient demographics and scanning parameters Tables  and 2. Tκ = 0.68). When patients with poor interobserver agreement were defined as “difference in subjective score between two graders being 2 or more in more than five segments,” we found that just four patients qualified as having poor interobserver agreement due to either the presence of dense calcification or multiple stents.Among the 1458 total segments captured for each group (18 segments in 81 patients), 137 segments were not evaluable because the segment was absent or too small . The subjective image quality scores were significantly better in Group CS, both for overall and for branch specific analyses . Branch p = 0.02) indicating weak positive correlation [This is the first report on the use of the CS diagnostic phase as the center of the CCTA acquisition window for Target CTA mode scanning. Group CS image quality was significantly better than that for Group 75% using both subjective and objective evaluations. The CS and CCTA diagnostic phases were both earlier than the empirically derived 75%, with the diagnostic phases considered to be outside the 75%-centered acquisition window in 19.5% of cases. The premise of this study of correlation between the CS and CTCAG diagnostic phases was also proven. The correlation efficiency between diagnostic phases of CS and CCTA was 0.351  and must be repeated for certain “difficult” cases. Therefore, the phase search usually requires the input of a radiologist or a technologist in addition to the scanning technologist.There is a worldwide trend to reduce radiation exposure during cardiac CT. Indeed, radiologists should make their best effort to achieve “as low as reasonable achievable (ALARA)” radiation exposure during every examination. Target CTA scan is a product of the response to this mandate. However, the present study showed wide individual variation in cardiac CT diagnostic phase. Radiologists should tailor the center of the acquisition window during Target CTA scanning or set the acquisition window wider than the narrowest setting to help achieve this goal. For instance, Steigner et al. suggest 72–81% acquisition window has a good probability of including the diagnostic phase for 95% coronary arteries . If TargThere are some limitations to our study. The heart usually straddles two volumes in CS, because CS needs to cover an area wider than the heart. First, because the RR intervals differ between those volumes, the reconstruction window becomes narrow when there is a large difference in the RR intervals. When this difference is too big, the reconstruction requires an artificial adjustment of the position of one of the R waves. In this study, cases that required such adjustment were considered to be arrhythmic and were excluded, because a longer CCTA acquisition window was applied to such cases. For the second limitation, the center of the CS acquisition window was fixed to 75%. This means that if the diagnostic phase existed at an extreme such as 55% or 92%, it would not be possible to include this phase, even when the center of the acquisition window was adjusted using CS. In fact, with some of our cases, the CS diagnostic phase was located at the earliest pole of the scan. Likewise, the best CCTA reconstruction phase was also found at the earliest pole. With these cases, there is likely to be and even better phase that occurred even earlier. The third study limitation was that many cases exhibited a gap between the CS and CCTA diagnostic phases, as was expected based on the correlation coefficient. In cases with large gaps, an even better phase may exist beyond the CCTA acquisition window. The fourth limitation pertains to the limited sample size because the average Group CS diagnostic phases and the percentage of patients that had values outside of the 75% fixed scan acquisition window were derived from a small number of patients. This point could be addressed by repeating the investigation in a larger population. In addition, further studies should be performed to determine whether the method described herein is also effective with other CT systems, such as 256-row CT or dual-source CT.This study found that CS and CCTA diagnostic phases were significantly correlated, with average diagnostic phase of 73.9% and 73.6%, respectively, although the phases showed substantial interindividual variation. The CCTA scan image quality using Target CTA mode was significantly better when the center of the acquisition window was adjusted using CS, compared with that using a fixed percentage.


The 17th International Conference on Human Retrovirology: HTLV and Related Retroviruses took place in Trois Ilets, Martinque (FWI) from June 18th to June 21th, 2015. The main topic covered during the meeting was human T-lymphotropic viruses (HTLVs) and was subdivided in distinct sessions: clinical research, animal models, immunology, molecular and cellular biology, and virology. The following abstracts were presented.Five of the presented abstracts are not included in this supplement as they have been published elsewhere -5.


Organ transplantation is a well-accepted treatment for patients with end-stage organ failure. Despite continued improvement in short-term graft survival, late allograft dysfunction remains a significant problem in the clinic, especially in kidney transplant patients. Many factors contribute to late graft dysfunction, and among them immunological factors are the leading cause of late grafts loss. In this special issue, we have solicited a set of interesting papers addressing some aspects of this important topic in the field.Here we focused on antibody-mediated rejection (AMR), as AMR is emerging as a major barrier to long-term graft survival, and the donor-specific antibodies are directly involved in AMR. The paper by Q. Sun and Y. Yang provides a comprehensive overview of the characteristics of AMR, both in acute rejection and late chronic rejection, and the current strategies in managing AMR. S. Lionaki et al. provide us with an excellent review on the incidence and clinical significance of de novo donor specific antibodies (DSA) after renal transplantation. It is well recognized that transplant glomerulopathy is a very special entity of late AMR, and Dr. W. Hanf from Australia discussed the effect of donor HLA antibodies on endothelium in transplant settings. These three review papers provide an extensive overview on antibody reactivity and its correlation with late graft injury.On the mechanistic side, while C4d remains a marker of a humoral response, recent evidence indicates that, in renal allografts, microvascular injury in the presence of donor antibodies is indicative of antibody mediated graft injury. X. Li et al. confirmed that AMR is characterized with early capillary dilation, which is strongly correlated with intracapillary inflammation. They also discussed the diagnostic value of transcription factors T-bet/GATA3 ratio in predicting AMR, which may be of value in diagnosis of C4d-negative AMR.The treatment of chronic ongoing AMR remains controversial. A group headed by C. W. Yang investigated the effect of combination therapy with rituximab and intravenous immunoglobulin on the progression of chronic AMR. They found that this therapy can delay the progression of chronic AMR. However, higher baseline proteinuria levels are associated with poor response to the treatment.In another paper, H. Petra et al. evaluated differences in the intrarenal expression patterns of immune related genes in acute and chronic rejections. They found that Banff 2007 chronic rejection categories did not differ in intrarenal expression of 376 selected genes associated with immune response.There are evidences that characters in early immune responses may also affect late graft function. L. Ma et al. reported that arterial lesions of donor kidneys had significant effects on the renal allograft function 2 years after transplantation, and correlations between donor age and arterial lesions were significant in this regard. Y. Wu and colleagues found that a novel tissue protective peptide, helix B surface peptide (HBSP) derived from erythropoietin, can effectively improve renal function by reducing tissue damage caused by ischemia reperfusion or cyclosporine A. The mechanism might be related to reduced caspase-3 activation, a key trigger in cell apoptosis and inflammation. Whether HBSP can display similar effect in clinical practice remains to be determined.It should be noted that liver transplantation invokes relatively weak immunological responses. E. Muñoz-Sáez et al. reported the experimental design of an in utero hepatocellular transplantation model in rats, which is an interesting tool for investigating immune responses in other settings as well. Concerning clinical liver transplantation, data from S. Mizuno et al. suggested that peripheral blood CD4+ adenosine triphosphate activity (ATP) assay (ImmuKnow assay) can be useful in monitoring immunological aspects of transplant responses, while Y. Hu et al. documented that APACHE IV is superior to MELD scoring system in prognosis of transplant outcomes in patients with liver transplants, which may be used to improve the outcome of liver transplantation.We anticipate that these outstanding papers will provide the readers with a comprehensive view on some of the challenging problems facing the transplant field. It is our hope that, by understanding the fundamental immune mechanisms in late allograft dysfunction, new and much improved strategies could be developed to further enhance transplant outcomes.Qiquan  SunQiquan  SunAkinlolu O.  OjoAkinlolu O.  OjoXian C.  LiXian C.  Li


Identifying relevant studies for inclusion in a systematic review (i.e. screening) is a complex, laborious and expensive task. Recently, a number of studies has shown that the use of machine learning and text mining methods to automatically identify relevant studies has the potential to drastically decrease the workload involved in the screening phase. The vast majority of these machine learning methods exploit the same underlying principle, i.e. a study is modelled as a bag-of-words (BOW).We explore the use of topic modelling methods to derive a more informative representation of studies. We apply Latent Dirichlet allocation (LDA), an unsupervised topic modelling approach, to automatically identify topics in a collection of studies. We then represent each study as a distribution of LDA topics. Additionally, we enrich topics derived using LDA with multi-word terms identified by using an automatic term recognition (ATR) tool. For evaluation purposes, we carry out automatic identification of relevant studies using support vector machine (SVM)-based classifiers that employ both our novel topic-based representation and the BOW representation.Our results show that the SVM classifier is able to identify a greater number of relevant studies when using the LDA representation than the BOW representation. These observations hold for two systematic reviews of the clinical domain and three reviews of the social science domain.A topic-based feature representation of documents outperforms the BOW representation when applied to the task of automatic citation screening. The proposed term-enriched topics are more informative and less ambiguous to systematic reviewers.The online version of this article (doi:10.1186/s13643-015-0117-0) contains supplementary material, which is available to authorized users. The screening phase of systematic reviews aims to identify citations relevant to a research topic, according to a certain pre-defined protocol –4 known w in a corpus D, while Table K topics ϕ∼Dir(nβ) Choose Choose topics proportions wn in document m:For each word Choose a topic wn,m from zn.Choose a word Topic analysis is currently gaining popularity in both machine learning and text mining applications –16. A toThe hyperparameters mentclass2pt{minimBesides LDA, there are many other approaches for discovering abstract information from a corpus. Latent semantic analysis  makes usn-grams and Medical Subject Headings (MeSH) [Automatic text classification for systematic reviews has been investigated by Bekhuis et al.  who focus (MeSH)  featuress (MeSH) . The ress (MeSH)  combineds (MeSH)  introducs (MeSH)  describes (MeSH)  exploites (MeSH)  showed ts (MeSH)  construcs (MeSH)  investigs (MeSH)  firstly s (MeSH)  investigTo investigate whether LDA can be successfully applied to text classification in support of the screening phase in systematic reviews.To compare the performance of two methods for text classification: one based on LDA topics and the other based on the BOW model.To evaluate the impact of using different numbers of topics in topic-based classification.Results obtained by Miwa et al.  showed tk-nearest neighbours) were also explored. However, since they failed to obtain robust results, we do not present further details.In order to carry out a systematic comparison of the two different approaches to text classification, our study is divided into two parts. Firstly, we evaluate the baseline approach, i.e. an SVM using BOW features. This SVM classifier is created using LIBSVM . The secF-score, accuracy, area under the receiver operating characteristic curve (ROC) and precision-recall curve (PRC). However, in our case, accuracy was found not to be a suitable indicator of an effective performance, due to the significant imbalance between relevant and irrelevant instances in the dataset; this ratio is 1:9 approximately for each corpus  tagged corpus according to C-value . CandidaAs for parameter tuning, all the experiments have been performed with default parameters for classifiers and symmetry hyperparameters for LDA, which means that every topic will be sampled with equal probability.We performed our experiments using five datasets corresponding to completed reviews, in domains of social science and clinical trials. These reviews constitute the “gold standard” data, in that for each domain, they include expert judgements about which documents are relevant or irrelevant to the study in question. The datasets were used as the basis for the intrinsic evaluation of the different text classification methods. Our conclusions are supported by the Friedman test Table  which isWe applied the models to three datasets provided by the Evidence Policy and Practice Information and Coordinating Center (EPPI-center)  and two F1-score. This can be attributed to the imbalanced nature of the corpora [Table  corpora . AdditioTopic-based classification was undertaken by firstly analysing and predicting the topic distribution for each document and then classifying the documents using topics as features. During the phase of training the model, the topic assigned to each word in a document can be considered as a hidden variable, this problem can be solved by using approximation methods such as Monte Carlo Markov chain (MCMC) or variational inference. However, these methods are sensitive to initial parameter settings which are usually set randomly before the first iteration. Consequently, the results could fluctuate within a certain range. The results produced by topic-based classification are all average results. However, our results show that topic distribution is an ideal replacement for the traditional BOW features. Besides other advantages, the most obvious advantage of which is to reduce the dimensions of features for representing a document. Experimental settings were identical in the evaluation of the two sets of classifiers, except for the features being topic distributions in one case and BOW in the other. The optimal LDA model was derived through experimentation with differing numbers of topics . In the experiments performed, several values for this parameter were explored.Table F-score, ROC and PRC but obtain higher recall. For this comparison, the best performing topic-based model (with topic density set to 150 for youth development corpus) was used. It can be observed from Fig. F-score. As noted earlier, high accuracy is not a good basis for judging performance due to the imbalance between positive and negative instances, i.e. even if a classifier labels every document as a negative sample, accuracy will still be around 90 %. Figure RBF>LINEAR. For a ranked list of feature types in terms of recall, it is: TPC >TE>BOW. Additionally, Figs. A comparison of the performance of the BOW-based model (BOW in legend) against the performance of models trained with topic-based model (TPC) and term enriched-topic model (TE) is presented in this section. According to the results of using a linear function for model training Fig. , models Our experiments demonstrated that the performance of BOW SVM with linear kernel function has produced the most robust results achieving the highest values in almost every metric, except for recall. But on any systematic reviews classification task, poor performance in recall needs to be addressed. The BOW model yielded a poor performance with RBF and POLY kernel functions due to the data imbalance and dimensionality issue. Topic-based classification significantly addresses this problem by dramatically reducing the dimensionality of the representation of a document (topic feature). The topic-based classifier yielded a higher recall, which means more relevant documents will be identified. Moreover, the topic features enable the classifier to work with RBF and POLY kernels and produce better recall comparing with a linear kernel. The same patterns were observed in all corpora, although there is only one example presented in this article.As future work, we will further investigate the generalisability of the model to diverse domains. Moreover, we plan to explore different machine learning and text mining techniques that can be used to support systematic reviews such as paragraph vectors and active learning. Also, further experiments will be performed in a more realistic situation. For example, whether topics could help reviewers’ decision in “live” systematic review would be an interesting research area in the future. An intuitive image of TE topics has been made in this article. For public health reviews where topics are multidimensional, the presence of diverse multi-word terms in a dataset can be an important element that affects the performance of classifiers. But TE topics have the potential to deal with these difficulties. Further investigation on TE topics will be performed, which would benefit reviewers and help them to understand topics more easily compared to ordinary topics.


C). In this study, we showed that dopamine treatment of neuronal cells reduced the number of viable cells and increased the production of reactive oxygen species (ROS) as demonstrated in previous studies. Overall PrPC expression level was not altered by dopamine treatment, but its unglycosylated form was consistently reduced at 100 μM of dopamine. At the same concentration, the level of phosphorylated mTOR and 4EBP1 was also reduced. Moreover, dopamine treatment decreased the solubility of PrPC, and increased its accumulation in autophagosomal compartments with concomitant induction of LC3-II and p62/SQSTM1 levels. In vitro oxidation of dopamine promoted formation of high-order oligomers of recombinant prion protein. These results suggest that dopamine metabolites alter the conformation of PrPC, which in turn is sorted to degradation pathway, causing autophagosome overload and attenuation of protein synthesis. Accumulation of PrPC aggregates is an important feature of prion diseases. Thus, this study brings new insight into the dopamine metabolism as a source of endogenous metabolites capable of altering PrPC solubility and its subcellular localization.Accumulation of protein aggregates is a histopathological hallmark of several neurodegenerative diseases, but in most cases the aggregation occurs without defined mutations or clinical histories, suggesting that certain endogenous metabolites can promote aggregation of specific proteins. One example that supports this hypothesis is dopamine and its metabolites. Dopamine metabolism generates several oxidative metabolites that induce aggregation of α-synuclein, and represents the main etiology of Parkinson's diseases. Because dopamine and its metabolites are unstable and can be highly reactive, we investigated whether these molecules can also affect other proteins that are prone to aggregate, such as cellular prion protein (PrP Aberrant protein aggregation is a common hallmark of many neurodegenerative diseases, while a specific protein predominantly aggregates in each type of diseases  is an essential event for development of transmissible spongiform encephalopathies (TSE). However, in its normal conformation, PrPC plays important roles in cell growth, differentiation and survival  were purchased from Life Technologies. Dopamine hydrochloride, thiazolyl blue tetrazolium bromide (MTT) and 2′, 7′-dichlorofluorescein diacetate (DCFDA) were purchased from Sigma-Aldrich. Complete Protease Inhibitor cocktail tablets were purchased from Roche and Pierce™ phosphatase inhibitor mini tablets were purchased from Thermo Scientific. All primary antibodies were purchased from Cell Signaling, except anti-prion SAF32, which was purchased from Cayman. Horseradish peroxidase conjugated secondary antibodies were purchased from Sigma-Aldrich and Alexa fluorophore conjugated antibodies and CellROX Green reagent were purchased from Life Technologies.2 in DMEM-Glutamax™-I (Dulbecco's Modified Eagle's Medium) supplemented with 10% FBS, Penicillin (100 U/mL) and Streptomycin (100 μg/mL). For dopamine treatment, 4 × 104 cells/cm2 were seeded. After 24 h, cells were treated with 50 or 100 μM dopamine diluted in DMEM containing 0.5% of FBS for 24 h.N2a cells were maintained at 37°C in a humidified atmosphere of 5% CO3 25 mM, NaH2PO4 1.2 mM, MgCl2 1.2 mM, CaCl2 2.5 mM, D-glucose 10 mM) for 2 h. The MTT formazan were solubilized in 100 μl of DMSO. Insoluble materials were removed by centrifugation at 20,000 g for 2 min and absorbance of supernatant was measured at 540 nm.Cells were treated with dopamine in 96-well plates for 24 h. After the treatment, cells were incubated with 100 μl of 1.2 mM MTT diluted in Krebs solution . CellRox Green was also analyzed by Operetta high content screening system (Perkin Elmer).C expression analysis was shown in supplementary data.Cells were lysed with lysis buffer , and post-nuclear supernatants (PNS) were collected. The protein content in PNS was quantified using BCA protein assay kit (Thermo Scientific Pierce). Equal amounts of proteins were resolved by SDS-PAGE and transferred to PVDF membrane. For immunodetection, membranes were incubated with TBS-T  containing 5% BSA for 1 h. Then, the membranes were incubated with primary antibody for 1 h at room temperature or for 16 h at 4°C, then washed three times with TBS-T. Secondary antibody conjugated with peroxidase and SuperSignal™ West Pico Chemiluminescent Substrate were used to detect antigens labeled with specific antibodies. Images were digitalized and quantified using Alliance mini 4 m (UVITEC Cambridge). For each protein, at least three independent experiments were performed. In every experiment, the band intensity of the proteins of interest (PI) was normalized by the intensity of the GAPDH bands. Western blot is semi-quantitative assay and direct comparison of PI/GAPDH ratio between independent experiments is not possible. Thus, in order to enable this comparison, the average of PI/GAPDH ratio of three experimental groups  was set as 100%, and the percentage of each group was calculated in each independent experiment. The mean percentage of all independent experiments was plotted with respective 95% confidence interval (CI95). An example of PrPC in each fraction was assessed by western blot. To combine the results of multiple independent experiments, percentage of PrPC observed in each sample was calculated considering the average of six samples  as 100%. This normalization was necessary because the absolute value of the band intensity is not comparable from one blot to another. The mean percentage of all independent experiments was plotted with respective CI95.Post-nuclear supernatants were incubated with 1% sarkosyl for 10 min on ice, then ultracentrifuged for 2 h at 100,000 × g and at 4°C. Pellets were dissolved in sample buffer 4x , and supernatants were incubated with 4 volumes of methanol for 2 h at −20°C for protein precipitation. After centrifugation for 20 min at 25,000× g and 4°C, methanol precipitated pellets were dissolved in Sample Buffer 4x. The level of PrPC was detected by western blot using SAF32 antibody.Cell surface proteins were biotinylated using Pierce Cell Surface Protein Isolation Kit (Thermo Scientific). The cells were harvested at time zero or after 1 h incubation in the presence or absence of 50 μM of dopamine. Biotinylated proteins were purified from the cell lysates using NeutrAvidin-agarose, and PrPLeica TCS SP8). Images were analyzed using Image J 1.48r. In each image, total area stained by anti-PrPC was defined as 100% and percentage of the area co-stained by anti-LC3-II was assessed using Colocalization Threshold plugin with default parameters  for 5 min and then with alkalinized 3.7% paraformaldehyde (pH 10) for 15 min. After washing twice with PBS, excess of paraformaldehyde was inactivated with glycine 100 mM and cells were permeabilized with Triton X-100 0.1% diluted in PBS for 10 min. To avoid unspecific bindings, cells were incubated with 1% BSA diluted in PBS for 1 h and then with primary antibodies diluted in PBS containing Triton X-100 0.1% for 1 h. After washing three times with PBS, cells were incubated with secondary antibody conjugated with Alexa 488 or Alexa 594 fluorophore for 1 h and then washed five times with PBS. Average images of six frames were acquired for each visual field using confocal microscope  is known to evoke cytotoxic effects  together with 4EBP1 (a repressor of cap-dependent translation upon dephosphorylation). As shown in Figures The treatment with 50 and 100 μM of dopamine did not alter the total amount of PrP Figures . However Figures . This baAll protein fold changes were calculated based on the loading control GAPDH. Thus, to ensure the constitutive expression of GAPDH in our experimental conditions, we compared the GAPDH expression to α-tubulin, another frequently used loading control. As shown in Figure C.Altogether, these data indicate that 100 μM of dopamine compromises cellular viability, redox balance and protein synthesis, which may affect the synthesis of PrPC. One possibility is that dopamine treatment may reduce the turnover of PrPC. To test this hypothesis, we biotinylated cell surface protein and observed a turnover of PrPC. After 1 h of incubation, a substantial amount of biotinylated PrPC was degraded in both dopamine-treated (50 μM) and untreated cells compared to input . Dopamine induced the formation of SDS-resistant higher-order oligomers of rPrP in a time and concentration-dependent manner . As shown in Figure C and LC3-II was increased by dopamine treatment  is an essential event for the development of TSE, molecular mechanisms of conformational transition between PrPC and PrPSc are poorly understood. Nevertheless, previous studies have demonstrated that PrPSc-like aggregates were found in normal brains at low levels (Yuan et al., Sc-like aggregates (Korth et al., C in response to redox alteration has also been proposed as a cytoprotective mechanism (Das et al., C was also accumulated in autophagosomes. These data indicate that the degradation of autophagosomal cargo by lysosome was not effective. Therefore, it is plausible to speculate that the reduced cell viability observed after dopamine treatment is at least partially due to the accumulation of PrPC aggregates in autophagosomes. Similarly, PrPC aggregation might have negatively affected protein synthesis since a previous study has demonstrated that protein synthesis was corrupted in N2a cells infected with prions (Roffe et al., Although the conversion of PrPC can be stimulated by several compounds such as Cu2+, nucleic acids and heme (Lee et al., C and confer cytotoxicity at high concentration (Thakur et al., C might function as a scavenging receptor for toxic molecules. Dopamine can induce toxicity by rapid auto-oxidation producing reactive dopamine-quinone (Asanuma et al., C, including dopamine metabolites, might induce structural alterations, which in turn, may trigger endocytosis for further degradation. Frequent binding of toxic molecules that cause conformational alterations of PrPC can eventually overload the degradation pathways, instigating the accumulation of protein aggregates.Endocytosis of PrPC aggregation. Possibly, dopamine and its oxidative metabolites can have more general roles in other protein aggregation, but the specificity of the target can be ruled by subcellular compartmentalization, brain region specificity and susceptibility of aggregation. Identification of endogenous metabolites that induce aggregation of a specific protein can contribute to better understanding of idiopathic neurodegenerative diseases and provide new molecular targets for treatment.Certain conditions, such as stress, drug addiction, iron deficiency, L-DOPA treatment or schizophrenia are known to increase dopamine metabolism (Nelson et al., Marcio H. M. da Luz conducted all experiments except rPrP oligomerization and analyzed the results. Italo T. Peres performed rPrP oligomerization assay. Tiago G. Santos acquired confocal images. Vilma R. Martins participated in study design and interpretation of data and revised the manuscript. Marcelo Y. Icimoto purified rPrP. Kil S. Lee participated in study design, data analysis and interpretation, and wrote the manuscript.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.


TFR was significantly higher in CML patients with acRTL ≤0.09 . CML stem cells harboring longer telomeres possibly maintain a proliferative potential after treatment discontinuation.We studied telomere length in 32 CML patients who discontinued imatinib after achieving complete molecular remission and 32 age-sex-matched controls. The relative telomere length (RTL) was determined by q-PCR as the telomere to single copy gene (36B4) ratio normalized to a reference sample (K-562 DNA). Age-corrected RTL (acRTL) was also obtained. The 36-month probability of treatment-free remission (TFR) was 59.4 %. TFR patients showed shorter acRTL compared to relapsed  contains supplementary material, which is available to authorized users. Telomeres are specialized nucleoprotein structures composed of long arrays of TTAGGG repeats localized at the ends of human chromosomes able to maintain genome stability and integrity and to protect the cell from progressive DNA shortening during repeated division . TelomerThirty-two chronic-phase CML patients discontinued TKI treatment after achieving complete molecular remission (CMR) for at least 18 months. All patients received imatinib therapy for more than 24 months. Two patients underwent second-line treatment with nilotinib because of molecular relapse. The median follow-up after discontinuation was 30 months (range 18–60). A complete molecular response was defined as undetectable breakpoint cluster region-Abelson (BCR/ABL1) by real-time quantitative polymerase chain reaction (qRT-PCR) with a sensitivity of the assay corresponding to molecular response (MR)4 and MR4.5. Peripheral blood samples from 32 age- and sex-matched healthy individuals were used for control purposes. The relative telomere length (RTL) was determined by q-PCR according to the technique described by Cawthon in 2002 [U test showed shorter acRTL in TFR patients compared to patients with molecular relapse    progenitors would result in telomere shortening, leading to genetic instability. Later, CML cells would escape senescence and apoptosis through upregulation of telomerase and restored telomere length. This would promote the occurrence of genetically unstable CML subclones with a selective growth advantage . DiscontCML, chronic myeloid leukemia; TFR, treatment-free remission; CMR, complete molecular remission; MR, molecular response; qRT-PCR, real-time quantitative polymerase chain reaction; BCR/ABL1, breakpoint cluster region-Abelson; TKIs, tyrosine kinase inhibitors; RTL, relative telomere length; acRTL, age-corrected relative telomere length; WBC, white blood cell; PLT, platelets


Mycobacterium bovis infection and other pathogens in wild boar (Sus scrofa), a recognized reservoir of bovine tuberculosis (bTB) in Mediterranean ecosystems. For this purpose, it has been assessed whether contacts with common concomitant pathogens are associated with the development of severe bTB lesions in 165 wild boar from mid-western Spain. The presence of bTB lesions affecting only one anatomic location , or more severe patterns affecting more than one location , was assessed in infected animals. In addition, the existence of contacts with other pathogens such as porcine circovirus type 2 (PCV2), Aujeszky's disease virus (ADV), swine influenza virus, porcine reproductive and respiratory syndrome virus, Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, Haemophilus parasuis and Metastrongylus spp, was evaluated by means of serological, microbiological and parasitological techniques. The existence of contacts with a structured community of pathogens in wild boar infected by M. bovis was statistically investigated by null models. Association between this community of pathogens and bTB severity was examined using a Partial Least Squares regression approach. Results showed that adult wild boar infected by M. bovis had contacted with some specific, non-random pathogen combinations. Contact with PCV2, ADV and infection by Metastrongylus spp, was positively correlated to tuberculosis severity. Therefore, measures against these concomitant pathogens such as vaccination or deworming, might be useful in tuberculosis control programmes in the wild boar. However, given the unexpected consequences of altering any community of organisms, further research should evaluate the impact of such measures under controlled conditions. Furthermore, more research including other important pathogens, such as gastro-intestinal nematodes, will be necessary to complete this picture.Co-infections with parasites or viruses drive tuberculosis dynamics in humans, but little is known about their effects in other non-human hosts. This work aims to investigate the relationship between  Co-infections  are ubiquitous in nature but most research on relevant diseases largely relies on a “one-disease-one-pathogen” perspective. From the point of view of community ecology, a host can be considered a complex ecosystem composed of parasites that directly or indirectly interact among themselves and with their own environment, the host Oryctolagus cuniculus). In this host-parasite model, respiratory infection by Bordetella bronchiseptica facilitates secondary helminth (Graphidium strigosum) infections that, at the same time, collaborate in maintaining the bacterial persistence in the upper respiratory tract B. bronchiseptica infection does not only facilitate Heligmosomoides polygyrus reproduction, another gastrointestinal nematode Trichostrongylus retortaeformis) from the small intestine Among all possible interactions, bacteria-helminth co-infections are one of the most studied models for exploring how co-infection drives disease dynamics and severity. Helminths mostly induce cytokines associated with a T-helper cell type 2 (Th2) immune response, which simultaneously tends to down-regulate T-helper cell type 1 (Th1) cytokines involved in intracellular microparasite control Mycobacterium tuberculosis), susceptibility and severity are shaped by co-infection with different types of pathogens. Since the first report describing severe pulmonary Mycobacterium spp-helminth co-infected patients in the mid 1940's Mycobacterium spp co-infection in humans is one of the best-known examples. In fact, the HIV infection is considered one of the main risk factors predisposing patients to tuberculosis as well as the progression to active disease, increasing the risk of latent tuberculosis reactivation 20-fold Shifts in disease severity are also common in a broad range of co-infected hosts. Concomitant infections often exacerbate the effects of single infections, independently of the diversity in parasite groups involved in the infection process. For example, in human tuberculosis (caused by Mycobacterium bovis is one of them and it is present in a broad range of wild hosts across different geographic regions Meles meles) in Great Britain, brush tailed possums (Trichosurus vulpecula) in New Zealand, buffalo (Syncerus cafer) in South Africa and wild boar (Sus scrofa) in the Iberian Peninsula are common reservoirs of this infectious disease Wildlife is an excellent model for exploring whether co-infection drives infectiousness of major diseases since they are almost always co-infected by several pathogens Mycoplasma hyopneumoniae, Haemophilus parasuis and Actinobacillus pleuropneumoniae) and a nematode (Metastrongylus spp) in 165 wild boar. Two hypotheses were tested. The first investigated whether contact with a selected group of pathogens in Mycobacterium spp infected wild boar occurred by chance or, on the contrary, was due to a structured community of pathogens (hypothesis i). The second was supported by links between tuberculosis severity and concomitant viral and nematode infections observed in both human ii).The aim of this work was to assess whether bTB severity in wild boar from mid-western Spain is associated with the contact with a selected group of common pathogens. Evidence of infection by means of serology and/or pathogen detection was carried out for viruses , bacteria . This study did not need to be approved by any animal ethics committee since animals were not killed for scientific purposes.Quercus ilex and Q. suber trees with understoreys dominated by Q. coccifera, Cistus ladanifer and Erica arborea. Wild boar density in the studied area ranged between 6.5 and 30 wild boar/hectare Cervus elaphus) and, in some cases, with fallow deer (Dama dama), roe deer (Capreolus capreolus) or extensive herds of cattle.This study was carried out on 20 wild boar game estates in mid-western Spain . In thisA total of 165 hunter harvested wild boar were collected between October 2011 and February 2013. The sex and age of these animals were determined on the basis of the observation of their sexual organs and the eruption of dentition pattern, respectively M. bovis as well as on the presence of microscopic granulomatous bTB lesions. Since the combination of microbiological culture and histopathology increases the sensitivity and specificity of bTB wild boar surveys Diagnosis of bTB in wild boar was carried out based on the isolation of M. bovis, microbiological cultures from intact (not handled or cut) submandibular or retropharyngeal lymph nodes and from a piece of caudal lung lobes (both with gross bTB-like lesions when possible) of each animal were carried out. For bacterial culture, tissue samples were sectioned and dissected, trimming the fat and connective tissue, using sterile scissors and forceps for each individual sample. Two grams of tissue were homogenized in 10 ml of sterile water with 0.2% albumin  for 4 minutes in a mechanic homogenizer . The homogenized material was then decontaminated by the hexadecyl pyridinium chloride method M. tuberculosis complex by PCR and “Spoligotyped” following standard methods M. bovis.To detect the presence of In addition, to assess the presence of tuberculosis granulomas, a piece of submandibular or retropharyngeal lymph node and lung of each animal sampled were fixed by immersion in neutral, buffered-formalin  and sections of 4 µm were cut and stained with hematoxylin and eosin for histopathological examination. The tissue pieces used for the histopathological analysis were chosen based on the presence of macroscopic bTB-like lesions when present. For wild boar in which bTB-like lesions were not found, a piece of submandibular lymph node and caudal lung lobe were identically processed for histopathology.To consider the extent of bTB, wild boar were classified into two groups: animals with a localized lesion pattern and animals with a generalized lesion pattern. Based on the distribution of lesions, generalized bTB implies more severe disease and a greater bacterial load than localized bTB Animals showing a localized pattern were those with bTB lesions in one location, mainly submandibular or retropharyngeal lymph nodes . On the A complete lesion assessment could not be carried out in 25 of 165 animals included in this study, since these animals were partially eviscerated upon arrival at the inspection area. This meant we could not ensure the lack of bTB-like lesions in abdominal organs and, therefore, their lesion pattern could not be completely determined.Haemophilus parasuis and Actinobacillus pleuropneumoniae, was determined in lungs of the sampled animals. DNA from a piece of cranial lobe from one of the lungs was extracted using a commercial QIAamp DNA Mini kit  following the manufacturer's recommendations. Later, specific PCRs were carried out in order to detect the presence of H. parasuisA. pleuropneumoniaeM. hyopneumoniae were detected using a commercial blocking-ELISA assay for swine  that was carried out using duplicate serum samples from each animal, following the protocol and cut-off values proposed by the manufacturers to differentiate seropositive and seronegative animals  <0.40× negative control OD).The presence of concomitant bacterial respiratory pathogens, such as Concerning viruses, a serologic survey for contacts with viral pathogens was carried out using commercial ELISA kits for swine and also following the manufacturer's recommendations to differentiate seropositive and seronegative animals. The presence of antibodies against PCV2 , ADV  >0.35), SIV  and PRRSV  was evaluated using duplicate samples of sera obtained from blood samples.Pulmonary nematodes were collected by lung dissection. During examination, the trachea and main bronchi were opened longitudinally with scissors, carefully examined and then placed under running water to collect adult worms on a sieve. In addition, the pulmonary parenchyma – and in particular the affected areas – were dissected carefully under a dissecting microscope to extract adult nematodes. Permanent preparations of adult specimens were made with lactophenol cotton blue solution and genus identification was based on previous descriptions A brief summary of the techniques used for antibodies and pathogen detection and the clinical picture produced by bacteria, viruses and parasites assessed in this work are shown in M. bovis, PCV2, ADV, SIV and Metastrongylus spp. Neither differences in pathogen prevalences, pathogen community structure nor in the effect of co-infection on bTB severity were determined at the game estate scale, in part because the sample size never exceeded 30 individuals per estate.For the analyses described below, all estates showed the presence of the most prevalent pathogens, e.g., Mycobacterium spp occurred by chance was studied using the null model analysis. Data were organised as presence/absence matrices in which each row represented a pathogen species and each column represented an individual wild boar. In a presence/absence matrix, “1” indicates that a species is present at a particular site or host, and “0” indicates that a species is absent Whether or not contact with other pathogens in wild boar infected by The C-score was used as a co-occurrence index for exploring co-occurrence patterns In addition, to compare the degree of co-occurrence across data, a standardised effect size (SES) for each matrix was calculated. The SES measures the number of standard deviations that the observed index (C-score) is above or below the mean index of the simulated communities.The association between viruses, bacteria and nematode species  and bTB severity  was assessed by a Partial Least Squares regression approach (PLSr). This statistical tool is an extension of multiple regression analysis, where associations between groups of variables are established with factors, i.e., combinations of dependent variables extracted from predictor variables that maximise the explained variance in the dependent variables. PLSr is probably the least restrictive of the multivariate techniques In the present study, bTB severity was considered as a single explanatory variable, while concomitant pathogens represented the × predictor factor. For PLSr modelling, the age of animals was considered in months. The “plspm” library version 0.3.7 M. bovis isolates were obtained from 85 animals (51.51%). Within infected animals, 28 showed M. bovis infection in both submandibular/retropharyngeal lymph nodes and lungs , whereas 57 only showed M. bovis infection in submandibular/retropharyngeal lymph nodes . On the other hand, bTB-like microscopic lesions were observed in 80 submandibular/retropharyngeal lymph nodes  and 28 lungs . Nine out of 85 animals infected by M. bovis (10.58%) did not show evidence of microscopic bTB-like lesions, while this microorganism could not be isolated from four animals that showed typical bTB granulomatous lesions in their lymph nodes (5%). Thus, since the combination of microbiological culture and histopathology increases the sensitivity of bTB diagnosis in wild boar M. bovis and showed 12 different spoligotype patterns (SB0119 (15.29%), SB0121 (25.88%), SB0134 (4.71%), SB0296 (3.53%), SB0339 (23.53%), SB1091 (8.23%), SB1142 (8.23%), SB0120 (1.18%), SB0152 (3.53%), SB0848 (3.53%), SB1142 (8.23%), SB1174 (2.35%)).The A detailed lesion severity assessment was carried out in 71 out of 89 animals positive to bTB. Generalized lesion patterns were detected in 28 bTB affected animals (40%), whereas localized lesions were observed in 43 affected animals (60%). Some of the animals with generalized patterns also displayed gross bTB-like lesions in organs such as liver, spleen or mesenteric lymph nodes; however, no bTB-like lesions were found in these organs in animals that did not show bTB-like lesions in the lungs (see ).M. hyopneumoniae (13.94%). A. pleuropneumoniae and Metastrongylus spp were detected in 4.84% and 50.51% of the animals, respectively, whereas evidence of infections with PRRSV or H. parasuis was not detected.The percentage of animals positive for selected respiratory pathogens is shown in M. bovis infected juvenile, yearling and adult wild boar are shown in M. bovis infected showed antibodies against PCV2 and ADV.The most common helminth, bacteria and viruses assemblages observed in The null model analysis showed that the observed C-scores were greater than expected by chance (O >E) indicating the existence of a competitively structured community; that is, bTB-infected wild boar have contacted with some specific, non-random pathogen combinations . This faMetastrongylus spp, sex and age provided a first PLSr X's component explaining 20.90% of the observed variability  Mycobacterium spp. later Regarding the order and timing of infections, the current study does not allow the determination of whether contact with these other pathogens was previous, simultaneous or subsequent to the precise time of infection by Diagnosis of some of the pathogens assessed in this work was based on serological techniques. Detection of antibodies against one pathogen does not necessarily mean a current infection since high titers of antibodies may remain for a long time after the clearance of the agent. However, this limitation might not influence the results obtained in this study since bTB is a chronic disease and lesions may persist in an affected wild boar for a long time Differentiation between seropositive and seronegative animals was carried out using the cut off values recommended by the ELISA's manufacturers, as has been previously done in similar surveys carried out in wild boar Metastrongylus spp and ADV on bTB severity suggests that sanitary measures focused on the control of these agents , may help to reduce the bTB prevalence in the affected areas.According to our results, certain pathogen combinations are correlated to more severe bTB lesions in wild boar. Since the presence of animals displaying severe bTB lesion patterns has been recently related to higher bTB prevalence in wild boar populations M. bovis may influence the success of measures applied to reduce bTB prevalence in wild boar populations, such as bTB vaccination Metastrongylus spp in wild boar vaccinated against bTB may reduce the effectiveness of this vaccine whereas measures such as previous deworming may be useful in the estates where vaccination will be carried out. In fact, a significant improvement in mycobacterial-specific immune responses occurs following anthelmintic therapy in vaccinated humans Importantly, the interaction between the above-mentioned pathogens and M. bovis in these populations.On the other hand, it is noteworthy that the greatest effects of co-infections in other wild hosts have been observed in seasons of food shortage To conclude, results obtained in this work provide a new point of view for bTB control based on community ecology principles. Removing specific members of the wild boar pathogen community could be considered in further bTB management plans in wild boar. However, given the unexpected consequences of altering any community of organisms, further research should evaluate the impact of such measures under controlled conditions. Furthermore, agents assessed in this work represent a limited group of wild boar pathogens. Therefore, the influence that other agents  have in wild boar bTB severity should be explored in future studies to obtain a more complete picture.Table S1Results obtained in characterisation, laboratory diagnosis and lesional assessment carried out in the 165 wild boar included in the study.(XLSX)Click here for additional data file.


Gastric cancer (GC) is a highly aggressive and life-threatening malignancy. Even with radical surgical removal and front-line chemotherapy, more than half of GCs locally relapse and metastasize at a distant site. The dismal outcomes reflect the ineffectiveness of a one-size-fits-all approach for a highly heterogeneous disease with diverse etiological causes and complex molecular underpinnings. The recent comprehensive genomic and molecular profiling has led to our deepened understanding of GC. The emerging molecular classification schemes based on the genetic, epigenetic, and molecular signatures are providing great promise for the development of more effective therapeutic strategies in a more personalized and precise manner. To this end, the Cancer Genome Atlas (TCGA) research network conducted a comprehensive molecular evaluation of primary GCs and proposed a new molecular classification dividing GCs into four subtypes: Epstein-Barr virus-associated tumors, microsatellite unstable tumors, genomically stable tumors, and tumors with chromosomal instability. This review primarily focuses on the TCGA molecular classification of GCs and discusses the implications on novel targeted therapy strategies. We believe that these fundamental findings will support the future application of targeted therapies and will guide our efforts to develop more efficacious drugs to treat human GCs. Helicobacter pylori and Epstein-Barr virus (EBV) infection], and genomics . In. In14]. stigated , 33 and survival . HoweverII study , Bang etII study  completeII study . The medII study –41.Fig. VEGF) gene. Studies suggest that angiogenesis is a malignant hallmark, and angiogenesis has served as a common therapeutic target [Angiogenesis may be highly relevant to the CIN subtype based on the recurrent amplification of vascular endothelial growth factor . Preclinical work has demonstrated that hotspot PIK3CA mutations led to constitutive PIK3CA pathway signaling in the absence of growth factors [PIK3CA-mutated GCs must be explored.The EBV subtype highlights the viral etiology of GCs; the TCGA characterization of this subtype suggests potential therapeutic targets for this subgroup of cancers. Of therapeutic importance, there is a strong predilection for  factors –46. Pers factors , 48, incTCGA analysis also showed that PD-1/PD-L1 was overexpressed in EBVaGCs. It has been reported that patients with cancers expressing high levels of PD-L1 were more sensitive to anti-PD-1 therapy than those with low levels of PD-L1 –51. PD-1AURK)A/B and polo-like kinase (PLK). In contrast, MSI cases generally lacked targetable amplifications, and mutations in ERBB1-3 and PIK3CA were noted, with many mutations at “hotspot” sites observed in other types of cancers [The GS subtype exhibited elevated expression of cell adhesion pathways, including the B1/B3 integrins, syndecan-1-mediated signaling, and angiogenesis-related pathways . These r cancers . AURKA a cancers , colorec cancers , pancrea cancers , esophag cancers , and lun cancers . MLN8237 cancers , 68. It  cancers . In some cancers . Other A cancers .PLKs, mitotic kinases of the polo family, play a critical role in the normal cell cycle, and their overexpression is involved in the pathogenesis of multiple human cancers –74. AmonThe deep understanding of GC molecular characterizations has led to new therapeutic strategies. Furthermore, the TCGA molecular classification that shows GC heterogeneity and distinct salient genomic features provides a guide to targeted agents for GC individualized therapy. Specifically for immune checkpoints, PD-L1/PD-1 appears to be Achilles’ heels for the EBV subtype of GC. However, it should also be noted that much work is needed to fully understand the clinical impact of this new classification. Therefore, a major unfulfilled task is to determine the clinical associations of the molecular signatures given that the cases in the TCGA cohort lacked sufficient clinical follow-up data. Nevertheless, the TCGA report is expected to provide valuable foundation and motivation to explore and refine molecular classification and tailored therapies to significantly decrease mortality and prolong survival of GC patients.


The central idea observes a recursive mapping of  The implementation of computer code for realistically simulating the configurations and motion of molecular objects requires modelling of many-body through-bond interactions. In turn, it is necessary to identify the participating atoms in each interaction. This paper presents a novel and exhaustive enumeration procedure exploiting the line graph transformation of the graph that encodes the molecular structure. In principle, by virtue of the recursive nature of the algorithm, straightforward extension to arbitrarily high order interactions is possible.Application of graph theoretic methods to the general study of molecular structure, and to equilibrium statistical mechanics in particular, are not new. Significant examples include the development of molecular branching rules , the enuintegral .define the molecular framework, while the higher order terms in  such thent}G is \documentcument}G . Hence, We recall the following definitions and terminology. A cycle graph We will also have occasion to consider directed graphs In a molecular structure, covalently bonded atom pairs are considered to be adjacent. Similarly, a pair of adjacent bonds sharing a common “hinge” atom form a more or less flexible bend. The corresponding nge atom . A \docupossible  (see Figmentclass2pt{minimif if if otherwise, c” graph  so that Ghebleh and Khatirinejad [In graph theoretical terms, this hierarchical organization of interactions is precisely captured by iterated application of the line graph construction inductively defined byen shown  that theirinejad  have propossible .Given a molecular graph ng lemma : the numCombining these results gives the useful consistency checksumsBy definition of the line graph transformation, for For concreteness, specify a maximum order fined by  is itselmentclass2pt{minimmentclass2pt{minimmentclass2pt{minimmentclass2pt{minimThe molecular graph entclass1pt{minimaFor added clarity, the edge index associated with each adjacent vertex pair is indicated by the superscript. From these matrices, the DAG obtained that represents the line graph hierarchy is shown in Fig. f Wagner  that \doentclass1pt{minimairinejad .A chemically relevant example, central to the hydrolysis and solubilisation of lipid associated with food digestion in the human lower gastrointestinal tract, are the bile salt and bile acid surfactants. Vila Verde and Frenkel  have promentclass2pt{minimOverall, the counts of bonds, bends, proper torsions and improper dihedrals are obtained as follows, theorem , it follirinejad .The line graph transformation provides a practical and elegant theoretical tool for exhaustively enumerating and indexing many-body intramolecular interactions. Given a suitable graphical representation of a molecular structure, an explicit pseudo-code implementation of the recursive line graph algorithm is given for automatically generating complete canonical lists of atomic indexes associated with each interaction order. No attempt has been made to computationally optimize this algorithm or the associated data structures. Instead, clarity of exposition is the main objective here. We anticipate the main application will involve embedding the algorithm within a Monte Carlo or Molecular Dynamics simulation code where other implementation details will determine the most efficient realization. In accord with common practice, intramolecular interactions up to order ile salt  that is