bluuebunny/crossref_metadata_2025_split huggingface dataset:
Starved Guts
Authors: Attia Suzanna , Feenstra Marjon , Swain Nathan , Cuesta Melina , Bandsma Robert H.J. 
Published: May 2017

ABSTRACTMalnutrition contributes significantly to death and illness worldwide and especially to the deaths of children younger than 5 years. The relation between intestinal changes in malnutrition and morbidity and mortality has not been well characterized; however, recent research indicates that the functional and morphologic changes of the intestine secondary to malnutrition itself contribute significantly to these negative clinical outcomes and may be potent targets of intervention. The aim of this review was to summarize current knowledge of experimental and clinically observed changes in the intestine from malnutrition preclinical models and human studies. Limited clinical studies have shown villous blunting, intestinal inflammation, and changes in the intestinal microbiome of malnourished children. In addition to these findings, experimental data using various animal models of malnutrition have found evidence of increased intestinal permeability, upregulated intestinal inflammation, and loss of goblet cells. More mechanistic studies are urgently needed to improve our understanding of malnutrition‐related intestinal dysfunction and to identify potential novel targets for intervention.
Gunshot Wound in an 18-Year-Old Woman, Inflicted With a Hunting Weapon Through an Obstacle (Mobile Phone)
Authors: Smędra Anna , Sidelnik Przemysław , Goryca Wojciech , Berent Jarosław 
Published: May 2017

AbstractThe article presents a case of an 18-year-old woman wounded by a shot fired from a distance with a hunting weapon. Because the location of the entrance and exit wounds initially seemed inconsistent with the reports (both wounds were described as “large and irregular in shape”) and no photographs documenting the inflicted injuries were taken, the case was referred for an opinion to the Department of Forensic Medicine in Lodz. After a review of the medical records, radiology, the victim's clothing, and performance of an experiment using the gun and ammunition, it was established that the entrance wound was located on the abdomen, and the exit wound was located on the buttock. The initial problems with recognizing the entrance and exit wounds encountered by the surgical team were caused by bullet deformation. Before hitting the body, the projectile pierced a mobile phone that was in the pocket of the woman's jacket, subsequently causing a large atypical secondary entrance wound. The experiment confirmed that, when the projectile passed through an obstacle with consequent deformation, it caused more extensive gunshot wounds, both at the entrance and at the exit, as well as more severe damage to the bones.
An Adolescent Presenting With Seizures as a Symptom of Gliomatosis Cerebri
Authors: Blanco-Iglesias Elena , Cabeza Beatriz , Esparza Elena Garcia , de Prada Inmaculada , Lassaletta Alvaro , Budke Marcelo , Serrano Ana 
Published: May 2017

Abstract
Gliomatosis cerebri is a diffuse infiltrating glioma of neuroepithelial origin that affects more than 2 cerebral lobes. This is rarely seen in pediatric patients. The clinical presentation and imaging are very unspecific, and a biopsy is typically needed for the diagnosis. Given the widespread nature of the disease, surgical treatment is not possible and has a poor overall prognosis. A pediatric patient presented with elevated intracranial pressure. All initial studies were negative, and the imaging showed a symmetrical affection involving the supratentorial and infratentorial regions. A biopsy ultimately confirmed gliomatosis cerebri. This case describes a unique clinical presentation of gliomatosis cerebri in a pediatric patient.
Influence of Visceral Interoceptive Experience on the Brain's Response to Food Images in Anorexia Nervosa
Authors: Kerr Kara L. , Moseman Scott E. , Avery Jason A. , Bodurka Jerzy , Simmons W. Kyle 
Published: May 2017

ABSTRACTObjectiveThe aim of the study was to determine how visceral sensations affect responses to food stimuli in anorexia nervosa (AN).MethodsTwenty weight-restored, unmedicated adolescent and young adult women with AN and twenty healthy control participants completed an interoceptive attention task during which they focused on sensations from the heart, stomach, and bladder and made ratings of these sensations. They then underwent functional magnetic resonance imaging scanning while viewing pictures of food and nonfood objects. Between-groupsttests were employed to investigate group differences in the relationship between interoceptive sensation ratings and brain hemodynamic response to food pictures and, specifically, to highly palatable foods.ResultsIn response to food pictures, AN participants exhibited a positive relationship between stomach sensation ratings and posterior insula activation (peakt= 4.30). AN participants displayed negative relationships between stomach sensation ratings and amygdala activation (peakt= −4.05) and heart sensation ratings and ventromedial prefrontal cortex activation (peakt= −3.52). In response to highly palatable foods, AN was associated with positive relationships between stomach sensation ratings and activity in the subgenual anterior cingulate (peakt= 3.88) and amygdala (peakt= 4.83), and negative relationships in the ventral pallidum (peakt= −3.99) and ventral tegmental area (peakt= −4.03). AN participants also exhibited negative relationships between cardiac sensations and activation in response to highly palatable foods in the putamen (peakt= −3.41) and ventromedial prefrontal cortex (peakt= −3.61). Healthy participants exhibited the opposite pattern in all of these regions.ConclusionsHedonic and interoceptive inferences made by individuals with AN at the sight of food may be influenced by atypical visceral interoceptive experience, which could contribute to restrictive eating.
Improving Retention in Care Among Pregnant Women and Mothers Living With HIV: Lessons From INSPIRE and Implications for Future WHO Guidance and Monitoring
Authors: Rollins Nigel C. , Essajee Shaffiq M. , Bellare Nita , Doherty Meg , Hirnschall Gottfried O. 
Published: May 2017

Abstract:
Identifying women living with HIV, initiating them on lifelong antiretroviral treatment (ART), and retaining them in care are among the important challenges facing this generation of health care managers and public health researchers. Implementation research attempts to solve a wide range of implementation problems by trying to understand and work within real-world conditions to find solutions that have a measureable impact on the outcomes of interest. Implementation research is distinct from clinical research in many ways yet demands similar standards of conceptual thinking and discipline to generate robust evidence that can be, to some extent, generalized to inform policy and service delivery. In 2011, the World Health Organization (WHO), with funding from Global Affairs Canada, began support to 6 implementation research projects in Malawi, Nigeria, and Zimbabwe. All focused on evaluating approaches for improving rates of retention in care among pregnant women and mothers living with HIV and ensuring their continuation of ART. This reflected the priority given by ministries of health, program implementers, and researchers in each country to the importance of women living with HIV returning to health facilities for routine care, adherence to ART, and improved health outcomes. Five of the studies were cluster randomized controlled trials, and 1 adopted a matched cohort design. Here, we summarize some of the main findings and key lessons learned. We also consider some of the broader implications, remaining knowledge gaps, and how implementation research is integral to, and essential for, global guideline development and to inform HIV/AIDS strategies.
Meta analysis of microbiome studies identifies shared and disease-specific patterns
Authors: Duvallet Claire , Gibbons Sean , Gurry Thomas , Irizarry Rafael , Alm Eric 
Published: May 2017

1AbstractHundreds of clinical studies have been published that demonstrate associations between the human microbiome and a variety of diseases. Yet, fundamental questions remain on how we can generalize this knowledge. For example, if diseases are mainly characterized by a small number of pathogenic species, then new targeted antimicrobial therapies may be called for. Alternatively, if diseases are characterized by a lack of healthy commensal bacteria, then new probiotic therapies might be a better option. Results from individual studies, however, can be inconsistent or in conflict, and comparing published data is further complicated by the lack of standard processing and analysis methods.Here, we introduce the MicrobiomeHD database, which includes 29 published case-control gut microbiome studies spanning ten different diseases. Using standardized data processing and analyses, we perform a comprehensive crossdisease meta-analysis of these studies. We find consistent and specific patterns of disease-associated microbiome changes. A few diseases are associated with many individual bacterial associations, while most show only around 20 genus-level changes. Some diseases are marked by the presence of pathogenic microbes whereas others are characterized by a depletion of health-associated bacteria. Furthermore, over 60% of microbes associated with individual diseases fall into a set of “core” health and disease-associated microbes, which are associated with multiple disease states. This suggests a universal microbial response to disease.
The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals its Role in Community Composition
Authors: Verster Adrian J. , Ross Benjamin D. , Radey Matthew C. , Bao Yiqiao , Goodman Andrew L. , Mougous Joseph D. , Borenstein Elhanan 
Published: May 2017

AbstractWhile the composition of the human gut microbiome has been well defined, the forces governing its assembly are poorly understood. Recently, prominent members of this community from the orderBacteroidaleswere shown to possess the type VI secretion system (T6SS), which mediates contact-dependent antagonism between Gram-negative bacteria. However, the distribution of the T6SS in human gut microbiomes and its role have not yet been characterized. To address this challenge, we construct an extensive catalog of T6SS effector/immunity (E-I) genes from three genetic architectures (GA1-3) found inBacteroidalesgenomes. We then use metagenomic analysis to assess the abundances of these genes across a large set of gut microbiome samples. We find that despite E–I diversity across reference strains, each individual microbiome harbors a limited set of E-I genes representing a single E–I genotype. Importantly, for GA1-2, these genotypes are not associated with a specific species, suggesting selection for compatibility. GA3, in contrast, is restricted toB. fragilis, and its low diversity reflects a singleB. fragilisstrain per sample. We further show that in infant microbiomes GA3 is enriched andB. fragilisstrains are replaced over time, suggesting competition for dominance in developing microbiomes. Finally, we find a strong association between the presence of GA3 and increased abundance ofBacteroides,indicating that this system confers a selective advantagein vivoinBacteroidesrich ecosystems. Combined, our findings provide the first comprehensive characterization of the T6SS landscape in the human microbiome, implicating it in both intra- and inter-species interactions.
Copb2is essential for embryogenesis and hypomorphic mutations cause human microcephaly
Authors: DiStasio Andrew , Driver Ashley , Sund Kristen , Donlin Milene , Muraleedharan Ranjith M. , Pooya Shabnam , Kline-Fath Beth , Kaufman Kenneth M. , Prows Cynthia A. , Schorry Elizabeth , DasGupta Biplab , Stottmann Rolf W. 
Published: May 2017

AbstractPrimary microcephaly is a congenital brain malformation characterized by a head circumference less than three standard deviations below the mean for age and sex and results in moderate to severe mental deficiencies and decreased lifespan. We recently studied two children with primary microcephaly in an otherwise unaffected family. Exome sequencing identified an autosomal recessive mutation leading to an amino acid substitution in a WD40 domain of the highly conservedCoatomer Protein Complex, Subunit Beta 2 (COPB2). To study the role ofCopb2in neural development, we utilized genome editing technology to generate an allelic series in the mouse. Two independent null alleles revealed thatCopb2is essential for early stages of embryogenesis. Mice homozygous for the patient variant (Copb2R254C/R254C) appear to have a grossly normal phenotype, likely due to differences in corticogenesis between the two species. Strikingly, mice heterozygous for the patient mutation and a null allele (Copb2R254C/Znf) show a severe perinatal phenotype including low neonatal weight, significantly increased apoptosis in the brain, and death within the first week of life. Immunostaining of theCopb2R254C/Znfbrain revealed a reduction in layer V (CTIP2+) neurons, while the overall cell density of the cortex is unchanged. Moreover, disruption ofCopb2in mouse neurospheres resulted in reduced proliferation. These results identify a general requirement forCOPB2in embryogenesis and a specific role in corticogenesis. We further demonstrate the utility of CRISPR-Cas9 generated mouse models in the study of potential pathogenicity of variants of potential clinical interest.
Basal Ganglia Control of Reflexive Saccades: A Computational Model Integrating Physiology Anatomy and Behaviour
Authors: Cope Alex J. , Chambers Jonathan M. , Prescott Tony J. , Gurney Kevin N. 
Published: May 2017

AbstractIt is hypothesised that the basal ganglia play a key role in solving the problem of action selection. Here we investigate this hypothesis through computational modelling of the primate saccadic oculomotor system. This system is an excellent target for computational modelling because it is supported by a reasonably well understood functional anatomy, has limited degrees of freedom, and there is a wealth of behavioural and electrophysiological data for model comparison. Here, we describe a computational model of the reflexive saccadic oculomotor system incorporating the basal ganglia, key structures in motor control and competition between possible actions. To restrict the likelihood of overfitting the model it is structured and parameterised by the known anatomy and neurophysiology along with data from a single experimental behavioural paradigm, then validated by testing against several additional behavioural experimental data without modification of the parameters. With this model we reproduce a range of fundamental reflexive saccadic results both qualitatively and quantitatively, comprising: the distribution of saccadic latencies; the effect of eccentricity, luminance and fixation-target interactions on saccadic latencies; and the effect of competing targets on saccadic endpoint. By investigating the model dynamics we are able to provide mechanistic explanations for the sources of these behaviours. Further, because of its accesibility, the oculomotor system has also been used to study general principle of sensorimotor control. We interpret the ability of the basal ganglia to successfully control saccade selection in our model as further evidence for the action selection hypothesis.
Inverse Modeling for MEG/EEG Data
Authors: Sorrentino Alberto , Piana Michele 
Published: May 2017

AbstractWe provide an overview of the state-of-the-art for mathematical methods that are used to reconstruct brain activity from neurophysiological data. After a brief introduction on the mathematics of the forward problem, we discuss standard and recently proposed regularization methods, as well as Monte Carlo techniques for Bayesian inference. We classify the inverse methods based on the underlying source model, and discuss advantages and disadvantages. Finally we describe an application to the pre–surgical evaluation of epileptic patients.
Kinship governs fertility with pre-and post-zygotic mechanisms mediated by match of methylation patterns
Authors: Herbert M. 
Published: May 2017

AbstractIt has been shown that kinship normally determines fertility in humans and animals. At smaller populations the curve of fertility against kinship rises steeply as kinship rises until inbreeding is reached. In large and progressively larger populations, fertility slowly falls. At an equilibrium point fertility matches replacement. Away from that, fertility changes by one of four published time courses. Earlier we demonstrated damped oscillation in a population of captive fruit flies. I hypothesized that since fertility changes so rapidly, DNA base mutations could not be the cause. The mechanism must be epigenetic, the control of genes, and gave varying doses of a methylating cocktail to the same flies. The fly population changed in a complex way, which only happens when there are pre-zygotic and post-zygotic processes in effect together.One Sentence SummaryThere is evidence for an epigenetic effect – with both pre-zygotic and post-zygotic components – of kinship on fertility of flies (Drosophila melanogaster)induced by a methylating cocktail.
Dynamic Current Clamp Experiments Define the Functional Roles of IK1 and Ito,f in Human Induced Pluripotent Stem Cell Derived Cardiomyocytes
Authors: Marrus Scott B. , Springer Steven , Johnson Eric , Martinez Rita J. , Dranoff Edward J. , Mellor Rebecca , Yamada Kathryn 
Published: May 2017

AbstractThe transient outward potassium current (Ito) plays a key, albeit incompletely defined, role in cardiomyocyte physiology and pathophysiology. In light of the technical challenges of studying adult human cardiomyocytes, this study examines the use of induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) as a system which potentially preserves the native cellular milieu of human cardiomyocytes. ISPC-CMs express a robust Ito with slow recovery kinetics and fail to express the rapidly recovering Ito,f which is implicated in human disease. Overexpression of the accessory subunit KChIP2 (which is not expressed in iPSC-CMs) resulted in restoration of a rapid component of recovery. To define the functional role of Ito, dynamic current clamp was used to introduce computationally modeled currents into iPSC-CMs while recording action potentials. However, iPSC-CMs exhibit action potentials with multiple immature physiological properties, including slow upstroke velocity, heterogeneous action potential waveforms, and the absence of a phase 1 notch, thus potentially limiting the utility of these cells as a model of adult cardiomyocytes. Importantly, the introduction of modeled inwardly rectified current (IK1) ameliorated these immature properties by restoring a hyperpolarized resting membrane potential. In this context of normalized action potential morphologies, dynamic current clamp experiments introducing Ito,f demonstrated that there is significant cell-to-cell heterogeneity and that the functional effect of Ito,f is highly sensitive to the action potential plateau voltage in each cell.
Revealing Complete ComplexKIRHaplotypes Phased by Long-read Sequencing Technology
Authors: Roe D. , Vierra-Green C. , Pyo C.-W. , Eng K. , Kuang R. , Spellman S. , Ranade S. , Geraghty D.E. , Maiers M. 
Published: May 2017

AbstractThe killer cell immunoglobulin-like receptor (KIR) region of human chromosome 19 contains up to sixteen genes for natural killer (NK) cell receptors that recognize human leukocyte antigen (HLA)/peptide complexes and other ligands. TheKIRproteins fulfill functional roles in infections, pregnancy, autoimmune diseases, and transplantation. However, their characterization remains a constant challenge. Not only are the genes highly homologous due to their recent evolution by tandem duplications, but the region is structurally dynamic due to frequent transposon-mediated recombination. A sequencing approach that precisely captures the complexity ofKIRhaplotypes for functional annotation is desirable.We present a unique approach to haplotype theKIRloci using Single Molecule, Real-Time (SMRT®) Sequencing. Using this method, we have – for the first time – comprehensively sequenced and phased sixteenKIRhaplotypes from eight individuals without imputation. The information revealed four novel haplotype structures, a novel gene-fusion allele, novel and confirmed insertion/deletion events, a homozygous individual, and overall diversity for the structural haplotypes and their alleles.TheseKIRhaplotypes augment our existing knowledge by providing high-quality references, evolutionary informers, and source material for imputation. The haplotype sequences and gene annotations provide alternative loci for theKIRregion in the human genome reference GrCh38.p8.Author contributionsDR, CVG, SS, SR, DEG, MM designed the project. CWP, KE, RH performed the preparation and sequencing experiments. DR, CVG, RK, SR, DWG wrote the majority of the manuscript.
cyTRONandcyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models
Authors: Patruno Lucrezia , Galimberti Edoardo , Ramazzotti Daniele , Caravagna Giulio , De Sano Luca , Antoniotti Marco , Graudenzi Alex 
Published: May 2017

AbstractThe increasing availability of sequencing data of cancer samples is fueling the development of algorithmic strategies to investigate tumor heterogeneity and infer reliable models of cancer evolution. We here build up on previous works on cancer progression inference from genomic alteration data, to deliver two distinctCytoscape-based applications, which allow to produce, visualize and manipulate cancer evolution models, also by interacting with public genomic and proteomics databases. In particular, we here introducecyTRON, a stand-aloneCytoscapeapp, andcyTRON/JS, a web application which employs the functionalities ofCytoscape/JS.cyTRON was developed in Java; the code is available athttps://github.com/BIMIB-DISCo/cyTRONand on the Cytoscape App Storehttp://apps.cytoscape.org/apps/cytron. cyTRON/JS was developed in JavaScript and R; the source code of the tool is available athttps://github.com/BIMIB-DISCo/cyTRON-jsand the tool is accessible fromhttps://bimib.disco.unimib.it/cytronjs/welcome.