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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Inspiratory breathing movements depend on pre-Bötzinger complex ( preBötC ) interneurons that express calcium ( Ca2+ ) -activated nonselective cationic current ( ICAN ) to generate robust neural bursts . Hypothesized to be rhythmogenic , reducing ICAN is predicted to slow down or stop breathing; its contributions to mo...	Breathing behavior consists of periodic movements of the chest and airways that ventilate the lungs . The brain must generate a rhythm and form a motor output pattern to make breathing movements happen . Here , we address the ion channel–level neural origins of breathing , particularly the role of a class of transient ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "membrane", "potential", "vertebrates", "electrophysiology", "mice", "neuroscience", "animals", "mammals", "motor", "neurons", "physiological", "processes", "receptor", "potentials", "ion", "channels", "transient", "receptor", "pot...	2019	Trpm4 ion channels in pre-Bötzinger complex interneurons are essential for breathing motor pattern but not rhythm
Herpes simplex virus ( HSV ) entry into the cells requires glycoproteins gD , gH/gL and gB , activated in a cascade fashion by conformational modifications induced by cognate receptors and intermolecular signaling . The receptors are nectin1 and HVEM ( Herpes virus entry mediator ) for gD , and αvβ6 or αvβ8 integrin fo...	Herpes simplex virus encodes an entry apparatus made of the glycoproteins gD , gH/gL and gB . gD is the major determinant of HSV tropism . Receptor-induced modifications to gD and gH/gL activate in a cascade fashion gB , the conserved fusogenic glycoprotein across the Herpesviridae family . In herpesviruses other than ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "herpes", "simplex", "virus", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "viral", "structure", "viruses", "integrins", "dna", "viruses", ...	2017	Insertion of a ligand to HER2 in gB retargets HSV tropism and obviates the need for activation of the other entry glycoproteins
Prior experiences can influence future actions . These experiences can not only drive adaptive changes in motor output , but they can also modulate the rate at which these adaptive changes occur . Here we studied anterograde interference in motor adaptation – the ability of a previously learned motor task ( Task A ) to...	The act of learning one task can not only have direct effects on the performance of other tasks , but it can also affect the ability to learn other tasks . One example of the latter is the phenomenon of anterograde interference in motor adaptation , in which the learning of one adaptation can substantially reduce the r...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience", "neuroscience/motor", "systems" ]	2010	Reduction in Learning Rates Associated with Anterograde Interference Results from Interactions between Different Timescales in Motor Adaptation
Computational analysis of neural systems is at its most useful when it uncovers principles that provide a unified account of phenomena across multiple scales and levels of description . Here we analyse a widely used model of the cerebellar contribution to sensori-motor learning to demonstrate both that its response to ...	The cerebellum or “little brain” is a fist-sized structure located towards the rear of the brain , containing as many neurons as the rest of the brain combined , whose functions include learning to perform skilled motor tasks accurately and automatically . It is wired up into repeating microcircuits , sometimes referre...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/motor", "systems", "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience" ]	2008	Silent Synapses, LTP, and the Indirect Parallel-Fibre Pathway: Computational Consequences of Optimal Cerebellar Noise-Processing
The conserved DAF-16/FOXO transcription factors and SIR-2 . 1/SIRT1 deacetylases are critical for diverse biological processes , particularly longevity and stress response; and complex regulation of DAF-16/FOXO by SIR-2 . 1/SIRT1 is central to appropriate biological outcomes . Caenorhabditis elegans Host Cell Factor 1 ...	The nematode C . elegans has been instrumental in identifying and characterizing genetic components that influence aging . Studies in worms have been successfully extended to complex mammalian organisms allowing for the identification of genetic factors that impact longevity in mammals . DAF-16/FOXO transcription facto...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	The Evolutionarily Conserved Longevity Determinants HCF-1 and SIR-2.1/SIRT1 Collaborate to Regulate DAF-16/FOXO
Reunion Island is a French overseas territory located in the south-western of Indian Ocean , 700 km east of Madagascar . Leprosy first arrived on Reunion Island in the early 1700s with the African slaves and immigration from Madagascar . The disease was endemic until 1980 but improvement of health care and life conditi...	Leprosy was still endemic on Reunion Island 30 years ago but improvements in health care and treatments led to a significant decrease in the number of new cases of leprosy . Nevertheless , the long-standing lack of a surveillance system prevents a real evaluation of endemicity . This is the first study to evaluate erad...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "disabilities", "biopsy", "tropical", "diseases", "oceans", "geographical", "locations", "surgical", "and", "invasive", "medical", "procedures", "bacterial", "diseases", "research", "design", "comoros", "bodies", "of", "water", ...	2016	Leprosy on Reunion Island, 2005-2013: Situation and Perspectives
There is no effective vaccine against Buruli ulcer . In experimental footpad infection of C57BL/6 mice with M . ulcerans , a prime-boost vaccination protocol using plasmid DNA encoding mycolyltransferase Ag85A of M . ulcerans and a homologous protein boost has shown significant , albeit transient protection , comparabl...	Buruli ulcer ( BU ) is an infectious disease , characterized by deep , ulcerating skin lesions , particularly on arms and legs , which are provoked by a toxin . BU is caused by a microbe of the genus that also cause tuberculosis and leprosy . The 33 countries where Buruli ulcer has been detected , especially in West Af...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2014	Analysis of the Vaccine Potential of Plasmid DNA Encoding Nine Mycolactone Polyketide Synthase Domains in Mycobacterium ulcerans Infected Mice
Increased ambient temperature is inhibitory to plant immunity including auto-immunity . SNC1-dependent auto-immunity is , for example , fully suppressed at 28°C . We found that the Arabidopsis sumoylation mutant siz1 displays SNC1-dependent auto-immunity at 22°C but also at 28°C , which was EDS1 dependent at both tempe...	Ambient temperature is a major actor in plant immunity and in growth regulation . Foremost , high temperature ( >27°C ) is known to block plant defence responses . High temperature also alters the plant morphology by inducing elongation growth , which facilitates plant ‘cooling’ . This process is called thermomorphogen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "plant", "anatomy", "plant", "growth", "and", "development", "plant", "embryo", "anatomy", "cell", "processes", "brassica", "membrane", "proteins", "developmental", "biology", "plant", "science", "model", "organisms", "sumoylation", "experimental", "o...	2018	The Arabidopsis SUMO E3 ligase SIZ1 mediates the temperature dependent trade-off between plant immunity and growth
True incidence of leprosy and its impact on transmission will not be understood until a tool is available to measure pre-symptomatic infection . Diagnosis of leprosy disease is currently based on clinical symptoms , which on average take 3–10 years to manifest . The fact that incidence , as defined by new case detectio...	Despite reaching the global elimination target for leprosy , the need for a diagnostic tool to detect pre-symptomatic disease remains . Transmission has not been completely intercepted despite over 30 years of extensive curative treatment . With limited resources , two new leprosy skin test antigens , MLSA-LAM and MLCw...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "research", "design", "infectious", "diseases", "medicine", "and", "health", "sciences", "clinical", "medicine", "clinical", "research", "design", "clinical", "trials", "biology", "and", "life", "sciences", "microbiology", "research", "and", "analysis",...	2014	The Challenge of Producing Skin Test Antigens with Minimal Resources Suitable for Human Application against a Neglected Tropical Disease; Leprosy
A single co-administered dose of ivermectin ( IVM ) plus diethylcarbamazine ( DEC ) plus albendazole ( ALB ) , or triple-drug therapy , was recently found to be more effective for clearing microfilariae ( Mf ) than standard DEC plus ALB currently used for mass drug administration programs for lymphatic filariasis ( LF ...	Lymphatic filariasis is a mosquito-borne infection that causes disability in the form of lymphedema , hydroceles , and elephantiasis . It has been targeted for global elimination based on mass drug administration in the total population at risk including many people uninfected with LF . Recently , a single co-administe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "clinical", "research", "design", "tropical", "diseases", "parasitic", "diseases", "animals", "research", "design", "signs", "and", "symptoms", "p...	2019	Pharmacokinetics, safety, and efficacy of a single co-administered dose of diethylcarbamazine, albendazole and ivermectin in adults with and without Wuchereria bancrofti infection in Côte d’Ivoire
By necessity , the ancient activity of type II topoisomerases co-evolved with the double-helical structure of DNA , at least in organisms with circular genomes . In humans , the strand passage reaction of DNA topoisomerase II ( Topo II ) is the target of several major classes of cancer drugs which both poison Topo II a...	Several major classes of anti-cancer drugs kill tumor cells by binding to the enzyme DNA topoisomerase II , but at the same time , cellular responses are activated that protect the tumor cells . How checkpoint activation occurs under circumstances of topoisomerase II perturbation is not well understood . We show that a...	[ "Abstract", "Introduction", "Results/Discussion", "Material", "and", "Methods" ]	[]	2013	Direct Monitoring of the Strand Passage Reaction of DNA Topoisomerase II Triggers Checkpoint Activation
To follow the fate of CD8+ T cells responsive to Plasmodium berghei ANKA ( PbA ) infection , we generated an MHC I-restricted TCR transgenic mouse line against this pathogen . T cells from this line , termed PbT-I T cells , were able to respond to blood-stage infection by PbA and two other rodent malaria species , P . ...	Malaria is a disease caused by Plasmodium species , which have a highly complex life cycle involving both liver and blood stages of mammalian infection . To prevent disease , one strategy has been to induce CD8+ T cells against liver-stage parasites , usually by immunization with stage-specific antigens . Here we descr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "immunopathology", "clinical", "immunology", "immunity", "immunity", "to", "infections", "biology", "and", "life", "sciences", "immunology", "acquired", "immune", "system", "immune", "response", "immune", "system" ]	2014	CD8+ T Cells from a Novel T Cell Receptor Transgenic Mouse Induce Liver-Stage Immunity That Can Be Boosted by Blood-Stage Infection in Rodent Malaria
As infectious disease surveillance systems expand to include digital , crowd-sourced , and social network data , public health agencies are gaining unprecedented access to high-resolution data and have an opportunity to selectively monitor informative individuals . Contact networks , which are the webs of interaction t...	As public health agencies strive to harness big data to improve outbreak surveillance , they face the challenge of extracting meaningful information that can be directly used to improve public health , without incurring additional costs . In this article , we address the question: Which nodes in a social network should...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "sociology", "social", "sciences", "mathematical", "models", "mathematics", "scale-free", "networks", "algebra", "network", "analysis", "social", "networks", "infectious", "disease", "contro...	2016	Disease Surveillance on Complex Social Networks
The actin capping protein ( CP ) tightly binds to the barbed end of actin filaments , thus playing a key role in actin-based lamellipodial dynamics . V-1 and CARMIL proteins directly bind to CP and inhibit the filament capping activity of CP . V-1 completely inhibits CP from interacting with the barbed end , whereas CA...	Actin is a ubiquitous eukaryotic protein that polymerizes into bidirectional filaments and plays essential roles in a variety of biological processes , including cell division , muscle contraction , neuronal development , and cell motility . The actin capping protein ( CP ) tightly binds to the fast-growing end of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "cell", "biology/cytoskeleton" ]	2010	Two Distinct Mechanisms for Actin Capping Protein Regulation—Steric and Allosteric Inhibition
Tanzania is among the Rift Valley fever ( RVF ) epizootic/endemic countries in sub Saharan Africa , where RVF disease outbreaks occur within a range of 3 to 17-year intervals . Detection of Rift Valley fever virus ( RVFV ) antibodies in animals in regions with no previous history of outbreaks raises the question of whe...	The RVFV maintenance between inter-epizootic/inter-epidemic periods is not fully understood , despite the widely hypothesized belief of maintenance via transovarially infected Aedes mosquito eggs . Increasing serological evidence however , suggests that there could be continuous virus circulation throughout these perio...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion", "and", "recommendations" ]	[ "livestock", "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "ruminants", "pathogens", "immunology", "geographical", "locations", "microbiol...	2018	Serological evidence of inter-epizootic/inter-epidemic circulation of Rift Valley fever virus in domestic cattle in Kyela and Morogoro, Tanzania
Virtually all DNA viruses including hepatitis B viruses ( HBV ) replicate their genome inside the nucleus . In non-dividing cells , the genome has to pass through the nuclear pore complexes ( NPCs ) by the aid of nuclear transport receptors as e . g . importin β ( karyopherin ) . Most viruses release their genome in th...	Viral capsids facilitate protection of the enclosed viral genome and participate in the intracellular transport of the genome . At the site of replication capsids have to release the genome . The particular factors triggering genome liberation are not well understood . Like other karyophilic cargos , hepatitis B virus ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "invasion", "and", "cell", "entry" ]	2010	Nucleoporin 153 Arrests the Nuclear Import of Hepatitis B Virus Capsids in the Nuclear Basket
Microsporidia are obligate intracellular parasites of most animal groups including humans , but despite their significant economic and medical importance there are major gaps in our understanding of how they exploit infected host cells . We have investigated the evolution , cellular locations and substrate specificitie...	Microsporidians are highly reduced obligate intracellular eukaryotic parasites that cause significant disease in humans , animals and commercially relevant insects . Despite their medical and economic interest the mechanisms whereby microsporidians exploit the cells they infect are mainly unknown . We have characterise...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	Plasma Membrane-Located Purine Nucleotide Transport Proteins Are Key Components for Host Exploitation by Microsporidian Intracellular Parasites
Co-expression analysis has been employed to predict gene function , identify functional modules , and determine tumor subtypes . Previous co-expression analysis was mainly conducted at bulk tissue level . It is unclear whether co-expression analysis at the single-cell level will provide novel insights into transcriptio...	With the development of single-cell sequencing , an increasing number of biological insights were revealed at the single-cell resolution . Here we integrated the expression profiles from single cells and bulk tissues to discover that a majority of gene pairs were specifically co-expressed at single-cell and bulk levels...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "blastomas", "cancers", "and", "neoplasms", "oncology", "neurological", "tumors", "genome", "analysis", "epigenetics", "chromatin", "genomics", "chromosome", "biology", "proteins", "gene", "expression", "chr...	2016	Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes
The Mediator complex provides an interface between gene-specific regulatory proteins and the general transcription machinery including RNA polymerase II ( RNAP II ) . The complex has a modular architecture ( Head , Middle , and Tail ) and cryoelectron microscopy analysis suggested that it undergoes dramatic conformatio...	Intrinsically disordered proteins/regions do not adopt well-defined three dimensional structures; instead , they function as conformational ensembles . They are distinguished in molecular recognition and involved in various regulatory processes . Several components in the transcription machinery–for example , the trans...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/macromolecular", "sequence", "analysis", "computational", "biology/sequence", "motif", "analysis", "computational", "biology/transcriptional", "regulation" ]	2008	Malleable Machines in Transcription Regulation: The Mediator Complex
Mutations in the cystic fibrosis transmembrane conductance regulator ( CFTR ) gene cause cystic fibrosis ( CF ) and are associated with congenital bilateral absence of the vas deferens ( CBAVD ) , which is the major cause of infertility in male patients with CF . However , most Taiwanese patients with CBAVD do not carr...	Cystic fibrosis ( CF ) is the most common inherited life-threatening disease in Caucasians . The most well-known cause of CF is a genetic defect in CFTR , an apical membrane chloride and bicarbonate channel . The symptoms of CF include defects in the respiratory , digestive , and male reproductive systems . Most male p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "urology", "medicine", "and", "health", "sciences", "reproductive", "system", "male", "infertility", "genetic", "diseases", "fibrosis", "pulmonology", "germ", "cells", "animal", "models", "physiological", "processes", "developmental", "biology", "model", "organisms", "c...	2017	Loss of SLC9A3 decreases CFTR protein and causes obstructed azoospermia in mice
Infection of host cells by pathogenic microbes triggers signal transduction pathways leading to a multitude of host cell responses including actin cytoskeletal re-arrangements and transcriptional programs . The diarrheagenic pathogens Enteropathogenic E . coli ( EPEC ) and the related Enterohemorrhagic E . coli ( EHEC ...	Many significant immune diseases are caused by bacterial pathogens that deliver effector proteins into their host . The pathogen uses these proteins to subvert the hosts' normal cytosolic defense in a way that services the pathogen . It is therefore important to understand the normal processes of a cell and how they ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "microbiology/cellular", "microbiology", "and", "pathogenesis", "molecular", "biology/transcription", "initiation", "and", "activation", "cell", "biology/cytoskeleton" ]	2011	Bacterial and Host Determinants of MAL Activation upon EPEC Infection: The Roles of Tir, ABRA, and FLRT3
The FoxA family of pioneer transcription factors regulates hepatitis B virus ( HBV ) transcription , and hence viral replication . Hepatocyte-specific FoxA-deficiency in the HBV transgenic mouse model of chronic infection prevents the transcription of the viral DNA genome as a result of the failure of the developmental...	This study demonstrates the connection between FoxA expression and gene silencing by DNA methylation in vivo during liver maturation . Insufficient FoxA expression results in selective developmentally regulated hepatitis B virus ( HBV ) silencing by DNA methylation . To our knowledge , this is the first in vivo demonst...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "liver", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "dna", "transcription", "animal", "models", "model", "organisms", "dna", "replication", "experimental", "organism", "systems", "transcription", "...	2017	Hepatic deficiency of the pioneer transcription factor FoxA restricts hepatitis B virus biosynthesis by the developmental regulation of viral DNA methylation
Chromosome missegregation in germ cells is an important cause of unexplained infertility , miscarriages , and congenital birth defects in humans . However , the molecular defects that lead to production of aneuploid gametes are largely unknown . Cdc20 , the activating subunit of the anaphase-promoting complex/cyclosome...	Aneuploidy , an abnormal number of chromosomes , is a common defect in sperm and egg cells that is responsible for human infertility , miscarriage , and congenital birth defects . Although these developmental outcomes are prevalent in human reproduction , little is known about the molecular defects that may cause aneup...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "cell", "biology/cell", "growth", "and", "division", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/chromosome", "biology" ]	2010	Cdc20 Is Critical for Meiosis I and Fertility of Female Mice
Taenia solium ( T . solium ) cysticercosis remains a neglected zoonotic disease in India . The current study was planned to estimate the prevalence of T . solium porcine cysticercosis in the Punjab state of India , to compare this prevalence with the disease prevalence in pigs reared outside Punjab and to assess the di...	Taenia solium cysticercosis is a neglected zoonosis and severely affects pork production and public health in India . The current study was conducted to estimate the prevalence and distribution of T . solium porcine cysticercosis in the Punjab state of India and to compare the disease prevalence in pigs reared within a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "vertebrates", "india", "parasitic", "diseases", "animals", "animal", "slaughter", "mammals", "tongue", "neglected", "tropical", "diseases", "animal", "management", "cardiac", ...	2018	Prevalence and distribution of Taenia solium cysticercosis in naturally infected pigs in Punjab, India
Bacteria engage in contact-dependent activities to coordinate cellular activities that aid their survival . Cells of Myxococcus xanthus move over surfaces by means of type IV pili and gliding motility . Upon direct contact , cells physically exchange outer membrane ( OM ) lipoproteins , and this transfer can rescue mot...	Motility facilitates a wide variety of processes such as virulence , biofilm formation and development in bacteria . Bacteria have evolved at least three mechanisms for motility on surfaces: swarming motility , twitching motility and gliding motility . Mechanistically , gliding motility is poorly understood . Here , we...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Contact- and Protein Transfer-Dependent Stimulation of Assembly of the Gliding Motility Machinery in Myxococcus xanthus
Questionnaires of reported blood in urine ( BIU ) distributed through the existing school system provide a rapid and reliable method to classify schools according to the prevalence of Schistosoma haematobium , thereby helping in the targeting of schistosomiasis control . However , not all schools return questionnaires ...	The highly focal nature of schistosomiasis means that treatment is most cost-effective when delivered on a school-by-school basis . Questionnaires of reported blood in urine ( BIU ) distributed through the existing school system are a rapid , valid method to classify schools according to WHO treatment thresholds . Thei...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "disease", "mapping", "public", "health", "and", "epidemiology", "epidemiology", "spatial", "epidemiology" ]	2013	The Use of Bivariate Spatial Modeling of Questionnaire and Parasitology Data to Predict the Distribution of Schistosoma haematobium in Coastal Kenya
The discrepancy between structural and functional connectivity in neural systems forms the challenge in understanding general brain functioning . To pinpoint a mapping between structure and function , we investigated the effects of ( in ) homogeneity in coupling structure and delays on synchronization behavior in netwo...	Separating the time scale of oscillations from that of the phase dynamics allowed for reducing a network of coupled neural mass models to a system of phase oscillators . We studied the dynamics of networks of phases and their synchronization characteristics as being seminal for functional neural networks . We put parti...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computer", "and", "information", "sciences", "systems", "science", "mathematics", "neuroanatomy", "anatomy", "neural", "networks", "computational", "neuroscience", "nervous", "system", "biology", "and", "life", "sciences", "physical", "sciences", "computational", "biolog...	2014	Structure-Function Discrepancy: Inhomogeneity and Delays in Synchronized Neural Networks
Palpalis group tsetse flies are the major vectors of human African trypanosomiasis , and visually-attractive targets and traps are important tools for their control . Considerable efforts are underway to optimise these visual baits , and one factor that has been investigated is coloration . Analyses of the link between...	Tsetse flies transmit sleeping sickness ( human African trypanosomiasis ) , and visually attractive targets and traps are important tools for the control of the flies and prevention of disease . Previous studies have tried to determine the best colour for visual baits by relating their light reflectance properties to t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "vector-borne", "diseases", "geographical", "locations", "neuroscience", "animal", "behavior", "vision", "insect", "vectors", "zoology", "africa", "infectious", "diseases", "epidemiology", "neuroethology", "disease", "vectors", "be...	2014	A Colour Opponent Model That Explains Tsetse Fly Attraction to Visual Baits and Can Be Used to Investigate More Efficacious Bait Materials
Spontaneous canine head and neck squamous cell carcinoma ( HNSCC ) represents an excellent model of human HNSCC but is greatly understudied . To better understand and utilize this valuable resource , we performed a pilot study that represents its first genome-wide characterization by investigating 12 canine HNSCC cases...	Head and neck squamous cell carcinoma ( HNSCC ) represents the sixth leading cancer by incidence in humans; thus , developing effective therapeutic interventions is important . Although great advance has been made in our understanding of the biology of HNSCC over the past several decades , translating the research find...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Canine Spontaneous Head and Neck Squamous Cell Carcinomas Represent Their Human Counterparts at the Molecular Level
We present an approach for identifying genes under natural selection using polymorphism and divergence data from synonymous and non-synonymous sites within genes . A generalized linear mixed model is used to model the genome-wide variability among categories of mutations and estimate its functional consequence . We dem...	We present a new methodology , SnIPRE , for identifying genes under natural selection . SnIPRE is a “McDonald-Kreitman” type of analysis , in that it is based on MK table data and has an advantage over other types of statistics because it is robust to demography . Similar to the MKprf method , SnIPRE makes use of genom...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "mathematics", "theoretical", "biology", "natural", "selection", "statistics", "genetics", "population", "genetics", "biology", "biostatistics", "statistical", "methods", "genetics", "and", "genomics" ]	2012	SnIPRE: Selection Inference Using a Poisson Random Effects Model
Mobile group II introns , which are found in bacterial and organellar genomes , are site-specific retroelments hypothesized to be evolutionary ancestors of spliceosomal introns and retrotransposons in higher organisms . Most bacteria , however , contain no more than one or a few group II introns , making it unclear how...	Group II introns are bacterial mobile elements thought to be ancestors of introns and retroelements in higher organisms . They comprise a catalytically active intron RNA and an intron-encoded reverse transcriptase , which promotes splicing of the intron from precursor RNA and integration of the excised intron into new ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/rna-protein", "interactions", "biochemistry/rna", "structure", "molecular", "biology/molecular", "evolution", "molecular", "biology/rna", "splicing", "molecular", "biology/bioinformatics" ]	2010	Mechanisms Used for Genomic Proliferation by Thermophilic Group II Introns
The acid-sensing ion channel 1 ( ASIC1 ) is a key receptor for extracellular protons . Although numerous structural and functional studies have been performed on this channel , the structural dynamics underlying the gating mechanism remains unknown . We used normal mode analysis , mutagenesis , and electrophysiological...	The acid-sensing ion channels ( ASICs ) are key receptors for extracellular protons and are becoming increasingly important drug targets . However , their gating mechanism is still not fully understood . The crystallographic structure of the ASIC1 protein provides a clue , but the dynamics of the channel remains to be ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/molecular", "dynamics", "biophysics", "neuroscience" ]	2009	Inherent Dynamics of the Acid-Sensing Ion Channel 1 Correlates with the Gating Mechanism
The yellow fever ( YF ) 17D vaccine is one of the most effective human vaccines ever created . The YF vaccine has been produced since 1937 in embryonated chicken eggs inoculated with the YF 17D virus . Yet , little information is available about the infection mechanism of YF 17DD virus in this biological model . To bet...	Since 1937 , the vaccine against yellow fever has been produced in chicken embryos without any critical modification . Despite this highly available and effective vaccine , yellow fever remains an important cause of morbidity and mortality in tropical regions of Africa and South America , mainly by maintaining the sylv...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Yellow Fever 17DD Vaccine Virus Infection Causes Detectable Changes in Chicken Embryos
Disruption of proteostasis , or protein homeostasis , is often associated with aberrant accumulation of misfolded proteins or protein aggregates . Autophagy offers protection to cells by removing toxic protein aggregates and injured organelles in response to proteotoxic stress . However , the exact mechanism whereby au...	Accumulation of misfolded proteins deposited in the form of inclusion bodies is a common pathological hallmark for many human genetic diseases , particularly for the neurodegenerative disorders . The aggregation of the disease related proteins suggests a failure of the cellular machineries that maintain the protein hom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Proteotoxic Stress Induces Phosphorylation of p62/SQSTM1 by ULK1 to Regulate Selective Autophagic Clearance of Protein Aggregates
KSHV is the etiological agent of Kaposi's sarcoma ( KS ) , primary effusion lymphoma ( PEL ) , and a subset of multicentricCastleman's disease ( MCD ) . The fact that KSHV-encoded miRNAs are readily detectable in all KSHV-associated tumors suggests a potential role in viral pathogenesis and tumorigenesis . MiRNA-mediat...	Kaposi's sarcoma-associated herpesvirus is the etiological agent of KS and two lymphoproliferative diseases: multicentricCastleman's disease and primary effusion lymphomas ( PEL ) . KSHV tumors are the most prevalent AIDS malignancies and within Sub-Saharan Africa KS is the most common cancer in males , both in the pre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "rna", "nucleic", "acids", "viral", "immune", "evasion", "virology", "viral", "persistence", "and", "latency", "viruses", "and", "cancer", "biology", "rna", "stability", "microbiology" ]	2012	Ago HITS-CLIP Expands Understanding of Kaposi's Sarcoma-associated Herpesvirus miRNA Function in Primary Effusion Lymphomas
The introduction of forensic autosomal DNA profiles was controversial , but the problems were successfully addressed , and DNA profiling has gone on to revolutionise forensic science . Y-chromosome profiles are valuable when there is a mixture of male-source and female-source DNA , and interest centres on the identity ...	Y-chromosome DNA profiles are important in forensic science , particularly when a male has been accused of assaulting a female . However , unlike for autosomal profiles , the problem of evaluating weight-of-evidence for Y profiles has not been satisfactorily resolved despite many attempts . The key idea missing from cu...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "crime", "clinical", "laboratory", "sciences", "sociology", "geographical", "locations", "social", "sciences", "genetic", "mapping", "simulation", "and", "modeling", "mutation", "criminology", "mutation", "databases", "population",...	2017	How convincing is a matching Y-chromosome profile?
Rhodococcus equi causes fatal pyogranulomatous pneumonia in foals and immunocompromised animals and humans . Despite its importance , there is currently no effective vaccine against the disease . The actinobacteria R . equi and the human pathogen Mycobacterium tuberculosis are related , and both cause pulmonary disease...	Rhodococcus equi causes fatal pyogranulomatous bronchopneumonia in young foals and is an emerging opportunistic pathogen of immunocompromised humans . Despite its importance , there is currently no safe and effective vaccine against R . equi infections . Like Mycobacterium tuberculosis , the causative agent of human tu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "medicine", "infectious", "diseases", "veterinary", "diseases", "veterinary", "microbiology", "genetics", "biology", "genomics", "microbiology", "genetics", "and", "genomics", "veterinary", "science" ]	2011	The Steroid Catabolic Pathway of the Intracellular Pathogen Rhodococcus equi Is Important for Pathogenesis and a Target for Vaccine Development
The prenatal development of neural circuits must provide sufficient configuration to support at least a set of core postnatal behaviors . Although knowledge of various genetic and cellular aspects of development is accumulating rapidly , there is less systematic understanding of how these various processes play togethe...	Models of learning in artificial neural networks generally assume that the neurons and approximate network are given , and then learning tunes the synaptic weights . By contrast , we address the question of how an entire functional neuronal network containing many differentiated neurons and connections can develop from...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "neuroscience", "neurogenesis", "cellular", "neuroscience", "synaptic", "plasticity", "computer", "and", "information", "sciences", "neural", "networks", "biology", "and", "life", "sciences", "computational", "biology", "computerized", "simulations", "neuro...	2014	Developmental Self-Construction and -Configuration of Functional Neocortical Neuronal Networks
Allelic imbalance ( AI ) is a phenomenon where the two alleles of a given gene are expressed at different levels in a given cell , either because of epigenetic inactivation of one of the two alleles , or because of genetic variation in regulatory regions . Recently , Bing et al . have described the use of genotyping ar...	Measures of gene expression , and the search for regulatory regions in the genome responsible for differences in levels of gene expression , is one of the key paths of research used to identify disease causing genes , as well as explain differences between healthy individuals . Typically , experiments have measured and...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genomics", "computational", "biology/population", "genetics", "genetics", "and", "genomics/gene", "expression", "computational", "biology/molecular", "genetics", "computational", "biology/genomics", "genetics", "and", "genomics/epigenetics", "genetics...	2010	Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human
Neurons spike when their membrane potential exceeds a threshold value . In central neurons , the spike threshold is not constant but depends on the stimulation . Thus , input-output properties of neurons depend both on the effect of presynaptic spikes on the membrane potential and on the dynamics of the spike threshold...	Neurons spike when their combined inputs exceed a threshold value , but recent experimental findings have shown that this value also depends on the inputs . Thus , to understand how neurons respond to input spikes , it is important to know how inputs modify the spike threshold . Spikes are generated by sodium channels ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/neuronal", "signaling", "mechanisms", "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2011	Impact of Fast Sodium Channel Inactivation on Spike Threshold Dynamics and Synaptic Integration
The shift from outcrossing to self-fertilization is among the most common evolutionary transitions in flowering plants . Until recently , however , a genome-wide view of this transition has been obscured by both a dearth of appropriate data and the lack of appropriate population genomic methods to interpret such data ....	While many plants require pollen from another individual to set seed , in some species self-pollination is the norm . This evolutionary shift from outcrossing to self-fertilization is among the most common transitions in flowering plants . Here , we use dense genome sequence data to identify where in the genome two ind...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Genomic Identification of Founding Haplotypes Reveals the History of the Selfing Species Capsella rubella
Zoonoses are increasingly recognized as an important burden on global public health in the 21st century . High-resolution , long-term field studies are critical for assessing both the baseline and future risk scenarios in a world of rapid changes . We have used a three-decade-long field study on hantavirus , a rodent-b...	Pathogens shared with wildlife cause more than 60% of human infectious diseases . However , there is a scarcity of comprehensive modeling of zoonotic disease dynamics at the wildlife-human interface . Here , we use 30 years of monthly rodent-hantavirus monitoring to show that the complex seasonality in human spillover ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "population", "dynamics", "immunology", "microbiology", "vertebrates", "animals", "mammals", "viruses", "preventive", "medicine", "seasons", "hemorrhagic...	2017	Anthropogenically driven environmental changes shift the ecological dynamics of hemorrhagic fever with renal syndrome
Conflict destabilizes social interactions and impedes cooperation at multiple scales of biological organization . Of fundamental interest are the causes of turbulent periods of conflict . We analyze conflict dynamics in an monkey society model system . We develop a technique , Inductive Game Theory , to extract directl...	Persistent conflict is one of the most important contemporary challenges to the integrity of society and to individual quality of life . Yet surprisingly little is understood about conflict . Is resource scarcity and competition the major cause of conflict , or are other factors , such as memory for past conflicts , th...	[ "Abstract", "Introduction", "Results", "Methods" ]	[ "evolutionary", "biology", "evolutionary", "biology/animal", "behavior", "computational", "biology" ]	2010	Inductive Game Theory and the Dynamics of Animal Conflict
It has long been recognized that oncogenic viruses often integrate close to common fragile sites . The papillomavirus E2 protein , in complex with BRD4 , tethers the viral genome to host chromatin to ensure persistent replication . Here , we map these targets to a number of large regions of the human genome and name th...	Papillomavirus cause persistent , but mostly self-limiting , infections of the host epithelium . However , a subset of oncogenic papillomaviruses is the causative agent of certain human cancers . In persistent infection the viral genomes are tethered to host chromosomes to maintain and partition the extrachromosomal vi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "medicine", "and", "health", "sciences", "chromosome", "structure", "and", "function", "viruses", "and", "cancer", "dna-binding", "proteins", "microbiology", "cancers", "and", "neoplasms", "genitourinary", "tract", "tumors", "histone"...	2014	Papillomavirus Genomes Associate with BRD4 to Replicate at Fragile Sites in the Host Genome
Genome-wide association studies have identified hundreds of loci for type 2 diabetes , coronary artery disease and myocardial infarction , as well as for related traits such as body mass index , glucose and insulin levels , lipid levels , and blood pressure . These studies also have pointed to thousands of loci with pr...	Recent genetic studies have identified hundreds of regions of the human genome that contribute to risk for type 2 diabetes , coronary artery disease and myocardial infarction , and to related quantitative traits such as body mass index , glucose and insulin levels , blood lipid levels , and blood pressure . These resul...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "diabetes", "mellitus", "type", "2", "mathematics", "diabetic", "endocrinology", "statistics", "genetics", "endocrinology", "genetics", "and", "genomics", "biology", "human", "genetics", "diabetes", "and", "endocrinology", "metabolic", "disorders", "cardiovasc...	2012	The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits
Understanding any brain circuit will require a categorization of its constituent neurons . In hippocampal area CA1 , at least 23 classes of GABAergic neuron have been proposed to date . However , this list may be incomplete; additionally , it is unclear whether discrete classes are sufficient to describe the diversity ...	Single-cell RNA sequencing allows scientists to count the number of copies of each gene expressed in multiple individually isolated cells . Because different cell types express genes in different amounts , “clusters” of cells with similar expression patterns are likely to correspond to different cell types . As well as...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "methods", "and", "resources", "applied", "mathematics", "neuroscience", "factor", "analysis", "simulation", "and", "modeling", "algorithms", "mathematics", "clustering", "algorithms", "statistics", "(mathematics)", "genome", "analysis", "interneurons", "neuronal", "dendrit...	2018	Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics
Many cellular stress-responsive signaling systems exhibit highly dynamic behavior with oscillatory features mediated by delayed negative feedback loops . What remains unclear is whether oscillatory behavior is the basis for a signaling code based on frequency modulation ( FM ) or whether the negative feedback control m...	Many signaling events are controlled by negative feedback circuits: as a result they are highly dynamic and in some cases show oscillations The presence of oscillations has led to the hypothesis that signaling pathways convey information about the stimulus via the frequency of oscillations and spikes of activity , anal...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemical", "simulations", "signal", "transduction", "signaling", "in", "cellular", "processes", "immunological", "signaling", "signaling", "cascades", "regulatory", "networks", "immunology", "signaling", "pathways", "signaling", "networks", "biology", "molecular", "cell...	2013	Dual Delayed Feedback Provides Sensitivity and Robustness to the NF-κB Signaling Module
Hepatitis C virus ( HCV ) p7 is a membrane-associated oligomeric protein harboring ion channel activity . It is essential for effective assembly and release of infectious HCV particles and an attractive target for antiviral intervention . Yet , the self-assembly and molecular mechanism of p7 ion channelling are current...	Hepatitis C remains a serious global health problem affecting more than 2% of the world's population , and current therapies are effective in only a subset of patients , necessitating an ongoing search for new treatments . The p7 viroporin is considered to be an attractive possible drug target , but rational drug desig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "computational", "chemistry", "chemistry", "biology", "computational", "biology", "biophysics" ]	2012	The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels
The ultimate stage of the transmission of Dengue Virus ( DENV ) to man is strongly dependent on crosstalk between the virus and the immune system of its vector Aedes aegypti ( Ae . aegypti ) . Infection of the mosquito's salivary glands by DENV is the final step prior to viral transmission . Therefore , in the present ...	Dengue viruses ( DENV ) are generally maintained in a cycle which requires horizontal transmission via their arthropod vector , Ae . aegypti , to the vertebrate host . One important consequence of this process is the interference of the virus with the immune systems of both the mosquito and its host . While infection o...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "virology/emerging", "viral", "diseases", "infectious", "diseases", "virology" ]	2011	Induction of a Peptide with Activity against a Broad Spectrum of Pathogens in the Aedes aegypti Salivary Gland, following Infection with Dengue Virus
The gene expression pattern specified by an animal regulatory sequence is generally viewed as arising from the particular arrangement of transcription factor binding sites it contains . However , we demonstrate here that regulatory sequences whose binding sites have been almost completely rearranged can still produce i...	The transformation of a fertilized egg into a complex , multicellular organism is a carefully choreographed process in which thousands of genes are turned on and off in specific spatial and temporal patterns that confer distinct physical properties and behaviors on emerging cells and tissues . To understand how an orga...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology/embryology", "genetics", "and", "genomics/comparative", "genomics", "computational", "biology/transcriptional", "regulation", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "computational", "biology/comparative", "sequence", "ana...	2008	Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation
Recent research has demonstrated the use of the structural connectome as a powerful tool to characterize the network architecture of the brain and potentially generate biomarkers for neurologic and psychiatric disorders . In particular , the anatomic embedding of the edges of the cerebral graph have been postulated to ...	While the structural connectome of the brain has emerged as a powerful tool towards understanding the progression of neurologic and psychiatric disorders , links between the anatomy of connections within the brain and the effects of localized white matter pathology on cognition are still an active area of investigation...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "neural", "networks", "nervous", "system", "brain", "neuroscience", "magnetic", "resonance", "imaging", "mathematics", "algebra", "brain", "mapping", "research", "and", "analysis", "methods", "computer"...	2017	Brain network eigenmodes provide a robust and compact representation of the structural connectome in health and disease
SSG&PM over 17 days is recommended as first line treatment for visceral leishmaniasis in eastern Africa , but is painful and requires hospitalization . Combination regimens including AmBisome and miltefosine are safe and effective in India , but there are no published data from trials of combination therapies including...	Visceral leishmaniasis , or kala-azar , is a parasitic disease which is fatal without treatment . A 17-day treatment of sodium stibogluconate ( SSG ) with paromomycin ( PM ) is the recommended treatment in eastern Africa , but requires painful injections , causes adverse events , and patients need to stay in the hospit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "body", "weight", "medicine", "and", "health", "sciences", "body", "fluids", "clinical", "research", "design", "tropical", "diseases", "parasitic", "diseases", "research", "design", "physiological", "parameters", "pharmaceutics", "neglected", "tropical", "d...	2016	Efficacy and Safety of AmBisome in Combination with Sodium Stibogluconate or Miltefosine and Miltefosine Monotherapy for African Visceral Leishmaniasis: Phase II Randomized Trial
IgG antibodies can organize into ordered hexamers on cell surfaces after binding their antigen . These hexamers bind the first component of complement C1 inducing complement-dependent target cell killing . Here , we translated this natural concept into a novel technology platform ( HexaBody technology ) for therapeutic...	Immunotherapy is a powerful and rapidly expanding field that makes use of the body’s natural defense mechanisms to eliminate disease entities such as infectious agents or cancer cells . Circulating antibodies bind aberrant structures in a highly target-specific manner and “flag” disease cells for destruction by killing...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	A Novel Platform for the Potentiation of Therapeutic Antibodies Based on Antigen-Dependent Formation of IgG Hexamers at the Cell Surface
V-ATPases are part of the membrane components of pathogen-containing vacuoles , although their function in intracellular infection remains elusive . In addition to organelle acidification , V-ATPases are alternatively implicated in membrane fusion and anti-inflammatory functions controlled by ATP6V0d2 , the d subunit v...	V-ATPases control acidification and other processes at intracellular vesicles that bacteria and parasites exploit as compartments for replication and immune evasion . We report that the protozoan intracellular parasite Leishmania amazonensis resists inflammatory macrophage immune responses and upregulates an alternativ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "lysosomes", "immune", "cells", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "vacuoles", "pathogens", "immunology", "parasitic", "diseases", "parasitic", "protozoans", "protozoans", ...	2019	ATP6V0d2 controls Leishmania parasitophorous vacuole biogenesis via cholesterol homeostasis
Pathogenic fungi constitute a growing threat to both plant and animal species on a global scale . Despite a clonal mode of reproduction dominating the population genetic structure of many fungi , putatively asexual species are known to adapt rapidly when confronted by efforts to control their growth and transmission . ...	Pathogenic fungi constitute a growing threat to both plant and animal species on a global scale . However , many features of the fungal genome that enable them to successfully adapt to infect diverse hosts and ecological niches remain cryptic , especially for newly evolved emerging lineages . In this paper , we report ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mutation", "haplotypes", "genome", "evolution", "natural", "selection", "genetics", "population", "genetics", "ploidy", "biology", "genomics", "evolutionary", "biology", "genomic", "evolution", "comparative", "genomics" ]	2013	Chromosomal Copy Number Variation, Selection and Uneven Rates of Recombination Reveal Cryptic Genome Diversity Linked to Pathogenicity
To date , Alphavirus infections and their most prominent member , chikungunya fever , a viral disease which first became apparent in Tanzania in 1953 , have been very little investigated in regions without epidemic occurrence . Few data exist on burden of disease and socio-economic and environmental covariates disposin...	The origin of febrile disease is often difficult to diagnose . In tropical countries , viral infections that are transmitted by arthropods include , among others , Alphavirus infections ( e . g . chikungunya fever ) , dengue , West Nile , Yellow Fever and Rift Valley fever . In malaria endemic areas , these diseases ar...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "travel-associated", "diseases", "infectious", "disease", "control", "viral", "diseases" ]	2014	Seroprevalence of Alphavirus Antibodies in a Cross-Sectional Study in Southwestern Tanzania Suggests Endemic Circulation of Chikungunya
The immune system can recognize virtually any antigen , yet T cell responses against several pathogens , including Mycobacterium tuberculosis , are restricted to a limited number of immunodominant epitopes . The host factors that affect immunodominance are incompletely understood . Whether immunodominant epitopes elici...	While T cells are required for protection against Mycobacterium tuberculosis infection , attempts to prevent tuberculosis by vaccines designed to elicit memory T cells have only been partially successful . Several vaccine candidates are in clinical trials , but progress has been slow because their ability to prevent di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Human and Murine Clonal CD8+ T Cell Expansions Arise during Tuberculosis Because of TCR Selection
Coordination of growth between and within organs contributes to the generation of well-proportioned organs and functionally integrated adults . The mechanisms that help to coordinate the growth between different organs start to be unravelled . However , whether an organ is able to respond in a coordinated manner to loc...	The coordination of growth within and between organs contributes to the generation of functionally integrated structures and well-proportioned animals and plants . Though these issues have fascinated biologists for centuries , the responsible molecular mechanisms remain largely uncharacterized . In this work , we have ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/molecular", "development", "developmental", "biology/organogenesis" ]	2010	A dp53-Dependent Mechanism Involved in Coordinating Tissue Growth in Drosophila
Upon viral infection , the production of type I interferon ( IFN ) and the subsequent upregulation of IFN stimulated genes ( ISGs ) generate an antiviral state with an important role in the activation of innate and adaptive host immune responses . The ubiquitin-like protein ( UBL ) ISG15 is a critical IFN-induced antiv...	Modification of proteins by ubiquitin ( UB ) and ubiquitin-like proteins ( UBLs ) are key regulatory processes of the innate and adaptive immune response . Interferon ( IFN ) stimulated gene product 15 ( ISG15 ) is an ubiquitin-like protein modifier , which is reversibly conjugated to different viral and cellular prote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	ISG15 Regulates Peritoneal Macrophages Functionality against Viral Infection
CONSTITUTIVE PHOTOMORPHOGENIC 1 ( COP1 ) functions as an E3 ubiquitin ligase and mediates a variety of developmental processes in Arabidopsis by targeting a number of key regulators for ubiquitination and degradation . Here , we identify a novel COP1 interacting protein , COP1 SUPPRESSOR 2 ( CSU2 ) . Loss of function m...	CONSTITUTIVE PHOTOMORPHOGENIC 1 ( COP1 ) is a key regulator of light mediated developmental processes and it works as an E3 ubiquitin ligase controlling the abundance of multiple transcription factors . In the work presented here , we identified a novel repressor of COP1 , the COP1 SUPPRESSOR 2 ( CSU2 ) , via a forward...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Arabidopsis COP1 SUPPRESSOR 2 Represses COP1 E3 Ubiquitin Ligase Activity through Their Coiled-Coil Domains Association
White blood cells ( WBCs ) mediate immune systems and consist of various subtypes with distinct roles . Elucidation of the mechanism that regulates the counts of the WBC subtypes would provide useful insights into both the etiology of the immune system and disease pathogenesis . In this study , we report results of gen...	White blood cells ( WBCs ) are blood cells that mediate immune systems and defend the body against foreign microorganisms . It is well known that WBCs consist of various subtypes of cells with distinct roles , although the genetic background of each of the WBC subtypes has yet to be examined . In this study , we report...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "genome-wide", "association", "studies", "medicine", "quantitative", "traits", "genome", "analysis", "tools", "biology", "hematology", "cell", "biology", "heredity", "genetics", "cellular", "types", "genomics", "molecular", "cell", "biology", "genetics...	2011	Identification of Nine Novel Loci Associated with White Blood Cell Subtypes in a Japanese Population
Adaptive evolution is generally assumed to progress through the accumulation of beneficial mutations . However , as deleterious mutations are common in natural populations , they generate a strong selection pressure to mitigate their detrimental effects through compensatory genetic changes . This process can potentiall...	While core cellular processes are generally conserved during evolution , the constituent genes differ somewhat between related species with similar lifestyles . Why should this be so ? In this work , we propose that gene loss may initially be deleterious , but organisms can recover fitness by the accumulation of compen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology", "and", "life", "sciences", "evolutionary", "theory", "evolutionary", "biology", "evolutionary", "genetics" ]	2014	The Genomic Landscape of Compensatory Evolution
Nuclear receptors of the Hepatocyte Nuclear Factor-4 ( HNF4 ) subtype have been linked to a host of developmental and metabolic functions in animals ranging from worms to humans; however , the full spectrum of physiological activities carried out by this nuclear receptor subfamily is far from established . We have foun...	The function of many important biological structures requires the construction of very complex cellular shapes . For example , mammalian kidneys or related renal systems in other animals rely on the formation of elongated tubes that maximize surface area to facilitate the exchange of ions between the body and excreted ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/molecular", "development", "molecular", "biology/translational", "regulation", "developmental", "biology/pattern", "formation", "developmental", "biology/morphogenesis", "and", "cell", "biology" ]	2009	The Caenorhabditis elegans HNF4α Homolog, NHR-31, Mediates Excretory Tube Growth and Function through Coordinate Regulation of the Vacuolar ATPase
Although effective rabies virus vaccines have been existing for decades , each year , rabies virus infections still cause around 50 . 000 fatalities worldwide . Most of these cases occur in developing countries , where these vaccines are not available . The reasons for this are the prohibitive high costs of cell cultur...	Conventional prophylactic vaccines require transport and storage under controlled temperatures in an unbroken cold chain . Therefore , distribution of many vaccines is restricted to areas where the cold chain can be maintained which excludes especially rural areas in many countries from continues vaccine supply . Unfor...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "viral", "vaccines", "medicine", "and", "health", "sciences", "body", "weight", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "european", "union", "pathogens", "immunology", "geographical", "locations", "microbiology", "vaccines", "viruses", "phy...	2017	A thermostable messenger RNA based vaccine against rabies
We previously reported that foetuses congenitally infected with Trypanosoma cruzi , the agent of Chagas disease , mount an adult-like parasite-specific CD8+ T-cell response , producing IFN-g , and present an altered NK cell phenotype , possibly reflecting a post-activation state supported by the ability of the parasite...	IFN-g release by NK cells is essential in early control of infections with intracellular pathogens by driving protective type 1 immune response . NK cell activation requires integration of signals delivered by cytokines , dendritic cells , monocytes/macrophages and/or pathogens . Little information is available about t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology", "parasitology", "biology", "microbiology" ]	2013	Monocytes Play an IL-12-Dependent Crucial Role in Driving Cord Blood NK Cells to Produce IFN-g in Response to Trypanosoma cruzi
Nipah virus ( NiV ) is a paramyxovirus ( genus Henipavirus ) that emerged in the late 1990s in Malaysia and has since been identified as the cause of sporadic outbreaks of severe febrile disease in Bangladesh and India . NiV infection is frequently associated with severe respiratory or neurological disease in infected ...	Nipah virus ( NiV ) was identified in the late 1990s as the causative agent of severe respiratory and neurological disease in Malaysia and Bangladesh . The virus is transmitted by inhalation , contact or consumption of contaminated material . In this study , our objective was to characterize NiV-induced disease progres...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "respiratory", "infections", "cytokines", "pathology", "and", "laboratory", "medicine", "diagnostic", "radiology", "immunology", "pulmonol...	2017	Loss in lung volume and changes in the immune response demonstrate disease progression in African green monkeys infected by small-particle aerosol and intratracheal exposure to Nipah virus
Active matter systems , and in particular the cell cytoskeleton , exhibit complex mechanochemical dynamics that are still not well understood . While prior computational models of cytoskeletal dynamics have lead to many conceptual insights , an important niche still needs to be filled with a high-resolution structural ...	Active matter systems have the distinct ability to convert energy from their surroundings into mechanical work , which gives rise to them having highly dynamic properties . Modeling active matter systems and capturing their complex behavior has been a great challenge in past years due to the many coupled interactions b...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "cell", "motility", "actin", "filaments", "simulation", "and", "modeling", "molecular", "motors", "actin", "motors", "materials", "science", "cellular", "structures", "and", "organelles", "macromolecules", "cytoskeleton", "motor", "proteins", "materials", "by", "structu...	2016	MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks
To identify parameters of Leishmania infection within a population of infected sand flies that reliably predict subsequent transmission to the mammalian host , we sampled groups of infected flies and compared infection intensity and degree of metacyclogenesis with the frequency of transmission . The percentage of paras...	Many infectious diseases are initiated when pathogenic organisms are deposited into the skin of the human host by the bite of an insect . In the case of the parasite Leishmania , the causative agent of Leishmaniasis , factors associated with the bite of the infected sand fly vector influence infection outcome , suggest...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "emerging", "infectious", "diseases", "vector", "biology", "biology", "microbiology", "host-pathogen", "interaction", "parasitology" ]	2011	Infection Parameters in the Sand Fly Vector That Predict Transmission of Leishmania major
Respiratory syncytial virus ( RSV ) is the most common cause of infant hospitalizations and severe RSV infections are a significant risk factor for childhood asthma . The pathogenic mechanisms responsible for RSV induced immunopathophysiology remain elusive . Using an age-appropriate mouse model of RSV , we show that I...	IL-33 is responsible for the immunopathophysiological response observed following neonatal RSV infection in mice . Its presence in nasal aspirates of human infants with severe RSV and suggests its role in disease severity and asthma .	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Respiratory Syncytial Virus Disease Is Mediated by Age-Variable IL-33
Many enveloped viruses invade cells via endocytosis and use different environmental factors as triggers for virus-endosome fusion that delivers viral genome into cytosol . Intriguingly , dengue virus ( DEN ) , the most prevalent mosquito-borne virus that infects up to 100 million people each year , fuses only in late e...	Dengue virus infection is a growing public health problem with up to 100 million cases annually , and neither vaccines nor effective therapies are available . To search for the ways of preventing and treating dengue infections we need to better understand their molecular mechanisms . As with many other viruses , dengue...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "invasion", "and", "cell", "entry" ]	2010	Dengue Virus Ensures Its Fusion in Late Endosomes Using Compartment-Specific Lipids
Zika virus ( ZIKV ) is an emerging flavivirus typically causing a dengue-like febrile illness , but neurological complications , such as microcephaly in newborns , have potentially been linked to this viral infection . We established a panel of in vitro assays to allow the identification of ZIKV inhibitors and demonstr...	A robust cell-based antiviral assay was developed that allows to screen for and validate novel inhibitors of Zika virus ( ZIKV ) replication . The viral polymerase inhibitor 7-deaza-2’-C-methyladenosine ( 7DMA ) was identified as a potent ZIKV inhibitor . A mouse model for ZIKV infections , which was validated for anti...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "vero", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "pathogens", "animal", "models", "of", "disease", "biological", "cultures", "rna", "extraction", ...	2016	The Viral Polymerase Inhibitor 7-Deaza-2’-C-Methyladenosine Is a Potent Inhibitor of In Vitro Zika Virus Replication and Delays Disease Progression in a Robust Mouse Infection Model
Gammaherpesviruses chronically infect their host and are tightly associated with the development of lymphoproliferative diseases and lymphomas , as well as several other types of cancer . Mechanisms involved in maintaining chronic gammaherpesvirus infections are poorly understood and , in particular , little is known a...	Gammaherpesviruses are associated with the development of lymphomas , particularly in immunosuppressed individuals , as well as several other types of cancers . Like all herpesviruses , once a host is infected these viruses cannot be cleared and , as such , infected individuals harbor these viruses for life . One of th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/persistence", "and", "latency", "infectious", "diseases", "virology/animal", "models", "of", "infection", "virology", "immunology", "microbiology" ]	2009	Gammaherpesvirus-Driven Plasma Cell Differentiation Regulates Virus Reactivation from Latently Infected B Lymphocytes
The average human genome contains a small cohort of active L1 retrotransposons that encode two proteins ( ORF1p and ORF2p ) required for their mobility ( i . e . , retrotransposition ) . Prior studies demonstrated that human ORF1p , L1 RNA , and an ORF2p-encoded reverse transcriptase activity are present in ribonucleop...	Long Interspersed Element-1 ( LINE-1 or L1 ) sequences are the predominant class of autonomous retrotransposons in the human genome and comprise an astounding 17% of human DNA . Although the majority of L1s are considered to be “dead , ” an average human genome contains ∼80–100 active L1s . Active L1s encode two protei...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/rna-protein", "interactions", "genetics", "and", "genomics", "biochemistry/macromolecular", "assemblies", "and", "machines" ]	2010	Characterization of LINE-1 Ribonucleoprotein Particles
Cortical firing rates frequently display elaborate and heterogeneous temporal structure . One often wishes to compute quantitative summaries of such structure—a basic example is the frequency spectrum—and compare with model-based predictions . The advent of large-scale population recordings affords the opportunity to d...	Neuroscientists commonly measure the time-varying activity of neurons in the brain . Early studies explored how such activity directly encodes sensory stimuli . Since then neural responses have also been found to encode abstract parameters such as expected reward . Yet not all aspects of neural activity directly encode...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "decision", "making", "population", "dynamics", "vertebrates", "neuroscience", "animals", "mammals", "simulation", "and", "modeling", "primates", "systems", "science", "mathematics", "cognition", "computational", "neuroscience", "population", "biology", "neuronal", "tuning"...	2016	Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1
Kyasanur Forest disease virus ( KFDV ) and Alkhumra hemorrhagic fever virus ( AHFV ) are genetically closely-related , tick-borne flaviviruses that cause severe , often fatal disease in humans . Flaviviruses in the tick-borne encephalitis ( TBE ) complex typically cause neurological disease in humans whereas patients i...	Kyasanur Forest disease virus ( KFDV ) and Alkhumra hemorrhagic fever virus ( AHFV ) are tick-borne flaviviruses that cause severe hemorrhagic disease in humans . The pathogenesis of the disease is still not very well understood mostly due to the lack of suitable animal models . Despite sharing a high degree of genetic...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "classification", "emerging", "viral", "diseases", "tropical", "diseases", "microbiology", "viruses", "rna", "viruses", "neglected", "tropical", "diseases", "veterinary", "sc...	2014	Comparative Pathogenesis of Alkhumra Hemorrhagic Fever and Kyasanur Forest Disease Viruses in a Mouse Model
Trypanosoma cruzi , the etiological agent of Chagas disease , is highly genetically diverse . Numerous lines of evidence point to the existence of six stable genetic lineages or DTUs: TcI , TcIIa , TcIIb , TcIIc , TcIId , and TcIIe . Molecular dating suggests that T . cruzi is likely to have been an endemic infection o...	Trypanosoma cruzi , the etiological agent of Chagas disease , infects over 10 million people in Latin America . Six major genetic lineages of the parasite have been identified with differential geographic distributions , ecological associations and epidemiological importance . With the advent of the T . cruzi genome se...	[ "Abstract", "Introduction", "Methods", "and", "Analyses", "Results", "Discussion" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "ecology/evolutionary", "ecology", "molecular", "biology/molecular", "evolution", "public", "health", "and", "epidemiology/infectious", "diseases", "microbiology/parasitology", "ecology/population", "ecology" ]	2009	Trypanosoma cruzi IIc: Phylogenetic and Phylogeographic Insights from Sequence and Microsatellite Analysis and Potential Impact on Emergent Chagas Disease
Increasing evidence has indicated that microRNAs ( miRNAs ) play vital roles in various pathological processes and thus are closely related with many complex human diseases . The identification of potential disease-related miRNAs offers new opportunities to understand disease etiology and pathogenesis . Although there ...	MiRNAs are a class of small non-coding RNAs that are associated with a variety of complex biological processes . Increasing studies have shown that miRNAs have close relationships with many human diseases . The prediction of the associations between miRNAs and diseases has thus become a hot topic . Although traditional...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "linguistics", "medicine", "and", "health", "sciences", "natural", "antisense", "transcripts", "gene", "regulation", "endocrine", "tumors", "carcinomas", "applied", "mathematics", "cancers", "and", "neoplasms", "social", "sciences", "biomarkers", "simulation", "and", "m...	2019	Adaptive multi-view multi-label learning for identifying disease-associated candidate miRNAs
Septic shock caused by Neisseria meningitidis is typically rapidly evolving and often fatal despite antibiotic therapy . Further understanding of the mechanisms underlying the disease is necessary to reduce fatality rates . Postmortem samples from the characteristic purpuric rashes of the infection show bacterial aggre...	Certain bacterial pathogens access the bloodstream during infection and this is associated with extremely severe conditions such as septic shock . A central feature of these infections is the rapid alteration of blood vessel function with deregulated inflammation , coagulation and loss of vessel integrity . Studying th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens" ]	2013	Adhesion of Neisseria meningitidis to Dermal Vessels Leads to Local Vascular Damage and Purpura in a Humanized Mouse Model
Genetic recombination during meiosis functions to increase genetic diversity , promotes elimination of deleterious alleles , and helps assure proper segregation of chromatids . Mammalian recombination events are concentrated at specialized sites , termed hotspots , whose locations are determined by PRDM9 , a zinc finge...	During formation of sperm and eggs chromosomes exchange DNA in a process known as recombination , creating new combinations responsible for much of the enormous diversity in populations . In some mammals , including humans , the locations of recombination are chosen by a DNA-binding protein named PRDM9 . Importantly , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots
Protein–protein interaction and gene regulatory networks are likely to be locked in a state corresponding to a disease by the behavior of one or more bistable circuits exhibiting switch-like behavior . Sets of genes could be over-expressed or repressed when anomalies due to disease appear , and the circuits responsible...	Since most disease states exhibit a certain level of resilience against therapeutic interventions , each disease state can be considered to be homeostatic to some extent . There must be one or more mechanisms that cause the gene-regulatory network to maintain a certain state , and one such mechanism is a bistable switc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology/lung", "cancer", "computational", "biology/systems", "biology", "oncology/gastrointestinal", "cancers" ]	2010	Large-Scale Analysis of Network Bistability for Human Cancers
Numerous constraints significantly hamper the experimental study of hepatitis C virus ( HCV ) . Robust replication in cell culture occurs with only a few strains , and is invariably accompanied by adaptive mutations that impair in vivo infectivity/replication . This problem complicates the production and study of authe...	Two decades after its identification , hepatitis C virus ( HCV ) remains a leading cause of serious liver diseases worldwide . The poor in vitro propagation of patient isolates has impaired their study . Conversely , viral strains of the most prevalent ( ∼70% of total infections ) and clinically problematic ( ∼45% cure...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "virology/virion", "structure,", "assembly,", "and", "egress", "gastroenterology", "and", "hepatology/hepatology", "infectious", "diseases/viral", "infections", "virology/host", "invasion", "and", "cell", "entry" ]	2011	A New Model to Produce Infectious Hepatitis C Virus without the Replication Requirement
Recent genome-wide association ( GWA ) studies have identified dozens of common variants associated with adult height . However , it is unknown how these variants influence height growth during childhood . We derived peak height velocity in infancy ( PHV1 ) and puberty ( PHV2 ) and timing of pubertal height growth spur...	Family studies have shown that adult height is largely genetically determined . Identification of common genetic factors has been expedited with recent advances in genotyping techniques . However , factors regulating childhood height growth remain unclear . We investigated genetic variants of adult height for associati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "public", "health", "and", "epidemiology/epidemiology", "genetics", "and", "genomics/complex", "traits" ]	2009	Genetic Determinants of Height Growth Assessed Longitudinally from Infancy to Adulthood in the Northern Finland Birth Cohort 1966
We know a great deal about the genes used by the model pathogen Salmonella enterica serovar Typhimurium to cause disease , but less about global gene regulation . New tools for studying transcripts at the single nucleotide level now offer an unparalleled opportunity to understand the bacterial transcriptome , and expre...	The transcriptional networks and the functions of small regulatory RNAs of Salmonella enterica serovar Typhimurium are being studied intensively . S . Typhimurium is becoming the ideal model pathogen for linking transcriptional and post-transcriptional gene regulation to bacterial virulence . Here , we systematically d...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "regulatory", "proteins", "microbiology", "dna-binding", "proteins", "dna", "transcription", "bacterial", "diseases", "regulator", "genes", "post-tran...	2016	The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium
Cancers arise from successive rounds of mutation and selection , generating clonal populations that vary in size , mutational content and drug responsiveness . Ascertaining the clonal composition of a tumor is therefore important both for prognosis and therapy . Mutation counts and frequencies resulting from next-gener...	Cancers arise from a series of mutations that occur over time . As a result , as a tumor grows each cell inherits a distinctive genotype , defined by the set of all somatic mutations that distinguish the tumor cell from normal cells . Acertaining these genotype patterns , and identifying which ones are associated with ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "and", "health", "sciences", "cancer", "genetics", "basic", "cancer", "research", "genetics", "biology", "and", "life", "sciences", "genomics", "genomic", "medicine" ]	2014	Inferring Clonal Composition from Multiple Sections of a Breast Cancer
Gene expression controls how the brain develops and functions . Understanding control processes in the brain is particularly hard since they involve numerous types of neurons and glia , and very little is known about which genes are expressed in which cells and brain layers . Here we describe an approach to detect gene...	The way gene expression is spatially distributed across the brain reflects the function and micro-structure of neural tissues . Measuring these patterns is hard because brain tissues are composed of many types of neurons and glia cells , and average gene expression across a region mixes transcripts from many different ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "gene", "expression", "molecular", "genetics", "biology", "computational", "biology" ]	2012	Localizing Genes to Cerebellar Layers by Classifying ISH Images
Neurocysticercosis is a common helminthic infection of the central nervous system and an important cause of adult-onset epilepsy in endemic countries . However , few studies have examined associations between neurologic symptoms , serology and radiographic findings on a community-level . We conducted a population-based...	Neurocysticercosis is a parasitic infection of the brain and a common cause of epilepsy in many countries in Latin America , Asia and Africa . In this study , we applied a combination of head CT , serology and symptoms screening in a rural village in northern Peru . We found that the infection was very common in this c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "neuroscience", "parasitic", "diseases", "peru", "headaches", "physiological", "processes", "signs", "and...	2016	High Prevalence of Asymptomatic Neurocysticercosis in an Endemic Rural Community in Peru
Holometabolous insects undergo a radical anatomical re-organisation during metamorphosis . This poses a developmental challenge: the host must replace the larval gut but at the same time retain symbiotic gut microbes and avoid infection by opportunistic pathogens . By manipulating host immunity and bacterial competitiv...	The majority of animals are holometabolous insects and change dramatically through development . They undergo a dramatic transformation from a larval stage , adapted to feed , to an adult separated by a pupal stage . During this pupal stage the majority of the organs are renewed including the gut . This creates a risky...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Host and Symbiont Jointly Control Gut Microbiota during Complete Metamorphosis
Schistosomiasis is a major endemic disease that affects hundreds of millions worldwide . Since the treatment and control of this parasitic disease rely on a single drug , praziquantel , it is imperative that new effective drugs are developed . Here , we report that phytol , a diterpene alcohol from chlorophyll widely u...	Schistosomiasis is an infectious parasitic disease caused by helminths from the genus Schistosoma , which affects hundreds of millions of people , mainly the poor . Despite schistosomiasis being one of the most prevalent and debilitating neglected tropical diseases , the treatment and control of this disease relies on ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2014	Phytol, a Diterpene Alcohol from Chlorophyll, as a Drug against Neglected Tropical Disease Schistosomiasis Mansoni
In vitro , dendritic cells ( DCs ) bind and transfer intact , infectious HIV to CD4 T cells without first becoming infected , a process known as trans-infection . trans-infection is accomplished by recruitment of HIV and its receptors to the site of DC–T cell contact and transfer of virions at a structure known as the ...	Dendritic cells ( DCs ) patrol mucosal areas of the body , where they engulf invading pathogens and transport them to immune tissues . There the DCs degrade the microbes and present antigenic peptides to T lymphocytes to elicit specific immune responses . HIV-1 has appropriated this feature of the immune system to bett...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/immunodeficiency", "viruses", "cell", "biology" ]	2008	HIV Traffics through a Specialized, Surface-Accessible Intracellular Compartment during trans-Infection of T Cells by Mature Dendritic Cells
Prions , characterized by self-propagating protease-resistant prion protein ( PrP ) conformations , are agents causing prion disease . Recent studies generated several such self-propagating protease-resistant recombinant PrP ( rPrP-res ) conformers . While some cause prion disease , others fail to induce any pathology ...	Many neurodegenerative disorders , including Alzheimer’s disease , Parkinson’s disease and Prion disease , are caused by misfolded proteins that can self-propagate in vivo and in vitro . Misfolded self-replicating recombinant prion protein ( PrP ) conformers have been generated in vitro with defined cofactors , some of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "animal", "diseases", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "enzymology", "animal", "prion", "diseases", "immunoprecipitation", "immunologic", "techniques", "zoology", "enzyme", ...	2017	Self-propagating, protease-resistant, recombinant prion protein conformers with or without in vivo pathogenicity
The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors , including histone modifications , DNA methylation , and the incorporation of histone variants . H2A . Z , one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes ...	Eukaryotes package their DNA to fit within the nucleus using well-conserved proteins , called histones , that form the building blocks of nucleosomes , the fundamental units of chromatin . Histone variants are specialized versions of these proteins that change the chromatin landscape by altering the biochemical propert...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "expression", "analysis", "functional", "genomics", "retrotransposons", "plant", "growth", "and", "development", "plant", "biology", "dna", "transcription", "gene", "function", "histone", "modification", "genome", "sequen...	2012	Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes
Polycomb-group ( PcG ) and Trithorax-group proteins together form a maintenance machinery that is responsible for stable heritable states of gene activity . While the best-studied target genes are the Hox genes of the Antennapedia and Bithorax complexes , a large number of key developmental genes are also Polycomb ( Pc...	Cells make fate decisions as they progressively differentiate into specific cell types during development . The stability of these decisions is important and is achieved , in part , by changes to the chromatin that packages DNA in the nucleus . A key set of protein complexes that together constitute the Polycomb-group/...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "developmental", "biology/molecular", "development", "genetics", "and", "genomics/epigenetics", "molecular", "biology", "genetics", "and", "genomics", "developmental", "biology/developmental", "molecular", "mechanisms" ]	2008	Stability and Dynamics of Polycomb Target Sites in Drosophila Development
Food shortage was associated with leprosy in two recent studies investigating the relation between socioeconomic factors and leprosy . Inadequate intake of nutrients due to food shortage may affect the immune system and influence the progression of infection to clinical leprosy . We aimed to identify possible differenc...	Even though leprosy is one of the oldest diseases known to mankind , there is still a lot unknown about its transmission and why some people develop the disease and others do not . Leprosy is often seen as a disease of the poor , but which aspects of poverty are associated with leprosy are still under study . Recently ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Diet-Related Risk Factors for Leprosy: A Case-Control Study
Principal components analysis , PCA , is a statistical method commonly used in population genetics to identify structure in the distribution of genetic variation across geographical location and ethnic background . However , while the method is often used to inform about historical demographic processes , little is kno...	Genetic variation in natural populations typically demonstrates structure arising from diverse processes including geographical isolation , founder events , migration , and admixture . One technique commonly used to uncover such structure is principal components analysis , which identifies the primary axes of variation...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology/human", "evolution", "genetics", "and", "genomics/population", "genetics" ]	2009	A Genealogical Interpretation of Principal Components Analysis
Buruli Ulcer ( BU ) is a neglected , necrotizing skin disease caused by Mycobacterium ulcerans . Currently , there is no vaccine against M . ulcerans infection . Although the World Health Organization recommends a combination of rifampicin and streptomycin for the treatment of BU , clinical management of advanced stage...	Buruli Ulcer ( BU ) , caused by Mycobacterium ulcerans , is a necrotizing disease of the skin , subcutaneous tissue and bone . Standard treatment of BU patients consists of a combination of the antibiotics rifampicin and streptomycin for 8 weeks . However , in advanced stages of the disease , surgical resection of the ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "buruli", "ulcer", "cytokines", "microbial", "control", "immunology", "neglected", "tropical", "diseases", "microbiology", "biology", "immune", "system" ]	2013	Phage Therapy Is Effective against Infection by Mycobacterium ulcerans in a Murine Footpad Model
Scrub typhus , a bacterial infection caused by Orientia tsutsugamushi , is increasingly recognized as an important cause of fever in Asia , with an estimated one million infections occurring each year . Limited access to health care and the disease’s non-specific symptoms mean that many patients are undiagnosed and unt...	Scrub typhus is a common cause of fever in rural Asia where there is limited access to healthcare , diagnostics , and treatment . It is thought that up to 1 million cases occur per year , but the disease is difficult to differentiate clinically from other infections , such as leptospirosis and dengue , meaning that man...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	A Systematic Review of Mortality from Untreated Scrub Typhus (Orientia tsutsugamushi)
The mechanisms that ensure fertilization of egg by a sperm are not fully understood . In all teleosts , a channel called the ‘micropyle’ is the only route of entry for sperm to enter and fertilize the egg . The micropyle forms by penetration of the vitelline envelope by a single specialized follicle cell , the micropyl...	In many fish , sperm enters eggs through a specialized channel called the ‘micropyle’ . The micropyle is formed by a special follicle cell , the ‘micropylar cell’ , which sits on the top of the developing egg during oogenesis , and forms the sperm entry canal . The underlying mechanisms of this process are unknown . We...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "fish", "reproductive", "system", "vertebrates", "animals", "reproductive", "physiology", "germ", "cells", "animal", "models", "osteichthyes", "developmental", "biology", "oocytes", "model", "organisms", "experimental", "organism",...	2019	The effector of Hippo signaling, Taz, is required for formation of the micropyle and fertilization in zebrafish
Homeostatic synaptic plasticity is a negative-feedback mechanism for compensating excessive excitation or inhibition of neuronal activity . When neuronal activity is chronically suppressed , neurons increase synaptic strength across all affected synapses via synaptic scaling . One mechanism for this change is alteratio...	Synaptic scaling is a form of homeostatic plasticity that normalizes the strength of synapses ( the structure that allows nerve cells to communicate ) and is triggered by chronic inhibition of neuronal activity . Although extensive studies have been conducted , the molecular mechanism of this synaptic adaptation is not...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "neuronal", "plasticity", "biology", "and", "life", "sciences", "cellular", "neuroscience" ]	2014	Calcineurin Mediates Synaptic Scaling Via Synaptic Trafficking of Ca2+-Permeable AMPA Receptors
Calcium/calmodulin-dependent protein kinase II ( CaMKII ) holoenzymes play a critical role in decoding Ca2+ signals in neurons . Understanding how this occurs has been the focus of numerous studies including many that use models . However , CaMKII is notoriously difficult to simulate in detail because of its multi-subu...	Ca2+ signals are commonly used by cells for various types of activities . In neurons , Ca2+ can regulate gene expression and dendritic spine enlargement , strengthen synaptic connectivity , and promote neural growth or even death . One important Ca2+ binding protein is calmodulin , which has a wide range of downstream ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "single", "channel", "recording", "action", "potentials", "medicine", "and", "health", "sciences", "membrane", "potential", "electrophysiology", "reactants", "neuroscience", "network", "analysis", "membrane", "electrophysiology", "bioassays", "and", "phys...	2018	Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach
Hepatitis C virus ( HCV ) depends on liver-specific microRNA miR-122 for efficient viral RNA amplification in liver cells . This microRNA interacts with two different conserved sites at the very 5’ end of the viral RNA , enhancing miR-122 stability and promoting replication of the viral RNA . Treatment of HCV patients ...	With the advent of potent direct-acting antivirals ( DAA ) , hepatitis C virus ( HCV ) can now be eliminated from the majority of patients , using multidrug therapy with DAAs . However , such DAAs are not available for the treatment of most RNA virus infections . The main problem is the high error rate by which RNA-dep...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "microbial", "mutation", "nucleic", "acid", "synthesis", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "hepacivirus", "pathogens", "microbiology", "rna", "stability", "viruses", "rna", "virus...	2019	Impact of a patient-derived hepatitis C viral RNA genome with a mutated microRNA binding site

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