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The role of the pore-forming Staphylococcus aureus toxin Panton-Valentine leukocidin ( PVL ) in severe necrotizing diseases is debated due to conflicting data from epidemiological studies of community-associated methicillin-resistant S . aureus ( CA-MRSA ) infections and various murine disease-models . In this study , ...	Staphylococcus aureus can cause serious diseases , including necrotizing pneumonia , which often affects young immunocompetent patients and has a high lethality rate . Several clinical studies demonstrated a clear association between this form of pneumonia and S . aureus strains carrying the gene for the pore-forming t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/innate", "immunity" ]	2010	Staphylococcus aureus Panton-Valentine Leukocidin Is a Very Potent Cytotoxic Factor for Human Neutrophils
The Gram-negative soil dwelling bacterium Burkholderia pseudomallei is the etiological agent of melioidosis . The disease is endemic in most parts of Southeast Asia and northern Australia . Over last few years , there has been an increase in number of melioidosis cases from India; however the disease epidemiology is le...	Burkholderia pseudomallei , a gram negative bacterium , is the causative agent of melioidosis . B . pseudomallei is a soil saprophyte and causes infections in humans by percutaneous inoculation , inhalation or ingestion . Melioidosis is a life threatening disease , which requires prolonged antibiotic treatment and is c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biogeography", "taxonomy", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "melioidosis", "population", "genetics", "geographical", "locations", "india", "australia", "bacterial", "diseases", "phylogenetics", "data", "management", ...	2018	Molecular analysis of clinical Burkholderia pseudomallei isolates from southwestern coastal region of India, using multi-locus sequence typing
Since the two eutherian sex chromosomes diverged from an ancestral autosomal pair , the X has remained relatively gene-rich , while the Y has lost most of its genes through the accumulation of deleterious mutations in nonrecombining regions . Presently , it is unclear what is distinctive about genes that remain on the ...	Using recently available marsupial and monotreme genomes , we investigated nascent sex chromosome evolution in mammals . We show that , in eutherian mammals , X and Y genes acquired distinct evolutionary rates and functional constraints immediately after recombination suppression; X-linked genes maintained lower , ance...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/bioinformatics", "genetics", "and", "genomics/bioinformatics", "computational", "biology/genomics" ]	2009	Evolution and Survival on Eutherian Sex Chromosomes
Although many human diseases have a genetic component involving many loci , the majority of studies are statistically underpowered to isolate the many contributing variants , raising the question of the existence of alternate processes to identify disease mutations . To address this question , we collect ancestral tran...	A central goal of personal genomics is to interpret an individual’s genome to identify variants that confer disease risk , an aim that has far-reaching implications for personalized , precision medicine . Here , we leverage next generation sequencing , health records , and functional genome annotations to develop stati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories
This study describes two longitudinal serological surveys of European Bat Lyssavirus type 1 ( EBLV-1 ) antibodies in serotine bat ( Eptesicus serotinus ) maternity colonies located in the North-East of France . This species is currently considered as the main EBLV-1 reservoir . Multievent capture-recapture models were ...	A multi-annual survey of two serotine bat ( Eptesicus serotinus ) maternity colonies previously found exposed to European Bat Lyssavirus type 1 ( EBLV-1 ) was assessed using capture-recapture methodology . The two roosting site were located in the North-East of France . Animals were trapped , banded , and blood samples...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "european", "union", "pathogens", "immunology", "geographical", "locations", "microbiology", "vertebrates", "saliva", "animals", "mammals", "...	2017	Longitudinal survey of two serotine bat (Eptesicus serotinus) maternity colonies exposed to EBLV-1 (European Bat Lyssavirus type 1): Assessment of survival and serological status variations using capture-recapture models
Clustered , Regularly Interspaced Short Palindromic Repeats ( CRISPR ) abound in the genomes of almost all archaebacteria and nearly half the eubacteria sequenced . Through a genetic interference mechanism , bacteria with CRISPR regions carrying copies of the DNA of previously encountered phage and plasmids abort the r...	CRISPR is the acronym for the adaptive immune system that has been found in almost all archaebacteria and nearly half the eubacteria examined . Unlike the other defenses bacteria have for protection from phage and other deleterious DNAs , CRISPR has the virtues of specificity , memory , and the capacity to abort infect...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "molecular", "biology/molecular", "evolution", "microbiology/microbial", "evolution", "and", "genomics", "ecology/population", "ecology", "genetics", "and", "genomics/population", "genetics" ]	2010	Nasty Viruses, Costly Plasmids, Population Dynamics, and the Conditions for Establishing and Maintaining CRISPR-Mediated Adaptive Immunity in Bacteria
Polar auxin transport lies at the core of many self-organizing phenomena sustaining continuous plant organogenesis . In angiosperms , the shoot apical meristem is a potentially unique system in which the two main modes of auxin-driven patterning—convergence and canalization—co-occur in a coordinated manner and in a ful...	The regularity of leaf arrangement around stems has long puzzled scientists . The key role played by the plant hormone auxin is now well established . On the surface of the tissue responsible for leaf formation , auxin accumulates at several points , from which new leaves eventually emerge . Auxin also guides the progr...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "plant", "anatomy", "apoplastic", "space", "cell", "processes", "hormones", "plant", "science", "plant", "hormones", "cellular", "structures", "and", "organelles", "leaf", "veins", "leaves", "biophysics", "exocytosis", "cell", "membranes", "physics", "biochemistry", "...	2019	Toward a 3D model of phyllotaxis based on a biochemically plausible auxin-transport mechanism
Tropical infectious diseases like dengue , scrub typhus , murine typhus , leptospirosis , and enteric fever continue to contribute substantially to the febrile disease burden throughout Southeast Asia while malaria is declining . Recently , there has been increasing focus on biomarkers ( i . e . C-reactive protein ( CR...	Fever remains an important reason why people are hospitalised in Southeast Asia . We do not know the most common causes of fever in many regions of the tropics . This knowledge would help doctors decide on the most appropriate treatment in areas where access to diagnostics is difficult . Establishing diagnostic tests f...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "antimicrobials", "dermatology", "typhus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "drugs", "tropical", "diseases", "microbiology", "bacterial", "diseases", "signs", "and", "symp...	2018	Causes of acute undifferentiated fever and the utility of biomarkers in Chiangrai, northern Thailand
The abundance of different SSU rRNA ( “16S” ) gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity . However , the genomic copy number of the 16S gene varies greatly – from one in many species to up to 15 in some bacteria and ...	Microbial ecologists cannot observe their study organisms directly , so they use molecular sequencing to measure the abundance of different microbes living in the wild . The most commonly used method for measuring the abundance of different microbes is to collect a DNA sample from an environment and sequence a particul...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "phylogenetics", "ecology", "biology", "evolutionary", "biology", "microbiology", "evolutionary", "systematics", "microbial", "ecology" ]	2012	Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
Plasticity studies suggest that behavioral relevance can change the cortical processing of trained or conditioned sensory stimuli . However , whether this occurs in the context of natural communication , where stimulus significance is acquired through social interaction , has not been well investigated , perhaps becaus...	Like a student in a foreign country immersed in an unfamiliar language or a young mother trying to decipher her baby's cries , we all encounter initially meaningless sounds that in fact carry meaning . As these sounds gain significance , we become better at detecting and discriminating between them . How does this occu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology", "mus", "(mouse)", "neuroscience" ]	2007	Auditory Cortical Detection and Discrimination Correlates with Communicative Significance
Cortical networks , in-vitro as well as in-vivo , can spontaneously generate a variety of collective dynamical events such as network spikes , UP and DOWN states , global oscillations , and avalanches . Though each of them has been variously recognized in previous works as expression of the excitability of the cortical...	The spontaneous neural activity is the dynamic floor on which the cortex builds its response to incoming stimuli and organizes its information processing , thereby the importance of understanding its dynamical underpinnings . In-vitro preparations , as well as the intact cortex in deep sleep or anesthesia , display a v...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[]	2015	Network Events on Multiple Space and Time Scales in Cultured Neural Networks and in a Stochastic Rate Model
The prevailing paradigm of T lymphocyte control of viral replication is that the protective capacity of virus-specific CD8+ T cells is directly proportional to the number of functions they can perform , with IL-2 production capacity considered critical . Having recently defined rapid perforin upregulation as a novel ef...	Although CD8+ T cells are thought to be largely responsible for the control of viral infections , exactly how they mediate protection is uncertain . One approach to assessing their protective capacity is to measure several of their functions simultaneously . Generally , it is believed the more functions a cell can perf...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immunity", "to", "infections", "immunology/immune", "response" ]	2010	Perforin and IL-2 Upregulation Define Qualitative Differences among Highly Functional Virus-Specific Human CD8+ T Cells
While it has been established that a number of microenvironment components can affect the likelihood of metastasis , the link between microenvironment and tumor cell phenotypes is poorly understood . Here we have examined microenvironment control over two different tumor cell motility phenotypes required for metastasis...	A large proportion of cancer deaths are due to metastasis—the spread of cancer from the primary tumor to other parts of the body . Movement of cells may require the formation of protrusions called invadopodia , which degrade extracellular matrix . Although some studies have reported on locomotion in primary tumors , th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "systems", "biology", "medicine", "and", "health", "sciences", "cell", "biology", "molecular", "biology", "biology", "and", "life", "sciences", "computational", "biology", "biomechanics" ]	2014	Multiparametric Classification Links Tumor Microenvironments with Tumor Cell Phenotype
Hepatitis C virus ( HCV ) infection remains a major cause of hepatic inflammation and liver disease . HCV triggers NLRP3 inflammasome activation and interleukin-1β ( IL-1β ) production from hepatic macrophages , or Kupffer cells , to drive the hepatic inflammatory response . Here we examined HCV activation of the NLRP3...	This study deciphers the molecular mechanism of Hepatitis C virus ( HCV ) -induced hepatic inflammation . HCV triggers NLRP3 inflammasome activation and IL-1β release from hepatic macrophages , thus driving liver inflammation . Using biochemical , virological , and genetic approaches we identified the HCV core protein ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "method" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "hepacivirus", "pathogens", "immunology", "microbiology", "viral", "structure", "immune", "receptor", "signaling", ...	2019	Modulation of calcium signaling pathway by hepatitis C virus core protein stimulates NLRP3 inflammasome activation
This study focused on the savannah tsetse species Glossina swynnertoni and G . morsitans centralis , both efficient vectors of human and animal trypanosomiasis in , respectively , East and Central Africa . The aim was to develop long-lasting , practical and cost-effective visually attractive devices that induce the str...	Glossina swynnertoni is restricted to open savannah in northwestern Tanzania and southwestern Kenya whereas G . morsitans centralis has a much wider distribution from western Tanzania/southern Uganda westwards through Zambia and southeast of the Democratic Republic of the Congo ( DRC ) to Angola . Both are savannah tse...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "african", "trypanosomiasis", "angola", "geographical", "locations", "tropical", "diseases", "parasitic", "diseases", "animals", "parasitic", "protozoans", "glossina", "research", "design", "protozoans",...	2018	Standardising visual control devices for Tsetse: East and Central African Savannah species Glossina swynnertoni, Glossina morsitans centralis and Glossina pallidipes
An accurate early warning system to predict impending epidemics enhances the effectiveness of preventive measures against dengue fever . The aim of this study was to develop and validate a forecasting model that could predict dengue cases and provide timely early warning in Singapore . We developed a time series Poisso...	Without effective drugs or a vaccine , vector control remains the only method of controlling dengue fever outbreaks in Singapore . Based on our previous findings on the effects of weather on dengue cases and optimal timing for issuing dengue early warning in Singapore , the purpose of this study was to develop a dengue...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "global", "health", "public", "health" ]	2012	Forecast of Dengue Incidence Using Temperature and Rainfall
The World Health Organization currently recommends combined streptomycin and rifampicin antibiotic treatment as first-line therapy for Mycobacterium ulcerans infections . Alternatives are needed when these are not tolerated or accepted by patients , contraindicated , or neither accessible nor affordable . Despite in vi...	Buruli ulcer is a necrotizing infection of skin and subcutaneous tissue caused by Mycobacterium ulcerans and is the third most common mycobacterial disease worldwide ( after tuberculosis and leprosy ) . In recent years its treatment has radically changed , evolving from a predominantly surgically to a predominantly med...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases" ]	2012	Successful Outcomes with Oral Fluoroquinolones Combined with Rifampicin in the Treatment of Mycobacterium ulcerans: An Observational Cohort Study
H9N2 subtype influenza viruses have been detected in different species of wild birds and domestic poultry in many countries for several decades . Because these viruses are of low pathogenicity in poultry , their eradication is not a priority for animal disease control in many countries , which has allowed them to conti...	Avian influenza viruses continue to present challenges to human health . Recently the H7N9 and H10N8 viruses that are of low pathogenicity for poultry have caused human infections and deaths in China . H9N2 influenza virus have been isolated worldwide from wild and domestic avian species for several decades , and their...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "viral", "transmission", "and", "infection", "microbial", "evolution", "virology", "biology", "and", "life", "sciences", "microbiology", "evolutionary", "biology", "viral", "evolution" ]	2014	Genetics, Receptor Binding Property, and Transmissibility in Mammals of Naturally Isolated H9N2 Avian Influenza Viruses
The cornerstone of current schistosomiasis control programmes is delivery of praziquantel to at-risk populations . Such preventive chemotherapy requires accurate information on the geographic distribution of infection , yet the performance of alternative survey designs for estimating prevalence and converting this into...	Many countries are currently scaling up efforts to control schistosomiasis , a helminthic disease for which preventive chemotherapy with praziquantel is the main control tool . In order to apply WHO guidelines on how frequently to treat a given district or similar geographic unit for schistosomiasis , survey-based esti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "education", "helminths", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "malawi", "parasitic", "diseases", "animals", "health", "ca...	2017	Optimising cluster survey design for planning schistosomiasis preventive chemotherapy
We have previously reported that Vivax Malaria Protein 001 ( VMP001 ) , a vaccine candidate based on the circumsporozoite protein of Plasmodium vivax , is immunogenic in mice and rhesus monkeys in the presence of various adjuvants . In the present study , we evaluated the immunogenicity and efficacy of VMP001 formulate...	Plasmodium vivax is responsible for causing malaria in large parts of the globe , including regions with temperate climates not suited for the transmission of other Plasmodium species . In addition , P . vivax has the propensity to form dormant forms , known as hypnozoites , that can remain latent for weeks to months a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "humoral", "immunity", "infectious", "disease", "immunology", "clinical", "immunology", "immunity", "biology", "and", "life", "sciences", "immunology", "humoral", "immune", "response" ]	2014	Protective Efficacy of a Plasmodium vivax Circumsporozoite Protein-Based Vaccine in Aotus nancymaae Is Associated with Antibodies to the Repeat Region
Neurons receive excitatory or sensory inputs through their dendrites , which often branch extensively to form unique neuron-specific structures . How neurons regulate the formation of their particular arbor is only partially understood . In genetic screens using the multidendritic arbor of PVD somatosensory neurons in ...	Sensory neurons sample their environment through highly branched structures termed dendritic arbors or trees . The precise patterning of dendritic arbors is important for the proper functioning of the nervous system , and evidence indicates an involvement of sensory neurons in neuropsychiatric disease such as autism sp...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "caenorhabditis", "gene", "regulation", "regulatory", "proteins", "endoplasmic", "reticulum", "cell", "processes", "dna-binding", "proteins", "neuroscience", "animals", "animal", "models", "physiological", "processes...	2017	Reduced Insulin/Insulin-Like Growth Factor Receptor Signaling Mitigates Defective Dendrite Morphogenesis in Mutants of the ER Stress Sensor IRE-1
The circadian oscillator , an internal time-keeping device found in most organisms , enables timely regulation of daily biological activities by maintaining synchrony with the external environment . The mechanistic basis underlying the adjustment of circadian rhythms to changing external conditions , however , has yet ...	Circadian oscillators are internal timing devices that produce rhythms with a period of about 24 hours to regulate a wide range of biological processes for nearly all organisms . Circadian oscillators adjust phase and period in response to external cues such as light and temperatures and internal cues such as metabolit...	[ "Abstract", "Introduction", "Methods", "Results" ]	[ "genetic", "networks", "gene", "regulation", "brassica", "light", "electromagnetic", "radiation", "circadian", "oscillators", "model", "organisms", "network", "analysis", "experimental", "organism", "systems", "chronobiology", "plants", "arabidopsis", "thaliana", "research"...	2019	Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator
Recent computational and behavioral studies suggest that motor adaptation results from the update of multiple memories with different timescales . Here , we designed a model-based functional magnetic resonance imaging ( fMRI ) experiment in which subjects adapted to two opposing visuomotor rotations . A computational m...	Motor adaptation , a form of motor learning in which motor commands are modified to compensate for disturbances in the external environment , usually proceeds at a rapid pace initially and is then followed by more gradual adjustments . This suggests that at least two learning processes are involved , but little is know...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Neural Substrates Related to Motor Memory with Multiple Timescales in Sensorimotor Adaptation
The Sec system is responsible for protein insertion , translocation and secretion across membranes in all cells . The bacterial actin homolog MreB controls various processes , including cell wall synthesis , membrane organization and polarity establishment . Here we show that the two systems genetically interact and th...	The notion that bacterial cells have intricate spatial organization , which affects many vital processes , is relatively new and , hence , the underlying mechanisms are largely unknown . The general secretion system and the cytoskeleton are central systems , each known to organize functions associated with certain cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "walls", "fluorescence", "imaging", "cell", "cycle", "and", "cell", "division", "cell", "processes", "membrane", "staining", "light", "microscopy", "membrane", "proteins", "microscopy", "cellular", "structures", "and", "organelles", "cytoskeleton", "research", ...	2017	The bacterial Sec system is required for the organization and function of the MreB cytoskeleton
Centromeres are critically important for chromosome stability and integrity . Most eukaryotes have regional centromeres that include long tracts of repetitive DNA packaged into pericentric heterochromatin . Neocentromeres , new sites of functional kinetochore assembly , can form at ectopic loci because no DNA sequence ...	Centromere function is essential for proper chromosomal segregation . Most organisms , including humans , have regional centromeres in which centromere function is not strictly dependent on DNA sequence . Upon alteration of chromosomes , new functional centromeres ( neocentromeres ) can form at ectopic positions . The ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/microbial", "growth", "and", "development", "microbiology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/chromosome", "biology", "molecular", "biology/centromeres" ]	2009	Neocentromeres Form Efficiently at Multiple Possible Loci in Candida albicans
Spermatogenesis consists broadly of three phases: proliferation of diploid germ cells , meiosis , and finally extensive differentiation of the haploid cells into effective delivery vehicles for the paternal genome . Despite detailed characterization of many haploid developmental steps leading to sperm , only fragmentar...	Failure of spermatogenesis , which is presumed to often result from genetic defects , is a common cause of male sterility . Although numerous genes associated with defects in male spermatogenesis have been identified , numerous cases of genetic male infertility remain unelucidated . We report here that the transcriptio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	RFX2 Is a Major Transcriptional Regulator of Spermiogenesis
Mexicans are a recent admixture of Amerindians , Europeans , and Africans . We performed local ancestry analysis of Mexican samples from two genome-wide association studies obtained from dbGaP , and discovered that at the MHC region Mexicans have excessive African ancestral alleles compared to the rest of the genome , ...	Whether or not there exists recent selection since admixture in Latinos has been a subject of debate . To detect selection signal , a method uniquely applicable to recently admixed samples is local ancestry analysis . We infer local ancestry of admixed samples ( in our study , Mexicans ) , and look for regions where th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "population", "genetics", "immunology", "ethnicities", "clinical", "medicine", "genome", "analysis", "population", "biology", "chromosome", "6", "genomic", "signal", "processing", "lipids", ...	2016	Strong Selection at MHC in Mexicans since Admixture
Modern agriculture favours the selection and spread of novel plant diseases . Furthermore , crop genetic resistance against pathogens is often rendered ineffective within a few years of its commercial deployment . Leptosphaeria maculans , the cause of phoma stem canker of oilseed rape , develops gene-for-gene interacti...	Plant disease resistance often relies on simple “gene-for-gene” systems and , in the pathogen , a mutation in a single “avirulence” gene matching the plant resistance gene is sufficient to render the resistance ineffective . In agricultural systems , breeding for resistance is challenged by both the high evolutionary p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mutation", "mycology", "fungi", "plant", "microbiology", "evolutionary", "biology", "plant", "biology", "crops", "population", "genetics", "crop", "diseases", "biology", "microbiology", "host-pathogen", "interaction", "agriculture" ]	2012	Genome Structure and Reproductive Behaviour Influence the Evolutionary Potential of a Fungal Phytopathogen
The mechanisms generating stably differentiated cell-types from multipotent precursors are key to understanding normal development and have implications for treatment of cancer and the therapeutic use of stem cells . Pigment cells are a major derivative of neural crest stem cells and a key model cell-type for our under...	In a multicellular organism , one genome is used to make numerous different cell-types . This must require the activity of all these genes to be configured into multiple distinct and stable active states , each corresponding to one of the different cell-types characteristic of a tissue . The stable active states of dif...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "cell", "differentiation", "gene", "function", "animal", "models", "developmental", "biology", "model", "organisms", "gene", "expression", "biology", "systems", "biology", "zebrafish", "genetics", "gene", "networks", "genetics", "and", "genomics", ...	2011	An Iterative Genetic and Dynamical Modelling Approach Identifies Novel Features of the Gene Regulatory Network Underlying Melanocyte Development
To date there are no approved antiviral drugs for the treatment of Ebola virus disease ( EVD ) . While a number of candidate drugs have shown limited efficacy in vitro and/or in non-human primate studies , differences in experimental methodologies make it difficult to compare their therapeutic effectiveness . Using an ...	Studies to evaluate the effectiveness of candidate antiviral drugs to inhibit Ebola virus infection have been hampered by the availability and access to level 4 containment facilities . Using a mini-genome model system that generates Ebola virus-like particles that infect cells , we have been able to screen a panel of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	A Rapid Screening Assay Identifies Monotherapy with Interferon-ß and Combination Therapies with Nucleoside Analogs as Effective Inhibitors of Ebola Virus
The molecular composition of the cannabinoid type 1 ( CB1 ) receptor complex beyond the classical G-protein signaling components is not known . Using proteomics on mouse cortex in vivo , we pulled down proteins interacting with CB1 in neurons and show that the CB1 receptor assembles with multiple members of the WAVE1 c...	One of the most interesting features of the endocannabinoid system ( a group of neuromodulatory lipids and their receptors , which promotes homeostasis in a variety of physiological processes ) is its ability to counteract nociception or pain . This function is largely mediated by the receptor component of the endocann...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Cannabinoid Receptor CB1 Interacts with the WAVE1 Complex and Plays a Role in Actin Dynamics and Structural Plasticity in Neurons
Chromosome movements are a general feature of mid-prophase of meiosis . In budding yeast , meiotic chromosomes exhibit dynamic movements , led by nuclear envelope ( NE ) -associated telomeres , throughout the zygotene and pachytene stages . Zygotene motion underlies the global tendency for colocalization of NE-associat...	In meiosis , cells specified to become gametes ( eggs or sperm ) undergo a single round of DNA replication followed by two consecutive chromosomal divisions . In most organisms , the proper segregation of chromosomes at the first meiotic division is mechanically dependent upon genetic exchange , or crossing over , at h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "molecular", "biology/recombination", "cell", "biology/cell", "growth", "and", "division", "cell", "biology", "genetics", "and", "genomics/nuclear", "structure", "and", "function", "molecular", "biology/chromosome", "structure", "ge...	2008	Csm4, in Collaboration with Ndj1, Mediates Telomere-Led Chromosome Dynamics and Recombination during Yeast Meiosis
The primate visual system consists of a ventral stream , specialized for object recognition , and a dorsal visual stream , which is crucial for spatial vision and actions . However , little is known about the interactions and information flow between these two streams . We investigated these interactions within the net...	Many different areas of the brain are utilized to analyze the three-dimensional shape of the objects we see and grasp ( e . g . , a sphere compared to a disk ) . In this study , we temporarily inactivated one of these areas in the monkey parietal cortex and measured the effect on the network of brain areas involved in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "brain", "vertebrates", "social", "sciences", "neuroscience", "animals", "mammals", "cerebral", "hemispheres", "magnetic", "resonance", "imaging", "primat...	2016	Posterior Parietal Cortex Drives Inferotemporal Activations During Three-Dimensional Object Vision
Cascading activity is commonly found in complex systems with directed interactions such as metabolic networks , neuronal networks , or disease spreading in social networks . Substantial insight into a system's organization can be obtained by reconstructing the underlying functional network architecture from the observe...	In many complex systems found across disciplines , such as biological cells and organisms , social networks , economic systems , and the Internet , individual elements interact with each other , thereby forming large networks whose structure is often not known . In these complex networks , local events can easily propa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "mathematics/statistics", "computational", "biology/computational", "neuroscience", "computational", "biology/metabolic", "networks", "computational", "biology", "computational", "biology/signaling", "networks", "neuroscience", "neuroscience/theoretical", "neuroscience" ]	2009	Efficient Network Reconstruction from Dynamical Cascades Identifies Small-World Topology of Neuronal Avalanches
The On-Off direction-selective ganglion cell ( DSGC ) in mammalian retinas responds most strongly to a stimulus moving in a specific direction . The DSGC initiates spikes in its dendritic tree , which are thought to propagate to the soma with high probability . Both dendritic and somatic spikes in the DSGC display stro...	The On-Off direction-selective ganglion cell ( DSGC ) found in mammalian retinas generates a directional signal , responding most strongly to a stimulus moving in a specific direction . The DSGC initiates spikes in its dendritic tree which are thought to propagate to the soma and brain with high probability . Both dend...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physiology/sensory", "systems", "neuroscience/sensory", "systems", "physiology/neuronal", "signaling", "mechanisms", "biophysics/theory", "and", "simulation", "computational", "biology/computational", "neuroscience", "neuroscience/neuronal", "signaling", "mechanisms", "neuroscience/...	2010	Dendritic Spikes Amplify the Synaptic Signal to Enhance Detection of Motion in a Simulation of the Direction-Selective Ganglion Cell
Recently , enterovirus 71 ( EV71 ) has caused life-threatening outbreaks involving neurological and cardiopulmonary complications in Asian children with unknown mechanism . EV71 has one single serotype but can be phylogenetically classified into 3 main genogroups ( A , B and C ) and 11 genotypes ( A , B1∼B5 and C1∼C5 )...	Recently , enterovirus 71 ( EV71 ) has caused life-threatening outbreaks in tropical Asia . EV71 has one single serotype but can be phylogenetically classified into 3 main genogroups and 11 genotypes ( A , B1∼B5 and C1∼C5 ) . In Taiwan , nationwide EV71 epidemics with different predominant genotypes occurred in 1998 ( ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "pediatrics", "and", "child", "health", "pediatrics" ]	2013	Cross-reactive Neutralizing Antibody Responses to Enterovirus 71 Infections in Young Children: Implications for Vaccine Development
Rabies is a viral zoonosis affecting mammal species and causes large economic losses . Included among the neglected diseases , it is still insufficiently addressed by governments and the international community , despite formal surveillance and control programs . This study used a dataset of 10 , 112 rabies diagnoses i...	The approach proposed in this study can provide a valuable contribution to strengthen the efforts to reduce rabies incidence , a relevant public health problem worldwide . In Brazil during the period from 2001–2012 , 129 human cases of rabies were notified , with 128 deaths . It is imperative to decrease rabies virus c...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Trends in Animal Rabies Surveillance in the Endemic State of Minas Gerais, Brazil
The Eph receptor tyrosine kinases ( RTKs ) are regulators of cell migration and axon guidance . However , our understanding of the molecular mechanisms by which Eph RTKs regulate these processes is still incomplete . To understand how Eph receptors regulate axon guidance in Caenorhabditis elegans , we screened for supp...	The correct wiring of the nervous system depends on the ability of axons to properly interpret extracellular cues that guide them to their targets . The Eph receptor tyrosine kinases ( RTKs ) have roles in guiding axons , but their signaling pathways are not completely understood . In this study , we used the nematode ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "molecular", "cell", "biology", "molecular", "development", "genetics", "molecular", "genetics", "biology", "morphogenesis", "neuroscience", "genetics", "and", "genomics" ]	2012	The Caenorhabditis elegans Eph Receptor Activates NCK and N-WASP, and Inhibits Ena/VASP to Regulate Growth Cone Dynamics during Axon Guidance
Organisms have increased in complexity through a series of major evolutionary transitions , in which formerly autonomous entities become parts of a novel higher-level entity . One intriguing feature of the higher-level entity after some major transitions is a division of reproductive labor among its lower-level units i...	A major transition in evolution occurs when previously autonomous entities become co-dependent in the context of a higher-level entity . Such transitions include the evolution of multicellular organisms from unicellular ancestors and eusocial “superorganisms” from multicellular ancestors . The evolution of reproductive...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "evolutionary", "biology", "theoretical", "biology", "biology", "and", "life", "sciences", "microbiology" ]	2014	Geometry Shapes Evolution of Early Multicellularity
To understand the complex relationship governing transcript abundance and the level of the encoded protein , we integrate genome-wide experimental data of ribosomal density on mRNAs with a novel stochastic model describing ribosome traffic dynamics during translation elongation . This analysis reveals that codon arrang...	Gene expression regulation is central to all living systems . Here we introduce a new framework and methodology to study the last stage of protein production in cells , where the genetic information encoded in the mRNAs is translated from the language of nucleotides into functional proteins . The process , on each mRNA...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "systems", "biology", "molecular", "cell", "biology", "statistical", "mechanics", "theoretical", "biology", "protein", "translation", "gene", "expression", "biology", "computational", "biology", "molecular", "biology" ]	2013	Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation
Gene expression variation is extensive in nature , and is hypothesized to play a major role in shaping phenotypic diversity . However , connecting differences in gene expression across individuals to higher-order organismal traits is not trivial . In many cases , gene expression variation may be evolutionarily neutral ...	A major goal in genetics is to understand how individuals with different genetic makeups respond to their environment . Understanding these “gene-environment interactions” is important for the development of personalized medicine . For example , gene-environment interactions can explain why some people are more sensiti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "peroxidases", "chemical", "compounds", "quantitative", "trait", "loci", "enzymes", "gene", "regulation", "regulatory", "proteins", "enzymology", "dna-binding", "proteins", "organic", "compounds", "fungi", "transcription", "factors", "alcohols", "proteins", "gene", "expre...	2018	Linkage mapping of yeast cross protection connects gene expression variation to a higher-order organismal trait
Lymphatic filariasis is caused by the parasitic worms Wuchereria bancrofti , Brugia malayi or B . timori , which are transmitted via the bites from infected mosquitoes . Once in the human body , the parasites develop into adult worms in the lymphatic vessels , causing severe damage and swelling of the affected tissues ...	We have developed and validated a yeast-based high-throughput screening assay for the identification of specific inhibitors of filarial targets . We engineered yeast strains to functionally express parasite and human enzymes , labeling these with fluorescent proteins and growing them in competition in the presence of t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "cloning", "animals", "drug", "screening", "complementary", "dna", "cloning", "age", "groups", "fungi", "adults", "model", "organisms", "brugia", "forms", "of", "dna", "pharmacology", "dna", "molecular", "bio...	2016	Yeast-Based High-Throughput Screens to Identify Novel Compounds Active against Brugia malayi
Lymphatic filariasis ( LF ) infects approximately 120 million people worldwide . As many as 40 million have symptoms of LF disease , including lymphedema , elephantiasis , and hydrocele . India constitutes approximately 45% of the world's burden of LF . The Indian NGO Church's Auxiliary for Social Action ( CASA ) has b...	Lymphatic filariasis ( LF ) is the world's second-leading cause of disability and causes limb lymphedema and elephantiasis in up to 15 million people and lymphedema or hydrocele in over 40 million people , worldwide . A massive global effort has been undertaken to eliminate LF as a public health problem . LF eliminatio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "clinical", "research", "design", "behavioral", "and", "social", "aspects", "of", "health", "infectious", "disease", "epidemiology", "parasitic", "diseases", "preventive", "medicine", "skin", "infections", "global",...	2013	Impact of Community-Based Lymphedema Management on Perceived Disability among Patients with Lymphatic Filariasis in Orissa State, India
The high rates of RNA virus evolution are generally attributed to replication with error-prone RNA-dependent RNA polymerases . However , these long-term nucleotide substitution rates span three orders of magnitude and do not correlate well with mutation rates or selection pressures . This substitution rate variation ma...	RNA viruses are the fastest evolving human pathogens , making their treatment and control difficult . Compared to DNA viruses , RNA viruses replicate with much lower fidelity , which can explain why RNA viruses evolve significantly faster than most DNA viruses . However , there is tremendous variation among the evoluti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "viruses", "viral", "classification", "virology", "biology", "microbiology", "viral", "evolution" ]	2014	Cell Tropism Predicts Long-term Nucleotide Substitution Rates of Mammalian RNA Viruses
In Drosophila , the MSL ( Male Specific Lethal ) complex up regulates transcription of active genes on the single male X-chromosome to equalize gene expression between sexes . One model argues that the MSL complex acts upon the elongation step of transcription rather than initiation . In an unbiased forward genetic scr...	Drosophila males hypertranscribe most of the genes along their single X chromosome to match the output of females with two X chromosomes . It had been difficult to imagine how the MSL dosage compensation complex could impose a modest , but essential , ∼two-fold increase by interacting with hundreds of different factors...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "genetic", "screens", "gene", "expression", "genetics", "gene", "regulation", "epigenetics", "biology", "molecular", "genetics", "chromatin", "genetics", "and", "genomics", "dna", "transcription", "histone", "modification" ]	2012	Mutations in the Transcription Elongation Factor SPT5 Disrupt a Reporter for Dosage Compensation in Drosophila
Timings of human activities are marked by circadian clocks which in turn are entrained to different environmental signals . In an urban environment the presence of artificial lighting and various social cues tend to disrupt the natural entrainment with the sunlight . However , it is not completely understood to what ex...	For humans living in urban areas , the modern daily life is very different from that of people who lived in ancient times , from which todays’ societies evolved . Mainly due to the availability of artificial lighting , modern humans have been able to modify their natural daily cycles . In addition , social rules , like...	[ "Abstract", "Introduction", "Results", "Discusion", "Materials", "and", "methods" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "sleep", "cell", "phones", "physiological", "processes", "probability", "distribution", "mathematics", "longitude", "chronobiology", "geography", "c...	2017	Tracking urban human activity from mobile phone calling patterns
Pattern formation during development is a highly dynamic process . In spite of this , few experimental and modelling approaches take into account the explicit time-dependence of the rules governing regulatory systems . We address this problem by studying dynamic morphogen interpretation by the gap gene network in Droso...	Animal development is a highly dynamic process . Biochemical or environmental signals can cause the rules that shape it to change over time . We know little about the effects of such changes . For the sake of simplicity , we usually leave them out of our models and experimental assays . Here , we do exactly the opposit...	[ "Abstract", "Introduction", "Models", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "gene", "regulation", "animals", "blastulas", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "systems", "science", "mathematics", "experimental", "organism", "systems", "molecular", "development", "embryo...	2017	Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression
The bacterial colicin-immunity proteins Im7 and Im9 fold by different mechanisms . Experimentally , at pH 7 . 0 and 10°C , Im7 folds in a three-state manner via an intermediate but Im9 folding is two-state-like . Accordingly , Im7 exhibits a chevron rollover , whereas the chevron arm for Im9 folding is linear . Here we...	In order to fold correctly , a globular protein must avoid being trapped in wrong , i . e . , nonnative conformations . Thus a biophysical account of how attractive nonnative interactions are bypassed by some amino acid sequences but not others is key to deciphering protein structure and function . We examine two close...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[]	2015	Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins
Fasciola hepatica is not only responsible for major economic losses in livestock farming , but is also a major food-borne zoonotic agent , with 180 million people being at risk of infection worldwide . This parasite is sophisticated in manipulating the hosts’ immune system to benefit its own survival . A better underst...	Fasciola hepatica ( liver fluke ) is not only of major health , welfare and economic importance in ruminants , but also an emerging zoonosis . This parasite is sophisticated in manipulating the host’s immune system to benefit its own survival . In this study we investigated global gene expression changes of the primary...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "immunology", "cell", "processes", "tropical", "diseases", "fascioliasis", "parasitic", "diseases", "regulator", "genes", "gene", "types", "ne...	2016	Transcriptomic Study on Ovine Immune Responses to Fasciola hepatica Infection
Overlaying differential changes in gene expression on protein interaction networks has proven to be a useful approach to interpreting the cell's dynamic response to a changing environment . Despite successes in finding active subnetworks in the context of a single species , the idea of overlaying lists of differentiall...	Microarrays are a powerful tool for discovering genes whose expression is associated with a particular biological process or phenotype . Differential expression analysis can often generate a list of several hundred or even thousands of significant genes . While these genes represent real expression differences , the la...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/gene", "discovery", "computer", "science/applications", "developmental", "biology/stem", "cells", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "genetics", "and", "genomics/function...	2010	A Scalable Approach for Discovering Conserved Active Subnetworks across Species
We previously showed that CD8+ T cells are required for optimal primary immunity to low dose Leishmania major infection . However , it is not known whether immunity induced by low dose infection is durable and whether CD8+ T cells contribute to secondary immunity following recovery from low dose infection . Here , we c...	It is known that CD8+ T cells are important for primary immunity to low dose L . major infection , but whether low dose-induced immunity is long lasting and whether CD8+ T cells are also important for memory immune response to low dose L . major is unknown . We studied whether infectious dose affects primary anti-Leish...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "leishmaniasis", "biology", "and", "life", "sciences", "immunology", "protozoan", "infections", "parasitic", "diseases", "veterinary", "science", "parasitology" ]	2014	CD8+ T cells Are Preferentially Activated during Primary Low Dose Leishmania major Infection but Are Completely Dispensable during Secondary Anti-Leishmania Immunity
It has been proposed that neural noise in the cortex arises from chaotic dynamics in the balanced state: in this model of cortical dynamics , the excitatory and inhibitory inputs to each neuron approximately cancel , and activity is driven by fluctuations of the synaptic inputs around their mean . It remains unclear wh...	This work studies the effects of chaotic dynamics , a prominent feature of the balanced state model , on storage of continuous parameters in working memory . We propose a simple model of a balanced network with mutual inhibition , and show that it possesses a continuum of steady states , a commonly proposed mechanism f...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cognitive", "science", "medicine", "and", "health", "sciences", "neural", "networks", "nervous", "system", "electrophysiology", "neuroscience", "learning", "and", "memory", "mathematics", "algebra", "cognition", "computational", "neuroscience", "memory", "neuronal", "tun...	2017	Slow diffusive dynamics in a chaotic balanced neural network
Atrial fibrillation ( AF ) is the most common cardiac arrhythmia at the clinic . Recent GWAS identified several variants associated with AF , but they account for <10% of heritability . Gene-gene interaction is assumed to account for a significant portion of missing heritability . Among GWAS loci for AF , only three we...	Gene-gene interaction is assumed to be critical to the pathogenesis of human disease , but its contribution to human disease phenotype needs definitive documentation . Moreover , the underlying molecular mechanism for gene-gene interaction is unknown . Here we use atrial fibrillation ( AF ) as a model to demonstrate th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Molecular Basis of Gene-Gene Interaction: Cyclic Cross-Regulation of Gene Expression and Post-GWAS Gene-Gene Interaction Involved in Atrial Fibrillation
Whether , when , how , and why increased complexity evolves in biological populations is a longstanding open question . In this work we combine a recently developed method for evolving virtual organisms with an information-theoretic metric of morphological complexity in order to investigate how the complexity of morpho...	The evolution of complexity , a central issue of evolutionary theory since Darwin's time , remains a controversial topic . One particular question of interest is how the complexity of an organism's body plan ( morphology ) is influenced by the complexity of the environment in which it evolved . Ideally , it would be de...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "organismal", "evolution", "computer", "science", "biology", "evolutionary", "biology", "computerized", "simulations", "evolutionary", "processes" ]	2014	Environmental Influence on the Evolution of Morphological Complexity in Machines
Significant progress has been made in defining the central signaling networks in many organisms , but collectively we know little about the downstream targets of these networks and the genes they regulate . To reconstruct the regulatory circuit of calcineurin signal transduction via MoCRZ1 , a Magnaporthe oryzae C2H2 t...	All organisms have the innate ability to perceive their environment and respond to it , largely through controlling gene expression . Tailored specificity of a response is primarily achieved through signal cascades involving unique receptors , downstream transcription factors ( proteins that bind to DNA to regulate gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/plant-biotic", "interactions", "plant", "biology/plant-biotic", "interactions", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "infectious", "diseases/fungal", "infections", "genetics", "and", "genomics/gene",...	2010	Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca2+/Calcineurin Signaling in the Rice Blast Fungus
Compensatory mutations between protein residues in physical contact can manifest themselves as statistical couplings between the corresponding columns in a multiple sequence alignment ( MSA ) of the protein family . Conversely , large coupling coefficients predict residue contacts . Methods for de-novo protein structur...	Knowledge about the three-dimensional structure of proteins is key to understanding their function and role in biological processes and diseases . The experimental structure determination techniques , such as X-ray crystallography or electron cryo-microscopy , are labour intensive , time-consuming and expensive . There...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "immune", "cells", "markov", "models", "statistics", "split-decomposition", "method", "antigen-presenting", "cells", "immunology", "multiple", "alignment", "calculation", "phylogenetics", "data", "management", "mathematic...	2018	Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction
Although there is tremendous interest in understanding the evolutionary roles of horizontal gene transfer ( HGT ) processes that occur during chronic polyclonal infections , to date there have been few studies that directly address this topic . We have characterized multiple HGT events that most likely occurred during ...	Bacterial infections have long been studied using Koch's postulates wherein the paradigm is that a single clone leads to a given infection . Over the past decade , it has become clear that chronic bacterial infections often do not fit this paradigm . Instead these are associated with the presence of multiple strains or...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "computer", "science/applications", "genetics", "and", "genomics/comparative", "genomics", "computational", "biology/comparative", "sequence", "analysis", "infectious", "diseases/bacterial", "infections", "micro...	2010	Generation of Genic Diversity among Streptococcus pneumoniae Strains via Horizontal Gene Transfer during a Chronic Polyclonal Pediatric Infection
Although evidence suggests that T cells are critical for immunity to malaria , reliable T cell correlates of exposure to and protection from malaria among children living in endemic areas are lacking . We used multiparameter flow cytometry to perform a detailed functional characterization of malaria-specific T cells in...	Despite reports of decreasing malaria morbidity across many parts of Africa , the incidence of malaria among children continues to be very high in Uganda , even in the setting of insecticide-treated bednets and artemisinin-based combination therapy . Additional control measures , including a vaccine , are sorely needed...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "adaptive", "immunity", "immune", "cells", "clinical", "immunology", "immunity", "t", "cells", "immunity", "to", "infections", "immune", "tolerance", "malaria", "plasmodium", "falciparum", "parasitic", "diseases", "immune", "respons...	2014	IFNγ/IL-10 Co-producing Cells Dominate the CD4 Response to Malaria in Highly Exposed Children
Channel noise is the dominant intrinsic noise source of neurons causing variability in the timing of action potentials and interspike intervals ( ISI ) . Slow adaptation currents are observed in many cells and strongly shape response properties of neurons . These currents are mediated by finite populations of ionic cha...	Neurons of sensory systems encode signals from the environment by sequences of electrical pulses — so-called spikes . This coding of information is fundamentally limited by the presence of intrinsic neural noise . One major noise source is “channel noise” that is generated by the random activity of various types of ion...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/theoretical", "neuroscience" ]	2010	How Noisy Adaptation of Neurons Shapes Interspike Interval Histograms and Correlations
Senescence is a universal barrier to immortalisation and tumorigenesis . As such , interest in the use of senescence-induction in a therapeutic context has been gaining momentum in the past few years; however , senescence and immortalisation remain underserved areas for drug discovery owing to a lack of robust senescen...	Cellular senescence is an irreversible arrest of cell proliferation . Senescence is understood to be a universal barrier that all cancers must overcome during their evolution . Developing ways to induce senescence in cancer cells is therefore an attractive strategy to identify targets for cancer therapy . However , a l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "medicine", "and", "health", "sciences", "senescence", "gene", "regulation", "cancer", "treatment", "biomarkers", "oncology", "physiological", "processes", "developmental", "biology", "organism", "development", "molecular", "biology", "techniques", "research...	2017	A ‘synthetic-sickness’ screen for senescence re-engagement targets in mutant cancer backgrounds
A multicellular organism is not a monolayer of cells in a flask; it is a complex , spatially structured environment , offering both challenges and opportunities for viruses to thrive . Whereas virus infection dynamics at the host and within-cell levels have been documented , the intermediate between-cell level remains ...	A great deal is understood about how a virus infects an individual cell and manages to replicate . Patterns of disease progression in plant and animal hosts , such as virus titers and the appearance of symptoms , have also been described in great detail . On other hand , very little is known about what is happening at ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "mutation", "plant", "microbiology", "genetic", "polymorphism", "effective", "population", "size", "disease", "dynamics", "microbial", "evolution", "virology", "natural", "selection", "genetics", "population", "dynamics", "population", "genetics", "host-pathogen", "interact...	2014	Within-Host Spatiotemporal Dynamics of Plant Virus Infection at the Cellular Level
The “reproductive ground plan” hypothesis ( RGPH ) proposes that reproductive division of labour in social insects had its antecedents in the ancient gene regulatory networks that evolved to regulate the foraging and reproductive phases of their solitary ancestors . Thus , queens express traits that are characteristic ...	In social insects , the evolution of the worker caste and the regulation of reproductive behaviour by workers are poorly understood . Evolution is conservative and often proceeds by adapting an existing gene network to a new function . The “reproductive ground plan” hypothesis ( RGPH ) suggests that social insects evol...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "evolutionary", "biology", "ecology" ]	2008	Effects of Selection for Honey Bee Worker Reproduction on Foraging Traits
Rabies continues to pose a significant threat to human and animal health in regions of Indonesia . Indonesia has an extensive network of veterinary diagnostic laboratories and the 8 National laboratories are equipped to undertake diagnostic testing for rabies using the commercially-procured direct fluorescent antibody ...	In Indonesia , veterinary diagnostic laboratories conduct tests for rabies on brain samples from animals suspected of being infected with rabies virus . National laboratories use internationally recommended tests for rabies virus that require expensive materials and equipment . Remote and smaller Provincial laboratorie...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vertebrates", "geographical", "locations", "animals", "mammals", "dogs", "indonesia", "viruse...	2017	Development and validation of an immunoperoxidase antigen detection test for improved diagnosis of rabies in Indonesia
SIRT1 is a member of the sirtuin family of NAD+-dependent deacetylases , which couple cellular metabolism to systemic physiology . Although studies in mouse models have defined a central role for SIRT1 in maintaining metabolic health , the molecular mechanisms remain unclear . Here we show that loss of the Drosophila S...	The sirtuins are a highly conserved family of deacetylases with targets that range from DNA-associated histones to transcription factors . The activities of these enzymes are dependent upon the energetic state of the cell as they utilize the coenzyme NAD+ , an important electron carrier in central metabolic pathways . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "carbohydrate", "metabolism", "invertebrates", "medicine", "and", "health", "sciences", "chemical", "compounds", "diabetic", "endocrinology", "hyperglycemia", "carbohydrates", "glucose", "metabolism", "animals", "organic", "compounds", "glucose", "hormones", "endocrine", "p...	2016	Sir2 Acts through Hepatocyte Nuclear Factor 4 to maintain insulin Signaling and Metabolic Homeostasis in Drosophila
Mass cytometry ( CyTOF ) has greatly expanded the capability of cytometry . It is now easy to generate multiple CyTOF samples in a single study , with each sample containing single-cell measurement on 50 markers for more than hundreds of thousands of cells . Current methods do not adequately address the issues concerni...	Recently , the cytometry field has experienced rapid advancement in the development of mass cytometry ( CyTOF ) . CyTOF enables a significant increase in the ability to monitor 50 or more cellular markers for millions of cells at the single-cell level . Initial studies with CyTOF focused on few samples , in which exper...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "medicine", "and", "health", "sciences", "split-decomposition", "method", "random", "variables", "covariance", "simulation", "and", "modeling", "bone", "marrow", "cells", "multiple", "alignment", "calculation", "lymph", "nodes", "mathematics", "lymp...	2017	Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks
Cathepsin-like enzymes have been identified as potential targets for drug or vaccine development in many parasites , as their functions appear to be essential in a variety of important biological processes within the host , such as molting , cuticle remodeling , embryogenesis , feeding and immune evasion . Functional a...	Filarial nematodes are an important group of human pathogens , causing lymphatic filariasis and onchocerciasis , and infecting around 150 million people throughout the tropics with more than 1 . 5 billion at risk of infection . Control of filariasis currently relies on mass drug administration ( MDA ) programs using dr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "molecular", "biology", "genetics", "and", "genomics/functional", "genomics" ]	2009	Functional Analysis of the Cathepsin-Like Cysteine Protease Genes in Adult Brugia malayi Using RNA Interference
Although neocortical connectivity is remarkably stereotyped , the abundance of some wiring motifs varies greatly between cortical areas . To examine if regional wiring differences represent functional adaptations , we have used optogenetic raster stimulation to map the laminar distribution of GABAergic interneurons pro...	Many natural and engineered networks contain recurring patterns of local connectivity . Although these so-called network motifs are thought to have functional significance , direct tests of the idea that network topology reflects function remain scarce . We have performed such a test in the area of mammalian neocortex ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "synapses", "neurotransmitters", "sensory", "systems", "biology", "neuroscience", "neurophysiology" ]	2014	Experience-Dependent Rewiring of Specific Inhibitory Connections in Adult Neocortex
Human endogenous retroviruses ( HERVs ) are remnants of ancient infectious agents that have integrated into the human genome . Under normal circumstances , HERVs are functionally defective or controlled by host factors . In HIV-1-infected individuals , intracellular defense mechanisms are compromised . We hypothesized ...	The human genome contains a number of remnants or fossils of ancient viral infections referred to as human endogenous retroviruses ( HERV ) . Like fossils , these HERV are considered to be dead or inert in most cases . However , we demonstrate that T cells in the human immune system respond to HERV when a person is inf...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Supporting", "Information" ]	[ "homo", "(human)", "immunology" ]	2007	T Cell Responses to Human Endogenous Retroviruses in HIV-1 Infection
Inflammatory caspase-11/4/5 recognize cytosolic LPS from invading Gram-negative bacteria and induce pyroptosis and cytokine release , forming rapid innate antibacterial defenses . Since extracellular or vacuole-constrained bacteria are thought to rarely access the cytoplasm , how their LPS are exposed to the cytosolic ...	Sensing of lipopolysaccharide ( LPS ) in the cytosol triggers non-canonical inflammasome-mediated innate responses . Recent work revealed that bacterial outer membrane vesicles ( OMVs ) enables LPS to access the cytosol for extracellular bacteria . However , since intracellular OMVs are generally constrained in endosom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vacuoles", "pathology", "and", "laboratory", "medicine", "hela", "cells", "pathogens", "immunology", "biological", "cultures", "microbiology", "physiological", "processes", "inflammasomes", "cell", "cultures", "caco-2", "cells", ...	2018	Dysregulated hemolysin liberates bacterial outer membrane vesicles for cytosolic lipopolysaccharide sensing
The Ku heterodimer associates with the Saccharomyces cerevisiae telomere , where it impacts several aspects of telomere structure and function . Although Ku avidly binds DNA ends via a preformed channel , its ability to associate with telomeres via this mechanism could be challenged by factors known to bind directly to...	The telomeric cap modulates telomere replication and prevents natural chromosome ends from being processed as DNA double-strand breaks ( DSBs ) . In multiple species , including budding yeast , a detailed picture exists of the factors that comprise the telomeric cap and how they associate with telomeric DNA . It is les...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "telomeres", "cell", "biology", "chromosome", "biology", "biology", "molecular", "cell", "biology" ]	2011	Ku Must Load Directly onto the Chromosome End in Order to Mediate Its Telomeric Functions
Allosteric modulators are ligands for proteins that exert their effects via a different binding site than the natural ( orthosteric ) ligand site and hence form a conceptually distinct class of ligands for a target of interest . Here , the physicochemical and structural features of a large set of allosteric and non-all...	The physicochemistry and topography of ligand binding sites is generally conserved amongst related proteins , however , comparisons of the pharmacology of related targets ( and even the same target ) are often confounded by the existence of multiple , distinct , binding sites within the same protein . Importantly , the...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biochemistry", "computer", "and", "information", "sciences", "medicinal", "chemistry", "computer", "modeling", "biology", "and", "life", "sciences", "chemistry", "physical", "sciences", "chemical", "biology" ]	2014	Chemical, Target, and Bioactive Properties of Allosteric Modulation
Aedes aegypti is a cosmopolite mosquito , vector of arboviruses . The worldwide studies of its insecticide resistance have demonstrated a strong loss of susceptibility to pyrethroids , the major class of insecticide used for vector control . French overseas territories such as French Guiana ( South America ) , Guadelou...	Aedes aegypti is vector of Dengue , Chikungunya and Zika viruses , all causing emerging or re-emerging diseases worldwide . Fighting these diseases relies on the control of the vector . Therefore , insecticides have been extensively used worldwide , resulting in the development of insecticide resistance . In the French...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Deltamethrin Resistance Mechanisms in Aedes aegypti Populations from Three French Overseas Territories Worldwide
Legionella pneumophila , the causative agent of Legionnaires' disease , invades and replicates within macrophages and protozoan cells inside a vacuole . The type IVB Icm/Dot secretion system is necessary for the translocation of effector proteins that modulate vesicle trafficking pathways in the host cell , thus avoidi...	Legionella pneumophila is a facultative intracellular bacterium that can cause an often fatal type of pneumonia known as Legionnaires' disease . In nature , L . pneumophila is found in both fresh water and soil where it parasitizes free-living protists . Upon inhalation of contaminated aerosols , L . pneumophila invade...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cellular", "structures", "cell", "biology", "biology", "microbiology", "molecular", "cell", "biology" ]	2012	The Legionella pneumophila Effector VipA Is an Actin Nucleator That Alters Host Cell Organelle Trafficking
Typical Martsolf syndrome is characterized by congenital cataracts , postnatal microcephaly , developmental delay , hypotonia , short stature and biallelic hypomorphic mutations in either RAB3GAP1 or RAB3GAP2 . Genetic analysis of 85 unrelated “mutation negative” probands with Martsolf or Martsolf-like syndromes identi...	Nucleotide triphosphate bases containing inosine , ITP and dITP , are continually produced within the cell as a consequence of various essential biosynthetic reactions . The enzyme inosine triphosphate pyrophosphatase ( ITPase ) scavenges ITP and dITP to prevent their incorporation into RNA and DNA . Here we describe t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "models" ]	[ "glycosylamines", "medicine", "and", "health", "sciences", "mitochondrial", "dna", "cardiovascular", "anatomy", "computational", "biology", "developmental", "biology", "inosine", "genome", "analysis", "forms", "of", "dna", "energy-producing", "organelles", "mammalian", "g...	2019	ITPase deficiency causes a Martsolf-like syndrome with a lethal infantile dilated cardiomyopathy
As a neutrophilic bacterium , Helicobacter pylori is growth deficient under extreme acidic conditions . The gastric pathogen is equipped with an acid survival kit , regulating urease activity by a pH-gated urea channel , opening below pH 6 . 5 . After overcoming acid stress , the bacterium’s multiplication site is situ...	Natural transformation , i . e . the capacity to take up DNA from the environment , is one of the crucial means for horizontal gene transfer and genetic diversity in bacteria . The human gastric pathogen Helicobacter pylori is confronted with acid stress before entering its multiplication site , the gastric mucosa . Th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "oxidative", "stress", "oxygen", "pathogens", "microbiology", "nucleotides", "organic", "compounds", "purines", "helicobacter", "bacterial", "ge...	2016	Genetic Diversity as Consequence of a Microaerobic and Neutrophilic Lifestyle
4C-Seq has proven to be a powerful technique to identify genome-wide interactions with a single locus of interest ( or “bait” ) that can be important for gene regulation . However , analysis of 4C-Seq data is complicated by the many biases inherent to the technique . An important consideration when dealing with 4C-Seq ...	Circularized chromosome conformation capture , or 4C-Seq is a technique developed to identify regions of the genome that are in close spatial proximity to a single locus of interest ( ‘bait’ ) . This technique is used to detect regulatory interactions between promoters and enhancers and to characterize the nuclear envi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "markov", "models", "immunology", "mathematics", "genome", "analysis", "genomic", "signal", "processing", "genomic", "libraries", "white", "blood", "cells", "animal", "cells", "chromosome", ...	2016	4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
While there has been much recent focus on the ecological causes of adaptive diversification , we know less about the genetic nature of the trade-offs in resource use that create and maintain stable , diversified ecotypes . Here we show how a regulatory genetic change can contribute to sympatric diversification caused b...	Understanding the origin of diversity is a fundamental problem in evolutionary biology . The past decade has seen a shift in our understanding of speciation , away from considering geographical isolation as the main cause and towards elucidating how ecological interactions can drive diversification in populations that ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "genetics", "and", "genomics", "eubacteria" ]	2007	Adaptive Diversification in Genes That Regulate Resource Use in Escherichia coli
We have developed an easy-to-use and memory-efficient method called PhenotypeSeeker that ( a ) identifies phenotype-specific k-mers , ( b ) generates a k-mer-based statistical model for predicting a given phenotype and ( c ) predicts the phenotype from the sequencing data of a given bacterial isolate . The method was v...	Predicting phenotypic properties of bacterial isolates from their genomic sequences has numerous potential applications . A good example would be prediction of antimicrobial resistance and virulence phenotypes for use in medical diagnostics . We have developed a method that is able to predict phenotypes of interest fro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "gut", "bacteria", "pathology", "and", "laboratory", "medicine", "statistics", "pathogens", "microbiology", "pseudomonas", "aeruginosa", "genome", "sequencing", "antibiotic", "resistance", "mathematics", ...	2018	A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria
Temperate phages have the ability to maintain their genome in their host , a process called lysogeny . For most , passive replication of the phage genome relies on integration into the host's chromosome and becoming a prophage . Prophages remain silent in the absence of stress and replicate passively within their host ...	Temperate bacteriophages are widespread bacterial viruses that have the ability to replicate passively in their hosts as long as no stressful conditions are encountered , a process called lysogeny . Prophage-encoded genes may benefit the host in several ways such as providing resistance to antibiotics , increased patho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/microbial", "growth", "and", "development", "microbiology/microbial", "evolution", "and", "genomics", "microbiology" ]	2010	Tight Regulation of the intS Gene of the KplE1 Prophage: A New Paradigm for Integrase Gene Regulation
Fascioliasis is a pathogenic disease transmitted by lymnaeid snails and recently emerging in humans , in part due to effects of climate changes , anthropogenic environment modifications , import/export and movements of livestock . South America is the continent presenting more human fascioliasis hyperendemic areas and ...	Fascioliasis is a highly pathogenic zoonotic disease emerging in recent decades , in part due to the effects of climate and global changes . South America is the continent presenting more numerous human fascioliasis endemic areas and the highest Fasciola hepatica infection prevalences and intensities known in humans . ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "ruminants", "geographical", "locations", "tropical", "diseases", "vertebrates", "fascioliasis", "parasitic", "diseases", "animals", "mammals", "genetic", "mapping", "physiological", "processes", "gastro...	2017	DNA multigene characterization of Fasciola hepatica and Lymnaea neotropica and its fascioliasis transmission capacity in Uruguay, with historical correlation, human report review and infection risk analysis
Hookworms ( Necator americanus and Ancylostoma duodenale ) remain a major public health problem worldwide . Infections with hookworms ( e . g . , A . caninum , A . ceylanicum and A . braziliense ) are also prevalent in dogs , but the role of dogs as a reservoir for zoonotic hookworm infections in humans needs to be fur...	Hookworm infections remain a major public health problem in both tropical and subtropical parts of the world . To control the disease burden attributable to hookworms , large-scale deworming programs , in which drugs are administered to schoolchildren regardless of their infection status , are currently being implement...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "invertebrates", "medicine", "and", "health", "sciences", "geographical", "locations", "vertebrates", "india", "parasitic", "diseases", "dogs", "animals", "mammals", "necator", "americanus", "physiological", "processes", "developmental", "biology...	2016	Molecular Identification of Hookworm Isolates in Humans, Dogs and Soil in a Tribal Area in Tamil Nadu, India
Chagas disease is a neglected tropical disease that continues to affect populations living in extreme poverty in Latin America . After successful vector control programs , congenital transmission remains as a challenge to disease elimination . We used the PRECEDE-PROCEED planning model to develop strategies for neonata...	Chagas disease is caused by a parasite transmitted by insects that infest households living in extreme poverty conditions . The parasite can also be transmitted from mother to child during pregnancy . If detected at birth , the infection can be treated effectively with available drugs . However , access to professional...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "medicine", "and", "health", "sciences", "midwives", "medical", "personnel", "tropical", "diseases", "parasitic", "diseases", "developmental", "biology", "neglected", "tropical", "diseases", "infectious", "disease", "control", "public", "and", "occupational", "health", ...	2017	Towards Chagas disease elimination: Neonatal screening for congenital transmission in rural communities
Recently , Wu and colleagues [1] proposed two novel statistics for genome-wide interaction analysis using case/control or case-only data . In computer simulations , their proposed case/control statistic outperformed competing approaches , including the fast-epistasis option in PLINK and logistic regression analysis und...	Gene–gene interactions are a topic of great interest to geneticists carrying out studies of how genetic factors influence the development of common , complex diseases . Genes that interact may not only make important biological contributions to underlying disease processes , but also be more difficult to detect when us...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "computer", "science", "mathematical", "computing", "mathematics", "epidemiology", "statistics", "genetics", "biology", "computational", "biology", "computerized", "simulations", "genetics", "and", "genomics", "numerica...	2012	Improved Statistics for Genome-Wide Interaction Analysis
Salmonella enterica serovar Weltevreden ( S . Weltevreden ) is an emerging cause of diarrheal and invasive disease in humans residing in tropical regions . Despite the regional and international emergence of this Salmonella serovar , relatively little is known about its genetic diversity , genomics or virulence potenti...	Organisms belonging to the species Salmonella enterica are a major cause of infection globally . Such infections can be zoonotic in origin or transmitted between humans . One of the most notable features of the genus Salmonella is that the dominant serovars that cause human infections change over time , with new threat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "taxonomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "salmonellosis", "sequence", "assembly", "tools", "bacterial", "diseases", "phylogenetics", "data", "management", "e...	2016	A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions
Infection with the human liver fluke Opisthorchis viverrini induces cancer of the bile ducts , cholangiocarcinoma ( CCA ) . Injury from feeding activities of this parasite within the human biliary tree causes extensive lesions , wounds that undergo protracted cycles of healing , and re-injury over years of chronic infe...	The oriental liver fluke Opisthorchis viverrini infects millions of people in SE-Asia and kills 26 , 000 people each year due to parasite-induced liver cancer . The mechanisms by which the parasite causes cancer are complex , but a role for excessive wound healing in response to feeding parasites in the bile ducts has ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Carcinogenic Parasite Secretes Growth Factor That Accelerates Wound Healing and Potentially Promotes Neoplasia
Oxidative stress serves as an important host/environmental signal that triggers a wide range of responses in microorganisms . Here , we identified an oxidative stress sensor and response regulator in the important multidrug-resistant nosocomial pathogen Enterococcus faecium belonging to the MarR family and called AsrR ...	Multiple antibiotic‐resistant isolates of the opportunistic pathogen Enterococcus faecium have emerged and spread worldwide . However , studies aimed at identifying mechanisms that underlie the transformation of E . faecium from its commensal nature into a nosocomial pathogen are scarce . We report pleiotropic roles fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "bacterial", "diseases", "pathogenesis", "infectious", "diseases", "enterococcus", "infection", "medical", "microbiology", "microbial", "pathogens", "biology", "microbiology", "bacterial", "pathogens", "gram", "positive" ]	2012	AsrR Is an Oxidative Stress Sensing Regulator Modulating Enterococcus faecium Opportunistic Traits, Antimicrobial Resistance, and Pathogenicity
Pluripotent cells such as embryonic stem ( ES ) and induced pluripotent stem ( iPS ) cells are the starting point from which to generate organ specific cell types . For example , converting pluripotent cells to retinal cells could provide an opportunity to treat retinal injuries and degenerations . In this study , we u...	The goal of regenerative medicine is to replace dead or dying cells . Successful cell replacement depends on the ability of donor cells to differentiate into all functional cell types lost in the target organ . Blindness resulting from retinal disease or damage , for example , would require the replacement of as many a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/cell", "differentiation", "neuroscience/neurodevelopment", "developmental", "biology/neurodevelopment", "developmental", "biology/molecular", "development", "developmental", "biology/organogenesis" ]	2009	Generation of Functional Eyes from Pluripotent Cells
Paramyosin is a thick myofibrillar protein found exclusively in invertebrates . Evidence suggested that paramyosin from helminths serves not only as a structural protein but also as an immunomodulatory agent . We previously reported that recombinant Trichinella spiralis paramyosin ( Ts-Pmy ) elicited a partial protecti...	Trichinellosis is a serious food borne parasitic disease caused by the consumption of meat contaminated with the infective larvae of Trichinella spiralis . The ability of the tissue-dwelling parasite to evade the host complement attack is essential for its survival and for establishing infection in the host . This stud...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "trichinellosis", "parasitic", "diseases" ]	2011	Trichinella spiralis Paramyosin Binds to C8 and C9 and Protects the Tissue-Dwelling Nematode from Being Attacked by Host Complement
Clostridium difficile is the primary cause of nosocomial diarrhea and pseudomembranous colitis . It produces dormant spores , which serve as an infectious vehicle responsible for transmission of the disease and persistence of the organism in the environment . In Bacillus subtilis , the sin locus coding SinR ( 113 aa ) ...	In Bacillus subtilis , sporulation , competence and biofilm formation are regulated by a pleiotropic regulator called SinR . Two sinR homologs are present in C . difficile genome as an operon and henceforth labeled as sinR and sinR’ . Our detailed investigation revealed that in C . difficile , the SinR and SinR’ are ke...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "gut", "bacteria", "toxins", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "bacillus", "microbiology", "vertebrates", "animals", "mammals", "toxicology", "toxic", "agents", "bact...	2018	Pleiotropic roles of Clostridium difficile sin locus
The accurate prediction of the structure and dynamics of DNA remains a major challenge in computational biology due to the dearth of precise experimental information on DNA free in solution and limitations in the DNA force-fields underpinning the simulations . A new generation of force-fields has been developed to bett...	The ability to simulate computationally the structure and dynamics of biomolecules is a major goal of structural biology . Such simulations require the calculation of the forces and energy of the system , typically with extensively parametrized functions called “force-fields” . Developing reliable force-fields has been...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics
For the past four decades the compositional organization of the mammalian genome posed a formidable challenge to molecular evolutionists attempting to explain it from an evolutionary perspective . Unfortunately , most of the explanations adhered to the “isochore theory , ” which has long been rebutted . Recently , an a...	The non-uniformity of DNA composition in mammalian genomes has been known for over four decades . Many attempts have been made to provide a concise description of this heterogeneity and to identify the evolutionary driving forces behind this compositional phenomenology . The first concise description of the genome sugg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "evolution", "evolutionary", "modeling", "biology", "and", "life", "sciences", "molecular", "evolution", "computational", "biology", "evolutionary", "biology", "genomics", "statistics", "evolutionary", "theory" ]	2014	A Comparative Study and a Phylogenetic Exploration of the Compositional Architectures of Mammalian Nuclear Genomes
The Schistosomiasis Consortium for Operational Research and Evaluation ( SCORE ) has launched several large-scale trials to determine the best strategies for gaining and sustaining control of schistosomiasis and transitioning toward elimination . In Côte d’Ivoire , a 5-year cluster-randomized trial is being implemented...	Schistosomiasis is a parasitic worm disease that is widespread in sub-Saharan Africa . To better understand how to gain and sustain the control of schistosomiasis and how to eliminate this disease in different epidemiologic settings , the Schistosomiasis Consortium for Operational Research and Evaluation ( SCORE ) has ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Sustaining Control of Schistosomiasis Mansoni in Western Côte d’Ivoire: Results from a SCORE Study, One Year after Initial Praziquantel Administration
Recent genome-wide experiments in different eukaryotic genomes provide an unprecedented view of transcription factor ( TF ) binding locations and of nucleosome occupancy . These experiments revealed that a large fraction of TF binding events occur in regions where only a small number of specific TF binding sites ( TFBS...	Interactions between proteins and DNA trigger many important biological processes . Therefore , to fully understand how the information encoded on the DNA transcribes into RNA , which in turn translates into proteins in the cell , we need to unravel the molecular design principles of protein-DNA interactions . It is kn...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes
Negative examples – genes that are known not to carry out a given protein function – are rarely recorded in genome and proteome annotation databases , such as the Gene Ontology database . Negative examples are required , however , for several of the most powerful machine learning methods for integrative protein functio...	Many machine learning methods have been applied to the task of predicting the biological function of proteins based on a variety of available data . The majority of these methods require negative examples: proteins that are known not to perform a function , in order to achieve meaningful predictions , but negative exam...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "Materials" ]	[ "algorithms", "computer", "and", "information", "sciences", "mathematics", "applied", "mathematics", "biology", "and", "life", "sciences", "physical", "sciences", "computational", "biology" ]	2014	Negative Example Selection for Protein Function Prediction: The NoGO Database
Almost 60 years ago , Severo Ochoa was awarded the Nobel Prize in Physiology or Medicine for his discovery of the enzymatic synthesis of RNA by polynucleotide phosphorylase ( PNPase ) . Although this discovery provided an important tool for deciphering the genetic code , subsequent work revealed that the predominant fu...	Widely distributed among bacteria and eukaryotes , including humans , polynucleotide phosphorylase ( PNPase ) is a critical enzyme in RNA metabolism that functions in most organisms as a 3ʹ to 5ʹ exoribonuclease . In bacteria , inactivation of the gene encoding PNPase results in a wide range of consequences , including...	[ "Abstract", "Introduction", "Conclusions" ]	[ "nucleic", "acid", "synthesis", "non-coding", "rna", "sequences", "nucleases", "enzymes", "dna-binding", "proteins", "enzymology", "polynucleotides", "nucleotides", "review", "mitochondria", "bioenergetics", "rna", "synthesis", "cellular", "structures", "and", "organelles",...	2018	Polynucleotide phosphorylase: Not merely an RNase but a pivotal post-transcriptional regulator
The fusion of the human immunodeficiency virus type 1 ( HIV-1 ) with its host cell is the target for new antiretroviral therapies . Viral particles interact with the flexible plasma membrane via viral surface protein gp120 which binds its primary cellular receptor CD4 and subsequently the coreceptor CCR5 . However , wh...	The entry of human immunodeficiency virus ( HIV ) into cells is the target for new therapies preventing HIV infection . While intermediate steps of viral entry have been characterized , the progression between these steps and how they result in productive infection are not well understood . By using stochastic modeling...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/molecular", "dynamics", "biophysics/biomacromolecule-ligand", "interactions", "cell", "biology/cell", "adhesion", "infectious", "diseases/hiv", "infection", "and", "aids" ]	2010	Organization of Cellular Receptors into a Nanoscale Junction during HIV-1 Adhesion
Among the Reduviidae family , triatomines are giant blood-sucking bugs . They are well known in Central and South America where they transmit Trypanosoma cruzi to mammals , including humans , through their feces . This parasitic protozoan is the causative agent of Chagas disease , a major public health issue in endemic...	Triatomines are hematophagous insects including vectors of T . cruzi , the agent of Chagas disease , a huge public health issue , especially in South America . Whether these arthropods carry other pathogenic microorganisms is currently unknown . We investigated the presence of different arthropod-borne pathogens , incl...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "parasitic", "protozoans", "animals", "mammals", "organisms", "protozoans", "phylogenetic", "analysis", "molecular", "biology"...	2017	Detection of a Potential New Bartonella Species “Candidatus Bartonella rondoniensis” in Human Biting Kissing Bugs (Reduviidae; Triatominae)
Intracellular pathogens must egress from the host cell to continue their infectious cycle . Apicomplexans are a phylum of intracellular protozoans that have evolved members of the membrane attack complex and perforin ( MACPF ) family of pore forming proteins to disrupt cellular membranes for traversing cells during tis...	The intracellular parasite Toxoplasma gondii infects many hosts including humans . Infected people with a weak immune system can suffer severe disease when the parasite replicates uncontrolled via repeated cycles of cell invasion , intracellular growth , and exit , resulting in cell death . Previous studies showed that...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vesicles", "immune", "cells", "chemical", "compounds", "crystal", "structure", "viral", "transmission", "and", "infection", "antigen-presenting", "cells", "immunology", "condensed", "matter", "physics", "microbiology", "parasitic"...	2018	Structural basis of Toxoplasma gondii perforin-like protein 1 membrane interaction and activity during egress
Technological advances have unraveled the existence of small clusters of co-active neurons in the neocortex . The functional implications of these microcircuits are in large part unexplored . Using a heavily constrained biophysical model of a L5 PFC microcircuit , we recently showed that these structures act as tunable...	Working memory , the ability to retain information for a short period of time , is a fundamental cognitive function that shapes behavior . The cellular correlate of working memory is the prolonged spiking ( persistent ) activity of neurons in the prefrontal cortex . Impairments of prefrontal cortex functionalities and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "circuit", "models", "computational", "neuroscience", "single", "neuron", "function", "biology", "and", "life", "sciences", "computational", "biology", "coding", "mechanisms" ]	2014	Dendritic Nonlinearities Reduce Network Size Requirements and Mediate ON and OFF States of Persistent Activity in a PFC Microcircuit Model
In murine neurocysticercosis ( NCC ) , caused by infection with the parasite Mesocestoides corti , the breakdown of the Blood Brain Barrier ( BBB ) and associated leukocyte infiltration into the CNS is dependent on the anatomical location and type of vascular bed . Prior studies of NCC show that the BBB comprised of pi...	Neurocysticercosis ( NCC ) is one of the most common parasitic diseases of the CNS caused by the metacestode ( larva ) of the tapeworm Taenia solium . Epidemiological studies show that among the various forms of NCC , subarachnoid NCC is associated with poor prognosis , more resistance to anti-helminthic drugs and more...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunopathology", "medicine", "cerebrovascular", "diseases", "emerging", "infectious", "diseases", "neurological", "disorders", "neurology", "immunology", "biology", "microbiology", "host-pathogen", "interaction" ]	2013	Changes in Gene Expression of Pial Vessels of the Blood Brain Barrier during Murine Neurocysticercosis

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