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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
We experimentally investigated the synchronized patterns of three people during sports activities and found that the activity corresponded to spatiotemporal patterns in rings of coupled biological oscillators derived from symmetric Hopf bifurcation theory , which is based on group theory . This theory can provide catal...	Synchronization is very interesting as both a natural phenomenon and scientific topic in physical and biological systems . Examples include the Belousov-Zhabotinsky ( BZ ) reaction , the oscillation of metronomes , the flash of fireflies , and the calling behavior of Japanese tree frogs . The symmetric Hopf bifurcation...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "physics", "motor", "systems", "psychology", "social", "and", "behavioral", "sciences", "human", "performance", "interdisciplinary", "physics", "behavior", "biology", "neuroscience" ]	2011	Three People Can Synchronize as Coupled Oscillators during Sports Activities
The quinoline-based allosteric HIV-1 integrase ( IN ) inhibitors ( ALLINIs ) are promising candidates for clinically useful antiviral agents . Studies using these compounds have highlighted the role of IN in both early and late stages of virus replication . However , dissecting the exact mechanism of action of the quin...	The administration of highly active-antiretroviral therapy ( HAART ) has changed what was once a terminal disease into a manageable chronic infection . The success of HAART is manifested by reduced mortality and morbidity of HIV-1 infected patients . However , evolution of HIV-1 strains resistant to current therapies i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "infectious", "diseases", "medicine", "and", "health", "sciences", "medicinal", "chemistry", "biology", "and", "life", "sciences", "chemistry", "microbiology", "physical", "sciences", "chemical", "biology" ]	2014	A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase
In Drosophila , the fat body , functionally equivalent to the mammalian liver and adipocytes , plays a central role in regulating systemic growth in response to nutrition . The fat body senses intracellular amino acids through Target of Rapamycin ( TOR ) signaling , and produces an unidentified humoral factor ( s ) to ...	Organisms adjust their development in response to environmental conditions to maximize important life history traits such as body size and survival . From work in the fruit fly , Drosophila melanogaster , we are beginning to resolve some of the molecular mechanisms through which environmental conditions , specifically ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "tor", "signaling", "animals", "endocrine", "physiology", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "physiological", "parameters", "nutrition", "drosophila", ...	2016	Growth-Blocking Peptides As Nutrition-Sensitive Signals for Insulin Secretion and Body Size Regulation
Human cancer is caused by the accumulation of genetic alterations in cells . Of special importance are changes that occur early during malignant transformation because they may result in oncogene addiction and thus represent promising targets for therapeutic intervention . We have previously described a computational a...	Cancer is a deadly disease that develops through the accumulation of genetic changes over time . Many biological models do not incorporate this temporal aspect of tumor formation and progression , in part due to the difficulty of determining the sequence of events through biological experimentation for most cancer type...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "algorithms", "medicine", "oncology", "computer", "science", "mathematics", "applied", "mathematics", "computing", "methods", "probability", "theory" ]	2012	A Mathematical Methodology for Determining the Temporal Order of Pathway Alterations Arising during Gliomagenesis
During its life cycle , Caulobacter crescentus undergoes a series of coordinated shape changes , including generation of a polar stalk and reshaping of the cell envelope to produce new daughter cells through the process of cytokinesis . The mechanisms by which these morphogenetic processes are coordinated in time and s...	Bacterial cell shape is genetically hardwired and is critical for fitness and , in certain cases , pathogenesis . In most bacteria , a semi-rigid structure called the cell wall surrounds the inner membrane , offering protection against cell lysis while simultaneously maintaining cell shape . A highly dynamic macromolec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "walls", "cell", "division", "analysis", "caulobacter", "cell", "cycle", "and", "cell", "division", "cell", "processes", "prokaryotic", "models", "microscopy", "experimental", "organism", "systems", "bioassays", "and", "physiological", "analysis", "cellular", ...	2017	FtsEX-mediated regulation of the final stages of cell division reveals morphogenetic plasticity in Caulobacter crescentus
The Notch pathway plays a vital role in determining whether cells in the intestinal epithelium adopt a secretory or an absorptive phenotype . Cell fate specification is coordinated via Notch’s interaction with the canonical Wnt pathway . Here , we propose a new mathematical model of the Notch and Wnt pathways , in whic...	Epithelial cells which line the intestine form finger-shaped structures called crypts; these undergo a process of renewal at the base , causing cells to migrate upwards until they die and are sloughed off into the gut . Much of our understanding of how crypts function rests upon two processes: proliferation , in which ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "models" ]	[ "medicine", "and", "health", "sciences", "immune", "cells", "antigen-presenting", "cells", "immunology", "mathematical", "models", "notch", "signaling", "simulation", "and", "modeling", "network", "analysis", "digestive", "system", "research", "and", "analysis", "method...	2017	The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt
Bacterial capsular polysaccharides are virulence factors and are considered T cell–independent antigens . However , the capsular polysaccharide Sp1 from Streptococcus pneumoniae serotype 1 has been shown to activate CD4+ T cells in a major histocompatibility complex ( MHC ) class II–dependent manner . The mechanism of ...	Microorganisms are comprised of proteins , carbohydrates , lipids , and nucleic acids . Current immunologic paradigms state that activation of T lymphocytes required for humoral and cellular immune responses resulting in immunologic memory to the pathogens is solely brought about by proteinaceous antigens , processed a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "in", "vitro", "immunology", "microbiology", "mus", "(mouse)", "eubacteria" ]	2007	Transport of Streptococcus pneumoniae Capsular Polysaccharide in MHC Class II Tubules
We describe the first large scale analysis of gene translation that is based on a model that takes into account the physical and dynamical nature of this process . The Ribosomal Flow Model ( RFM ) predicts fundamental features of the translation process , including translation rates , protein abundance levels , ribosom...	Gene translation is a central process in all living organisms . However , this process is still enigmatic , and contradicting conclusions regarding the essential parameters that determine translation rates appear in different studies . We introduce a new approach for modeling the process of translation elongation . Tak...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "systems", "biology", "computerized", "simulations", "biochemistry", "computer", "science", "computer", "modeling", "protein", "abundance", "genetics", "molecular", "genetics", "biology", "computational", "biology", "proteomics", "biophysics", "genetics", "...	2011	Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model
The dynamics of infectious diseases spread via direct person-to-person transmission ( such as influenza , smallpox , HIV/AIDS , etc . ) depends on the underlying host contact network . Human contact networks exhibit strong community structure . Understanding how such community structure affects epidemics may provide in...	Understanding the spread of infectious diseases in populations is key to controlling them . Computational simulations of epidemics provide a valuable tool for the study of the dynamics of epidemics . In such simulations , populations are represented by networks , where hosts and their interactions among each other are ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	Dynamics and Control of Diseases in Networks with Community Structure
Gastrointestinal nematode parasites infect over 1 billion humans , with little evidence for generation of sterilising immunity . These helminths are highly adapted to their mammalian host , following a developmental program through successive niches , while effectively down-modulating host immune responsiveness . Larva...	Intestinal helminth parasites are highly prevalent in humans and animals , and survive for long periods by deviating the host immune system . No vaccines are currently available to control these infections . Many helminths invade through barrier surfaces ( such as the skin or the digestive tract ) and develop through t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunity", "immunology", "proteomics", "biology", "parasitic", "diseases" ]	2013	Secretion of Protective Antigens by Tissue-Stage Nematode Larvae Revealed by Proteomic Analysis and Vaccination-Induced Sterile Immunity
ATP6V1H is a component of a large protein complex with vacuolar ATPase ( V-ATPase ) activity . We identified two generations of individuals in which short stature and osteoporosis co-segregated with a mutation in ATP6V1H . Since V-ATPases are highly conserved between human and zebrafish , we generated loss-of-function ...	Osteoporosis , a major health problem worldwide , is characterized by low bone mineral density ( BMD ) and a propensity to fracture . Genetic factors are clearly the major determinants of BMD , but their identification and contribution to osteoporosis risk have been difficult to assess in humans . Genome-wide associati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rheumatology", "medicine", "and", "health", "sciences", "osteoporosis", "gene", "regulation", "chondrocytes", "vertebrates", "animals", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "osteoblasts", "bone", "connective", "tissue", "c...	2017	ATP6V1H Deficiency Impairs Bone Development through Activation of MMP9 and MMP13
Preterm birth is the major cause of neonatal death and serious morbidity . Most preterm births are due to spontaneous onset of labor without a known cause or effective prevention . Both maternal and fetal genomes influence the predisposition to spontaneous preterm birth ( SPTB ) , but the susceptibility loci remain to ...	Preterm birth is the major cause of infant deaths and life-long neurologic and cardiopulmonary morbidity . More than 10% of births in the United States occur prematurely , and the rate is increasing without known effective prevention . Previous premature birth increases the risk 3-fold in subsequent pregnancies . We re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/medical", "genetics", "genetics", "and", "genomics/population", "genetics" ]	2011	Mapping a New Spontaneous Preterm Birth Susceptibility Gene, IGF1R, Using Linkage, Haplotype Sharing, and Association Analysis
We report the identification , functional expression , purification , reconstitution and electrophysiological characterization of a novel cation channel ( TcCat ) from Trypanosoma cruzi , the etiologic agent of Chagas disease . This channel is potassium permeable and shows inward rectification in the presence of magnes...	The use of high-resolution electrophysiological techniques to study ion channels has provided a large amount of information on functional aspects of these important membrane proteins . However , the study of ion channels in unicellular eukaryotes has been limited to detection of ion conductances in large cells , gene i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parastic", "protozoans", "trypanosoma", "protozoology", "biology", "microbiology" ]	2012	Molecular and Electrophysiological Characterization of a Novel Cation Channel of Trypanosoma cruzi
The formation or suppression of particular structures is a major change occurring in development and evolution . One example of such change is the absence of the seventh abdominal segment ( A7 ) in Drosophila males . We show here that there is a down-regulation of EGFR activity and fewer histoblasts in the male A7 in e...	Many species display sexually dimorphic characters in specific regions of their body . In Drosophila melanogaster , a striking difference between males and females is the development of the seventh abdominal segment ( A7 ) , absent in males . We have found that in the first 30 h of pupal development , proliferation in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "growth", "control", "body", "plan", "organization", "biology", "morphogenesis" ]	2012	Drosophila Hox and Sex-Determination Genes Control Segment Elimination through EGFR and extramacrochetae Activity
Plasmodium falciparum malaria is responsible for nearly one million annual deaths worldwide . Because of the difficulty in monitoring the pathogenesis of cerebral malaria in humans , we conducted a study in various mouse models to better understand disease progression in experimental cerebral malaria ( ECM ) . We compa...	Plasmodium falciparum , the deadliest of all human malaria parasites , can cause cerebral malaria , a severe and frequently fatal complication of this devastating disease . Young children are predominantly at risk and may progress rapidly from the first signs of neurological involvement to coma and death . Here we used...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "microbiology", "host-pathogen", "interaction", "parasitic", "diseases", "parasitology", "parastic", "protozoans", "infectious", "diseases", "infectious", "diseases", "of", "the", "nervous", "system", "biology", "infectious", "disease", "modeling", "pathogenesis...	2012	Neuroimmunological Blood Brain Barrier Opening in Experimental Cerebral Malaria
SUMO is a posttranslational modifier that can modulate protein activities , interactions , and localizations . As the GFP-Smt3p fusion protein has a preference for subnucleolar localization , especially when deconjugation is impaired , the nucleolar role of SUMO can be the key to its biological functions . Using condit...	Disruption of the SUMO ( small ubiquitin-like modifier ) pathway by mutations is lethal in mammals and in budding yeast; however , the essential nature of its role remains unknown , mainly because only a small fraction of most substrate proteins is SUMO-modified . We argue that the clustering of SUMO modifications amon...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "cell", "biology/cell", "growth", "and", "division", "genetics", "and", "genomics/chromosome", "biology", "biochemistry/macromolecular", "assemblies", "and", "machines", "genetics", "and", "genomics/epigenetics", "genetics...	2008	Cooperation of Sumoylated Chromosomal Proteins in rDNA Maintenance
Trypanosoma brucei is a protozoan parasite that lacks many transcription factors found in other eukaryotes , such as those whose binding demarcates enhancers . T . brucei retains histone variants and modifications , however , and it is hypothesized that it relies on epigenetic marks to define transcription-related boun...	In eukaryotes , DNA is wrapped around histones to form chromatin . Modifications on the DNA itself , or on the canonical histones around which the DNA is wrapped , can lead to changes in gene expression . Alternate histones are also used to regulate gene expression . The African trypanosome , the causative agent of Afr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Base J and H3.V Regulate Transcriptional Termination in Trypanosoma brucei
To combat and eventually eliminate the transmission of the liver fluke Opisthorchis viverrini , an accurate and practical diagnostic test is required . A recently established urine antigen detection test using monoclonal antibody-based enzyme-linked-immunosorbent assay ( mAb-ELISA ) has shown promise due to its high di...	Opisthorchiasis , caused by an infection with the liver fluke , Opisthorchis viverrini , is a neglected tropical disease endemic in Southeast Asia , particularly Thailand and Lao PDR . O . viverrini as well as Clonorchis sinensis have been classified as group I biological carcinogenic agents for cholangiocarcinoma ( CC...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "helminths", "tropical", "diseases", "hookworms", "parasitic", "diseases", "animals", "urine", "trematodes", "foodborne", "trematodiases", "neglected", "tropical", "diseases", "opisthorchis", "str...	2019	Comparing the performance of urine and copro-antigen detection in evaluating Opisthorchis viverrini infection in communities with different transmission levels in Northeast Thailand
Plasmodium falciparum is unique among human malarias in its ability to sequester in post-capillary venules of host organs . The main variant antigens implicated are the P . falciparum erythrocyte membrane protein 1 ( PfEMP1 ) , which can be divided into three major groups ( A–C ) . Our study was a unique examination of...	One of the most severe forms of malarial disease is cerebral malaria , which disproportionally affects young children . In this disease , the parasite places proteins on the red blood cell surface , providing a “smokescreen” by which they evade host immunity and hide in organ blood vessels , blocking them and causing t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "microbiology", "plasmodium", "falciparum", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "immunodeficiency", "viruses", "protozoans", "infec...	2014	Differential PfEMP1 Expression Is Associated with Cerebral Malaria Pathology
Microtubules are nano-machines that grow and shrink stochastically , making use of the coupling between chemical kinetics and mechanics of its constituent protofilaments ( PFs ) . We investigate the stability and shrinkage of microtubules taking into account inter-protofilament interactions and bending interactions of ...	Microtubules are cylindrical machines inside biological cells , and are crucial for many functions such as chromosome segregation , intra-cellular transport , and cell motility . They are made of 13 elastic filaments ( protofilaments ) that can be either in a straight or in a curved conformation depending on the chemic...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[]	2015	Statistical Mechanics Provides Novel Insights into Microtubule Stability and Mechanism of Shrinkage
Previous genetic studies have suggested a history of sub-Saharan African gene flow into some West Eurasian populations after the initial dispersal out of Africa that occurred at least 45 , 000 years ago . However , there has been no accurate characterization of the proportion of mixture , or of its date . We analyze ge...	Southern Europeans and Middle Eastern populations are known to have inherited a small percentage of their genetic material from recent sub-Saharan African migrations , but there has been no estimate of the exact proportion of this gene flow , or of its date . Here , we apply genomic methods to show that the proportion ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/human", "evolution", "computational", "biology/population", "genetics", "genetics", "and", "genomics/population", "genetics" ]	2011	The History of African Gene Flow into Southern Europeans, Levantines, and Jews
Treponema pallidum infections occur worldwide causing , among other diseases , syphilis and yaws . In particular sexually transmitted syphilis is regarded as a re-emerging infectious disease with millions of new infections annually . Here we present three historic T . pallidum genomes ( two from T . pallidum ssp . pall...	Among the worldwide prevalent treponemal diseases syphilis is a global threat that is currently re-emerging . The origins of syphilis and other treponemal diseases are as yet unresolved and are subject to an intensive scholarly debate . Until now , assumptions on its origins and evolutionary history could only be drawn...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "taxonomy", "urology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "ancient", "dna", "north", "america", "treponematoses", "bacterial", "diseases",...	2018	Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains
Lymphatic filariasis ( LF ) is a neglected tropical disease for which more than a billion people in 73 countries are thought to be at-risk . At a global level , the efforts against LF are designed as an elimination program . However , current efforts appear to aim for elimination in some but not all endemic areas . Wit...	Lymphatic filariasis ( LF ) is a disease caused by filarial worms transmitted by different types of mosquitos that can lead to massive disability , including elephantiasis and hydrocele . LF has no significant zoonotic reservoir and is thought to be a potentially eradicable disease through once yearly treatment distrib...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	What Is Needed to Eradicate Lymphatic Filariasis? A Model-Based Assessment on the Impact of Scaling Up Mass Drug Administration Programs
Sexual reproduction provides an evolutionary advantageous mechanism that combines favorable mutations that have arisen in separate lineages into the same individual . This advantage is especially pronounced in microparasites as allelic reassortment among individuals caused by sexual reproduction promotes allelic divers...	The rearrangement of alleles among individuals in a population during sexual reproduction maintains high allelic diversity within individuals in a population at polymorphic genes . Allelic diversity within individuals can be particularly important for parasites as it enhances their ability to evade host immune systems ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "homologous", "chromosomes", "population", "genetics", "sexual", "reproduction", "parasitic", "protozoans", "developmental", "biology", "protozoans", "dna", "population", "biology", "homologous", "recombination", "sex", "chromosomes", "chromosome", "biology", "homozygosity", ...	2019	Sexual reproduction in a natural Trypanosoma cruzi population
Chicken YF1 genes share a close sequence relationship with classical MHC class I loci but map outside of the core MHC region . To obtain insights into their function , we determined the structure of the YF1*7 . 1/β2-microgloblin complex by X-ray crystallography at 1 . 3 Å resolution . It exhibits the architecture typic...	Proteins encoded by the major histocompatibility complex ( MHC ) play crucial roles in vertebrate immune systems , presenting pathogen-derived protein fragments to receptors on effector cells . In contrast , some non-classical MHC class I proteins such as CD1 molecules possess a hydrophobic groove that allows them to d...	[ "Abstract", "Introduction", "Results/Discussion", "Conclusions", "Materials", "and", "Methods" ]	[ "immunology/antigen", "processing", "and", "recognition" ]	2010	Structure of a Classical MHC Class I Molecule That Binds “Non-Classical” Ligands
Soaring rates of systemic fungal infections worldwide underscore the need for vaccine prevention . An understanding of the elements that promote vaccine immunity is essential . We previously reported that Th17 cells are required for vaccine immunity to the systemic dimorphic fungi of North America , and that Card9 and ...	Despite several million new systemic fungal infections annually worldwide , there are no commercial vaccines available . The development of effective vaccines requires a fundamental understanding of how protective immune responses are induced . Using experimental vaccine strains , we previously demonstrated that popula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "t", "helper", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "spleen", "immunology", "cell", "differentiation", "vaccines", "preventive", "medicine", "immune", ...	2016	MyD88 Shapes Vaccine Immunity by Extrinsically Regulating Survival of CD4+ T Cells during the Contraction Phase
Vaccine candidates for HIV-1 so far have not been able to elicit broadly neutralizing antibodies ( bNAbs ) although they express the epitopes recognized by bNAbs to the HIV envelope glycoprotein ( Env ) . To understand whether and how Env immunogens interact with the predicted germline versions of known bNAbs , we scre...	Recombinant HIV Envelope glycoproteins ( Env ) , the sole target of anti-HIV neutralizing antibodies , have , so far , not been able to elicit broadly neutralizing antibodies ( bNAbs ) although they express the corresponding epitopes . Such constructs elicit neutralizing antibodies of very narrow neutralizing breadth; ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "sexually", "transmitted", "diseases", "viral", "diseases" ]	2013	Recombinant HIV Envelope Proteins Fail to Engage Germline Versions of Anti-CD4bs bNAbs
The effectiveness of seasonal influenza vaccination programs depends on individual-level compliance . Perceptions about risks associated with infection and vaccination can strongly influence vaccination decisions and thus the ultimate course of an epidemic . Here we investigate the interplay between contact patterns , ...	When influenza spreads through a human population , its dynamics are shaped by both the complex patterns of contact that arise through our daily activities and individual decisions about the prevention and treatment of flu infections . However , until recently , mathematical models of flu transmission have ignored comp...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/social", "and", "behavioral", "determinants", "of", "health", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2011	Erratic Flu Vaccination Emerges from Short-Sighted Behavior in Contact Networks
While much effort has focused on detecting positive and negative directional selection in the human genome , relatively little work has been devoted to balancing selection . This lack of attention is likely due to the paucity of sophisticated methods for identifying sites under balancing selection . Here we develop two...	In the past , balancing selection was a topic of great theoretical interest that received much attention . However , there has been little focus toward developing methods to identify regions of the genome that are under balancing selection . In this article , we present the first set of likelihood-based methods that ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "modeling", "genetics", "biology", "and", "life", "sciences", "population", "genetics", "computational", "biology", "evolutionary", "biology" ]	2014	A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data
Empiric evidence shows that Aedes aegypti abundance is spatially heterogeneous and that some areas and larval habitats produce more mosquitoes than others . There is a knowledge gap , however , with regards to the temporal persistence of such Ae . aegypti abundance hotspots . In this study , we used a longitudinal ento...	We carried out a comprehensive study of the long-term trends in household-level Aedes aegypti spatial distribution within a well-defined urban area endemic for dengue virus . By using a dataset consisting of 13 , 662 household entomological visits performed in two neighborhoods in Iquitos , Peru , we quantified the ∼3 ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "tropical", "diseases", "microbiology", "viruses", "neglected", "tropical", "diseases", "research", "and", "analysis", "methods", "infectious", "diseases", "medica...	2014	Shifting Patterns of Aedes aegypti Fine Scale Spatial Clustering in Iquitos, Peru
The epidermal growth factor receptor ( EGFR ) signaling pathway is probably the best-studied receptor system in mammalian cells , and it also has become a popular example for employing mathematical modeling to cellular signaling networks . Dynamic models have the highest explanatory and predictive potential; however , ...	The epidermal growth factor receptor ( EGFR ) signaling pathway is arguably the best-characterized receptor system in mammalian cells and has become a prime example for mathematical modeling of cellular signal transduction . Most of these models are constructed to describe dynamic and quantitative events but , due to t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/signaling", "networks", "computational", "biology", "computational", "biology/systems", "biology", "cell", "biology/cell", "signaling" ]	2009	The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data
Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide . The fungal pathogen is notorious for its ability to overcome host resistance . To better understand its genetic variation in nature , we sequenced the genomes of two field isolates , Y34 and P131 . In comparison with the...	Magnaporthe oryzae is the causal agent of rice blast that is mainly controlled with resistance cultivars . However , genetic variations in the pathogen often lead to overcoming R gene-mediated resistance in rice cultivars . In this study we sequenced two field isolates from China and Japan . In comparison with the labo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "genomics", "evolutionary", "biology", "genetics", "and", "genomics" ]	2012	Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae
Biotin-mediated carboxylation of short-chain fatty acid coenzyme A esters is a key step in lipid biosynthesis that is carried out by multienzyme complexes to extend fatty acids by one methylene group . Pathogenic mycobacteria have an unusually high redundancy of carboxyltransferase genes and biotin carboxylase genes , ...	Tuberculosis is deadly human disease caused by infection with the bacterium Mycobacterium tuberculosis . This pathogen has a complex metabolism with many genes required for the synthesis of components of its unique cell envelope . We have investigated a family of closely related genes coding for different acyl CoA carb...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Characterization of the Mycobacterial Acyl-CoA Carboxylase Holo Complexes Reveals Their Functional Expansion into Amino Acid Catabolism
The convergence of corticostriatal glutamate and dopamine from the midbrain in the striatal medium spiny neurons ( MSN ) triggers synaptic plasticity that underlies reinforcement learning and pathological conditions such as psychostimulant addiction . The increase in striatal dopamine produced by the acute administrati...	The molecular mechanisms by which a dog learns to associate a bell ring with incoming food and by which addiction to cocaine is developed have many things in common . In both cases , glutamate-mediated inputs from the cortex converge on striatal neurons with the neuromodulator dopamine whose level increases upon food d...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "biochemistry", "computer", "science", "computer", "modeling", "biology", "computational", "biology", "molecular", "cell", "biology", "computerized", "simulations", "neuroscience" ]	2014	Segregation and Crosstalk of D1 Receptor-Mediated Activation of ERK in Striatal Medium Spiny Neurons upon Acute Administration of Psychostimulants
During cell entry of flaviviruses , low endosomal pH triggers the rearrangement of the viral surface glycoproteins to a fusion-active state that allows the release of the infectious RNA into the cytoplasm . In this work , West Nile virus was complexed with Fab fragments of the neutralizing mAb E16 and was subsequently ...	West Nile Virus ( WNV ) and other related viruses such as dengue virus enter their host cell by a process that involves fusion between the viral membrane and the membrane of cellular vesicles ( endosomes ) resulting in the release of the viral genome into the cytoplasm of the cell . This fusion event is initiated by lo...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "biophysics/macromolecular", "assemblies", "and", "machines", "virology/virion", "structure,", "assembly,", "and", "egress", "virology", "infectious", "diseases/viral", "infections", "immunology", "biochemistry/m...	2009	Capturing a Flavivirus Pre-Fusion Intermediate
We present a novel analysis of compositional order ( CO ) based on the occurrence of Frequent amino-acid Triplets ( FTs ) that appear much more than random in protein sequences . The method captures all types of proteomic compositional order including single amino-acid runs , tandem repeats , periodic structure of moti...	Variations in compositionally ordered ( CO ) sections of proteins , such as amino acid runs , tandem repeats and low complexity regions , are often considered as a third type of genomic variation along with SNP and CNV . At the microevolutionary scale , they are involved in the rapid evolution of numerous biological fu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Systematic Analysis of Compositional Order of Proteins Reveals New Characteristics of Biological Functions and a Universal Correlate of Macroevolution
To overcome the current problems in leishmaniasis chemotherapy , natural products have become an interesting alternative over the past few decades . Flavonoids have been studied as promising family of compounds for leishmaniasis treatment . 2’-Hydroxyflavanone ( 2HF ) is a flavanone , a class of flavonoid that has show...	Leishmaniasis is a parasitic disease endemic to 98 countries , affecting more than 12 million people globally , and there are more than 350 million people in risk areas . Although there are many drugs available as alternatives for leishmaniasis treatment , they remain mostly ineffective , expensive and longstanding , i...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "tropical", "diseases", "microbiology", "parasitic", "diseases", "protozoan", "life", "cycles", "animal", "models", "developmental", "biology", "otology", "model", "organisms", ...	2018	2'-Hydroxyflavanone activity in vitro and in vivo against wild-type and antimony-resistant Leishmania amazonensis
Neural networks consisting of globally coupled excitatory and inhibitory nonidentical neurons may exhibit a complex dynamic behavior including synchronization , multiclustered solutions in phase space , and oscillator death . We investigate the conditions under which these behaviors occur in a multidimensional parametr...	Nowadays we know that most cognitive functions are not represented in the brain by the activation of a single area but rather by a complex and rich behavior of brain networks distributed over various cortical and subcortical areas . The communication between brain areas is not instantaneous but also undergoes significa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/cognitive", "neuroscience", "neuroscience/theoretical", "neuroscience", "physics/interdisciplinary", "physics", "biophysics/theory", "and", "simulation", "computational", "biology/computational", "neuroscience", "neuroscience/neuronal", "signaling", "mechanisms", "computa...	2008	A Low Dimensional Description of Globally Coupled Heterogeneous Neural Networks of Excitatory and Inhibitory Neurons
The binding of short disordered peptide stretches to globular protein domains is important for a wide range of cellular processes , including signal transduction , protein transport , and immune response . The often promiscuous nature of these interactions and the conformational flexibility of the peptide chain , somet...	The interactions between proteins play a crucial role for almost every undertaking of a cell . Many of these interactions are mediated by the binding of relatively short unstructured polypeptide segments , or peptides , in one protein to well-folded domains in other proteins . Such protein-peptide interactions have som...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[]	2013	Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening
The challenge of distinguishing genetic drift from selection remains a central focus of population genetics . Time-sampled data may provide a powerful tool for distinguishing these processes , and we here propose approximate Bayesian , maximum likelihood , and analytical methods for the inference of demography and sele...	In recent years , considerable attention has been given to the evolution of drug resistance in the influenza A H1N1 strain . As a major annual cause of morbidity and mortality , combined with the rapid global spread of drug resistance , influenza remains as one of the most important global health concerns . Our work he...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "mutation", "genetic", "polymorphism", "effective", "population", "size", "natural", "selection", "evolutionary", "modeling", "genetics", "population", "genetics", "biology", "computational", "biology", "evolutionary", "biology", "evolutionary", "genetics", "genetic", "drif...	2014	Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective
The etiologic agent of Chagas Disease is Trypanosoma cruzi . Acute infection results in patent parasitemia and polyclonal lymphocyte activation . Polyclonal B cell activation associated with hypergammaglobulinemia and delayed specific humoral immunity has been reported during T . cruzi infection in experimental mouse m...	Chagas disease , caused by the protozoan parasite Trypanosoma cruzi , affects 10–12 million people in Latin America . Patent parasitemia develops during acute disease . During this phase , polyclonal B cell activation has been reported to generate high levels of serum antibody with low parasite specificity , and delaye...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immune", "response", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections", "immunology/leukocyte", "activation" ]	2010	Specific Humoral Immunity versus Polyclonal B Cell Activation in Trypanosoma cruzi Infection of Susceptible and Resistant Mice
Variability in the risk of transmission for respiratory pathogens can result from several factors , including the intrinsic properties of the pathogen , the immune state of the host and the host's behaviour . It has been proposed that self-reported social mixing patterns can explain the behavioural component of this va...	For infections such as influenza , there are several aspects to the transmission process , including the properties of the pathogen itself , the host immune system and host behaviour . Although it has been proposed that self-reported social mixing patterns can be used to explain the behavioural component of infection –...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "ecology", "viral", "transmission", "and", "infection", "disease", "dynamics", "virology", "epidemiology", "infectious", "disease", "epidemiology", "population", "dynamics", "biology", "and", "life", "sciences", "population", "bi...	2014	The Contribution of Social Behaviour to the Transmission of Influenza A in a Human Population
Pluripotent epiblast ( EPI ) cells , present in the inner cell mass ( ICM ) of the mouse blastocyst , are progenitors of both embryonic stem ( ES ) cells and the fetus . Discovering how pluripotency genes regulate cell fate decisions in the blastocyst provides a valuable way to understand how pluripotency is normally e...	Pluripotent stem cells can give rise to any cell type in the body , making them an attractive tool for regenerative medicine . Pluripotent stem cells can be derived from the mammalian embryo at the blastocyst stage or they can be created from mature adult cells by reprogramming . During reprogramming , SOX2 helps estab...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "signal", "transduction", "developmental", "biology", "embryology", "stem", "cells", "animal", "cells", "cell", "biology", "molecular", "development", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "cellular", "types", "morphogenesis", "cell", ...	2014	HIPPO Pathway Members Restrict SOX2 to the Inner Cell Mass Where It Promotes ICM Fates in the Mouse Blastocyst
Interferon protects mice from vesicular stomatitis virus ( VSV ) infection and pathogenesis; however , it is not known which of the numerous interferon-stimulated genes ( ISG ) mediate the antiviral effect . A prominent family of ISGs is the interferon-induced with tetratricopeptide repeats ( Ifit ) genes comprising th...	In mammals , the first line of defense against virus infection is the interferon system . Viruses induce synthesis of interferon in the infected cells and its secretion to circulation . Interferon acts upon the as yet uninfected cells and protects them from oncoming infection by inducing the synthesis of hundreds of ne...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cytokines", "immunology", "microbiology", "animal", "models", "mechanisms", "of", "resistance", "and", "susceptibility", "model", "organisms", "immune", "defense", "animal", "models", "of", "infection", "biology", "mouse", "immune", "response", "immune", "system", "i...	2012	Interferon-Induced Ifit2/ISG54 Protects Mice from Lethal VSV Neuropathogenesis
A vast amount of work has been dedicated to the effects of hemodynamics and cytokines on leukocyte adhesion and trans-endothelial migration ( TEM ) and subsequent accumulation of leukocyte-derived foam cells in the artery wall . However , a comprehensive mechanobiological model to capture these spatiotemporal events an...	Atherosclerosis affects millions of people worldwide and is characterized by a maladaptive build-up of fatty material , leukocytes , and extracellular matrix inside the artery wall . With age this material , collectively called a plaque , enhances and blocks blood flow thereby altering the hemodynamics . If the plaque ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "body", "fluids", "cardiovascular", "anatomy", "immunology", "developmental", ...	2017	An agent-based model of leukocyte transendothelial migration during atherogenesis
Flagellar synthesis is a highly regulated process in all motile bacteria . In Escherichia coli and related species , the transcription factor FlhDC is the master regulator of a multi-tiered transcription network . FlhDC activates transcription of a number of genes , including some flagellar genes and the gene encoding ...	Flagella are surface-associated appendages that propel bacteria and are involved in diverse functions such as chemotaxis , surface attachment , and host cell invasion . Flagella are incredibly complex macromolecular machines that are energetically costly to produce , assemble , and power . Flagellar production is tight...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "sequencing", "techniques", "functional", "genomics", "transcription", "activators", "gene", "regulation", "rna", "analysis", "nucleic", "acid", "sequencing", "dna-binding", "proteins", "microbiology", "dna", "transcription", "genome", "analysis", "transcrip...	2014	Comprehensive Mapping of the Escherichia coli Flagellar Regulatory Network
Effective search strategies have evolved in many biological systems , including the immune system . T cells are key effectors of the immune response , required for clearance of pathogenic infection . T cell activation requires that T cells encounter antigen-bearing dendritic cells within lymph nodes , thus , T cell sea...	The immune system is responsible for clearing disease-causing infections , and T cells are an important immune cell type that helps eliminate viruses and bacteria . To become activated , T cells must encounter another type of immune cell called dendritic cells in the lymph node . T cell search for dendritic cells is si...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "cell", "motility", "medicine", "and", "health", "sciences", "immune", "cells", "classical", "mechanics", "fluid", "mechanics", "immunology", "mathematical", "models", "simulation", "and", "modeling", "lymph", "nodes", "mathematics", "animal", "behav...	2016	Persistence and Adaptation in Immunity: T Cells Balance the Extent and Thoroughness of Search
Down syndrome ( DS ) leads to complex phenotypes and is the main genetic cause of birth defects and heart diseases . The Ts65Dn DS mouse model is trisomic for the distal part of mouse chromosome 16 and displays similar features with post-natal lethality and cardiovascular defects . In order to better understand these d...	Down syndrome is a common cause of birth defects mainly due to heart diseases with an incidence of up to 50% . Nevertheless the pathophysiology of DS cardiac anomalies and complications are not well understood . Here we have been able to demonstrate using a series of DS mouse models that birth defects and changes in EC...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "model", "organisms", "chromosomal", "disorders", "mouse", "genetics", "biology", "human", "genetics", "down", "syndrome", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2012	The App-Runx1 Region Is Critical for Birth Defects and Electrocardiographic Dysfunctions Observed in a Down Syndrome Mouse Model
The large yellow croaker Larimichthys crocea ( L . crocea ) is one of the most economically important marine fish in China and East Asian countries . It also exhibits peculiar behavioral and physiological characteristics , especially sensitive to various environmental stresses , such as hypoxia and air exposure . These...	L . crocea is a temperate-water migratory fish that belongs to the order Perciformes and the family Sciaenidae . In China , the annual yield from L . crocea aquaculture exceeds that of any other net-cage-farmed marine fish species . L . crocea also exhibits peculiar behavioral and physiological characteristics and is e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation
The childhood epileptic encephalopathies ( EE’s ) are seizure disorders that broadly impact development including cognitive , sensory and motor progress with severe consequences and comorbidities . Recently , mutations in DNM1 ( dynamin 1 ) have been implicated in two EE syndromes , Lennox-Gastaut Syndrome and Infantil...	Childhood epilepsy syndromes , such as the early epileptic encephalopathies ( EE’s ) encompass seizure disorders that manifest early and negatively impact or completely block developmental progression . Recently , mutations in DNM1 ( dynamin 1 ) have been implicated in two EE syndromes , Lennox-Gastaut Syndrome and Inf...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Independent Neuronal Origin of Seizures and Behavioral Comorbidities in an Animal Model of a Severe Childhood Genetic Epileptic Encephalopathy
Polo is a conserved kinase that coordinates many events of mitosis and meiosis , but how it is regulated remains unclear . Drosophila females having only one wild-type allele of the polo kinase gene and the dominant Scant mutation produce embryos in which one of the centrosomes detaches from the nuclear envelope in lat...	Coordination of cell division in development requires a complex interplay between protein kinases , which catalyze the transfer of phosphates to specific substrate proteins to modify their activities . One of these kinases is the conserved Polo , which is the target of anticancer drugs . Using genetics in Drosophila ( ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "molecular", "biology", "drosophila", "genetics", "and", "genomics" ]	2007	Mutations in Drosophila Greatwall/Scant Reveal Its Roles in Mitosis and Meiosis and Interdependence with Polo Kinase
In the fungus Podospora anserina , the [Het-s] prion induces programmed cell death by activating the HET-S pore-forming protein . The HET-s β-solenoid prion fold serves as a template for converting the HET-S prion-forming domain into the same fold . This conversion , in turn , activates the HET-S pore-forming domain . ...	Although amyloids are best known as protein aggregates that are responsible for fatal neurodegenerative diseases , amyloid structures can also fulfill functional roles in cells . In particular , the controlled formation of amyloid structures appears to be involved in different signaling processes in the context of prog...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Signal Transduction by a Fungal NOD-Like Receptor Based on Propagation of a Prion Amyloid Fold
Currently , over 15% of new HIV infections occur in children . Breastfeeding is a major contributor to HIV infections in infants . This represents a major paradox in the field because in vitro , breast milk has been shown to have a strong inhibitory effect on HIV infectivity . However , this inhibitory effect has never...	Infected children acquire HIV from their mother in utero , intrapartum or by ingesting their mother's breast milk which can contain both HIV particles ( cell-free ) and HIV-infected cells ( cell-associated ) . Although breastfeeding is attributed to a significant number of HIV infections in children , most breastfed in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "viral", "transmission", "and", "infection", "microbiology", "host-pathogen", "interaction", "pediatrics", "immunodeficiency", "viruses", "histology", "model", "organisms", "women's", "health", "animal", "models", "of", "infection", "infectious", "diseases", "...	2012	Human Breast Milk and Antiretrovirals Dramatically Reduce Oral HIV-1 Transmission in BLT Humanized Mice
Mycobacterium tuberculosis bacilli display two signature features: acid-fast staining and the capacity to induce long-term latent infections in humans . However , the mechanisms governing these two important processes remain largely unknown . Ser/Thr phosphorylation has recently emerged as an important regulatory mecha...	Acid-fast staining has been used since 1882 as the hallmark diagnostic test for detecting Mycobacterium tuberculosis , the causative agent of tuberculosis . It has been attributed to the presence of a waxy cell envelope , and primarily to its key components , mycolic acids . Here , we report a new mechanism of regulati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "enzymology", "microbiology", "bacterial", "diseases", "enzyme", "chemistry", "bacterial", "pathogens", "animal", "models", "of", "infection", "infectious", "diseases", "...	2014	Phosphorylation of KasB Regulates Virulence and Acid-Fastness in Mycobacterium tuberculosis
Mycobacterium tuberculosis synthesizes intra- and extracellular α-glucans that were believed to originate from separate pathways . The extracellular glucose polymer is the main constituent of the mycobacterial capsule that is thought to be involved in immune evasion and virulence . However , the role of the α-glucan ca...	Capsule formation is critical for the virulence of many bacterial and fungal pathogens . Mycobacterium tuberculosis cells are known to be surrounded by a capsule layer that is mainly composed of an α-glucan glucose polymer that resembles glycogen . Progress in understanding its role in the virulence of this important h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemical", "compounds", "disaccharides", "nmr", "spectroscopy", "carbohydrates", "organic", "compounds", "glucose", "mutation", "bacteria", "research", "and", "analysis", "methods", "trehalose", "spectrum", "analysis", "techniques", "mutant", "strains", "chemistry", "act...	2016	Metabolic Network for the Biosynthesis of Intra- and Extracellular α-Glucans Required for Virulence of Mycobacterium tuberculosis
Genome-wide association studies ( GWAS ) have identified more than 100 genetic variants contributing to BMI , a measure of body size , or waist-to-hip ratio ( adjusted for BMI , WHRadjBMI ) , a measure of body shape . Body size and shape change as people grow older and these changes differ substantially between men and...	Adult body size and body shape differ substantially between men and women and change over time . More than 100 genetic variants that influence body mass index ( measure of body size ) or waist-to-hip ratio ( measure of body shape ) have been identified . While there is evidence that some genetic loci affect body shape ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study
Neuropilin-1 ( Nrp1 ) encodes the transmembrane cellular receptor neuropilin-1 , which is associated with cardiovascular and neuronal development and was within the peak SNP interval on chromosome 8 in our prior GWAS study on age-related hearing loss ( ARHL ) in mice . In this study , we generated and characterized an ...	Neuropilin-1 is a member of the neuropilin family acting as an essential cell surface receptor involved in semaphorin-dependent axon guidance and VEGF-dependent angiogenesis and lies within our previously identified ARHL GWAS interval . In this study , we investigated the role of Neuropilin-1/Semaphorin-3A signaling in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Conclusions" ]	[ "medicine", "and", "health", "sciences", "nervous", "system", "ears", "gene", "regulation", "electrophysiology", "neuroscience", "neurites", "animal", "models", "inner", "ear", "model", "organisms", "experimental", "organism", "systems", "nerve", "fibers", "neuronal", ...	2017	Role of Neuropilin-1/Semaphorin-3A signaling in the functional and morphological integrity of the cochlea
The parainfluenza viruses ( PIVs ) are highly contagious respiratory paramyxoviruses and a leading cause of lower respiratory tract ( LRT ) disease . Since no vaccines or antivirals exist , non-pharmaceutical interventions are the only means of control for these pathogens . Here we used bioluminescence imaging to visua...	Human parainfluenza viruses ( HPIVs ) are a leading cause of pediatric hospitalization for lower respiratory tract infection , yet it is unknown why primary infection typically induces immunity without causing severe pathology . To study the determinants of PIV spread within the respiratory tracts of living animals , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "viral", "transmission", "and", "infection", "microbiology", "host-pathogen", "interaction", "viral", "vectors", "mechanisms", "of", "resistance", "and", "susceptibility", "viral", "pneumonia", "human", "parainfluenza", "virus", "infection", "veterinary", "sci...	2011	Illumination of Parainfluenza Virus Infection and Transmission in Living Animals Reveals a Tissue-Specific Dichotomy
Salmonella spp . are Gram-negative enteropathogenic bacteria that infect a variety of vertebrate hosts . Like any other living organism , protein secretion is a fundamental process essential for various aspects of Salmonella biology . Herein we report the identification and characterization of a horizontally acquired ,...	Bacteria of the Salmonella genus are important human pathogens and a leading cause of food-borne illness . Like for all other living organisms , protein secretion is a fundamental process , which is required for many different aspects of Salmonella biology including biogenesis of organelles , nutrient acquisition , and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/microbial", "evolution", "and", "genomics", "infectious", "diseases" ]	2008	A Novel Secretion Pathway of Salmonella enterica Acts as an Antivirulence Modulator during Salmonellosis
The opportunistic pathogen Pseudomonas aeruginosa can establish life-long chronic infections in the airways of cystic fibrosis ( CF ) patients . Persistent lifestyle is established with P . aeruginosa patho-adaptive variants , which are clonal with the initially-acquired strains . Several reports indicated that P . aer...	Pseudomonas aeruginosa chronic infections cause persistent respiratory symptoms and decline of the lung functions in patients with cystic fibrosis ( CF ) . Despite the continuous immune response of the host defense and the aggressive antibiotics treatment , bacterial persistence is anyhow established after an acute inf...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "respiratory", "medicine/respiratory", "infections", "microbiology/immunity", "to", "infections", "infectious", "diseases/respiratory", "infections", "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2011	Positive Signature-Tagged Mutagenesis in Pseudomonas aeruginosa: Tracking Patho-Adaptive Mutations Promoting Airways Chronic Infection
Magnaporthe oryzae , which causes the devastating rice-blast disease , invades its host plants via a specialized infection structure called the appressorium . Previously , we showed that the ATP-Binding Cassette 3 transporter is necessary for appressorial function ( host penetration ) in M . oryzae . However , thus far...	Magnaporthe oryzae , the causal fungus of the devastating blast disease in rice , invades its host via specialized infection structures called appressoria . Previously , we showed that ATP-Binding Cassette 3 ( Abc3 ) transporter is indispensable for appresssorial function of host penetration in M . oryzae . However , t...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "developmental", "biology", "model", "organisms", "biology", "microbiology", "molecular", "cell", "biology" ]	2012	Abc3-Mediated Efflux of an Endogenous Digoxin-like Steroidal Glycoside by Magnaporthe oryzae Is Necessary for Host Invasion during Blast Disease
According to the integrated information theory , the quantity of consciousness is the amount of integrated information generated by a complex of elements , and the quality of experience is specified by the informational relationships it generates . This paper outlines a framework for characterizing the informational re...	In prior work , we suggested that consciousness has to do with integrated information , which was defined as the amount of information generated by a system in a given state , above and beyond the information generated independently by its parts . In the present paper , we move from computing the quantity of integrated...	[ "Abstract", "Introduction", "Model", "Results", "and", "Discussion" ]	[ "mathematics", "neuroscience/cognitive", "neuroscience", "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2009	Qualia: The Geometry of Integrated Information
Genomic data generated from clinical Vibrio cholerae O1 isolates collected over a five year period in an area of Kolkata , India with seasonal cholera outbreaks allowed a detailed genetic analysis of serotype switching that occurred from Ogawa to Inaba and back to Ogawa . The change from Ogawa to Inaba resulted from mu...	Cholera is a major health problem in many parts of the world causing seasonal outbreaks in endemic areas . Essentially only the O1 serogroup of Vibrio cholerae causes epidemic cholera . This serogroup has two immunologically distinguishable serotype variants called Ogawa and Inaba . The Inaba serotype is a consequence ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "insertion", "mutation", "pathogens", "vibrio", "tropical", "diseases", "microbiology", "bacterial", "diseases", "mutation", "vibrio", "cholerae", "methylation", "genome", "analysis", ...	2016	Retrospective Analysis of Serotype Switching of Vibrio cholerae O1 in a Cholera Endemic Region Shows It Is a Non-random Process
The endosymbiotic bacterium Wolbachia is being investigated as a potential control agent in several important vector insect species . Recent studies have shown that Wolbachia can protect the insect host against a wide variety of pathogens , resulting in reduced transmission of parasites and viruses . It has been propos...	Wolbachia are bacteria that infect many insect species , but do not infect Anopheles mosquitoes . These mosquitoes transmit Plasmodium parasites , which cause malaria in humans . Wolbachia infection in Aedes aegypti mosquitoes reduces their ability to transmit diverse pathogens including viruses , nematodes and bird ma...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "genetics", "and", "genomics/gene", "expression", "biotechnology/applied", "microbiology", "computational", "biology/genomics", "infectious", "diseases/tropical", ...	2011	Wolbachia Infections in Anopheles gambiae Cells: Transcriptomic Characterization of a Novel Host-Symbiont Interaction
Brain stimulation can modulate the activity of neural circuits impaired by Alzheimer’s disease ( AD ) , having promising clinical benefit . However , all individuals with the same condition currently receive identical brain stimulation , with limited theoretical basis for this generic approach . In this study , we intr...	This work aims to close the knowledge gap between theory and experiment in brain stimulation . Previous modeling approaches for stimulation have overlooked the nonlinear dynamical nature of the brain and failed to shed light on efficient mechanisms for the exogenous control of the brain . Amid the current efforts for d...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "neural", "networks", "neurodegenerative", "diseases", "brain", "electrophysiology", "electrophysiology", "neuroscience", "surgical", "and", "invasive", "medical", "procedures", "regression", "analysis", "clinical", "medicine", "syst...	2018	Design of optimal nonlinear network controllers for Alzheimer's disease
Bacteria switch only intermittently to motile planktonic lifestyles under favorable conditions . Under chronic nutrient deprivation , however , bacteria orchestrate a switch to stationary phase , conserving energy by altering metabolism and stopping motility . About two-thirds of bacteria use flagella to swim , but how...	In the face of starvation , bacteria must minimize their energy use . Here , we describe our unexpected finding that some bacteria take the drastic measure of ejecting their flagella in response to nutrient deficiency . Bacteria continually assemble flagella as propellers—unrelated to eukaryotic flagella—rotated by rot...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "physiology", "cell", "motility", "medicine", "and", "health", "sciences", "swimming", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "flagellar", "motility", "biological", "locomotion", "shigella", "cell", "polarity", "bacterial", "d...	2019	γ-proteobacteria eject their polar flagella under nutrient depletion, retaining flagellar motor relic structures
We have studied the in vivo role of SLIRP in regulation of mitochondrial DNA ( mtDNA ) gene expression and show here that it stabilizes its interacting partner protein LRPPRC by protecting it from degradation . Although SLIRP is completely dependent on LRPPRC for its stability , reduced levels of LRPPRC persist in the ...	Mitochondria provide most of the energy required for key metabolic and cellular processes that are essential for life . The biogenesis of the mitochondrial oxidative phosphorylation system , the site of energy conversion , is dependent on the coordinated expression of the mitochondrial and nuclear genomes . Mitochondri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	SLIRP Regulates the Rate of Mitochondrial Protein Synthesis and Protects LRPPRC from Degradation
A previous study identified MoRgs1 as an RGS protein that negative regulates G-protein signaling to control developmental processes such as conidiation and appressorium formation in Magnaporthe oryzae . Here , we characterized additional seven RGS and RGS-like proteins ( MoRgs2 through MoRgs8 ) . We found that MoRgs1 a...	Regulator of G-protein signaling ( RGS ) proteins play pivotal roles in modulating heterotrimeric G-protein signal transduction cascades that enable eukaryotic cells to perceive external cues and elicit appropriate physiological and biochemical responses . A previous study for one of the RGS proteins , MoRgs1 , has dem...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "fungi", "functional", "genomics", "plant", "microbiology", "fungal", "reproduction", "microbial", "pathogens", "biology", "genomics", "microbiology", "genetics", "and", "genomics", "pathogenesis" ]	2011	Eight RGS and RGS-like Proteins Orchestrate Growth, Differentiation, and Pathogenicity of Magnaporthe oryzae
Canonical WNT/β-catenin signaling is a central pathway in embryonic development , but it is also connected to a number of cancers and developmental disorders . Here we apply a combined in-vitro and in-silico approach to investigate the spatio-temporal regulation of WNT/β-catenin signaling during the early neural differ...	Human neural progenitor cells offer the promising perspective of using in-vitro grown neural cell populations for replacement therapies in the context of neurodegenerative diseases , such as Parkinson’s or Huntington’s disease . However , to control hNPC differentiation within the scope of stem cell engineering , a tho...	[ "Abstract", "Introduction", "Results/Discussion" ]	[]	2015	Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells
Campylobacter infections are among the leading bacterial causes of diarrhea and of ‘environmental enteropathy’ ( EE ) and growth failure worldwide . However , the lack of an inexpensive small animal model of enteric disease with Campylobacter has been a major limitation for understanding its pathogenesis , intervention...	Campylobacter jejuni has been identified as one of the leading causes of enteropathy and diarrhea . In developing countries , these repeated enteric infections often result in growth deficits and cognitive impairment . There is a lack of small animal models of Campylobacter infection . This is a major hurdle in underst...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "animal", "models", "of", "disease", "microbiology", "diet", "campylobacter", "jejuni", "animal", "models", "diarrhea", "model", "organisms", ...	2018	A novel mouse model of Campylobacter jejuni enteropathy and diarrhea
Many viral pathogens cycle between humans and insects . These viruses must have evolved strategies for rapid adaptation to different host environments . However , the mechanistic basis for the adaptation process remains poorly understood . To study the mosquito-human adaptation cycle , we examined changes in RNA struct...	Important viral pathogens , such as influenza and dengue , jump between species; however , it is still unclear how these viruses evolved for efficient replication in significantly different environments . Using dengue virus as a model , which naturally alternates between humans and mosquitoes , changes in the viral RNA...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Dengue Virus RNA Structure Specialization Facilitates Host Adaptation
Pathogens and hosts require rapid modulation of virulence and defense mechanisms at the infection axis , but monitoring such modulations is challenging . In studying the human fungal pathogen Cryptococcus neoformans , mouse and rabbit infection models are often employed to shed light on the disease mechanisms but that ...	The host-pathogen interaction is highly dynamic and tightly regulated , and yet is difficult to monitor . Traditional investigations provide valuable information for the understanding of pathogenic microbial biology but are time-consuming and often neglect the host immune responses . In addition , current animal models...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "fungal", "genetics", "gene", "regulation", "pathogens", "animal", "models", "of", "disease", "microbiology", ...	2019	Unveil the transcriptional landscape at the Cryptococcus-host axis in mice and nonhuman primates
In eukaryotes , the interphase nucleus is organized in morphologically and/or functionally distinct nuclear “compartments” . Numerous studies highlight functional relationships between the spatial organization of the nucleus and gene regulation . This raises the question of whether nuclear organization principles exist...	Several reports suggest functional relationships within the spatial organization of the nucleus , gene regulation and cell differentiation . However , it still remains difficult to extract common rules , mostly because i ) most data have been gathered on limited sets of nuclear elements and in nuclei outside their norm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics/statistics", "cell", "biology/nuclear", "structure", "and", "function" ]	2010	Statistical Analysis of 3D Images Detects Regular Spatial Distributions of Centromeres and Chromocenters in Animal and Plant Nuclei
Comparison of whole genomes has revealed large and frequent changes in the size of gene families . These changes occur because of high rates of both gene gain ( via duplication ) and loss ( via deletion or pseudogenization ) , as well as the evolution of entirely new genes . Here we use the genomes of 12 fully sequence...	Though comparative genome sequencing has revealed vast similarities in the total number of genes contained within closely related species , this similarity hides enormous complexities in the identity and number of constituent proteins . Species can differ in their complement of genes through both gene duplication and l...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "drosophila" ]	2007	Gene Family Evolution across 12 Drosophila Genomes
A better understanding of changes in HIV-1 population genetics with combination antiretroviral therapy ( cART ) is critical for designing eradication strategies . We therefore analyzed HIV-1 genetic variation and divergence in patients' plasma before cART , during suppression on cART , and after viral rebound . Single-...	Anti-HIV compounds are highly effective for preventing the onset of AIDS but they do not cure infected individuals . Very low levels of virus remain detectable in the blood of most patients despite antiviral treatment and levels surge if treatment is stopped . It is crucial to understand why current treatments are not ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunodeficiency", "viruses", "viral", "persistence", "and", "latency", "virology", "biology", "microbiology", "viral", "replication", "viral", "evolution" ]	2014	Lack of Detectable HIV-1 Molecular Evolution during Suppressive Antiretroviral Therapy
Individual cells take lineage commitment decisions in a way that is not necessarily uniform . We address this issue by characterising transcriptional changes in cord blood-derived CD34+ cells at the single-cell level and integrating data with cell division history and morphological changes determined by time-lapse micr...	Hematopoietic stem cells are classically defined as a specific category of cells at the top of the hierarchy that can differentiate all blood cell types following step-by-step the instructions of a deterministic program . We have analysed this process , and our findings support a much more dynamic view than previously ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "cell", "cycle", "and", "cell", "division", "cell", "processes", "immunology", "cloning", "cell", "differentiation", "dna", "transcription...	2017	Integrated time-lapse and single-cell transcription studies highlight the variable and dynamic nature of human hematopoietic cell fate commitment
Biological systems often display modularity , in the sense that they can be decomposed into nearly independent subsystems . Recent studies have suggested that modular structure can spontaneously emerge if goals ( environments ) change over time , such that each new goal shares the same set of sub-problems with previous...	Biological systems often display modularity , in the sense that they can be decomposed into nearly independent subsystems . The evolutionary origin of modularity has recently been the focus of renewed attention . A series of studies suggested that modularity can spontaneously emerge in environments that vary over time ...	[ "Abstract", "Introduction", "Model", "Discussion" ]	[ "mathematics", "computational", "biology/evolutionary", "modeling", "evolutionary", "biology", "physics/interdisciplinary", "physics" ]	2009	An Analytically Solvable Model for Rapid Evolution of Modular Structure
Coprinopsis cinerea ( also known as Coprinus cinereus ) is a multicellular basidiomycete mushroom particularly suited to the study of meiosis due to its synchronous meiotic development and prolonged prophase . We examined the 15-hour meiotic transcriptional program of C . cinerea , encompassing time points prior to hap...	Meiosis is the part of the sexual reproduction process in which the number of chromosomes in an organism is halved . This occurs in most plants , animals , and fungi; and many of the proteins involved are the same in the different organisms that have been studied . We wanted to ask whether the genes involved in the mei...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "genetics", "and", "genomics" ]	2010	Analysis of the Basidiomycete Coprinopsis cinerea Reveals Conservation of the Core Meiotic Expression Program over Half a Billion Years of Evolution
Left-sided congenital heart disease ( CHD ) encompasses a spectrum of malformations that range from bicuspid aortic valve to hypoplastic left heart syndrome . It contributes significantly to infant mortality and has serious implications in adult cardiology . Although left-sided CHD is known to be highly heritable , the...	Congenital heart disease ( CHD ) is the leading malformation among all newborns , and one of the leading causes of morbidity and mortality in Western countries . Left-sided CHD ( LS-CHD ) encompasses a spectrum ranging from bicuspid aortic valve to aortic stenosis and hypoplastic left heart syndrome with familial clust...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "aortic", "diseases", "clinical", "genetics", "pediatric", "cardiology", "chromosomal", "disorders", "pediatrics", "and", "child", "health", "pediatrics", "chromosomal", "deletions", "and", "duplications", "genetics", "and", "genomics", "congenital", "heart", ...	2012	Rare Copy Number Variants Contribute to Congenital Left-Sided Heart Disease
Whether initiation of antiretroviral therapy ( ART ) regimens aimed at achieving greater concentrations within gut associated lymphoid tissue ( GALT ) impacts the level of mucosal immune reconstitution , inflammatory markers and the viral reservoir remains unknown . We included 12 HIV- controls and 32 ART-naïve HIV pat...	Despite the efficacy of ART to suppress HIV replication in blood , HIV-infected individuals experience persistent immunologic dysfunction and inflammation that predict mortality and have been related to a chronically injured gut-associated lymphoid tissue . These gut abnormalities results in a ‘leaky gut’ , from which ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Effects of Combined CCR5/Integrase Inhibitors-Based Regimen on Mucosal Immunity in HIV-Infected Patients Naïve to Antiretroviral Therapy: A Pilot Randomized Trial
A proper immune response ensures survival in a hostile environment and promotes longevity . Recent evidence indicates that innate immunity , beyond antimicrobial effectors , also relies on host-defensive mechanisms . The Caenorhabditis elegans transcription factor SKN-1 regulates xenobiotic and oxidative stress respons...	Innate immunity promotes survival by combating pathogenic threat . During infection , tissue damage is induced both by invading pathogens and immune effectors such as toxins and free radicals . Therefore , it is important to elucidate by what self-protective mechanisms the host defends itself against pathogenic stress ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "stress", "responses", "aging", "and", "immunity", "immunity", "to", "infections", "immunology", "microbiology", "anatomy", "and", "physiology", "host-pathogen", "interaction", "animal", "models", "physiological", "processes", "caenorhabditis", "elegans", "mod...	2012	A Role for SKN-1/Nrf in Pathogen Resistance and Immunosenescence in Caenorhabditis elegans
SKN-1/Nrf are the primary antioxidant/detoxification response transcription factors in animals and they promote health and longevity in many contexts . SKN-1/Nrf are activated by a remarkably broad-range of natural and synthetic compounds and physiological conditions . Defining the signaling mechanisms that regulate SK...	Oxidative stress is the result of imbalanced control of reactive oxidative species in cells , is a common occurrence during aerobic metabolism , and must be managed to limit cellular damage and disease . Many details about the signaling mechanisms utilized by animal cells in response to pro-oxidants remain to be discov...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "And", "Methods" ]	[ "phosphorylation", "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "pathology", "and", "laboratory", "medicine", "caenorhabditis", "gene", "regulation", "animals", "toxicology", "animal", "models", "caenorhabditis", "elegans", "model", "or...	2016	The Skp1 Homologs SKR-1/2 Are Required for the Caenorhabditis elegans SKN-1 Antioxidant/Detoxification Response Independently of p38 MAPK
Contact-Dependent Growth Inhibition ( CDI ) is a phenomenon in which bacteria use the toxic C-terminus of a large exoprotein ( called BcpA in Burkholderia species ) to inhibit the growth of neighboring bacteria upon cell-cell contact . CDI systems are present in a wide range of Gram-negative proteobacteria and a hallma...	Contact-Dependent Growth Inhibition ( CDI ) systems are highly diverse interbacterial competition systems that bacteria use to kill neighboring bacteria upon cell-cell contact . In Burkholderia species , BcpA is the large exoprotein responsible for mediating CDI . BcpI proteins provide immunity against auto-inhibition ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "emerging", "infectious", "diseases", "ecology", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "microbiology", ...	2014	Kind Discrimination and Competitive Exclusion Mediated by Contact-Dependent Growth Inhibition Systems Shape Biofilm Community Structure
Transitive inference ( the ability to infer that B > D given that B > C and C > D ) is a widespread characteristic of serial learning , observed in dozens of species . Despite these robust behavioral effects , reinforcement learning models reliant on reward prediction error or associative strength routinely fail to per...	Although machine learning systems can solve a wide variety of problems , they remain limited in their ability to make logical inferences . We developed a new computational model , called betasort , which addresses these limitations for a certain class of problems: Those in which the algorithm must infer the order of a ...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[]	2015	Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model
The transcription factor TWIST1 plays a vital role in mesoderm development , particularly in limb and craniofacial formation . Accordingly , haploinsufficiency of TWIST1 can cause limb and craniofacial malformations as part of Saethre-Chotzen syndrome . However , the molecular basis of TWIST1 transcriptional regulation...	TWIST1 haploinsufficiency can cause limb and craniofacial malformations , such as Saethre-Chotzen syndrome . However , the DNA regulatory elements that control TWIST1 expression and prevent developmental abnormalities are not known . Here , we identified and characterized several TWIST1 transcriptional enhancers . Each...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fish", "medicine", "and", "health", "sciences", "gene", "regulation", "vertebrates", "animals", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "experimental", "organism", "systems", "mammalian", "genomics", "body", "limbs", "embry...	2018	Unraveling the transcriptional regulation of TWIST1 in limb development
The genetic control of common traits is rarely deterministic , with many genes contributing only to the chance of developing a given phenotype . This incomplete penetrance is poorly understood and is usually attributed to interactions between genes or interactions between genes and environmental conditions . Because ma...	Although most inter-individual phenotypic variabilities are largely attributable to DNA differences , a wealth of examples illustrate how a single biological system can vary stochastically over time and between individuals . Identical twins are not identical , and similarly , clonal microbial cells differ in many aspec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/complex", "traits", "molecular", "biology/transcription", "elongation", "genetics", "and", "genomics/bioinformatics" ]	2008	Cell-to-Cell Stochastic Variation in Gene Expression Is a Complex Genetic Trait
Disseminated histoplasmosis is the first AIDS-defining infection in French Guiana . A retrospective cohort study studied predictive factors of disseminated histoplasmosis in HIV-infected patients between 1996 and 2008 . Cox proportional hazards models were used . The variables studied were age , sex , last CD4/CD8 coun...	Disseminated histoplasmosis is the first AIDS-related disease in French Guiana , and probably in the Amazonian area . In order to determine the factors that are associated with histoplasmosis , a retrospective looked at a cohort of HIV-infected patients between 1996 and 2008 . Multiple models were used to study the rel...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2014	Risk Factors for Disseminated Histoplasmosis in a Cohort of HIV-Infected Patients in French Guiana
Buruli Ulcer ( BU ) is a neglected tropical skin infection caused by Mycobacterium ulcerans . Residence near aquatic areas has been identified as an important source of transmission of M . ulcerans with increased risk of contracting Buruli ulcer . However , the reservoir and the mode of transmission are not yet well kn...	Buruli ulcer is a skin disease caused by Mycobacterium ulcerans . Although residence near aquatic areas has been identified as an important source of increased risk of contracting Buruli ulcer , the reservoir and the mode of transmission are not well known . To improve the understanding of the mode of transmission of M...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "surface", "water", "rivers", "tropical", "diseases", "geographical", "locations", "bacterial", "diseases", "aquatic", "environments", "bodies", "of", "water", "neglected", "tropical...	2018	Molecular detection of Mycobacterium ulcerans in the environment and its relationship with Buruli ulcer occurrence in Zio and Yoto districts of maritime region in Togo
For optimal response selection , the consequences associated with behavioral success or failure must be appraised . To determine how monetary consequences influence the neural representations of motor preparation , human brain activity was scanned with fMRI while subjects performed a complex spatial visuomotor task . A...	The expected outcome of voluntary actions profoundly shapes human decision making . For instance , expected monetary reward and punishment are powerful modulators of human behavior . Yet how these factors influence brain activity responsible for the preparation of such behavior is not fully understood . This is especia...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/motor", "systems", "neuroscience", "neuroscience/cognitive", "neuroscience", "neuroscience/neuronal", "signaling", "mechanisms" ]	2010	Motor Preparatory Activity in Posterior Parietal Cortex is Modulated by Subjective Absolute Value
Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes . Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests . Because of their toxicity for the environment and danger for human health , these nematicides have now been ba...	Plant-parasitic nematodes are annually responsible for more than $100 billion crop yield loss worldwide and those considered as causing most of the damages are root-knot nematodes . These nematodes used to be controlled by chemicals that are now banned from use because of their poor specificity and high toxicity for th...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[]	2013	Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining
Streptococcal toxic shock syndrome ( STSS ) caused by Streptococcus pyogenes is a clinical condition with a high mortality rate despite modern intensive care . A key feature of STSS is excessive plasma leakage leading to hypovolemic hypotension , disturbed microcirculation and multiorgan failure . Previous work has ide...	Streptococcus pyogenes , also known as group A streptococcus , is a common bacterial pathogen mostly causing rather harmless infections such as pharyngitis ( “strep throat” ) and impetigo ( a superficial skin infection ) . However , sometimes these bacteria give rise to severe invasive infections , and one of the most ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "infectious", "diseases/bacterial", "infections", "immunology/immune", "response", "immunology/leukocyte", "activation" ]	2008	Antibodies against a Surface Protein of Streptococcus pyogenes Promote a Pathological Inflammatory Response
Gene expression profiling in E 11 mouse embryos identified high expression of the long noncoding RNA ( lncRNA ) , LNCRNA-HIT in the undifferentiated limb mesenchyme , gut , and developing genital tubercle . In the limb mesenchyme , LncRNA-HIT was found to be retained in the nucleus , forming a complex with p100 and CBP...	A fundamental problem studied by skeletal biologists is the development of regenerative therapies to replace cartilage tissues impacted by injury or disease , which for individuals affected by osteoarthritis represents nearly half of all of all adults over the age of sixty five . To date , no therapies exist to promote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes
Bipolar disorder is a common , heritable mental illness characterized by recurrent episodes of mania and depression . Despite considerable effort to elucidate the genetic underpinnings of bipolar disorder , causative genetic risk factors remain elusive . We conducted a comprehensive genomic analysis of bipolar disorder...	Bipolar disorder is a common , heritable mental illness characterized by recurrent episodes of mania and depression . Despite considerable efforts genetic studies have yet to reveal the precise genetic underpinnings of the disorder . In this study we have analyzed a large extended pedigree of Old Order Amish that segre...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "sequencing", "medicine", "genome", "analysis", "tools", "genomics", "genetic", "mutation", "mental", "health", "linkage", "maps", "genome", "scans", "genetic", "association", "studies", "genetics", "psychiatry", "biolo...	2014	Genomic View of Bipolar Disorder Revealed by Whole Genome Sequencing in a Genetic Isolate
Trypanosoma brucei gambiense , transmitted by the tsetse fly , is the main causative agent of Human African trypanosomosis in West Africa and poses a significant health risk to 70 million people . Disease progression varies depending on host immunity , but usually begins with a haemo-lymphatic phase , followed by paras...	Human African trypanosomosis ( HAT ) caused by Trypanosoma brucei gambiense is a serious disease threatening 70 million people in West Africa . The parasite is transmitted by the tsetse fly , and initially multiplies in the bloodstream of the mammalian host , before progressing to the central nervous system . Using a s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Trypanosoma brucei gambiense Infections in Mice Lead to Tropism to the Reproductive Organs, and Horizontal and Vertical Transmission
In an uncertain environment , probabilities are key to predicting future events and making adaptive choices . However , little is known about how humans learn such probabilities and where and how they are encoded in the brain , especially when they concern more than two outcomes . During functional magnetic resonance i...	In order to make adaptive choices , people need to gather evidence to predict what will happen next . In general , the more frequently an event is observed , the more likely it will occur in the future . Thus the probability of an event is useful to predict its future occurrence . Previous studies have identified regio...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cognitive", "neuroscience", "behavioral", "neuroscience", "decision", "theory", "mathematics", "social", "and", "behavioral", "sciences", "psychology", "cognitive", "psychology", "decision", "making", "computational", "neuroscience", "statistics", "biology", "neuroscience" ]	2013	Activity in Inferior Parietal and Medial Prefrontal Cortex Signals the Accumulation of Evidence in a Probability Learning Task
Cooperation in social dilemmas is essential for the functioning of systems at multiple levels of complexity , from the simplest biological organisms to the most sophisticated human societies . Cooperation , although widespread , is fundamentally challenging to explain evolutionarily , since natural selection typically ...	Social dilemmas embody the tension between individual self-interest on the one hand and the public good on the other that underlie many of the greatest challenges facing human and animal societies , such as the maintenance of altruism and the responsible use of common resources . Understanding the mechanisms through wh...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "game", "theory", "snowdrift", "game", "computer", "and", "information", "sciences", "psychology", "mathematics", "scale-free", "networks", "prisoner's", "dilemma", "network", "analysis", "internet", "social", "networks", "applied", "mathematics", "biology", "and", "lif...	2016	Evolution of Cooperation in Social Dilemmas on Complex Networks
Classically , the functional consequences of natural selection over genomes have been analyzed as the compound effects of individual genes . The current paradigm for large-scale analysis of adaptation is based on the observed significant deviations of rates of individual genes from neutral evolutionary expectation . Th...	Characterizing genome adaptation is paramount for understanding evolutionary genomics . Classically , the search for positively selected genes has been used to identify adaptive differences in morphology , physiology and behavior between species . However , this approach assumed gene independence and was unable to iden...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/human", "evolution", "evolutionary", "biology/genomics", "evolutionary", "biology/bioinformatics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2011	Natural Selection on Functional Modules, a Genome-Wide Analysis
Recognizing an object takes just a fraction of a second , less than the blink of an eye . Applying multivariate pattern analysis , or “brain decoding” , methods to magnetoencephalography ( MEG ) data has allowed researchers to characterize , in high temporal resolution , the emerging representation of object categories...	Recognizing an object in the world ( e . g . a cat ) takes just a fraction of a second . Recent advances in neuroscience have allowed researchers to measure the emergence and dynamics of time-varying neural signals that allow us to quickly recognize objects visually . At each moment in time , these neural signals can b...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Emerging Object Representations in the Visual System Predict Reaction Times for Categorization
The incidence of clinical and clinicopathological signs associated with the progression of infection was evaluated prospectively in 329 naïve young dogs exposed to Leishmania infantum transmission and examined periodically during 22 months ( M ) . The dogs were part of Leishmania vaccine investigations performed under ...	Despite dogs representing the main reservoir for the most widespread entity of human leishmaniasis ( zoonotic visceral leishmaniasis caused by Leishmania infantum , endemic in five continents ) , many aspects of canine leishmaniasis ( CanL ) are still poorly understood . Dog responses to the infection are complex and b...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "zoonoses", "veterinary", "epidemiology", "parasitic", "diseases", "veterinary", "science" ]	2013	Prospective Study on the Incidence and Progression of Clinical Signs in Naïve Dogs Naturally Infected by Leishmania infantum
Embodied Choice considers action performance as a proper part of the decision making process rather than merely as a means to report the decision . The central statement of embodied choice is the existence of bidirectional influences between action and decisions . This implies that for a decision expressed by an action...	The modern view of how we make perceptual decisions is of a process of accumulating sensory evidence until reaching a threshold level of certainty . However , this evidence accumulation model neglects the contribution of action and motor processes to the choice that is made . Recent novel studies that track the changin...	[ "Abstract", "Introduction", "Discussion", "Models" ]	[]	2015	Embodied Choice: How Action Influences Perceptual Decision Making

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