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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
Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function . Given the great diversity of bacteria and the ease of genome sequencing , high-throughput approaches to identify gene function experimentally are needed . Here , we use pools of tagged transposon mutants in the ...	Many computationally predicted gene annotations in bacteria are incomplete or wrong . Consequently , experimental methods to systematically determine gene function in bacteria are required . Here , we describe a genetic approach to meet this challenge . We constructed a large transposon mutant library in the metal-redu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbial", "metabolism", "functional", "genomics", "microbiology", "gene", "function", "genome", "analysis", "tools", "gene", "expression", "biology", "systems", "biology", "genetic", "screens", "genetics", "genomics", "gene", "prediction", "genetics", ...	2011	Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions
The isolation of neutralizing monoclonal antibodies ( nmAbs ) against the Zika virus ( ZIKV ) might lead to novel preventative strategies for infections in at-risk individuals , primarily pregnant women . Here we describe the characterization of human mAbs from the plasmablasts of an acutely infected patient . One of t...	Antibody affinity maturation through somatic hypermutation ( SHM ) is thought to be critical for the development of antibodies with virus-neutralizing activity . Contrary to this notion , we describe novel human anti-Zika virus ( ZIKV ) antibodies with very low mutation levels , isolated from plasmablasts early after t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "immune", "cells", "body", "fluids", "pathogens", "immunology", "microbiology", "cloning", "viruses", "rna",...	2017	A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus
Tetherin is a membrane protein of unusual topology expressed from rodents to humans that accumulates enveloped virus particles on the surface of infected cells . However , whether this ‘tethering’ activity promotes or restricts retroviral spread during acute retrovirus infection in vivo is controversial . We report her...	Significant portions of the human and mouse genomes are comprised of retroviral sequences , revealing the long history of conflict between mammalian hosts and retroviruses that led to the evolution of host restriction factors . Nucleotide mutations in restriction factor genes provide a glimpse of this ongoing evolution...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	A Single Nucleotide Polymorphism in Tetherin Promotes Retrovirus Restriction In Vivo
Polyparasitism can lead to severe disability in endemic populations . Yet , the association between soil-transmitted helminth ( STH ) and the cumulative incidence of Schistosoma japonicum infection has not been described . The aim of this work was to quantify the effect of misclassification error , which occurs when le...	Hookworm , roundworm , and whipworm are collectively known as soil-transmitted helminths . These worms are prevalent in most of the developing countries along with another parasitic infection called schistosomiasis . The tests commonly used to detect infection with these worms are less than 100% accurate . This leads t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology/infectious",...	2011	Assessing the Impact of Misclassification Error on an Epidemiological Association between Two Helminthic Infections
Identifying human genes relevant for the processing of pain requires difficult-to-conduct and expensive large-scale clinical trials . Here , we examine a novel integrative paradigm for data-driven discovery of pain gene candidates , taking advantage of the vast amount of existing disease-related clinical literature and...	The mechanisms underlying pain are incompletely understood , and are hard to study due to the subjective and complex nature of pain . From a genetics perspective , the discovery of genes relevant for the processing of pain in humans has been slow and genome-wide association studies have not been successful in yielding ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "text", "mining", "public", "health", "and", "epidemiology", "pain", "management", "genetic", "polymorphism", "epidemiology", "anesthesiology", "population", "genetics", "biology", "computational", "biology", "population", "biology", "anesthesiology", "and", "...	2012	Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases
We present a computer simulation and associated experimental validation of assembly of glial-like support cells into the interweaving hexagonal lattice that spans the Drosophila pupal eye . This process of cell movements organizes the ommatidial array into a functional pattern . Unlike earlier simulations that focused ...	During development , organs are assembled through a complex combination of cell proliferation , programmed cell death , cell movements , etc . These aspects of tissue maturation must be achieved with a limited gene set—to achieve complexity , tissues utilize patterning mechanisms . That is , “rules” are used to create ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/morphogenesis", "and", "cell", "biology", "developmental", "biology/pattern", "formation", "cell", "biology/developmental", "molecular", "mechanisms", "computational", "biology" ]	2010	Computer Simulation of Cellular Patterning Within the Drosophila Pupal Eye
Upon viral infection , the mitochondrial antiviral signaling ( MAVS ) -IKKβ pathway is activated to restrict viral replication . Manipulation of immune signaling events by pathogens has been an outstanding theme of host-pathogen interaction . Here we report that the loss of MAVS or IKKβ impaired the lytic replication o...	Innate immunity represents the first line of defense against pathogen infection . Recent studies uncovered an array of sensors that detect pathogen-associated molecular patterns and induce antiviral cytokine production via two closely related kinase complexes , i . e . , the IKKα/β/γ and TBK-1/IKKε . To counteract host...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/innate", "immunity" ]	2010	Murine Gamma-Herpesvirus 68 Hijacks MAVS and IKKβ to Initiate Lytic Replication
Tree cover is a fundamental structural characteristic and driver of ecosystem processes in terrestrial ecosystems , and trees are a major global carbon ( C ) sink . Fire and herbivores have been hypothesized to play dominant roles in regulating trees in African savannas , but the evidence for this is conflicting . Movi...	Diseases are known to play important roles in regulating and structuring populations , but the consequences of disease outbreaks for entire communities and ecosystems are not as well understood . The Serengeti wildebeest were historically kept at low numbers by the rinderpest virus , but underwent a population explosio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology/plant-environment", "interactions", "ecology/global", "change", "ecology", "infectious", "diseases", "ecology", "ecology/community", "ecology", "and", "biodiversity", "ecology/population", "ecology", "ecology/ecosystem", "ecology" ]	2009	A Disease-Mediated Trophic Cascade in the Serengeti and its Implications for Ecosystem C
Meteorological factors influence dengue virus ecology by modulating vector mosquito population dynamics , viral replication , and transmission . Dynamic modeling techniques can be used to examine how interactions among meteorological variables , vectors and the dengue virus influence transmission . We developed a dengu...	Numerous studies have investigated meteorological and climatic influences on mosquito transmitted viruses . However , dengue ecology is complex , necessitating an understanding of the interactions among components in the system . We estimate dengue fever cases in San Juan , Puerto Rico using a mathematical model inform...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Meteorologically Driven Simulations of Dengue Epidemics in San Juan, PR
The binding of human complement inhibitors to vaccine antigens in vivo could diminish their immunogenicity . A meningococcal ligand for the complement down-regulator , factor H ( fH ) , is fH-binding protein ( fHbp ) , which is specific for human fH . Vaccines containing recombinant fHbp or native outer membrane vesicl...	Vaccines containing factor H-binding protein ( fHbp ) are being developed for protection against bacterial meningitis and sepsis caused by meningococci . The antigen was identified from genomic sequences and only later found to bind a human complement protein , factor H ( fH ) , but not fH from non-human species . In p...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "vaccines", "medicine", "vaccination", "complement", "system", "clinical", "immunology", "immunity", "immunology", "biology", "microbiology", "immune", "system" ]	2012	The Effect of Human Factor H on Immunogenicity of Meningococcal Native Outer Membrane Vesicle Vaccines with Over-Expressed Factor H Binding Protein
Circadian disruption has multiple pathological consequences , but the underlying mechanisms are largely unknown . To address such mechanisms , we subjected transformed cultured cells to chronic circadian desynchrony ( CCD ) , mimicking a chronic jet-lag scheme , and assayed a range of cellular functions . The results i...	Circadian misalignment caused by altered sleep–wake cycles , shift work , or frequent jet lag increases susceptibility to several disorders , including cancer . However , the mechanisms by which circadian disruption contributes to disease are not well understood , and so we addressed this issue by investigating the mol...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "phosphorylation", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "circadian", "oscillators", "chronobiology", "molecular", "biology", "techniques", "rna", "sequencing", "research", "and", "analysis", "...	2019	G1/S cell cycle regulators mediate effects of circadian dysregulation on tumor growth and provide targets for timed anticancer treatment
While the geographic range of a species is a fundamental unit of macroecology and a leading predictor of extinction risk , the evolutionary dynamics of species' ranges remain poorly understood . Based on statistical associations between range size and species age , many studies have claimed support for general models o...	The changing distribution of species over the surface of the Earth , likened by Darwin to “a grand game of chess with the World for a board” , is a central theme in the evolution of life . Studies of the fossil record and molecular estimates of species ages appear to show that species follow a predictable trend of expa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology", "paleontology", "biology", "evolutionary", "biology" ]	2012	Speciation and Extinction Drive the Appearance of Directional Range Size Evolution in Phylogenies and the Fossil Record
In the city of Salvador , a large urban centre in Northeast Brazil , a city-wide sanitation intervention started in 1997 , aimed at improving the sewerage coverage of households from 26% to 80% . Our aim was to study the impact of the intervention on the prevalence and incidence of geohelminths in the school-aged popul...	In the city of Salvador , a large urban centre in Northeast Brazil , a city-wide sanitation intervention started in 1997 , aiming to improve the sewerage coverage of households from 26% to 80% . Our aim was to study the impact of the intervention on the prevalence and incidence of geohelminths in the school-aged popula...	[ "Abstract", "Introduction", "Methodology", "Results", "Discussion" ]	[ "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	Reductions in the Prevalence and Incidence of Geohelminth Infections following a City-wide Sanitation Program in a Brazilian Urban Centre
Implementation of ecosystem-based fisheries management ( EBFM ) requires a clear conceptual and quantitative framework for assessing how different harvest options can modify benefits to ecosystem and human beneficiaries . We address this social-ecological need for Pacific salmon fisheries , which are economically valua...	Commercial fisheries that harvest salmon for human consumption can end up diverting nutrients that would normally be directed to terrestrial and aquatic ecosystems . We examined this problem for Pacific salmon fisheries by using grizzly bears as indicators of salmon ecosystem function . Bear densities vary enormously d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology", "marine", "and", "aquatic", "sciences", "biology", "population", "biology", "marine", "biology" ]	2012	Using Grizzly Bears to Assess Harvest-Ecosystem Tradeoffs in Salmon Fisheries
Botulinum neurotoxin serotype C ( BoNT/C ) is a neuroparalytic toxin associated with outbreaks of animal botulism , particularly in birds , and is the only BoNT known to cleave two different SNARE proteins , SNAP-25 and syntaxin . BoNT/C was shown to be a good substitute for BoNT/A1 in human dystonia therapy because of...	The seven established Botulinum Neurotoxins serotypes ( BoNT/A to G ) and the many BoNT subtypes , the causative agents of botulism , are the most poisonous substances known ( lethal doses in the low ng/kg range ) . Due to their toxicological properties , BoNTs are Janus-faced toxins: potent pathogenic factors and pote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "soleus", "muscles", "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "metabolic", "processes", "neuroscience", "toxicology", "toxic", "agents", "paralysis", "signs", "and", "symptoms", "proteolysis", "bioassays", "and", ...	2017	Botulinum neurotoxin C mutants reveal different effects of syntaxin or SNAP-25 proteolysis on neuromuscular transmission
TSSA ( Trypomastigote Small Surface Antigen ) is an antigenic , adhesion molecule displayed on the surface of Trypanosoma cruzi trypomastigotes . TSSA displays substantial sequence identity to members of the TcMUC gene family , which code for the trypomastigote mucins ( tGPI-mucins ) . In addition , TSSA bears sequence...	Infection with Trypanosoma cruzi produces a chronic and debilitating infectious disease known as Chagas disease , of major significance in Latin America and an emergent threat to global public health . In the absence of vaccines and/or appropriate chemotherapies , the search for parasite effectors that support infectio...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "binding", "blood", "serum", "cell", "physiology", "medicine", "and", "health", "sciences", "body", "fluids", "viral", "transmission", "and", "infection", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cycles", "devel...	2017	The Trypomastigote Small Surface Antigen (TSSA) regulates Trypanosoma cruzi infectivity and differentiation
Visceral leishmaniasis ( VL ) is a parasitic disease , transmitted by the sand fly species Phlebotomus argentipes in the Indian sub-continent . Effective vector control is highly desirable to reduce vector density and human and vector contact in the endemic communities with the aim to curtail disease transmission . We ...	Visceral leishmaniasis ( VL ) is a deadly parasitic disease , transmitted by the sand fly species Phlebotomus argentipes in the Indian sub-continent . Humans are the only proven reservoir of the parasite , Leishmania donovani . Effective vector control is highly desirable to reduce vector density and human and vector c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "invertebrates", "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "sand", "flies", "parasitic", "diseases", "animals", "neglected", "tropical", "diseases", "infectious", "disease", "control", "insect", "vectors", ...	2019	Effect of insecticide-treated bed nets on visceral leishmaniasis incidence in Bangladesh. A retrospective cohort analysis
Human African trypanosomiasis progresses from an early ( hemolymphatic ) stage , through CNS invasion to the late ( meningoencephalitic ) stage . In experimental infections disease progression is associated with neuroinflammatory responses and neurological symptoms , but this concept requires evaluation in African tryp...	Human African trypanosomiasis , caused by the parasites Trypanosoma brucei rhodesiense and T . b . gambiense , is clinically defined by two diagnostic stages , an early stage where the parasites appear to be localised to the blood and lymphatic systems , and a late stage where the parasites are also localised in the ce...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "immunology", "parasitic", "diseases", "immune", "response" ]	2012	Stage Progression and Neurological Symptoms in Trypanosoma brucei rhodesiense Sleeping Sickness: Role of the CNS Inflammatory Response
Pentameric ligand-gated ion channels ( pLGICs ) are neurotransmitter-activated receptors that mediate fast synaptic transmission . In pLGICs , binding of agonist to the extracellular domain triggers a structural rearrangement that leads to the opening of an ion-conducting pore in the transmembrane domain and , in the c...	Ligand-gated ion channels reside in the membranes of nerve and muscle cells . These proteins form channels that span the membrane , where they transduce chemical signals into changes in electrical excitability . Neurotransmitters bind to the extracellular surface of these proteins to trigger global structural rearrange...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Site-Directed Spin Labeling Reveals Pentameric Ligand-Gated Ion Channel Gating Motions
To cause infections microbes need to evade host defense systems , one of these being the evolutionarily old and important arm of innate immunity , the alternative pathway of complement . It can attack all kinds of targets and is tightly controlled in plasma and on host cells by plasma complement regulator factor H ( FH...	Complement is an important arm of innate immunity . Activation of this plasma protein cascade leads to opsonization of targets for phagocytosis , direct lysis of Gram-negative bacteria , and enhancement of the inflammatory and acquired immune responses . No specific signal is needed for activation of the alternative pa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "complement", "system", "immunology", "microbiology", "host-pathogen", "interaction", "immune", "defense", "bacterial", "pathogens", "mycology", "medical", "microbiology", "microbial", "pathogens", "biology", "yeast", "immune", "system", "immunity", "innate", "immunity" ]	2013	Microbes Bind Complement Inhibitor Factor H via a Common Site
Assess the feasibility of engaging youth to disseminate accurate information about gene by environmental ( GxE ) influences on podoconiosis , a neglected tropical lymphedema endemic in southern Ethiopia . A cross sectional survey was conducted with 377 youth randomly selected from 2 districts of Southern Ethiopia . Mea...	This study considers the feasibility of engaging rural Ethiopian youth as lay health workers ( LHWs ) with the objective to improve community understanding of the joint influences of genetics and environment on health . Identifying LHWs to accurately convey contributors to the heritable but preventable neglected tropic...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "education", "behavioral", "and", "social", "aspects", "of", "health", "engineering", "and", "technology", "sociology", "tropical", "diseases", "social", "sciences", "neuroscience", "parasitic", "diseases", "health", "care", "a...	2018	Rural youths' understanding of gene x environmental contributors to heritable health conditions: The case of podoconiosis in Ethiopia
Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation . In this paper , a panel of 24 breast cell lines was grown in 3D culture , their morphology was imaged through phase contrast microscopy , and computational methods were developed to segment and represe...	Cell culture models are an important vehicle for understanding biological processes and evaluation of therapeutic reagents . More importantly , the literature suggests that tumor cells grown in 3D exhibit pronounced drug and radiation resistances that are remarkably similar to that of tumors in vivo . Therefore , the n...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "biology/bioinformatics", "cell", "biology/cell", "growth", "and", "division", "computational", "biology/synthetic", "biology", "computer", "science" ]	2010	Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture
Previous modeling studies have identified the vaccination coverage level necessary for preventing influenza epidemics , but have not shown whether this critical coverage can be reached . Here we use computational modeling to determine , for the first time , whether the critical coverage for influenza can be achieved by...	Currently , a major public health concern is the next influenza pandemic; yet it remains unclear how to control such a crisis . By using novel mathematical modeling techniques , here we predict the likely impact of voluntary vaccination programs on controlling influenza epidemics and pandemics . We construct an individ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "none", "infectious", "diseases", "public", "health", "and", "epidemiology", "computational", "biology" ]	2007	Can Influenza Epidemics Be Prevented by Voluntary Vaccination?
Subcellular compartmentation of the ubiquitous second messenger cAMP has been widely proposed as a mechanism to explain unique receptor-dependent functional responses . How exactly compartmentation is achieved , however , has remained a mystery for more than 40 years . In this study , we developed computational and mat...	Subcellular compartmentation of the ubiquitous second messenger cAMP has been widely proposed as a mechanism to explain how this one signaling molecule produces unique receptor-dependent functional responses . But , how exactly compartmentation occurs , is unknown . This is because there has been no way to measure the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "muscle", "tissue", "enzymes", "enzymology", "simulation", "and", "modeling", "camp", "signaling", "cascade", "lyases", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "animal", "cells",...	2016	A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation
Nature has shaped the make up of proteins since their appearance , 3 . 8 billion years ago . However , the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated . Here we explore if protein evolution affects folding speed . We estimated folding times ...	Nature has come up with an enormous variety of protein three-dimensional structures , each of which is thought to be optimized for its specific function . A fundamental biological endeavor is to uncover the driving evolutionary forces for discovering and optimizing new folds . A long-standing hypothesis is that fold ev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "protein", "folding", "evolutionary", "modeling", "biology", "computational", "biology", "evolutionary", "selection", "biophysics", "evolutionary", "processes" ]	2013	Evolutionary Optimization of Protein Folding
DEAD-box helicase proteins accelerate folding and rearrangements of highly structured RNAs and RNA–protein complexes ( RNPs ) in many essential cellular processes . Although DEAD-box proteins have been shown to use ATP to unwind short RNA helices , it is not known how they disrupt RNA tertiary structure . Here , we use...	In addition to carrying genetic information from DNA to protein , RNAs function in many essential cellular processes . This often requires the RNA to form a specific three-dimensional structure , and some functions require cycling between multiple structures . However , RNAs have a strong propensity to become trapped i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "rna", "rna", "structure", "proteins", "enzymes", "chaperone", "proteins", "biology", "and", "life", "sciences", "enzymology", "rna", "stability", "long", "non-coding", "rnas", "ribozymes" ]	2014	DEAD-Box Helicase Proteins Disrupt RNA Tertiary Structure Through Helix Capture
The dual toxicity/essentiality of copper forces cells to maintain a tightly regulated homeostasis for this metal in all living organisms , from bacteria to humans . Consequently , many genes have previously been reported to participate in copper detoxification in bacteria . Myxococcus xanthus , a prokaryote , encodes m...	Copper exerts a dual effect on living organisms . It is essential for life , but an excess provokes cell damage , forcing cells to maintain a regulated homeostasis for this metal . These two antagonistic biological effects of copper are clearly illustrated by two human genetic disorders , Menkes syndrome and Wilson dis...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "cellular", "stress", "responses", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "microbiology", "dna", "transcription", "gene", "function", "prokaryotic", "models", "model", "organisms", "molecular", "genetics", "applied", "microbiology", "co...	2011	CorE from Myxococcus xanthus Is a Copper-Dependent RNA Polymerase Sigma Factor
Successful perception depends on combining sensory input with prior knowledge . However , the underlying mechanism by which these two sources of information are combined is unknown . In speech perception , as in other domains , two functionally distinct coding schemes have been proposed for how expectations influence r...	Perception inevitably depends on combining sensory input with prior expectations . This is particularly critical for identifying degraded input . However , the underlying neural mechanism by which expectations influence sensory processing is unclear . Predictive Coding theories suggest that the brain passes forward the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "syllables", "linguistics", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "engineering", "and", "technology", "signal", "processing", "social", "sciences", "neuroscience", "magnetic", "resonance", "im...	2016	Prediction Errors but Not Sharpened Signals Simulate Multivoxel fMRI Patterns during Speech Perception
Candida albicans has an elaborate , yet efficient , mating system that promotes conjugation between diploid a and α strains . The product of mating is a tetraploid a/α cell that must undergo a reductional division to return to the diploid state . Despite the presence of several “meiosis-specific” genes in the C . albic...	Candida albicans is an important human fungal pathogen that has an unconventional sexual cycle . Efficient mating requires that diploid cells of opposite mating type first switch from the more common “white” phase to the “opaque” phase and then undergo cell fusion . The resulting tetraploid strains can return to the di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "microbiology", "genetics", "and", "genomics" ]	2008	The Parasexual Cycle in Candida albicans Provides an Alternative Pathway to Meiosis for the Formation of Recombinant Strains
Natural populations often grow , shrink , and migrate over time . Such demographic processes can affect genome-wide levels of genetic diversity . Additionally , genetic variation in functional regions of the genome can be altered by natural selection , which drives adaptive mutations to higher frequencies or purges del...	Patterns of genetic diversity within a species are affected at broad and fine scales by population size changes ( “demography” ) and natural selection . From both population genetics theory and observation on genomic sequence data , it is known that demography can alter genome-wide average neutral genetic diversity . A...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "ecology", "and", "environmental", "sciences", "population", "genetics", "geographical", "locations", "human", "genomics", "invertebrate", "genomics", "simulation", "and", "modeling", "dna", "population", "biology", "research", "and", "analysis", "methods", "europe", "e...	2018	Human demographic history has amplified the effects of background selection across the genome
T cell receptors ( TCRs ) are key to antigen-specific immunity and are increasingly being explored as therapeutics , most visibly in cancer immunotherapy . As TCRs typically possess only low-to-moderate affinity for their peptide/MHC ( pMHC ) ligands , there is a recognized need to develop affinity-enhanced TCR variant...	T cell receptors ( TCRs ) play a major role in immunity , recognizing peptide antigens presented by major histocompatibility complex proteins . Due to their capacity to target intracellularly produced proteins and initiate cell killing , there is significant interest developing TCR-based therapeutic strategies , partic...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "immune", "system", "proteins", "biochemistry", "protein", "interactions", "proteins", "protein", "structure", "biology", "computational", "biology", "proteomics", "protein", "engineering", "macromolecular", "structure", "analysis" ]	2014	Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor
The Ewing sarcoma family of tumors ( EFT ) is a group of highly malignant small round blue cell tumors occurring in children and young adults . We report here the largest genomic survey to date of 101 EFT ( 65 tumors and 36 cell lines ) . Using a combination of whole genome sequencing and targeted sequencing approaches...	The Ewing sarcoma family of tumors is a group of aggressive cancers that primarily affects the pediatric and young adult population . Increasingly , genomics are being used to better define the disease biology and to identify targets for therapy in many cancer types . Here , we report one of the first and largest genom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "and", "health", "sciences", "cancer", "genetics", "ewing", "sarcoma", "genetics", "biology", "and", "life", "sciences", "cancers", "and", "neoplasms", "sarcomas" ]	2014	The Genomic Landscape of the Ewing Sarcoma Family of Tumors Reveals Recurrent STAG2 Mutation
The tempo and mode of human knowledge expansion is an enduring yet poorly understood topic . Through a temporal network analysis of three decades of discoveries of protein interactions and genetic interactions in baker's yeast , we show that the growth of scientific knowledge is exponential over time and that important...	It is of great interest to understand the patterns and mechanisms of scientific knowledge growth , but such studies have been hampered by the lack of ideal cases in which the structure of the knowledge is known , the knowledge is quantifiable , and the process of knowledge discovery is well understood and documented . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/literature", "analysis", "computational", "biology/genomics" ]	2009	On the Growth of Scientific Knowledge: Yeast Biology as a Case Study
Analyses of stool from patients with acute watery diarrhea ( AWD ) using sensitive molecular diagnostics have challenged whether fecal microbiological cultures have acceptably high sensitivity for cholera diagnosis . If true , these findings imply that current estimates of the global burden of cholera , which rely larg...	Conventional microbiological culture has remained a relatively uncontested ‘gold standard’ for the diagnosis of cholera; however , emerging methods , including sensitive molecular tests , challenge the current paradigm . One pivotal article demonstrated that culture failed to detect cholera in one-third of the cholera-...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "microbial", "cultures", "pathogens", "vibrio", "biological", "cultures", "tropical", "diseases", "microbiology", "geographical", "locations", "vaccines", "diarrhea", "bacterial", "dise...	2019	Use of oral cholera vaccine as a vaccine probe to determine the burden of culture-negative cholera
Weather factors are widely studied for their effects on indicating dengue incidence trends . However , these studies have been limited due to the complex epidemiology of dengue , which involves dynamic interplay of multiple factors such as herd immunity within a population , distinct serotypes of the virus , environmen...	As dengue virus transmission is through a human-to-mosquito-to-human cycle , the influence of meteorological factors on dengue is likely to be associated with their impact on mosquito populations and behavior . Other than the influence of weather factors , the shift of dominant serotypes and pre-emptive measures taken ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "epidemiology", "biology", "and", "life", "sciences", "population", "biology" ]	2014	Statistical Modeling Reveals the Effect of Absolute Humidity on Dengue in Singapore
The genome of the fission yeast Schizosaccharomyces pombe encodes 17 kinases that are essential for cell growth . These include the cell-cycle regulator Cdc2 , as well as several kinases that coordinate cell growth , polarity , and morphogenesis during the cell cycle . In this study , we further characterized another o...	Prp4 is an essential protein kinase that is involved in the splicing of some introns . Using a conditional mutant of Prp4 , we showed that a subset of genes , including several cell cycle–regulatory genes , are dependent on Prp4 for splicing . Furthermore , we could convert genes between Prp4-dependent and -independent...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Prp4 Kinase Grants the License to Splice: Control of Weak Splice Sites during Spliceosome Activation
Low-frequency sound localization depends on the neural computation of interaural time differences ( ITD ) and relies on neurons in the auditory brain stem that integrate synaptic inputs delivered by the ipsi- and contralateral auditory pathways that start at the two ears . The first auditory neurons that respond select...	Animals can locate the source of a sound by detecting microsecond differences in the arrival time of sound at the two ears . Neurons encoding these interaural time differences ( ITDs ) receive an excitatory synaptic input from each ear . They can perform a microsecond computation with excitatory synapses that have mill...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience", "computational", "biology/systems", "biology" ]	2010	Asymmetric Excitatory Synaptic Dynamics Underlie Interaural Time Difference Processing in the Auditory System
Accumulated research has demonstrated the beneficial effects of dietary restriction on extending lifespan and increasing cellular stress resistance . However , reducing nutrient intake has also been shown to direct animal behaviors toward food acquisition . Under food-limiting conditions , behavioral changes suggest th...	We investigated the mechanisms used during dietary stress conditions that regulate the behavioral output of excitable cells . In the roundworm Caenorhabditis elegans , males must display the proper behavioral response to potential food sources or mating partners . This regulation is disrupted by loss of ERG-like K+ cha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "caenorhabditis", "neuroscience" ]	2007	Food Deprivation Attenuates Seizures through CaMKII and EAG K+ Channels
The ‘communication through coherence’ ( CTC ) hypothesis proposes that selective communication among neural networks is achieved by coherence between firing rate oscillation in a sending region and gain modulation in a receiving region . Although this hypothesis has stimulated extensive work , it remains unclear whethe...	Distributed regions of mammalian brains transiently engage in coherent oscillations , often at specific stages of behavioral or cognitive tasks . This activity may play a role in controlling information flow among connected regions , allowing the brain's connectivity structure to be flexibly reconfigured in response to...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "circuit", "models", "computational", "neuroscience", "biology", "neuroscience", "coding", "mechanisms" ]	2012	Efficient “Communication through Coherence” Requires Oscillations Structured to Minimize Interference between Signals
Sensory hair cells are essential for hearing and balance . Their development from epithelial precursors has been extensively characterized with respect to transcriptional regulation , but not in terms of posttranscriptional influences . Here we report on the identification and functional characterization of an alternat...	The identification of novel deafness-causing mutations has been instrumental in revealing unexpected mechanisms that are required for development of the sound- and gravity-sensing hair cells of the inner ear . The Bronx waltzer ( bv ) mouse is characterized by defects in hair-cell development , as well as by deafness a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "auditory", "system", "developmental", "biology", "gene", "identification", "and", "analysis", "genetics", "molecular", "genetics", "biology", "sensory", "systems", "neuroscience", "genetics", "and", "genomics", "cell", "differentiation", "gene", "function" ]	2012	A Mutation in the Srrm4 Gene Causes Alternative Splicing Defects and Deafness in the Bronx Waltzer Mouse
Viruses have evolved several strategies to modify cellular processes and evade the immune response in order to successfully infect , replicate , and persist in the host . By utilizing in-silico testing of a transmembrane sequence library derived from virus protein sequences , we have pin-pointed a nine amino-acid motif...	HIV uses several mechanisms that allow it to evade immune control , in order to successfully infect , replicate , and persist in the host . Here we report a new mechanism . We utilized bioinformatics and identified a region within the transmembrane domain ( TMD ) of the envelop proteins of viruses that has high similar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "immunology/immune", "response", "microbiology/immunity", "to", "infections" ]	2010	HIV-1 gp41 and TCRα Trans-Membrane Domains Share a Motif Exploited by the HIV Virus to Modulate T-Cell Proliferation
Ethosuximide is a medication used to treat seizure disorders in humans , and we previously demonstrated that ethosuximide can delay age-related changes and extend the lifespan of the nematode Caenorhabditis elegans . The mechanism of action of ethosuximide in lifespan extension is unknown , and elucidating how ethosuxi...	Aging is a major factor that contributes to disease and disability in humans , but no medicines have been demonstrated to delay human aging . We previously conducted a screen for FDA-approved drugs that can extend the lifespan of the nematode worm C . elegans , resulting in the identification of ethosuximide , a medici...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "developmental", "biology/aging" ]	2008	The Anticonvulsant Ethosuximide Disrupts Sensory Function to Extend C. elegans Lifespan
Infections of Echinococcus granulosus sensu stricto ( s . s ) , E . multilocularis and E . shiquicus are commonly found co-endemic on the Qinghai-Tibet plateau , China , and an efficient tool is needed to facilitate the detection of infected hosts and for species identification . A single-tube multiplex PCR assay was e...	The canid adapted intestinal tapeworms , Echinococcus granulosus , E . multilocularis and E . shuiqucus are well known to be endemic in Northwestern China . The first two species can cause fatal disease in humans . Although E . shiquicus has not been reported to infect humans , all three species can be transmitted by d...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Discrimination between E. granulosus sensu stricto, E. multilocularis and E. shiquicus Using a Multiplex PCR Assay
Tonotopy is a fundamental organizational feature of the auditory system . Sounds are encoded by the spatial and temporal patterns of electrical activity in spiral ganglion neurons ( SGNs ) and are transmitted via tonotopically ordered processes from the cochlea through the eighth nerve to the cochlear nuclei . Upon rea...	Millions of people suffer from debilitating hearing defects , ranging from a complete inability to detect sound to more subtle changes in how sounds are encoded by the nervous system . Many forms of deafness are due to mutations in genes that impair the development or function of hair cells , which are responsible for ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "auditory", "system", "developmental", "neuroscience", "biology", "and", "life", "sciences", "sensory", "systems", "neuroscience", "neural", "circuit", "formation" ]	2014	Mutation of Npr2 Leads to Blurred Tonotopic Organization of Central Auditory Circuits in Mice
A first line of defense against pathogen attack for both plants and animals involves the detection of microbe-associated molecular patterns ( MAMPs ) , followed by the induction of a complex immune response . Plants , like animals , encode several receptors that recognize different MAMPs . While these receptors are tho...	Specialized receptors encoded by plants detect different components of bacterial machinery , and initiate an immune response . These recognition events are thought to induce largely redundant defense signaling , the magnitude of which varies quantitatively among populations , perhaps in response to environment specific...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "variant", "genotypes", "brassica", "microbiology", "plant", "physiology", "genetic", "mapping", "plant", "science"...	2016	Differentiation between MAMP Triggered Defenses in Arabidopsis thaliana
To assess the prevalence of HTLV-1 and HTLV-2 infections in a cohort of immigrants living in southern Italy . We screened for antibody to HTLV-1/2 infection 1 , 498 consecutive immigrants born in endemic areas ( sub-Saharan Africa or southern-Asia ) by a commercial chemiluminescent microparticle immunoassay . If confir...	As in Italy the immigrants constitute one tenth of the whole population and its contribution to blood donation is strongly desired we believe that to start screening for HTLV-1 and HTLV-2 infections in all donors from endemic countries at least on their first donation is a practice useful for a correct cost-effectivene...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "european", "union", "cost-effectiveness", "analysis", "economic", "analysis", "pathogens", "blood", "counts", "geographical", "locations", "microbiology", "social", ...	2018	Low prevalence of HTLV1/2 infection in a population of immigrants living in southern Italy
Dengue has propagated widely through the Americas . Most countries have not been able to maintain permanent larval mosquito control programs , and the long-term effects of control actions have rarely been documented . The study design was based on a before-and-after citywide assessment of Aedes aegypti larval indices a...	Dengue has become the most important viral disease of humans transmitted by arthropods in tropical and subtropical urban regions . Most countries have not been able to maintain permanent larval mosquito control programs against Aedes aegypti , the main vector of dengue and yellow fever , partly because of misguided rel...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/viral", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "ecology/population", "ecology", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", ...	2009	Effects of a Five-Year Citywide Intervention Program To Control Aedes aegypti and Prevent Dengue Outbreaks in Northern Argentina
When Drosophila melanogaster embryos initiate zygotic transcription around mitotic cycle 10 , the dose-sensitive expression of specialized genes on the X chromosome triggers a sex-determination cascade that , among other things , compensates for differences in sex chromosome dose by hypertranscribing the single X chrom...	Variation in gene dose can have profound effects on animal development . Yet every generation , animals must cope with differences in sex chromosome numbers . Drosophila compensate for the difference in X chromosome dosage ( two in females , one in males ) with a mechanism that allows for more transcription of the sing...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "developmental", "biology/embryology", "genetics", "and", "genomics/gene", "expression", "developmental", "biology/pattern", "formation", "genetics", "and", "genomics/chromosome", "biology", "developmental", "biology/developmental", "molecu...	2011	Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq
Cone-rod homeobox ( CRX ) protein is a “paired-like” homeodomain transcription factor that is essential for regulating rod and cone photoreceptor transcription . Mutations in human CRX are associated with the dominant retinopathies Retinitis Pigmentosa ( RP ) , Cone-Rod Dystrophy ( CoRD ) and Leber Congenital Amaurosis...	The transcription factor Cone-Rod Homeobox ( CRX ) plays a central role in regulating gene expression of rod and cone photoreceptors , the primary light sensing cells of the retina . Mutations in the human CRX gene have been associated with the retinal degeneration diseases Retinitis Pigmentosa ( RP ) , Cone-Rod Dystro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "genome", "expression", "analysis", "neurobiology", "of", "disease", "and", "regeneration", "animal", "genetics", "genetic", "mutation", "gene", "regulation", "neuroscience", "dna", "transcription", "gene", "function", "animal", "models", "retinal", "disorde...	2014	Mechanistically Distinct Mouse Models for CRX-Associated Retinopathy
SARS-coronavirus ( CoV ) is a zoonotic agent derived from rhinolophid bats , in which a plethora of SARS-related , conspecific viral lineages exist . Whereas the variability of virulence among reservoir-borne viruses is unknown , it is generally assumed that the emergence of epidemic viruses from animal reservoirs requ...	Novel detection and sequencing technologies have greatly improved our knowledge of virus diversity in nature . Metaviromic screening of zoonotic animal reservoirs has become an established approach in pathogen surveillance and pandemic preparedness research . However , knowledge of viral genomes and host-associated vir...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "vero", "cells", "medicine", "and", "health", "sciences", "coronaviruses", "luciferase", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "sars", "coronavirus", "biological", "cultures", "microbiology", "enzymology", "viruses", "rna", "viruses", "re...	2018	The papain-like protease determines a virulence trait that varies among members of the SARS-coronavirus species
Pituitary endocrine cells fire action potentials ( APs ) to regulate their cytosolic Ca2+ concentration and hormone secretion rate . Depending on animal species , cell type , and biological conditions , pituitary APs are generated either by TTX-sensitive Na+ currents ( INa ) , high-voltage activated Ca2+ currents ( ICa...	Excitable cells elicit electrical pulses called action potentials ( APs ) , which are generated and shaped by a combination of ion channels in the cell membrane . Since one type of ion channels is permeable to Ca2+ ions , there is typically an influx of Ca2+ during an AP . Pituitary cells therefore use AP firing to reg...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "fish", "goldfish", "nervous", "system", "membrane", "potential", "vertebrates", "electrophysiology", "neuroscience", "animals", "simulation", "and", "modeling", "osteichthyes", "animal", "models", "ion", ...	2019	A computational model for gonadotropin releasing cells in the teleost fish medaka
Cutaneous leishmaniasis ( CL ) is treated with parenteral drugs for decades with decreasing rate cures . Miltefosine is an oral medication with anti-leishmania activity and may increase the cure rates and improve compliance . This study is a randomized , open-label , controlled clinical trial aimed to evaluate the effi...	Cutaneous leishmaniasis ( CL ) is characterized by skin ulcerations and occurs in rural poor areas of developing countries . It is treated with daily injections of antimony for 20 days , which is associated with irregular use and increasingly lower cure rates . Miltefosine is an oral medication with activity against th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/skin", "infections", "dermatology/skin", "infections" ]	2010	Miltefosine in the Treatment of Cutaneous Leishmaniasis Caused by Leishmania braziliensis in Brazil: A Randomized and Controlled Trial
North America is currently home to a number of grey wolf ( Canis lupus ) and wolf-like canid populations , including the coyote ( Canis latrans ) and the taxonomically controversial red , Eastern timber and Great Lakes wolves . We explored their population structure and regional gene flow using a dataset of 40 full gen...	Full genome sequencing is becoming an increasingly valuable tool for both the management of animal populations , as well as fundamental to improving our understanding of their evolutionary history . The grey wolf ( Canis lupus ) is a keystone species in North America whose population structure and admixture has yet to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "timber", "infographics", "taxonomy", "ecology", "and", "environmental", "sciences", "plant", "products", "wolves", "vertebrates", "animals", "mammals", "ethnicities", "phylogenetics", "data", "management", "aquatic", "environments", "phylogenetic", "analysis", "bodies", ...	2018	Population genomics of grey wolves and wolf-like canids in North America
Messenger RNA ( mRNA ) synthesis and export are tightly linked , but the molecular mechanisms of this coupling are largely unknown . In Saccharomyces cerevisiae , the conserved TREX complex couples transcription to mRNA export and mediates mRNP formation . Here , we show that TREX is recruited to the transcription mach...	Gene expression is a fundamental cellular process that translates the information stored in the DNA into proteins , the workhorses of the cell . Eukaryotic cells contain a nucleus , where the genetic information is stored and transcribed by RNA polymerase II into messenger ( m ) RNAs . These copies of the blueprint of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Recruitment of TREX to the Transcription Machinery by Its Direct Binding to the Phospho-CTD of RNA Polymerase II
Across the nervous system , certain population spiking patterns are observed far more frequently than others . A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell . We investigate this p...	Neurons in most parts of the nervous system represent and process information in a collective fashion , yet the nature of this collective code is poorly understood . An important constraint placed on any such collective processing comes from the fact that individual neurons’ signaling is prone to corruption by noise . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "markov", "models", "membrane", "potential", "ocular", "anatomy", "electrophysiology", "neuroscience", "probability", "distribution", "mathematics", "ganglion", "cells", "thermodynamics", "entropy", "animal", ...	2016	Error-Robust Modes of the Retinal Population Code
Spores are an essential cell type required for long-term survival across diverse organisms in the tree of life and are a hallmark of fungal reproduction , persistence , and dispersal . Among human fungal pathogens , spores are presumed infectious particles , but relatively little is known about this robust cell type . ...	Spores are a critical cell type that allow long-term survival of diverse organisms from bacteria to fungi to plants . Among fungi , spores are often formed when growth conditions are poor; spores can then disperse to more favorable environments and reinitiate growth . Spores of some environmental fungi can cause fatal ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Protein Composition of Infectious Spores Reveals Novel Sexual Development and Germination Factors in Cryptococcus
Aedes albopictus is a vector of increasing public health concern due to its rapid global range expansion and ability to transmit Dengue virus , Chikungunya virus and a wide range of additional arboviruses . Traditional vector control strategies have been largely ineffective against Ae . albopictus and novel approaches ...	The mosquito , Aedes albopictus , is an aggressive human biter capable of transmitting Dengue virus , Chikungunya virus and at least 22 additional viruses that cause human illness . Over the last 30 years , this mosquito has spread from its native Asian range to all continents except Antarctica . Efforts to control thi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Global Transcriptional Dynamics of Diapause Induction in Non-Blood-Fed and Blood-Fed Aedes albopictus
We have established two mouse models of central nervous system ( CNS ) demyelination that differ from most other available models of multiple sclerosis ( MS ) in that they represent a mixture of viral and immune triggers . In the first model , ocular infection of different strains of mice with a recombinant HSV-1 that ...	Several mouse models of multiple sclerosis ( MS ) are now available . We have established two new mouse models . In the first model , ocular infection of different strains of mice with HSV-IL-2 recombinant virus causes CNS demyelination . In the second model , CNS demyelination was induced by different strains of wild ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "multiple", "sclerosis", "nervous", "system", "neurodegenerative", "diseases", "immunology", "neuroscience", "demyelinating", "disorders", "clinical", "medicine", "optic", "nerve", "eye", "dis...	2017	Suppression of IL-12p70 formation by IL-2 or following macrophage depletion causes T-cell autoreactivity leading to CNS demyelination in HSV-1-infected mice
Alveolar echinococcosis ( AE ) is a lethal zoonosis caused by the metacestode larva of the tapeworm Echinococcus multilocularis . The infection is characterized by tumour-like growth of the metacestode within the host liver , leading to extensive fibrosis and organ-failure . The molecular mechanisms of parasite organ t...	To ensure proper communication between their different cell populations , animals rely on secreted hormones and cytokines that act on receptors of target cells . Most of the respective cytokines , such as FGFs , evolved over 500 million years ago and are present in similar form in all animals , including parasitic worm...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "vesicles", "electrochemical", "cells", "helminths", "parasite", "evolution", "vertebrates", "parasitic", "diseases", "animals", "echinococcus", "parasitology", "xenopus", "endocrine", "physiology", "animal", "models...	2019	The role of fibroblast growth factor signalling in Echinococcus multilocularis development and host-parasite interaction
Crimean-Congo haemorrhagic fever virus ( CCHFV ) is a member of the Orthonairovirus genus of the Nairoviridae family and is associated with haemorrhagic fever in humans . Although T lymphocyte responses are known to play a role in protection from and clearance of viral infections , specific T cell epitopes have yet to ...	Crimean-Congo haemorrhagic fever virus ( CCHFV ) is a tick-borne virus that causes haemorrhagic fever with fatalities in humans . Clinical disease has been described in Africa , Asia , Eastern Europe , the Middle East , Turkey and more recently Greece , India and Spain . In the absence of specific anti-virals and vacci...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "sequencing", "techniques", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "immune", "physiology", "immunology", "vaccines", "nucleoproteins", "protein", "sequencing", "cytotoxic", "t", "cells", "molecular", ...	2017	Long-lived CD8+ T cell responses following Crimean-Congo haemorrhagic fever virus infection
Pathogenic Leptospira transmits from animals to humans , causing the zoonotic life-threatening infection called leptospirosis . This infection is reported worldwide with higher risk in tropical regions . Symptoms of leptospirosis range from mild illness to severe illness such as liver damage , kidney failure , respirat...	Pathogenic Leptospira causes the life-threatening infection called leptospirosis worldwide . Symptoms of leptospirosis range from mild illness to severe illness such as organ damage , meningitis , and fatal hemorrhagic disease . Invasive species of Leptospira spread to multiple tissues , and damage the linings of blood...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "physiology", "cell", "motility", "medicine", "and", "health", "sciences", "leptospira", "actin", "filaments", "pathology", "and", "laboratory", "medicine", "pathogens", "endothelial", "cells", "microbiology", "junctional", "complexes", "epithelial", "cells", "t...	2017	Leptospira interrogans causes quantitative and morphological disturbances in adherens junctions and other biological groups of proteins in human endothelial cells
Integration and down-regulation of cell growth and differentiation signals rely on plasma membrane receptor endocytosis and sorting towards either recycling vesicles or degradative lysosomes via multivesicular bodies ( MVB ) . In this process , the endosomal sorting complex-III required for transport ( ESCRT-III ) cont...	In multicellular organisms , the interpretation and transmission of cell growth and differentiation signals strongly rely on plasma membrane receptors . Once activated by their ligands , these receptors activate downstream signaling cascades and are rapidly internalized into intracellular vesicles that fuse inside the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "chemical", "compounds", "hela", "cells", "molecular", "probe", "techniques", "biological", "cultures", "immunoblotting", "organic", "compounds", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "immunoprecipitation", "mate...	2018	CHMP1B is a target of USP8/UBPY regulated by ubiquitin during endocytosis
Proper development of the immune system is an intricate process dependent on many factors , including an intact DNA damage response . The DNA double-strand break signaling kinase ATM and its cofactor NBS1 are required during T cell development and for the maintenance of genomic stability . The role of a second ATM cofa...	Defects in DNA repair pathways can lead to pathogenesis within the immune system , an example of which is inflammatory bowel disease ( IBD ) . Yet the underlying genetic causes of IBD are often unclear . The DNA repair kinase ATM is crucial for the proper development and function of the immune system . ATM is regulated...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	DNA Repair Cofactors ATMIN and NBS1 Are Required to Suppress T Cell Activation
Heme-iron recycling from senescent red blood cells ( erythrophagocytosis ) accounts for the majority of total body iron in humans . Studies in cultured cells have ascribed a role for HRG1/SLC48A1 in heme-iron transport but the in vivo function of this heme transporter is unclear . Here we present genetic evidence in a ...	Total body iron stores in mammals is a composite of iron absorption from diet and iron recycled by macrophages from dying red blood cells ( RBCs ) . Upon erythrophagocytosis of RBCs , the hemoglobin is degraded and heme is imported from the phagosomal compartment into the cytoplasm so that the iron can be released from...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "heme", "fish", "medicine", "and", "health", "sciences", "immune", "physiology", "immune", "cells", "spleen", "immunology", "rna", "extraction", "vertebrates", "animals", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organ...	2018	Hrg1 promotes heme-iron recycling during hemolysis in the zebrafish kidney
Control and prevention of Chagas disease rely mostly on residual spraying of insecticides . In Argentina , vector control shifted from a vertical to a fully horizontal strategy based on community participation between 1992 and 2004 . The effects of such strategy on Triatoma infestans , the main domestic vector , and on...	Despite decreasing rates of prevalence and incidence , Chagas disease remains a serious problem in Latin America , especially for the rural poor . Without vaccines , control and prevention rely mostly on residual spraying of insecticides . Under the aegis of the Southern Cone Initiative , and in agreement with global t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/infectious", "diseases", "public", "health", "and", "epidemiology", "public", "health", "and", "epidemiology/health", "policy" ]	2009	Cost-Effectiveness of Chagas Disease Vector Control Strategies in Northwestern Argentina
Early identification of adverse effect of preclinical and commercial drugs is crucial in developing highly efficient therapeutics , since unexpected adverse drug effects account for one-third of all drug failures in drug development . To correlate protein–drug interactions at the molecule level with their clinical outc...	Early identification of the side effects of preclinical and commercial drugs is crucial in developing highly efficient therapeutics , as unexpected side effects account for one-third of all drug failures in drug development and lead to drugs being withdrawn from the market . Compared with the experimental identificatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Supporting", "Information" ]	[ "biotechnology", "oncology", "computational", "biology", "biophysics", "homo", "(human)" ]	2007	In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators
In female fruit flies , Sex-lethal ( Sxl ) turns off the X chromosome dosage compensation system by a mechanism involving a combination of alternative splicing and translational repression of the male specific lethal-2 ( msl-2 ) mRNA . A genetic screen identified the translation initiation factor eif4e as a gene that a...	Gene expression in eukaryotes is a complex process that occurs in several discrete steps . Some of those steps are separated into different sub-cellular compartments and thus might be expected to occur independently of one another and involve entirely distinct factors . For example pre-mRNA splicing takes place in the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2011	The Translation Initiation Factor eIF4E Regulates the Sex-Specific Expression of the Master Switch Gene Sxl in Drosophila melanogaster
We have established that HCMV acts as a specific ligand engaging and activating cellular integrins on monocytes . As a result , integrin signaling via Src activation leads to the functional activation of paxillin required for efficient viral entry and for the biological changes in monocytes needed for viral disseminati...	We previously demonstrated that HCMV , by engaging cellular receptors , changes the biology of blood monocytes , allowing for efficient viral entry into these cells and their use as virus-carriers in HCMV systemic spread . However , it was unclear how HCMV induces receptor-mediated signaling in infected cells . Here we...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2013	The HCMV gH/gL/UL128-131 Complex Triggers the Specific Cellular Activation Required for Efficient Viral Internalization into Target Monocytes
Allotetraploid cotton species are a vital source of spinnable fiber for textiles . The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes . We describe the evolution of the cotton genome ( SNPs and structural variants ) with the greatly improved r...	The polyploid genome of domesticated cotton contains two different copies of most genes because its genome is duplicated . Instead of 13 chromosomes like its wild relatives , domesticated cotton has 26 chromosomes ( 13 AT chromosomes and 13 DT chromosomes ) . Differences in the gene copies may hold keys to the genetic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "genome", "evolution", "plant", "products", "computational", "biology", "departures", "from", "diploidy", "sequence", "assembly", "tools", "plant", "science", "tetraploidy", "fiber", "crops", "phylogenetic", "analysis", "genome", "analysis", "crops", "p...	2016	DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton
Myocardium damage during Chagas' disease results from the immunological imbalance between pro- and production of anti-inflammatory cytokines and has been explained based on the Th1–Th2 dichotomy and regulatory T cell activity . Recently , we demonstrated that IL-17 produced during experimental T . cruzi infection regul...	Dilated cardiomyopathy is one of the clinical forms of Chagas' disease ( CD ) after the infection caused by the parasite Trypanosoma cruzi . Even though strategies adopted in most Latin-American countries in the last decades towards vector control have been effective in reducing the incidence of CD , active transmissio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "cardiomyopathies", "immune", "cells", "cytokines", "immunity", "to", "infections", "immunology", "parasitic", "diseases", "cardiovascular", "neglected", "tropical", "diseases", "immunoregulation", "infectious", "diseases", "t", "cells", "immune", "response", ...	2012	Deficient Regulatory T Cell Activity and Low Frequency of IL-17-Producing T Cells Correlate with the Extent of Cardiomyopathy in Human Chagas' Disease
DNA replication is fundamental for life , yet a detailed understanding of bacterial DNA replication is limited outside the organisms Escherichia coli and Bacillus subtilis . Many bacteria , including mycobacteria , encode no identified homologs of helicase loaders or regulators of the initiator protein DnaA , despite t...	DNA is the molecule that encodes all of the genetic information of an organism . In order to pass genes onto the next generation , DNA has to first be copied through a process called DNA replication . Most of the initial studies on bacterial DNA replication were performed in Escherichia coli and Bacillus subtilis . Whi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "nuclear", "staining", "pathology", "and", "laboratory", "medicine", "enzymes", "cell", "cycle", "and", "cell", "division", "pathogens", "cell", "processes", "bacillus", "dna-binding", "proteins", "microbiology", "enzymology", ...	2017	Rv0004 is a new essential member of the mycobacterial DNA replication machinery
Plants , as sessile organisms , survive environmental changes by prioritizing their responses to the most life-threatening stress by allocating limited resources . Previous studies showed that pathogen resistance was suppressed under abiotic stresses . Here , we show the mechanism underlying this phenomenon . Phosphory...	Chemical defence inducers make plants resistant to diseases such as rice blast . However , plants sometimes become more pathogen susceptible under abiotic stresses even in their presence . Because such regulation prioritizes the responses to the most life-threatening stress , it could be necessary for plants to survive...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Abiotic Stresses Antagonize the Rice Defence Pathway through the Tyrosine-Dephosphorylation of OsMPK6
During neurogenesis , transcription factors combinatorially specify neuronal fates and then differentiate subtype identities by inducing subtype-specific gene expression profiles . But how is neuronal subtype identity maintained in mature neurons ? Modeling this question in two Drosophila neuronal subtypes ( Tv1 and Tv...	For neurons to function properly , they must establish and then maintain their unique , subtype-specific gene expression profiles . These unique gene expression profiles are established during development by networks of DNA–binding proteins , termed transcription factors ( TFs ) . However , how neurons maintain their u...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "organism", "development", "genetics", "biology", "neuroscience", "genetics", "and", "genomics" ]	2012	Developmental Transcriptional Networks Are Required to Maintain Neuronal Subtype Identity in the Mature Nervous System
Trypanosoma brucei is a master of antigenic variation and immune response evasion . Utilizing a genomic repertoire of more than 1000 Variant Surface Glycoprotein-encoding genes ( VSGs ) , T . brucei can change its protein coat by “switching” from the expression of one VSG to another . Each active VSG is monoallelically...	A broad array of human pathogens ( including bacteria , fungi and parasites ) vary the proteins on their cell surface to escape the immune response of their hosts . This process , called antigenic variation , relies on a repertoire of variant protein encoding genes in the genome and the organism's ability to accurately...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	Telomere Length Affects the Frequency and Mechanism of Antigenic Variation in Trypanosoma brucei
The increasing prevalence of multi-drug–resistant ( MDR ) strains of Pseudomonas aeruginosa among critically ill humans is of significant concern . In the current study , we show that MDR clinical isolates of P . aeruginosa representing three distinct genotypes that display high virulence against intestinal epithelial ...	The resistance of bacteria to multiple antibiotics is a major problem in critically ill patients who often become colonized by highly lethal pathogens such as Pseudomonas aeruginosa . During the course of critical illness , as many as 50% of patients' intestinal tracts become colonized with P . aeruginosa , with as man...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "gastroenterology", "and", "hepatology", "microbiology", "animals", "eubacteria" ]	2008	Structure–Function Aspects of PstS in Multi-Drug–Resistant Pseudomonas aeruginosa
During meiosis , the maternal and paternal homologous chromosomes must align along their entire length and recombine to achieve faithful segregation in the gametes . Meiotic recombination is accomplished through the formation of DNA double-strand breaks , a subset of which can mature into crossovers to link the parenta...	Sexually reproducing species rely on meiosis to transmit their genetic information across generations . Parental chromosomes ( homologues ) undergo many distinctive processes in their complex journey from attachment to segregation . The physiological induction of DNA double strand breaks is crucial for promoting correc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "meiosis", "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "gonads", "caenorhabditis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "meiotic", "prophase", "animals", "animal", "models", "dna", "damage", "caenorha...	2018	BRCA1-BARD1 associate with the synaptonemal complex and pro-crossover factors and influence RAD-51 dynamics during Caenorhabditis elegans meiosis
Plasmodium falciparum , the causative agent of the most severe form of malaria in humans invades erythrocytes using multiple ligand-receptor interactions . The P . falciparum reticulocyte binding-like homologue proteins ( PfRh or PfRBL ) are important for entry of the invasive merozoite form of the parasite into red bl...	The causative agent of the most severe form of malaria in humans is the protozoan parasite Plasmodium falciparum . These parasites are carried by a mosquito that infects humans during feeding resulting in injection of sporozoite forms that infect and develop in the liver into the merozoite stage . The merozoites are re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2011	Plasmodium falciparum Merozoite Invasion Is Inhibited by Antibodies that Target the PfRh2a and b Binding Domains
Experiments that study neural encoding of stimuli at the level of individual neurons typically choose a small set of features present in the world—contrast and luminance for vision , pitch and intensity for sound—and assemble a stimulus set that systematically varies along these dimensions . Subsequent analysis of neur...	Many neuroscience experiments begin with a set of reduced stimuli designed to vary only along a small set of variables . Yet many phenomena of interest—natural movies , objects—are not easily parameterized by a small number of dimensions . Here , we develop a novel Bayesian model for clustering stimuli based solely on ...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "markov", "models", "membrane", "potential", "vertebrates", "electrophysiology", "neuroscience", "animals", "mammals", "primates", "optimization", "systems", "science", "mathematics", "old", "world", "monkey...	2017	Neuron’s eye view: Inferring features of complex stimuli from neural responses
In nature , arthropod-borne viruses ( arboviruses ) perpetuate through alternating replication in vertebrate and invertebrate hosts . The trade-off hypothesis proposes that these viruses maintain adequate replicative fitness in two disparate hosts in exchange for superior fitness in one host . Releasing the virus from ...	Arthropod-borne viruses , including West Nile virus ( WNV ) have long been considered to be subject to a fitness “trade-off” because they must replicate in at least two taxonomically divergent hosts in order to perpetuate . Results of studies testing this trade-off hypothesis have been inconsistent and largely dependen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "veterinary", "diseases", "zoology", "epidemiology", "biology", "microbiology", "evolutionary", "biology", "population", "biology", "public", "health", "veterinary", "science" ]	2011	West Nile Virus Experimental Evolution in vivo and the Trade-off Hypothesis
Craniofacial development requires signals from epithelia to pattern skeletogenic neural crest ( NC ) cells , such as the subdivision of each pharyngeal arch into distinct dorsal ( D ) and ventral ( V ) elements . Wnt signaling has been implicated in many aspects of NC and craniofacial development , but its roles in D-V...	Craniofacial abnormalities are among the most common birth defects . Understanding the molecular mechanisms underlying craniofacial disorders is crucial for developing treatment strategies . Much of the craniofacial skeleton arises from specialized embryonic structures known as pharyngeal arches . Patterning of these a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "genetics", "biology", "and", "life", "sciences", "research", "and", "analysis", "methods" ]	2014	Wnt Signaling Interacts with Bmp and Edn1 to Regulate Dorsal-Ventral Patterning and Growth of the Craniofacial Skeleton
Phylogenies of highly genetically variable viruses such as HIV-1 are potentially informative of epidemiological dynamics . Several studies have demonstrated the presence of clusters of highly related HIV-1 sequences , particularly among recently HIV-infected individuals , which have been used to argue for a high transm...	Diversity of viral genetic sequences depends on epidemiological mechanisms and dynamics , however the exact mechanisms responsible for patterns observed in phylogenies of HIV remain poorly understood . We observe that virus taken from patients with early/acute HIV infection are more likely to be closely related . By de...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "mathematics", "effective", "population", "size", "epidemiology", "infectious", "disease", "epidemiology", "genetics", "population", "genetics", "biology", "evolutionary", "biology", "nonlinear", "dynamics", "genetics",...	2012	Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection
Previous studies have demonstrated contact irritant and spatial repellent behaviors in Aedes aegypti following exposure to sublethal concentrations of chemicals . These sublethal actions are currently being evaluated in the development of a push-pull strategy for Ae . aegypti control . This study reports on mosquito es...	Dengue virus is spread by Aedes aegypti , a mosquito that prefers to feed on humans . Chemicals used at toxic levels is currently the only confirmed effective strategy for dengue vector control , but insecticide resistance issues are threatening this approach . Other chemical actions that break vector-human contact exi...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "biology" ]	2013	Contact Irritant Responses of Aedes aegypti Using Sublethal Concentration and Focal Application of Pyrethroid Chemicals
Praziquantel ( PZQ ) is a key therapy for treatment of parasitic flatworm infections of humans and livestock , but the mechanism of action of this drug is unresolved . Resolving PZQ-engaged targets and effectors is important for identifying new druggable pathways that may yield novel antiparasitic agents . Here we use ...	The parasitic infection schistosomiasis afflicts millions of people worldwide and is clinically treated using a single drug , praziquantel ( PZQ ) . Despite the fact that PZQ has served as a stalwart anthelmintic for decades , the molecular basis of action of this clinical agent is poorly understood . This lack of mech...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Ergot Alkaloids (Re)generate New Leads as Antiparasitics
Cell-cycle progression is governed by a series of essential regulatory proteins . Two major regulators are cell-division cycle protein 20 ( CDC20 ) and its homologue , CDC20 homologue 1 ( CDH1 ) , which activate the anaphase-promoting complex/cyclosome ( APC/C ) in mitosis , and facilitate degradation of mitotic APC/C ...	Malaria parasites are single cell organisms that multiply via asexual division at different stages in the life-cycle: in the liver and red blood cells of the vertebrate host and gut of the mosquito vector . The precursor sexual stages ( male and female gametocytes ) form in red blood cells , then following ingestion in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	A Putative Homologue of CDC20/CDH1 in the Malaria Parasite Is Essential for Male Gamete Development
Translation of RNA to protein is a core process for any living organism . While for some steps of this process the effect on protein production is understood , a holistic understanding of translation still remains elusive . In silico modelling is a promising approach for elucidating the process of protein synthesis . A...	Translation , the process of synthesizing proteins from mRNA templates , is an essential biological process in all living organisms . A better understanding of this process will have ramifications in various fields—from gene regulation , disease understanding and medicine to biotechnology and synthetic biology . Noneth...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data
Trichome patterning in Arabidopsis serves as a model system to study how single cells are selected within a field of initially equivalent cells . Current models explain this pattern by an activator–inhibitor feedback loop . Here , we report that also a newly discovered mechanism is involved by which patterning is gover...	Trichomes , the specialized hair cells found on plant leaves , represent a model system to study how cellular interactions coordinate the development and arrangement of a collection of initially equivalent cells into regularly placed specialized cells . It was assumed that a regulatory feedback loop of positively and n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "developmental", "biology" ]	2008	Two-Dimensional Patterning by a Trapping/Depletion Mechanism: The Role of TTG1 and GL3 in Arabidopsis Trichome Formation
Many species have experienced dramatic changes in their abundance and distribution during recent climate change , but it is often unclear whether such ecological responses are accompanied by evolutionary change . We used targeted exon sequencing of 294 museum specimens ( 160 historic , 134 modern ) to generate independ...	Museum specimens represent an irreplaceable archive that can be used to understand how species respond to rapid environmental change . We recovered genomic data from archived samples spanning a century of climate change in co-distributed declining versus stable species of montane chipmunks . Applying novel statistical ...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Conclusions", "Methods" ]	[ "genome", "evolution", "population", "genetics", "vertebrates", "social", "sciences", "animals", "mammals", "animal", "behavior", "evolutionary", "adaptation", "population", "biology", "zoology", "genomics", "genetic", "polymorphism", "behavior", "molecular", "evolution", ...	2019	Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change
Among the different faces of immune reconstitution inflammatory syndrome ( IRIS ) developing in HIV-patients , no clinical definition has been reported for Schistosomiasis-IRIS ( Schisto-IRIS ) . Although Schisto-IRIS remains largely uninvestigated , matrix metalloproteinases ( MMP ) and tissue inhibitors of metallopro...	A subset of HIV-patients starting antiretroviral therapy are at risk of developing immune-driven worsening symptoms of a previously treated opportunistic infection . This paradoxical immune reconstitution inflammatory syndrome ( IRIS ) has been abundantly described in common co-infections such as M . tuberculosis ( TB-...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "helminths", "antiviral", "therapy", "enzymes", "immunology", "tropical", "diseases", "enzymology", "metalloproteases", "parasiti...	2018	Aberrant plasma MMP and TIMP dynamics in Schistosoma - Immune reconstitution inflammatory syndrome (IRIS)
The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence . However , less is known about the functional consequences of this encoding . Here , we address this question using a genome-wide map of ∼380 , 000 yeast nucleosomes that we sequenced in their ent...	The detailed positions of nucleosomes along genomes have critical roles in transcriptional regulation . Consequently , it is important to understand the principles that govern the organization of nucleosomes in vivo and the functional consequences of this organization . Here we report on progress in identifying the fun...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/bioinformatics", "computational", "biology/genomics", "computational", "biology/transcriptional", "regulation" ]	2008	Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
Dermal hyperpigmentation or Fibromelanosis ( FM ) is one of the few examples of skin pigmentation phenotypes in the chicken , where most other pigmentation variants influence feather color and patterning . The Silkie chicken is the most widespread and well-studied breed displaying this phenotype . The presence of the d...	The process of animal domestication has been a long and ongoing effort of the human race to cultivate beneficial traits in agriculturally productive or otherwise beneficial species . We are just now beginning to understand the effect this type of selection pressure has had on genetic variation and overall genome archit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "trait", "locus", "heredity", "gene", "expression", "genetics", "molecular", "genetics", "biology", "genomics", "structural", "genomics", "genetics", "and", "genomics" ]	2011	A Complex Genomic Rearrangement Involving the Endothelin 3 Locus Causes Dermal Hyperpigmentation in the Chicken
Mouse papillomavirus type 1 ( MmuPV1 ) provides , for the first time , the opportunity to study infection and pathogenesis of papillomaviruses in the context of laboratory mice . In this report , we define the transcriptome of MmuPV1 genome present in papillomas arising in experimentally infected mice using a combinati...	Papillomavirus ( PV ) infections lead to development of both benign warts and cancers . Because PVs are epitheliotropic and species specific , it has been extremely challenging to study PV infection in the context of a naturally occurring infection in a tractable laboratory animal . The recent discovery of the papillom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "dermatology", "medicine", "and", "health", "sciences", "otology", "ear", "infections", "genome", "analysis", "molecular", "biology", "techniques", "mammalian", "genomics", "rna", "sequencing", "research", "and", "analysis", "methods", "genom...	2017	The full transcription map of mouse papillomavirus type 1 (MmuPV1) in mouse wart tissues
The potato late blight pathogen Phytophthora infestans secretes an array of effector proteins thought to act in its hosts by disarming defences and promoting pathogen colonisation . However , little is known about the host targets of these effectors and how they are manipulated by the pathogen . This work describes the...	The plant immune system is activated following the perception of exposed , essential and invariant microbial molecules that are recognised as non-self . A major component of plant immunity is the transcriptional induction of genes involved in a wide array of defence responses . In turn , adapted pathogens deliver effec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	An RxLR Effector from Phytophthora infestans Prevents Re-localisation of Two Plant NAC Transcription Factors from the Endoplasmic Reticulum to the Nucleus
Hematopoietic stem cells ( HSCs ) balance self-renewal and differentiation to maintain homeostasis . With aging , the frequency of polar HSCs decreases . Cell polarity in HSCs is controlled by the activity of the small RhoGTPase cell division control protein 42 ( Cdc42 ) . Here we demonstrate—using a comprehensive set ...	Stem cells are unique cells that can differentiate to produce more stem cells or other types of cells and can divide both symmetrically ( to produce daughter cells with the same fate ) and asymmetrically ( to produce one daughter cell that retains stem cell potential and one that differentiates ) . The mechanisms that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "cell", "division", "analysis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "cloning", "surgical", "and", "invasive", "medical", "procedures", "cell", "polarity", "stem", "cells", ...	2018	Aging alters the epigenetic asymmetry of HSC division
Dengue fever is a virus infection that is spread by the Aedes aegypti mosquito and can cause severe disease especially in children . Dengue fever is a major problem in tropical and sub-tropical regions of the world . We invited dengue experts from around the world to attend meetings to discuss dengue surveillance . We ...	The Pediatric Dengue Vaccine Initiative organized Dengue Prevention Boards in the Asia-Pacific and the Americas regions consisting of dengue experts from endemic countries . Both Boards convened meetings to review issues in surveillance . Through presentations , facilitated discussions , and surveys , the Boards identi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology" ]	2010	Best Practices in Dengue Surveillance: A Report from the Asia-Pacific and Americas Dengue Prevention Boards
Bdelloid rotifers are a class of microscopic invertebrates that have existed for millions of years apparently without sex or meiosis . They inhabit a variety of temporary and permanent freshwater habitats globally , and many species are remarkably tolerant of desiccation . Bdelloids offer an opportunity to better under...	Bdelloid rotifers are microscopic animals that live in freshwater habitats throughout the world . Two life history characteristics distinguish these common invertebrates as extraordinary . First , they have existed for millions of years apparently without sex: males have not been reported , and females produce genetica...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Concluding", "remarks", "Materials", "and", "methods" ]	[ "horizontal", "gene", "transfer", "genome", "evolution", "invertebrate", "genomics", "sequence", "assembly", "tools", "gene", "transfer", "genome", "analysis", "genomic", "libraries", "genomics", "molecular", "evolution", "comparative", "genomics", "animal", "genomics", ...	2018	Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species
In the study of circadian rhythms , it has been a puzzle how a limited number of circadian clock genes can control diverse aspects of physiology . Here we investigate circadian gene expression genome-wide using larval zebrafish as a model system . We made use of a spatial gene expression atlas to investigate the expres...	For most animals whose lives are dependent on the sun , circadian clocks govern their daily behaviors and physiology . In different animals , novel functions under the circadian clock's control can evolve as adaptations to their specific environment . A zebrafish demonstrates a remarkably high level of interplay betwee...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microarrays", "genome", "expression", "analysis", "genomics", "gene", "expression", "genetics", "molecular", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics", "dna", "transcription" ]	2013	Analysis of a Gene Regulatory Cascade Mediating Circadian Rhythm in Zebrafish
The caterpillar of the moth Premolis semirufa ( Lepidoptera: Arctiidae ) , commonly named Pararama , is endemic of the Amazon basin . Accidental contact with these caterpillar bristles causes local symptoms such as intense heat , pain , edema and itching which last for three to seven days; however , after multiples con...	Pararama , the popular name of the larval form of the moth Premolis semirufa inhabits rubber plantations in the Amazon region and the accidental contact of the skin with the caterpillar's bristles or cocoons results in immediate and intense heat , pain , edema , and itching . In many cases a chronic inflammatory reacti...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "immunology", "biology" ]	2012	Premolis semirufa (Walker, 1856) Envenomation, Disease Affecting Rubber Tappers of the Amazon: Searching for Caterpillar-Bristles Toxic Components
We propose a novel biologically constrained three-phase model of the brain microstructure . Designing a realistic model is tantamount to a packing problem , and for this reason , a number of techniques from the theory of random heterogeneous materials can be brought to bear on this problem . Our analysis strongly sugge...	The goal of the present work is to develop a biologically constrained three-dimensional model of the brain microstructure . This is an important task because the brain's three-dimensional microstructure cannot be directly visualized , yet a knowledge of its structure is essential for understanding normal brain function...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/theory", "and", "simulation", "computational", "biology" ]	2008	A Novel Three-Phase Model of Brain Tissue Microstructure
NF-κB plays a central role in modulating innate immune responses to bacterial infections . Therefore , many bacterial pathogens deploy multiple mechanisms to counteract NF-κB activation . The invasion of and subsequent replication of Shigella within epithelial cells is recognized by various pathogen recognition recepto...	In response to bacterial infection , host cells induce a plethora of innate immune responses to combat the infection . However , many bacterial pathogens have developed sophisticated mechanisms to evade the host's immune system . Because NF-κB is crucial for innate immune responses against bacterial infection , bacteri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacterial", "pathogens", "host-pathogen", "interaction", "biology", "microbiology" ]	2013	Shigella IpaH0722 E3 Ubiquitin Ligase Effector Targets TRAF2 to Inhibit PKC–NF-κB Activity in Invaded Epithelial Cells
In the rabbit model of syphilis , infection phenotypes associated with the Nichols and Chicago strains of Treponema pallidum ( T . pallidum ) , though similar , are not identical . Between these strains , significant differences are found in expression of , and antibody responses to some candidate virulence factors , s...	During infection , the agent of syphilis , Treponema pallidum subsp . pallidum ( T . pallidum ) , successfully evades the host immune defenses and establishes a persistent infection that can cause blindness , paralysis , or even death in some individuals that progress to the tertiary stage of the disease . The study of...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "biology", "genomics", "microbiology", "genetics", "and", "genomics" ]	2012	Footprint of Positive Selection in Treponema pallidum subsp. pallidum Genome Sequences Suggests Adaptive Microevolution of the Syphilis Pathogen

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