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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
Can deliberate interaction between the public and persons affected by leprosy reduce stigmatization ? The study described in this paper hypothesises that it can and assesses the effectiveness of a ‘contact intervention’ . This cluster-randomized controlled intervention study is part of the Stigma Assessment and Reducti...	Stigma plays an important role in several neglected tropical diseases such as leprosy , Buruli ulcer , lymphatic filariasis , onchocerciasis and leishmaniasis . It negatively impacts individuals affected , and often also their families , and even communities . There are different ways to address stigma . One promising ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	A Cluster-Randomized Controlled Intervention Study to Assess the Effect of a Contact Intervention in Reducing Leprosy-Related Stigma in Indonesia
Polyamines are essential for cell growth of eukaryotes including the etiologic agent of human African trypanosomiasis ( HAT ) , Trypanosoma brucei . In trypanosomatids , a key enzyme in the polyamine biosynthetic pathway , S-adenosylmethionine decarboxylase ( TbAdoMetDC ) heterodimerizes with a unique catalytically-dea...	Trypanosoma brucei is a single-celled eukaryotic pathogen and the causative agent of human African trypanosomiasis ( HAT ) . Polyamines are organic polycations that are essential for growth in T . brucei to facilitate protein translation and to maintain redox homeostasis . The pathway is the target of eflornithine , a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "rna", "interference", "protein", "metabolism", "chemical", "compounds", "aliphatic", "amino", "acids", "messenger", "rna", "enzymology", "parasitic", "protozoans", "organic", "compounds", "trypanosoma", "brucei", "leucine", "protozoans", "amino", "acids", "epigenetics", ...	2018	A dual regulatory circuit consisting of S-adenosylmethionine decarboxylase protein and its reaction product controls expression of the paralogous activator prozyme in Trypanosoma brucei
PCR-Restriction Fragment Length Polymorphism ( RFLP ) analyses targeting multiple nuclear genes were established for the simple and practical identification of Leishmania species without using expensive equipment . This method was applied to 92 clinical samples collected at 33 sites in 14 provinces of Ecuador , which h...	Leishmaniasis caused by intracellular protozoa of the genus Leishmania is a neglected tropical disease widely distributing worldwide , especially in tropical and subtropical areas . Approximately 20 species are known to be pathogenic to humans , of which eight species have been recorded as causative agents of cutaneous...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecuador", "geographical", "locations", "parasitic", "diseases", "parasitic", "protozoans", "protozoans", "leishmania", "molecular", "biology", "techniques", "cellular", "structures", "and", "organelles", "research", "and", "analys...	2019	PCR-RFLP analyses of Leishmania species causing cutaneous and mucocutaneous leishmaniasis revealed distribution of genetically complex strains with hybrid and mito-nuclear discordance in Ecuador
The Gram-negative bacterial plant pathogen Xanthomonas campestris pv . vesicatoria employs a type III secretion ( T3S ) system to inject bacterial effector proteins into the host cell cytoplasm . One essential pathogenicity factor is HrpB2 , which is secreted by the T3S system . We show that secretion of HrpB2 is suppr...	The Gram-negative plant pathogenic bacterium Xanthomonas campestris pv . vesicatoria is the causal agent of bacterial spot disease in pepper and tomato . Pathogenicity of X . campestris pv . vesicatoria depends on a type III protein secretion ( T3S ) system that injects bacterial effector proteins directly into the hos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/plant-biotic", "interactions" ]	2008	HpaC Controls Substrate Specificity of the Xanthomonas Type III Secretion System
Cyclic nucleotides ( cAMP and cGMP ) regulate multiple intracellular processes and are thus of a great general interest for molecular and structural biologists . To study the allosteric mechanism of different cyclic nucleotide binding ( CNB ) domains , we compared cAMP-bound and cAMP-free structures ( PKA , Epac , and ...	Cyclic nucleotides are small regulatory molecules which transmit signal from receptors positioned on a living cell membrane into the cell interior and regulate multiple biological processes ranging from bacteria to humans . Such regulation occurs through binding of the cyclic nucleotides to the corresponding proteins ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "cell", "biology/cell", "signaling", "molecular", "biology/bioinformatics", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "biochemistry/bioinformatics", "biochemistry/biomacromolecule-ligand", ...	2008	A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains
A significant number of environmental microorganisms can cause serious , even fatal , acute and chronic infections in humans . The severity and outcome of each type of infection depends on the expression of specific bacterial phenotypes controlled by complex regulatory networks that sense and respond to the host enviro...	P . aeruginosa causes acute as well as chronic infections in humans . In this paper we report the identification of a P . aeruginosa small molecule , 2-AA , that modulates this pathogen's virulence to promote chronic infections . We show that the synthesis of 2-AA , responsible for the grape-like odor of P . aeruginosa...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "gram", "negative", "microbial", "pathogens", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens", "pathogenesis" ]	2011	A Quorum Sensing Regulated Small Volatile Molecule Reduces Acute Virulence and Promotes Chronic Infection Phenotypes
Fibroblastic reticular cells ( FRCs ) form the cellular scaffold of lymph nodes ( LNs ) and establish distinct microenvironmental niches to provide key molecules that drive innate and adaptive immune responses and control immune regulatory processes . Here , we have used a graph theory-based systems biology approach to...	Fibroblastic reticular cells ( FRCs ) in lymph nodes are organized in a highly connected cellular network that not only acts as a scaffold for lymphocyte migration but also provides key factors for induction and maintenance of immune responses . By utilizing high-resolution microscopy coupled with computational approac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "infographics", "cell", "motility", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "developmental", "biology", "routes", "of", "administration", "luminescent", "proteins", "yellow", "fluorescent", "protei...	2016	Topological Small-World Organization of the Fibroblastic Reticular Cell Network Determines Lymph Node Functionality
Currently , the efficacy of syphilis treatment is measured with anti-lipid antibody tests . These can take months to indicate cure and , as a result , syphilis treatment trials require long periods of follow-up . The causative organism , Treponema pallidum ( T . pallidum ) , is detectable in the infectious lesions of e...	Syphilis is an infection that is spread both sexually and from mother-to-child . Worldwide , it affects an estimated 11 million people each year . Treatment is available , but relies heavily on penicillin and may not be as effective where the infection involves the brain or nervous system . Clinical trials are needed t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Rapid Treponema pallidum Clearance from Blood and Ulcer Samples following Single Dose Benzathine Penicillin Treatment of Early Syphilis
Colicins are protein antibiotics synthesised by Escherichia coli strains to target and kill related bacteria . To prevent host suicide , colicins are inactivated by binding to immunity proteins . Despite their high avidity ( Kd≈fM , lifetime ≈4 days ) , immunity protein release is a pre-requisite of colicin intoxicatio...	Many proteins interact with other proteins as part of their function . One method of modulating the activity of protein complexes is to break them apart . Some complexes , however , are extremely kinetically stable and it is unclear how these can dissociate on a biologically relevant timescale . In this study we addres...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "physics", "biochemistry", "protein", "interactions", "proteins", "biology", "microbiology", "biophysics", "bacterial", "pathogens" ]	2013	A Force-Activated Trip Switch Triggers Rapid Dissociation of a Colicin from Its Immunity Protein
Recently , genome sequencing of many isolates of genetically monomorphic bacterial human pathogens has given new insights into pathogen microevolution and phylogeography . Here , we report a genome-based micro-evolutionary study of a bacterial plant pathogen , Pseudomonas syringae pv . tomato . Only 267 mutations were ...	Our knowledge of the recent evolution of bacterial human pathogens has increased dramatically over the last five years . By comparison , relatively little is known about recent evolution of bacterial plant pathogens . Here , we analyze a large collection of isolates of the economically important plant pathogen Pseudomo...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "pest", "control", "plant", "biology", "genetics", "biology", "genomics", "evolutionary", "biology", "microbiology", "population", "biology", "genetics", "and", "genomics", "agriculture" ]	2011	The Plant Pathogen Pseudomonas syringae pv. tomato Is Genetically Monomorphic and under Strong Selection to Evade Tomato Immunity
The efficacies of many new T cell vaccines rely on generating large populations of long-lived pathogen-specific effector memory CD8 T cells . However , it is now increasingly recognized that prior infection history impacts on the host immune response . Additionally , the order in which these infections are acquired cou...	Many natural pathogens elicit large antigen-specific long-lived effector memory CD8 T cell responses that contribute to pathogen protection and control . This strategy is also employed by novel CD8 T cell vaccine vectors . In the real world , the host is likely to encounter a number of such pathogens at different times...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "animal", "models", "of", "disease", "immunology", "cell", "processes", "microbiology", "cytot...	2017	Adenoviral vaccine induction of CD8+ T cell memory inflation: Impact of co-infection and infection order
Cryptococcus neoformans is a heterothallic fungal pathogen of humans and animals . Although the fungus grows primarily as a yeast , hyphae are produced during the sexual phase and during a process called monokaryotic fruiting , which is also believed to involve sexual reproduction , but between cells of the same mating...	Fungi typically grow vegetatively as either yeast or hyphae . Many of the major human fungal pathogens can generate both morphologies and are referred to as the dimorphic fungi . Cryptococcus neoformans is a yeast-like fungus that has not been traditionally thought to be dimorphic since hyphae production typically occu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "fungi", "mycology", "medical", "microbiology", "biology", "microbiology" ]	2013	The Production of Monokaryotic Hyphae by Cryptococcus neoformans Can Be Induced by High Temperature Arrest of the Cell Cycle and Is Independent of Same-Sex Mating
Highly pathogenic H5N1 influenza A viruses have spread across Asia , Europe , and Africa . More than 500 cases of H5N1 virus infection in humans , with a high lethality rate , have been reported . To understand the molecular basis for the high virulence of H5N1 viruses in mammals , we tested the virulence in ferrets of...	Highly pathogenic H5N1 influenza A viruses have caused more than 500 human infections with approximately 60% lethality in 15 countries and continue to pose a pandemic threat . The recent worldwide spread of pandemic H1N1 influenza A viruses raises the concern of reassortment between the H5N1 viruses and other influenza...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "infectious", "diseases", "microbiology/immunity", "to", "infections", "respiratory", "medicine/respiratory", "infections", "pathology", "virology", "virology/animal", "models", "of", "infection", "infectious", "diseases/vir...	2010	The HA and NS Genes of Human H5N1 Influenza A Virus Contribute to High Virulence in Ferrets
Plasmodium spp parasites harbor an unusual plastid organelle called the apicoplast . Due to its prokaryotic origin and essential function , the apicoplast is a key target for development of new anti-malarials . Over 500 proteins are predicted to localize to this organelle and several prokaryotic biochemical pathways ha...	Malaria caused by Plasmodium spp parasites is a profound human health problem that has shaped our evolutionary past and continues to influence modern day with a disease burden that disproportionately affects the world's poorest and youngest . New anti-malarials are desperately needed in the face of existing or emerging...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "infectious", "diseases", "chemical", "biology", "chemistry", "biology", "microbiology", "molecular", "cell", "biology" ]	2011	Chemical Rescue of Malaria Parasites Lacking an Apicoplast Defines Organelle Function in Blood-Stage Plasmodium falciparum
The pig parasite Ascaris suum plays and important role in veterinary medicine and represents a suitable model for A . lumbricoides , which infects over 800 million people . In pigs , continued exposure to Ascaris induces immunity at the level of the gut , protecting the host against migrating larvae . The objective of ...	Roundworms infect millions of humans and pigs throughout the world . The pig roundworm A . suum is a good model for A . lumbricoides infection in humans due to similar host physiology and the close genetic relationship between the worms . The aim of this study was to identify and characterize early larval antigens that...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "helminths", "immunology", "vertebrates", "animals", "mammals", "developmental", "biology", "ascaris", "ascaris", "lumbricoides", "antibodies", "i...	2016	A Phosphorylcholine-Containing Glycolipid-like Antigen Present on the Surface of Infective Stage Larvae of Ascaris spp. Is a Major Antibody Target in Infected Pigs and Humans
In experimental assays of angiogenesis in three-dimensional fibrin matrices , a temporary scaffold formed during wound healing , the type and composition of fibrin impacts the level of sprouting . More sprouts form on high molecular weight ( HMW ) than on low molecular weight ( LMW ) fibrin . It is unclear what mechani...	Therapies for a range of medical conditions , including cancer , wound healing and diabetic retinopathy can benefit from a better control over the growth of blood vessels . The chemical properties of fibrin , the material that forms scabs in wounds and can also occur in large concentrations in tumors , can regulate the...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "cardiovascular", "physiology", "fibrinogen", "enzymes", "endothelial", "cells", "enzymology", "fibrin", "epithelial", "cells", "angiogenesis", "developmental", "biology", "glycoproteins", "plasmins", "cellular", "structures", "and",...	2018	A local uPAR-plasmin-TGFβ1 positive feedback loop in a qualitative computational model of angiogenic sprouting explains the in vitro effect of fibrinogen variants
Staphylococcus aureus is able to infect virtually all organ systems and is a frequently isolated etiologic agent of osteomyelitis , a common and debilitating invasive infection of bone . Treatment of osteomyelitis requires invasive surgical procedures and prolonged antibiotic therapy , yet is frequently unsuccessful du...	Osteomyelitis is a common , debilitating infection of bone that rarely resolves without prolonged antibiotics and invasive surgical procedures . This study explores the role of host inflammation during osteomyelitis . Our findings highlight innate immune responses that are critical for control of S . aureus burdens in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	MyD88 and IL-1R signaling drive antibacterial immunity and osteoclast-driven bone loss during Staphylococcus aureus osteomyelitis
Human African trypanosomiasis ( HAT ) , a parasitic protozoal disease , is caused primarily by two subspecies of Trypanosoma brucei . HAT is a re-emerging disease and currently threatens millions of people in sub-Saharan Africa . Many affected people live in remote areas with limited access to health services and , the...	Traditional herbal medicine continues to play a key role in health , particularly in remote areas with limited access to “modern medicines” . Many plants are used in traditional Nigerian medicine to treat parasitic diseases . While many of these plants have shown notable activity against parasitic protozoa , in most ca...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "medicinal", "chemistry", "phytochemistry", "chemistry", "computational", "chemistry" ]	2012	In-silico Investigation of Antitrypanosomal Phytochemicals from Nigerian Medicinal Plants
During intracellular infections , autophagy significantly contributes to the elimination of pathogens , regulation of pro-inflammatory signaling , secretion of immune mediators and in coordinating the adaptive immune system . Intracellular pathogens such as S . Typhimurium have evolved mechanisms to circumvent autophag...	S . Typhimurium is a facultative intracellular pathogen which uses its type III secretion system to avoid cell-autonomous defense mechanisms such as autophagy . Here we show that S . Typhimurium induces energy depletion resulting in an early but transient activation of AMPK and autophagy . Salmonella virulence factors ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "phosphorylation", "cell", "death", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "lysosomes", "immune", "cells", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "pathogens", "cell", "processes", ...	2017	Salmonella Typhimurium disrupts Sirt1/AMPK checkpoint control of mTOR to impair autophagy
Fragile sites are loci of recurrent chromosome breakage in the genome . They are found in organisms ranging from bacteria to humans and are implicated in genome instability , evolution , and cancer . In budding yeast , inactivation of Mec1 , a homolog of mammalian ATR , leads to chromosome breakage at fragile sites ref...	Chromosome breakage can occur during normal cell division . When it occurs , the breaks do not arise randomly throughout the genome , but at preferred locations referred to as fragile sites . Chromosome breakage at fragile sites is an evolutionarily conserved phenomenon , implicated in evolution and speciation . In hum...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "microbiology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Topoisomerase II– and Condensin-Dependent Breakage of MEC1ATR-Sensitive Fragile Sites Occurs Independently of Spindle Tension, Anaphase, or Cytokinesis
In order to cross a street without being run over , we need to be able to extract very fast hidden causes of dynamically changing multi-modal sensory stimuli , and to predict their future evolution . We show here that a generic cortical microcircuit motif , pyramidal cells with lateral excitation and inhibition , provi...	It has recently been shown that STDP installs in ensembles of pyramidal cells with lateral inhibition networks for Bayesian inference that are theoretically optimal for the case of stationary spike input patterns . We show here that if the experimentally found lateral excitatory connections between pyramidal cells are ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "circuit", "models", "computer", "and", "information", "sciences", "neural", "homeostasis", "neural", "networks", "computational", "neuroscience", "biology", "and", "life", "sciences", "computational", "biology", "neuroscience" ]	2014	STDP Installs in Winner-Take-All Circuits an Online Approximation to Hidden Markov Model Learning
Lipid droplets ( LDs ) are important cellular organelles that govern the storage and turnover of lipids . Little is known about how the size of LDs is controlled , although LDs of diverse sizes have been observed in different tissues and under different ( patho ) physiological conditions . Recent studies have indicated...	Lipid droplets ( LD ) are primary lipid storage structures that also function in membrane and lipid trafficking , protein turnover , and the reproduction of deadly viruses . Increased LD accumulation in liver , skeletal muscle , and adipose tissue is a hallmark of the metabolic syndrome . Enlarged LDs are often found i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "lipids", "model", "organisms", "genetic", "screens", "genetics", "biology", "genetics", "and", "genomics" ]	2011	A Role for Phosphatidic Acid in the Formation of “Supersized” Lipid Droplets
Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans , yet little is known about how natural selection acts on genome arrangement . Pathogenic bacteria such as Yersinia pestis , which causes bubonic and pneumonic plague , often exhibit a high degree of genomic rearra...	Whole-genome sequencing has revealed that organisms exhibit extreme variability in chromosome structure . One common type of chromosome structure variation is genome arrangement variation: changes in the ordering of genes on the chromosome . Not only do we find differences in genome arrangement across species , but in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "genetics", "and", "genomics/chromosome", "biology", "evolutionary", "biology/genomics", "computational", "biology/evolutionary", "...	2008	Dynamics of Genome Rearrangement in Bacterial Populations
Clonorchiasis is among the most neglected tropical diseases . It is caused by ingesting raw or undercooked fish or shrimp containing the larval of Clonorchis sinensis and mainly endemic in Southeast Asia including China , Korea and Vietnam . The global estimations for population at risk and infected are 601 million and...	Clonorchiasis is caused by eating incompletely cooked fishery product which carries the larval of Clonorchis sinensis . Millions of people are estimated to suffer in Southeast Asia . However , it is still among the most neglected tropical diseases due to the lack of clear evaluation , of which no disease burden availab...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "neglected", "tropical", "diseases", "clonorchiasis", "parasitic", "diseases", "disease", "informatics" ]	2011	Disability Weight of Clonorchis sinensis Infection: Captured from Community Study and Model Simulation
Fascioliasis , caused by the liver fluke Fasciola hepatica , is a neglected tropical disease infecting over 1 million individuals annually with 17 million people at risk of infection . Like other helminths , F . hepatica employs mechanisms of immune suppression in order to evade its host immune system . In this study t...	Fascioliasis , caused by the liver fluke Fasciola hepatica , is a neglected tropical disease infecting over 1 million individuals annually with 17 million people at risk of infection . These worms infect the liver and can survive for many years in its animal or human host because they supress the host’s immune system t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "binding", "phosphorylation", "cell", "physiology", "invertebrates", "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "helminths", "rna", "extraction", "carbohydrates", "organic", "compounds", "animals...	2016	Fasciola hepatica Surface Coat Glycoproteins Contain Mannosylated and Phosphorylated N-glycans and Exhibit Immune Modulatory Properties Independent of the Mannose Receptor
Neurosteroids are endogenous modulators of neuronal excitability and nervous system development and are being developed as anesthetic agents and treatments for psychiatric diseases . While gamma amino-butyric acid Type A ( GABAA ) receptors are the primary molecular targets of neurosteroid action , the structural detai...	Neurosteroids are cholesterol metabolites produced by neurons and glial cells that participate in central nervous system ( CNS ) development , regulate neuronal excitability , and modulate complex behaviors such as mood . Exogenously administered neurosteroid analogues are effective sedative hypnotics and are being dev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "neurochemistry", "crystal", "structure", "chemical", "compounds", "condensed", "matter", "physics", "vertebrates", "electrophysiology", "neuroscience", "organic", "compounds", "animals", "xenopus", "membrane", "proteins", "animal", ...	2019	Multiple functional neurosteroid binding sites on GABAA receptors
Myosin Ic is thought to be the principal constituent of the motor that adjusts mechanical responsiveness during adaptation to prolonged stimuli by hair cells , the sensory receptors of the inner ear . In this context myosin molecules operate neither as filaments , as occurs in muscles , nor as single or few molecules ,...	Myosin molecules are biological nanomachines that transduce chemical energy into mechanical work and thus produce directed motion in living cells . These molecules proceed through cyclic reactions in which they change their conformational states upon the binding and release of nucleotides while attaching to and detachi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "stiffness", "cell", "motility", "mechanical", "properties", "actin", "filaments", "classical", "mechanics", "chemical", "compounds", "phosphates", "nucleotides", "mechanical", "energy", "molecular", "motors", "actin", "motors", "mathematics", "statistics", "(mathematics)",...	2017	Chemomechanical regulation of myosin Ic cross-bridges: Deducing the elastic properties of an ensemble from single-molecule mechanisms
The dendritic spines of pyramidal neurons are the targets of most excitatory synapses in the cerebral cortex . They have a wide variety of morphologies , and their morphology appears to be critical from the functional point of view . To further characterize dendritic spine geometry , we used in this paper over 7 , 000 ...	Dendritic spines of pyramidal neurons are the targets of most excitatory synapses in the cerebral cortex and their morphology appears to be critical from the functional point of view . Thus , characterizing this morphology is necessary to link structural and functional spine data and thus interpret and make them more m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "ellipses", "dendritic", "structure", "light", "microscopy", "geometry", "neuroscience", "probability", "distribution", "mathematics", "ganglion", "cells", "microscopy", "neuronal", "dendrites", "research", "and", "analysis", "methods", "animal", "cells", "fluorescence", ...	2018	3D morphology-based clustering and simulation of human pyramidal cell dendritic spines
Enterohemorrhagic Escherichia coli O157:H7 ( EHEC ) is an important food-borne pathogen that colonizes the colon . Transposon-insertion sequencing ( TIS ) was used to identify genes required for EHEC and E . coli K-12 growth in vitro and for EHEC growth in vivo in the infant rabbit colon . Surprisingly , many conserved...	Enterohemorrhagic E . coli ( EHEC ) is an important food-borne pathogen that infects the colon . We created a dense EHEC transposon library and used transposon-insertion sequencing to identify the genes required for EHEC growth in vitro and in vivo in the infant rabbit colon . We found that there is a large infection b...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "bile", "vertebrates", "rabbits", "animals", "mammals", "animal", "models", "bacterial", "diseases", "experimental", "organism", "systems", "genetic", "elements", "enterohaemorrhagic", "escherichia", "coli", "di...	2019	Transposon-insertion sequencing screens unveil requirements for EHEC growth and intestinal colonization
The B1 SOX transcription factors SOX1/2/3/19 have been implicated in various processes of early embryogenesis . However , their regulatory functions in stages from the blastula to early neurula remain largely unknown , primarily because loss-of-function studies have not been informative to date . In our present study ,...	In the developing embryo , various processes such as cell fate specification , embryo patterning , and morphogenesis take place concurrently . The embryo must control gene expression in order to coordinate these processes and thereby enable the proper organization of its structures . The B1 sox transcription factor gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/stem", "cells", "developmental", "biology/morphogenesis", "and", "cell", "biology", "genetics", "and", "genomics/gene", "expression", "developmental", "biology/pattern", "formation", "developmental", "biology/cell", "differentiation", "neuroscience/neuro...	2010	B1 SOX Coordinate Cell Specification with Patterning and Morphogenesis in the Early Zebrafish Embryo
Yellow fever ( YF ) , transmitted via bites of infected mosquitoes , is a life-threatening viral disease endemic to tropical and subtropical regions of Africa and South America . YF has largely been controlled by widespread national vaccination campaigns . Nevertheless , between December 2015 and August 2016 , YF resur...	An epidemic model for the transmission of yellow fever virus ( YFV ) in urban areas is formulated and implemented to study the 2016 yellow fever ( YF ) outbreak in Luanda , Angola . We explore the complex vector-host dynamics of this system taking into account mosquito abundance , vaccination and asymptomatic infection...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "atmospheric", "science", "angola", "immunology", "geographical", "locations", "animals", "preventive", "medicine", "el", "ni単o-southern", "oscillation", "infectious", "disease", "control", "vaccination", "and", "i...	2018	Modelling the large-scale yellow fever outbreak in Luanda, Angola, and the impact of vaccination
Despite the central role of alternative sigma factors in bacterial stress response and virulence their regulation remains incompletely understood . Here we investigate one of the best-studied examples of alternative sigma factors: the σB network that controls the general stress response of Bacillus subtilis to uncover ...	Understanding the regulation of bacterial stress response holds the key to tackling the problems of emerging resistance to anti-bacteria’s and antibiotics . To this end , here we study one of the longest serving model systems of bacterial stress response: the σB pathway of Bacillus subtilis . The sigma factor σB contro...	[ "Abstract", "Introduction", "Results", "Methods" ]	[ "cellular", "stress", "responses", "engineering", "and", "technology", "enzymes", "signal", "processing", "cell", "processes", "enzymology", "operons", "dna-binding", "proteins", "phosphatases", "polymerases", "network", "analysis", "dna", "computer", "and", "information"...	2016	Role of Autoregulation and Relative Synthesis of Operon Partners in Alternative Sigma Factor Networks
Identification of drug-target interactions ( DTIs ) plays a key role in drug discovery . The high cost and labor-intensive nature of in vitro and in vivo experiments have highlighted the importance of in silico-based DTI prediction approaches . In several computational models , conventional protein descriptors have bee...	Drugs work by interacting with target proteins to activate or inhibit a target’s biological process . Therefore , identification of DTIs is a crucial step in drug discovery . However , identifying drug candidates via biological assays is very time and cost consuming , which introduces the need for a computational predi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "neural", "networks", "statistics", "enzymes", "enzymology", "neuroscience", "mathematics", "forecasting", "artificial", "intelligence", "convolution", "sequence", "motif", "analysis", "pharmacology", "extraction", "techniques", "res...	2019	DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences
The rate at which HIV-1 infected individuals progress to AIDS is highly variable and impacted by T cell immunity . CD8 T cell inhibitory molecules are up-regulated in HIV-1 infection and associate with immune dysfunction . We evaluated participants ( n = 122 ) recruited to the SPARTAC randomised clinical trial to deter...	After being infected with HIV , the pace of disease progression is highly variable between individuals . Some stay well with functioning immune systems for many years , whilst others progress to AIDS quickly . Understanding the factors that underpin these differences is important and may relate to factors such as viral...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "t", "helper", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "antiviral", "therapy", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "i...	2016	Exhaustion of Activated CD8 T Cells Predicts Disease Progression in Primary HIV-1 Infection
The NF-κB-like velvet domain protein VosA ( viability of spores ) binds to more than 1 , 500 promoter sequences in the filamentous fungus Aspergillus nidulans . VosA inhibits premature induction of the developmental activator gene brlA , which promotes asexual spore formation in response to environmental cues as light ...	Velvet domain proteins of filamentous fungi are structurally similar to Rel-homology domains of mammalian NF-κB proteins . Velvet and NF-κB proteins control regulatory circuits of downstream transcriptional networks for cellular differentiation , survival and stress responses . Velvet proteins interconnect developmenta...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "fungal", "spores", "secondary", "metabolism", "aspergillus", "fungal", "genetics", "gene", "regulation", "oxidative", "stress", "regulatory", "proteins", "dna-binding", "proteins", "aspergillus", "nidulans", "fungi", "experimental", "organism", "systems", "transcription", ...	2018	Velvet domain protein VosA represses the zinc cluster transcription factor SclB regulatory network for Aspergillus nidulans asexual development, oxidative stress response and secondary metabolism
Chronic chagasic cardiomyopathy ( CCC ) develops years after acute infection by Trypanosoma cruzi and does not improve after trypanocidal therapy , despite reduction of parasite burden . During disease , the heart undergoes oxidative stress , a potential causative factor for arrhythmias and contractile dysfunction . He...	Protection against functional damage , i . e . disease tolerance , is a successful strategy against pathogens the immune system fails to eliminate . In Chagas disease , Trypanosoma cruzi infects the heart and many years after parasite burden is reduced to a minimum by the immune response , a cardiomyopathy ensues , oft...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "cardiovascular", "anatomy", "oxidative", "stress", "cardiac", "ventricles", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "cardiovascular", "medicine", "organisms", "electrocardiography", "protozoans", ...	2016	Resveratrol Reverses Functional Chagas Heart Disease in Mice
The essential coenzyme nicotinamide adenine dinucleotide ( NAD+ ) plays important roles in metabolic reactions and cell regulation in all organisms . Bacteria , fungi , plants , and animals use different pathways to synthesize NAD+ . Our molecular and genetic data demonstrate that in the unicellular green alga Chlamydo...	Nicotinamide adenine dinucleotide ( NAD+ ) is an essential coenzyme . NAD+ is necessary for electron transfer in many metabolic reactions . NAD+ functions as a substrate for several enzymes , one of which is sirtuin , an enzyme involved in gene regulation and aging . NAD+ can be synthesized either from amino acids ( de...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "cell", "biology/gene", "expression", "computational", "biology/molecular", "genetics", "genetics", "and", "genomics/gene", "function", "genetics", "and", "genomics/plant", "genomes", "and", "evolution", "genetics", "and", ...	2010	Synthesizing and Salvaging NAD+: Lessons Learned from Chlamydomonas reinhardtii
A balance between excitatory and inhibitory synaptic currents is thought to be important for several aspects of information processing in cortical neurons in vivo , including gain control , bandwidth and receptive field structure . These factors will affect the firing rate of cortical neurons and their reliability , wi...	The adult human brain consumes more than 20% of the resting metabolism . With ∼19–23 billion neurons , the cerebral cortex consumes much of this energy , mainly to restore ion gradients across membranes for electrical signaling . Even small increases in the average spike rate of cortical neurons could cause the cortex ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Balanced Excitatory and Inhibitory Synaptic Currents Promote Efficient Coding and Metabolic Efficiency
The genome-scale models of metabolic networks have been broadly applied in phenotype prediction , evolutionary reconstruction , community functional analysis , and metabolic engineering . Despite the development of tools that support individual steps along the modeling procedure , it is still difficult to associate mat...	The broad application of genome-scale metabolic modeling has made it a useful technique for tackling fundamental questions in biological research and engineering . Today over 100 models have been constructed for organisms that carry out a diverse array of metabolic activities spanning all three kingdoms of life . These...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "xenobiotic", "metabolism", "metabolic", "networks", "mathematical", "models", "simulation", "and", "modeling", "network", "analysis", "exchange", "reactions", "lipid", "metabolism", "research", "and", "analysis", "methods", "computer", "and", "information", "sciences", ...	2016	PSAMM: A Portable System for the Analysis of Metabolic Models
Despite causing considerable damage to host tissue during the onset of parasitism , nematodes establish remarkably persistent infections in both animals and plants . It is thought that an elaborate repertoire of effector proteins in nematode secretions suppresses damage-triggered immune responses of the host . However ...	Plant-parasitic nematodes have a major impact on global food security , as they reduce the annual yield of food crops by approximately 10 percent . For decades , the application of non-selective toxic chemicals to infested soils controlled outbreaks of plant-parasitic nematodes . The recent bans on most of these chemic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immune", "system", "proteins", "biochemistry", "plant", "science", "proteins", "plant", "pathogens", "plant", "pathology", "biology", "and", "life", "sciences", "immunology", "nematology", "zoology", "immunomodulation", "agriculture" ]	2014	Apoplastic Venom Allergen-like Proteins of Cyst Nematodes Modulate the Activation of Basal Plant Innate Immunity by Cell Surface Receptors
The rapid accumulation of biological networks poses new challenges and calls for powerful integrative analysis tools . Most existing methods capable of simultaneously analyzing a large number of networks were primarily designed for unweighted networks , and cannot easily be extended to weighted networks . However , it ...	To study complex cellular networks , we need to consider their dynamic topologies under many different experimental or physiological conditions . Integrative analysis over large numbers of massive biological networks thus emerges as a new challenge in data mining . Recently , we and others have proposed several algorit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology" ]	2011	Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation
Dengue is one of the most important infectious diseases of humans and has spread throughout much of the tropical and subtropical world . Despite this widespread dispersal , the determinants of dengue transmission in endemic populations are not well understood , although essential for virus control . To address this iss...	Although dengue is a major cause of morbidity in many tropical and subtropical regions of the world , little is known about how the causative virus ( dengue virus , DENV ) spreads through endemic populations . To address this issue we undertook a phylogeny-based analysis of 751 complete genome sequences of DENV-1 sampl...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequence", "analysis", "phylogenetics", "emergence", "evolutionary", "biology", "population", "genetics", "biology", "computational", "biology", "gene", "flow", "evolutionary", "systematics", "evolutionary", "processes", "evolutionary", "genetics" ]	2011	Endemic Dengue Associated with the Co-Circulation of Multiple Viral Lineages and Localized Density-Dependent Transmission
We perform a large-scale study of intrinsically disordered regions in proteins and protein complexes using a non-redundant set of hundreds of different protein complexes . In accordance with the conventional view that folding and binding are coupled , in many of our cases the disorder-to-order transition occurs upon co...	Traditionally , protein structure is believed to determine function . Recently , it was observed that many proteins contain regions without well-defined structure ( intrinsically disordered regions ) , including a large fraction of eukaryotic proteins . Intrinsic disorder has been associated with particular functions i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics/structural", "genomics", "biophysics/protein", "folding", "biophysics/biomacromolecule-ligand", "interactions", "evolutionary", "biology/bioinformatics", "computational", "biology/systems", "biology" ]	2009	Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis
Melioidosis , caused by Burkholderia pseudomallei , is an endemic disease in Bangladesh . No systematic study has yet been done to detect the environmental source of the organism and its true extent in Bangladesh . The present study attempted to isolate B . pseudomallei in soil samples and to determine its seroprevalen...	Melioidosis , caused by B . pseudomallei , can be a fatal disease if not treated with appropriate antibiotics . The organism is mainly present in soil and water in endemic areas , and people become infected through skin inoculation , inhalation or ingestion . The disease has been sporadically detected in Bangladesh ove...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2016	Burkholderia pseudomallei: Its Detection in Soil and Seroprevalence in Bangladesh
Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks , and are often the only accessible way to explore their behavior . The development of fast algorithms is paramount to allow large-scale simulations . The Gillespie algorithm can be used for fast simulation of ...	When studying how e . g . diseases spread in a population , intermittent contacts taking place between individuals—through which the infection spreads—are best described by a time-varying network . This object captures both their complex structure and dynamics , which crucially affect spreading in the population . The ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks
Thrombocytopenia is a major side-effect of cytotoxic cancer therapies . The aim of precision medicine is to develop therapy modifications accounting for the individual’s risk . To solve this task , we develop an individualized bio-mechanistic model of the dynamics of bone marrow thrombopoiesis , circulating platelets a...	Chemotherapy is ubiquitously used to treat cancer diseases . Due to general toxicity of the drugs , chemotherapy results in a number of side effects especially with respect to blood formation . Here we study the loss of platelets during chemotherapy which is dose limiting in many situations . However , this side-effect...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "population", "genetics", "ploidy", "toxicology", "bone", "marrow", "cells", "toxicity", "osteoblasts", "pharmaceutics", "connective", "tissue", ...	2019	Modeling individual time courses of thrombopoiesis during multi-cyclic chemotherapy
Cleft palate is among the most common birth defects in humans . Previous studies have shown that Shh signaling plays critical roles in palate development and regulates expression of several members of the forkhead-box ( Fox ) family transcription factors , including Foxf1 and Foxf2 , in the facial primordia . Although ...	Cleft lip and/or cleft palate ( CL/P ) are among the most common birth defects in humans , occurring at a frequency of about 1 in 500–2500 live births . The etiology and pathogenesis of CL/P are complex and poorly understood . Generation and analysis of mice carrying targeted null and conditional mutations in many gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	A Shh-Foxf-Fgf18-Shh Molecular Circuit Regulating Palate Development
The interferon inducible protein , BST-2 ( or , tetherin ) , plays an important role in the innate antiviral defense system by inhibiting the release of many enveloped viruses . Consequently , viruses have evolved strategies to counteract the anti-viral activity of this protein . While the mechanisms by which BST-2 pre...	BST-2 ( or , tetherin ) is an antiviral protein that inhibits the release and spread of many enveloped viruses and is upregulated as part of the innate immune defense against infections . By studying the lymphocytic choriomeningitis virus ( LCMV ) model of infection , we sought insights into how BST-2 shapes the early ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "hela", "cells", "293t", "cells", "spleen", "immunology", "biological", "cultures", "microbiology", "viral", "structure", "cell", "cultures", "cytotoxic", "t", "cel...	2018	BST-2 controls T cell proliferation and exhaustion by shaping the early distribution of a persistent viral infection
Herpesviruses infect most humans . Their infections can be associated with pathological conditions and significant changes in T cell repertoire but evidences of symbiotic effects of herpesvirus latency have never been demonstrated . We tested the hypothesis that HCMV and EBV-specific CD8 T cells contribute to the heter...	The majority of humans are infected by herpesviruses , such as Epstein-Barr virus and Human Cytomegalovirus , which rarely cause severe pathology but heavily distort the human T cell repertoire . Up to 20% of cytotoxic T cells can be specific to Epstein-Barr and Cytomegalovirus . It is believed that all these herpesvir...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases", "immunology/immune", "response", "virology", "infectious", "diseases/viral", "infections", "immunology", "immunology/immunity", "to", "infections", "infectious", "diseases/gastrointestinal", "infections" ]	2010	Contribution of Herpesvirus Specific CD8 T Cells to Anti-Viral T Cell Response in Humans
Fatty acid synthesis in plants occurs in plastids , and thus , export for subsequent acyl editing and lipid assembly in the cytosol and endoplasmatic reticulum is required . Yet , the transport mechanism for plastid fatty acids still remains enigmatic . We isolated FAX1 ( fatty acid export 1 ) , a novel protein , which...	Fatty acid synthesis in plants occurs in chloroplasts—the organelle more commonly known for conducting photosynthesis . For subsequent lipid assembly to be possible in the endoplasmatic reticulum ( ER ) , export of these fatty acids across the chloroplast envelope membranes is required . The mechanism of this transport...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	FAX1, a Novel Membrane Protein Mediating Plastid Fatty Acid Export
Stress granules ( SGs ) are non-membranous cytoplasmic aggregates of mRNAs and related proteins , assembled in response to environmental stresses such as heat shock , hypoxia , endoplasmic reticulum ( ER ) stress , chemicals ( e . g . arsenite ) , and viral infections . SGs are hypothesized as a loci of mRNA triage and...	Cells suffer from various environmental stresses such as heat shock and viral infection . In response to a stress , small non-membranous cytoplasmic aggregates , stress granules ( SGs ) , are assembled . SGs contain mRNAs and related proteins . Hippocampal CA1 neurons located in the brain , which are vulnerable to isch...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Spatio-temporal Dynamics and Mechanisms of Stress Granule Assembly
Multiple syndromes share congenital heart and craniofacial muscle defects , indicating there is an intimate relationship between the adjacent cardiac and pharyngeal muscle ( PM ) progenitor fields . However , mechanisms that direct antagonistic lineage decisions of the cardiac and PM progenitors within the anterior mes...	Many developmental syndromes include both congenital heart and craniofacial defects , necessitating a better understanding of the mechanisms underlying the correlation of these defects . During early vertebrate development , cardiac and pharyngeal muscle cells originate from adjacent , partially overlapping progenitor ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "fish", "medicine", "and", "health", "sciences", "cardiovascular", "anatomy", "skeletal", "muscles", "vertebrates", "pharyngeal", "muscles", "animals", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "heart", "experimental", "organism...	2019	Nr2f-dependent allocation of ventricular cardiomyocyte and pharyngeal muscle progenitors
In Caenorhabditis elegans ( C . elegans ) , the promotion of longevity by the transcription factor DAF-16 requires reduced insulin/IGF receptor ( IIR ) signaling or the ablation of the germline , although the reason for the negative impact of germ cells is unknown . FOXO/DAF-16 activity inhibits germline proliferation ...	Previous studies have shown that DAF–16/FOXO transcription factor promotes longevity and stress resistance and inhibits tumor progression in the absence of insulin signaling . Here we show that active DAF-16 in the epidermis can shorten lifespan by promoting a tumorous germline phenotype . In contrast to the known inhi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Cell-Nonautonomous Signaling of FOXO/DAF-16 to the Stem Cells of Caenorhabditis elegans
Male circumcision reduces acquisition of HIV-1 by 60% . Hence , the foreskin is an HIV-1 entry portal during sexual transmission . We recently reported that efficient HIV-1 transmission occurs following 1 h of polarized exposure of the inner , but not outer , foreskin to HIV-1-infected cells , but not to cell-free viru...	Circumcision reduces HIV-1 acquisition in men , suggesting that the foreskin is an HIV-1 entry site . We previously showed that two types of immune cells in the foreskin epidermis are the first ones targeted by HIV-1 . Hence , Langerhans cells ( LCs ) positioned in proximity to the external surface rapidly capture inco...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "sexually", "transmitted", "diseases", "aids", "biology" ]	2011	HIV-1 Efficient Entry in Inner Foreskin Is Mediated by Elevated CCL5/RANTES that Recruits T Cells and Fuels Conjugate Formation with Langerhans Cells
Most individuals exposed to hepatitis C virus ( HCV ) become persistently infected while a minority spontaneously eliminate the virus . Although early immune events influence infection outcome , the cellular composition , molecular effectors , and timeframe of the host response active shortly after viral exposure remai...	Hepatitis C virus ( HCV ) is a leading cause of liver disease , with an estimated 71 million people infected worldwide . Following exposure , a subset of individuals spontaneously clears the virus while a majority progress to chronic infection . The immune functions active during the initial , acute infection by HCV ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "hepacivirus", "pathogens", "immunology", "computational", "biology", "microbiology", "viruses", "multivariate", "analysis", "vaccines", "mathematic...	2018	Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance
The pro-apoptotic proteins Bax and Bak are essential for executing programmed cell death ( apoptosis ) , yet the mechanism of their activation is not properly understood at the structural level . For the first time in cell death research , we calculated intra-protein charge transfer in order to study the structural alt...	Apoptosis is a physiological form of cell death that is fundamental for development , growth and homeostasis in multi-cellular organisms . Deviations in the apoptosis machinery are known to be involved in cancer , neurodegenerative disorders , and autoimmune diseases . The proteins Bax and Bak are essential for executi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "empirical", "methods", "biochemistry", "protein", "chemistry", "computational", "chemistry", "protein", "interactions", "proteins", "ab", "initio", "methods", "protein", "structure", "regulatory", "proteins", "macromolecular", "assemblies", "biology", "chemistry", "drug", ...	2012	Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation
Aneuploidy is known to be deleterious and underlies several common human diseases , including cancer and genetic disorders such as trisomy 21 in Down's syndrome . In contrast , aneuploidy can also be advantageous and in fungi confers antifungal drug resistance and enables rapid adaptive evolution . We report here that ...	Aneuploidy refers to increases or decreases in the copy number of individual chromosomes ( rather than of the entire haploid or diploid genome ) . In humans , aneuploidy is well known to be deleterious , causing genetic disorders such as Down syndrome ( trisomy 21 ) , and frequently occurring during mitosis in the gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "genomics", "emerging", "infectious", "diseases", "medical", "microbiology", "genetics", "microbiology", "biology" ]	2013	Unisexual and Heterosexual Meiotic Reproduction Generate Aneuploidy and Phenotypic Diversity De Novo in the Yeast Cryptococcus neoformans
Sporadic Creutzfeldt-Jakob disease ( sCJD ) is the most prevalent of the human prion diseases , which are fatal and transmissible neurodegenerative diseases caused by the infectious prion protein ( PrPSc ) . The origin of sCJD is unknown , although the initiating event is thought to be the stochastic misfolding of endo...	In Creutzfeldt-Jakob disease ( CJD ) , heterozygosity at residue 129 for methionine or valine in normal prion protein may affect disease phenotype , onset and progression . However , the relative contribution of each prion protein allotype to the infectious , disease associated form of prion protein ( PrPSc ) is unknow...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "valine", "chemical", "compounds", "aliphatic", "amino", "acids", "neurodegenerative", "diseases", "cerebellar", "cortex", "brain", "organic", "compounds", "amino", "acids", "infectious", "diseases", "zoonoses", "proteins", "homo...	2016	The Distribution of Prion Protein Allotypes Differs Between Sporadic and Iatrogenic Creutzfeldt-Jakob Disease Patients
In natural ecosystems , hundreds of species typically share the same environment and are connected by a dense network of interactions such as predation or competition for resources . Much is known about how fixed ecological niches can determine species abundances in such systems , but far less attention has been paid t...	In natural ecosystems , hundreds of species with different characteristics typically live side by side , some competing for the same foods and some preying on others . A central question in ecology is how the abundance of a given species in such an ecosystem depends on its particular characteristics ( its phenotype ) ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "ecology", "ecosystems", "population", "modeling", "population", "dynamics", "theoretical", "ecology", "biology", "population", "ecology", "population", "biology", "microbial", "ecology" ]	2011	Dynamic Phenotypic Clustering in Noisy Ecosystems
HIV-1 does not persistently infect macaques due in part to restriction by several macaque host factors . This has been partially circumvented by generating chimeric SIV/HIV-1 viruses ( SHIVs ) that encode SIV antagonist of known restriction factors . However , most SHIVs replicate poorly in macaques unless they are fur...	Macaque model systems are critical gatekeepers for testing HIV-1 prevention methods and for studies of HIV-1 transmission and pathogenesis . HIV-1 does not persistently infect macaques due to inhibition of the virus by several macaque-specific restriction factors necessitating the use of chimeric SIV/HIV-1 viruses ( SH...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vertebrates", "viral", "structure", "animals", "mammals", "retroviruses", "primates", "immunodeficiency"...	2019	Macaque interferon-induced transmembrane proteins limit replication of SHIV strains in an Envelope-dependent manner
The cores of globular proteins are densely packed , resulting in complicated networks of structural interactions . These interactions in turn give rise to dynamic structural correlations over a wide range of time scales . Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanis...	Biological macromolecules comprise extensive networks of interconnected atoms . These complex coupled networks result in correlated structural dynamics , where atoms and residues move and evolve together as concerted conformational changes . The availability of a wealth of macromolecular structures necessitates the use...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "archaea", "yeast", "and", "fungi", "computational", "biology", "eukaryotes", "paramecium", "etc)", "molecular", "biology", "ciliates", "(tetrahymena" ]	2008	Accurate Structural Correlations from Maximum Likelihood Superpositions
Dengue is associated with significant economic expenditure and it is estimated that the Asia Pacific region accounts for >50% of the global cost . Indonesia has one of the world’s highest dengue burdens; Aedes aegypti and Aedes albopictus are the primary and secondary vectors . In the absence of local data on disease c...	Dengue , an infection transmitted by mosquitos , is a public health concern particularly in tropical/subtropical areas and the Asia Pacific region where it is associated with a significant cost to society . Indonesia has one of the world’s highest dengue burdens but Indonesia-specific data on cost are lacking . To esti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "geographical", "locations", "tropical", "diseases", "social", "sciences", "indonesia", "health", "care", "inpatients", "global", "health", "neglected", "tropical", "diseases", "patients", "public", "and", "occupational", "health...	2019	Economic burden of dengue in Indonesia
Although sleep appears to be broadly conserved in animals , the physiological functions of sleep remain unclear . In this study , we sought to identify a physiological defect common to a diverse group of short-sleeping Drosophila mutants , which might provide insight into the function and regulation of sleep . We found...	Most animals sleep; humans sleep nearly a third of their lives . Yet the fundamental functions of sleep remain unknown . Here , we used short-sleeping Drosophila mutants to uncover a role for sleep in resistance to oxidative stress . Oxidative stress is an imbalance of reactive oxygen species and antioxidant responses ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "sleep", "deprivation", "rna", "interference", "oxidative", "stress", "sleep", "enzymes", "enzymology", "dismutases", "animals", "sleep", "disorders", "animal", "models", "physiological", "processes", "drosophila",...	2018	A bidirectional relationship between sleep and oxidative stress in Drosophila
The Kaposi's sarcoma-associated herpesvirus gene products K3 and K5 are viral ubiquitin E3 ligases which downregulate MHC-I and additional cell surface immunoreceptors . To identify novel cellular genes required for K5 function we performed a forward genetic screen in near-haploid human KBM7 cells . The screen identifi...	Viruses manipulate the cellular machinery of the host to facilitate their replication and evade the host immune response . Kaposi's sarcoma-associated herpesvirus ( KSHV ) , a gammaherpesvirus linked to the development of Kaposi's sarcoma , encodes two viral E3 ubiquitin ligases K3 and K5 which target multiple cell sur...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Haploid Genetic Screens Identify an Essential Role for PLP2 in the Downregulation of Novel Plasma Membrane Targets by Viral E3 Ubiquitin Ligases
Heterozygous mutations in the PRPF31 gene cause autosomal dominant retinitis pigmentosa ( adRP ) , a hereditary disorder leading to progressive blindness . In some cases , such mutations display incomplete penetrance , implying that certain carriers develop retinal degeneration while others have no symptoms at all . As...	Retinitis pigmentosa ( RP ) is an inherited disorder of the retina that is caused by mutations in more than 50 genes . Dominant mutations in one of these , PRPF31 , can be non-penetrant . That is , some carriers of mutations suffer from the disease while others do not display any symptoms . In these particular individu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "human", "genetics", "genetics", "and", "genomics" ]	2012	CNOT3 Is a Modifier of PRPF31 Mutations in Retinitis Pigmentosa with Incomplete Penetrance
The granular layer , which mainly consists of granule and Golgi cells , is the first stage of the cerebellar cortex and processes spatiotemporal information transmitted by mossy fiber inputs with a wide variety of firing patterns . To study its dynamics at multiple time scales in response to inputs approximating real s...	The cerebellum is an organ of peculiar geometrical properties , and has been attributed the function of applying spatiotemporal transforms to sensorimotor data since Eccles . In this work we have analyzed the spatiotemporal response properties of the first part of the cerebellar circuit , the granule layer . On the bas...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "action", "potentials", "nervous", "system", "membrane", "potential", "junctional", "complexes", "electrophysiology", "neuroscience", "gap", "junctions", "nerve", "fibers", "neuronal", "dendrites", "animal", ...	2017	Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer
Several mechanisms have been proposed to explain how ion channels and transporters distinguish between similar ions , a process crucial for maintaining proper cell function . Of these , three can be broadly classed as mechanisms involving specific positional constraints on the ion coordinating ligands which arise throu...	Differentiating between Na+ and K+ ions is important for many cellular processes , such as nerve conduction and the regulation of membrane potentials . Different biological molecules utilise different methods to discriminate between ions . In this work , the reduced ligand fluctuation mechanism of ion selectivity is de...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "molecular", "mechanics", "molecular", "dynamics", "chemistry", "biology", "computational", "chemistry", "biophysics", "simulations", "biophysics" ]	2013	An Entropic Mechanism of Generating Selective Ion Binding in Macromolecules
Semi-conservative segregation of nucleosomes to sister chromatids during DNA replication creates gaps that must be filled by new nucleosome assembly . We analyzed the cell-cycle timing of centromeric chromatin assembly in Drosophila , which contains the H3 variant CID ( CENP-A in humans ) , as well as CENP-C and CAL1 ,...	The centromere is essential for kinetochore formation , chromosome attachment to spindle microtubules , and equal segregation of the genome to daughter cells . Centromeres are epigenetically inherited through a unique type of chromatin which contains centromere-specific proteins . At each round of DNA replication , cen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	Assembly of Drosophila Centromeric Chromatin Proteins during Mitosis
In both insects and mammals , spermatids eliminate their bulk cytoplasm as they undergo terminal differentiation . In Drosophila , this process of dramatic cellular remodeling requires apoptotic proteins , including caspases . To gain further insight into the regulation of caspases , we screened a large collection of s...	Caspases are a family of proteases that play important roles in programmed cell death ( apoptosis ) . These enzymes also have nonlethal functions , for example , in inflammation , cell differentiation , and cellular morphogenesis . During maturation , sperm cells eliminate the majority of their cytoplasm and organelles...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "drosophila" ]	2007	A Ubiquitin Ligase Complex Regulates Caspase Activation During Sperm Differentiation in Drosophila
The honeybee olfactory system is a well-established model for understanding functional mechanisms of learning and memory . Olfactory stimuli are first processed in the antennal lobe , and then transferred to the mushroom body and lateral horn through dual pathways termed medial and lateral antennal lobe tracts ( m-ALT ...	The honeybee olfactory system offers the opportunity to study different levels of learning complexity in a small size network . Odour information is transferred from the antennae to the antennal lobes , and from there to the mushroom bodies and the lateral horn via parallel medial and lateral tracts of projection neuro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "invertebrates", "honey", "bees", "social", "sciences", "neuroscience", "learning", "and", "memory", "animals", "synaptic", "plasticity", "cognitive", "psychology", "odorants", "materials", "science", "neuronal", "plasticity", "bees", "developmental", "neurosc...	2017	Olfactory learning without the mushroom bodies: Spiking neural network models of the honeybee lateral antennal lobe tract reveal its capacities in odour memory tasks of varied complexities
Nontyphoidal Salmonellae ( NTS ) are responsible for a huge burden of bloodstream infection in Sub-Saharan African children . Recent reports of a decline in invasive NTS ( iNTS ) disease from Kenya and The Gambia have emphasised an association with malaria control . Following a similar decline in iNTS disease in Malawi...	Invasive nontyphoidal Salmonella ( iNTS ) disease is estimated to be responsible for 680 , 000 deaths/year and yet this is widely under-recognised by clinicians , epidemiologists and policymakers in Sub-Saharan Africa . Recently there have been reports of a decline in childhood iNTS disease from both Kenya and The Gamb...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Modelling the Contributions of Malaria, HIV, Malnutrition and Rainfall to the Decline in Paediatric Invasive Non-typhoidal Salmonella Disease in Malawi
Buruli ulcer ( BU ) is a progressive disease of subcutaneous tissues caused by Mycobacterium ulcerans . The pathology of BU lesions is associated with the local production of a diffusible substance , mycolactone , with cytocidal and immunosuppressive properties . The defective inflammatory responses in BU lesions refle...	Mycolactone is a lipophilic molecule produced by Mycobacterium ulcerans , the causative agent of the skin disease Buruli ulcer ( BU ) . Mycolactone displays unique cytocidal and immunosuppressive properties that are reflected locally by massive tissue necrosis and minimal inflammation . Here we investigated whether myc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "pathology/immunology" ]	2008	Mycolactone Diffuses from Mycobacterium ulcerans–Infected Tissues and Targets Mononuclear Cells in Peripheral Blood and Lymphoid Organs
Recent studies of the HapMap lymphoblastoid cell lines have identified large numbers of quantitative trait loci for gene expression ( eQTLs ) . Reanalyzing these data using a novel Bayesian hierarchical model , we were able to create a surprisingly high-resolution map of the typical locations of sites that affect mRNA ...	Individual phenotypes within natural populations generally exhibit a large diversity resulting from a complex interplay of genes and environmental factors . Since the advent of molecular markers in the 1980s , quantitative genetics has made a significant step toward unraveling the genetic bases of such complex traits ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/gene", "expression" ]	2008	High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation
We quantified Leishmania infantum parasites transmitted by natural vectors for the first time . Both L . infantum strains studied , dermotropic CUK3 and viscerotropic IMT373 , developed well in Phlebotomus perniciosus and Lutzomyia longipalpis . They produced heavy late-stage infection and colonized the stomodeal valve...	Leishmaniasis is a disease caused by protozoan parasites which are transmitted through the bites of infected insects called sand flies . The World Health Organization has estimated that leishmaniases cause 1 . 6 million new cases annually , of which an estimated 1 . 1 million are cutaneous or mucocutaneous , and 500 , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parastic", "protozoans", "medicine", "infectious", "diseases", "veterinary", "diseases", "zoonotic", "diseases", "neglected", "tropical", "diseases", "protozoology", "biology", "microbiology", "veterinary", "science" ]	2011	Experimental Transmission of Leishmania infantum by Two Major Vectors: A Comparison between a Viscerotropic and a Dermotropic Strain
To support the Bangladesh National Kala-azar Elimination Programme ( NKEP ) , we investigated the feasibility of using trained village volunteers for detecting post-kala-azar dermal leishmaniasis ( PKDL ) cases , using polymerase chain reaction ( PCR ) for confirmation of diagnosis and treatment compliance by PKDL pati...	PKDL is a skin disorder which usually develops in 10–20% and about 60% of patients with visceral leishmaniasis ( VL ) after treatment respectively in the Indian subcontinent and Sudan . However , cases among people without prior VL have also been reported . Except skin lesion , PKDL patients are healthy and usually do ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "public", "health", "and", "epidemiology/screening", "public", "health", "and", "epidemiology/health", "policy" ]	2010	Enhanced Case Detection and Improved Diagnosis of PKDL in a Kala-azar-Endemic Area of Bangladesh
The regulation of filopodia plays a crucial role during neuronal development and synaptogenesis . Axonal filopodia , which are known to originate presynaptic specializations , are regulated in response to neurotrophic factors . The structural components of filopodia are actin filaments , whose dynamics and organization...	Neurons communicate with each other via specialized cell–cell junctions called synapses . The proper formation of synapses ( “synaptogenesis” ) is crucial to the development of the nervous system , but the molecular pathways that regulate this process are not fully understood . External cues , such as brain-derived neu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "cell", "biology/neuronal", "signaling", "mechanisms", "neuroscience/neuronal", "signaling", "mechanisms", "neuroscience/neuronal", "and", "glial", "cell", "biology", "cell", "biology/cytoskeleton" ]	2009	Eps8 Regulates Axonal Filopodia in Hippocampal Neurons in Response to Brain-Derived Neurotrophic Factor (BDNF)
The role of adult hippocampal neurogenesis in spatial learning remains a matter of debate . Here , we show that spatial learning modifies neurogenesis by inducing a cascade of events that resembles the selective stabilization process characterizing development . Learning promotes survival of relatively mature neurons ,...	The birth of adult hippocampal neurons is associated with enhanced learning and memory performance . In particular , spatial learning increases the survival and the proliferation of newborn cells , but surprisingly , it also decreases their number . Here , we hypothesized that spatial learning also depends upon the dea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "rattus", "(rat)" ]	2007	Spatial Learning Depends on Both the Addition and Removal of New Hippocampal Neurons
Synchronization between neuronal populations plays an important role in information transmission between brain areas . In particular , collective oscillations emerging from the synchronized activity of thousands of neurons can increase the functional connectivity between neural assemblies by coherently coordinating the...	The correct operation of the brain requires a carefully orchestrated activity , which includes the establishment of synchronized behavior among multiple neuronal populations . Synchronization of collective neuronal oscillations , in particular , has been suggested to mediate communication between brain areas , with the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "neuroscience", "neuroscience", "biology", "and", "life", "sciences", "computational", "biology" ]	2014	Phase-Coherence Transitions and Communication in the Gamma Range between Delay-Coupled Neuronal Populations
Myelin is essential for rapid saltatory conduction and is produced by Schwann cells in the peripheral nervous system and oligodendrocytes in the central nervous system . In both cell types the transcription factor Sox10 is an essential component of the myelin-specific regulatory network . Here we identify Myrf as an ol...	In recent years it has become clear that complex developmental processes are not regulated by single transcription factors but rather by combinations of transcription factors that interact in intricate regulatory networks . Here , we analyze the regulatory network that drives terminal differentiation of oligodendrocyte...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Transcription Factors Sox10 and Myrf Define an Essential Regulatory Network Module in Differentiating Oligodendrocytes
Genome-wide association studies and follow-up meta-analyses in Crohn's disease ( CD ) and ulcerative colitis ( UC ) have recently identified 163 disease-associated loci that meet genome-wide significance for these two inflammatory bowel diseases ( IBD ) . These discoveries have already had a tremendous impact on our un...	Genetic studies of common diseases have seen tremendous progress in the last half-decade primarily due to recent technologies that enable a systematic examination of genetic markers across the entire genome in large numbers of patients and healthy controls . The studies , while identifying genomic regions that influenc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis
The first reported Far East scarlet-like fever ( FESLF ) epidemic swept the Pacific coastal region of Russia in the late 1950s . Symptoms of the severe infection included erythematous skin rash and desquamation , exanthema , hyperhemic tongue , and a toxic shock syndrome . The term FESLF was coined for the infection be...	We have analyzed the genome sequence of a Y . pseudotuberculosis isolate responsible for Far East scarlet-like fever ( FESLF ) . FESLF leads to severe clinical manifestations , including scarlet-like skin rash , from which this illness gets its name , and , most importantly , a toxic shock syndrome not seen in common p...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "public", "health", "and", "epidemiology", "microbiology", "evolutionary", "biology", "genetics", "and", "genomics", "eubacteria" ]	2007	The Complete Genome Sequence of Yersinia pseudotuberculosis IP31758, the Causative Agent of Far East Scarlet-Like Fever
In this paper we use a hybrid multiscale mathematical model that incorporates both individual cell behaviour through the cell-cycle and the effects of the changing microenvironment through oxygen dynamics to study the multiple effects of radiation therapy . The oxygenation status of the cells is considered as one of th...	Anti-cancer treatments such as radiotherapy and chemotherapy have evolved through clinical trial-and-error over decades , and although they cure some cases and are partially effective in many , the majority of such cancers ultimately recur . Doctors turn to new , expensive drugs as they emerge , but perhaps fail to stu...	[ "Abstract", "Introduction", "Results/Discussion", "Methods", "Microenvironment", "and", "tumour", "growth" ]	[ "oncology", "medicine", "mathematics", "radiation", "therapy", "applied", "mathematics", "cancer", "treatment", "chemotherapy", "and", "drug", "treatment", "biology", "computational", "biology" ]	2013	Towards Predicting the Response of a Solid Tumour to Chemotherapy and Radiotherapy Treatments: Clinical Insights from a Computational Model
High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence , but not its copy number , varies among individuals . To explore such balanced structural polymorphisms , we used array-based Comparative Genomic Hybridization ( aCGH ) to conduct a ...	Balanced structural polymorphisms are differences in the relative arrangement of genomic features within species that do not affect DNA copy number . Little is known about their prevalence or importance because they are difficult to observe . Here , we present a novel methodology for systematically identifying such pol...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/chromosome", "biology", "evolutionary", "biology/genomics" ]	2009	Systematic Identification of Balanced Transposition Polymorphisms in Saccharomyces cerevisiae
A major goal of systems biology is to understand how organism-level behavior arises from a myriad of molecular interactions . Often this involves complex sets of rules describing interactions among a large number of components . As an alternative , we have developed a simple , macro-level model to describe how chronic ...	Dynamic response to changing conditions in the environment is an essential property of all biological systems . Whereas extensive research over the last several decades has elucidated numerous molecular responses to environmental stress , there is much less known how these translate into organismal-level responses . Tw...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "chemistry", "biology", "computational", "biology", "chemical", "engineering", "genetics", "and", "genomics", "engineering" ]	2012	Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress
Genome-scale metabolic reconstructions are currently available for hundreds of organisms . Constraint-based modeling enables the analysis of the phenotypic landscape of these organisms , predicting the response to genetic and environmental perturbations . However , since constraint-based models can only describe the me...	Genome-scale models of metabolism enable the exploration of the phenotypic landscape of an organism . Unlike probabilistic approaches such as genome-wide association studies , these models describe the mechanistic link between genotype and phenotype , predicting the response to genetic and environmental perturbations ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "deletion", "mutation", "medicine", "and", "health", "sciences", "enzymes", "enzymology", "simulation", "and", "modeling", "mutation", "enzyme", "metabolism", "genome", "analysis", "isozymes", "pharmacology", "drug", "metabolism", "enzyme", "chemistry", "research", "and...	2016	Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction
Vaccinia virus A33 is an extracellular enveloped virus ( EEV ) -specific type II membrane glycoprotein that is essential for efficient EEV formation and long-range viral spread within the host . A33 is a target for neutralizing antibody responses against EEV . In this study , we produced seven murine anti-A33 monoclona...	Before the eradication of smallpox ( variola virus ) from nature , hundreds of million of people succumbed to the infection . The discovery of vaccinia virus ( VACV ) , the active ingredient of the smallpox vaccine , ultimately led to the eradiation of smallpox from the human population . Vaccination with VACV leads to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Structural and Functional Characterization of Anti-A33 Antibodies Reveal a Potent Cross-Species Orthopoxviruses Neutralizer
Turkey is located in an important geographical location , in terms of the epidemiology of vector-borne diseases , linking Asia and Europe . Cutaneous leishmaniasis ( CL ) is one of the endemic diseases in a Turkey and according to the Ministry Health of Turkey , 45% of CL patients originate from Şanlıurfa province loca...	Turkey is one of the endemic countries for leishmaniasis , cutaneous and visceral . Cutaneous leishmaniasis caused by Leishmania tropica is a serious public health problem with more than two thousands of local cases each year . Moreover , with the civil war in Syria more than three million refugees were accepted to res...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "turkey", "(country)", "heterozygosity", "medicine", "and", "health", "sciences", "geographical", "locations", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "alleles", "microsatellite", "loci", "protozoans", "leishmania", "gene", "types", "ne...	2017	Epidemiological analysis of Leishmania tropica strains and giemsa-stained smears from Syrian and Turkish leishmaniasis patients using multilocus microsatellite typing (MLMT)
Human visceral leishmaniasis ( VL ) caused by L . infantum and cutaneous leishmaniasis ( CL ) caused by L . tropica and L . infantum have been reported in Turkey . L . infantum is also responsible for canine leishmaniasis ( CanL ) and it is widely common in the country . The main aim of the present study was to design ...	Leishmaniasis caused by Leishmania parasites are seen as cutaneous ( CL ) and visceral ( VL ) clinical forms in Turkey . Leishmania ( L . ) tropica and L . infantum were determined as CL agents , while L . infantum was incriminated for VL in the country . Canine leishmaniasis ( CanL ) is widely common throughout the co...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "leishmaniasis", "medicine", "neglected", "tropical", "diseases", "infectious", "diseases" ]	2013	A Real-Time ITS1-PCR Based Method in the Diagnosis and Species Identification of Leishmania Parasite from Human and Dog Clinical Samples in Turkey
Ticks are distributed worldwide and affect human and animal health by transmitting diverse infectious agents . Effective vaccines against most tick-borne pathogens are not currently available . In this study , we characterized a tick histamine release factor ( tHRF ) from Ixodes scapularis and addressed the vaccine pot...	Ticks are distributed worldwide and affect human and animal health by transmitting diverse infectious agents . Safe and effective vaccines against most tick-borne pathogens are not currently available . Typical vaccines target microbes directly , using extracts of the organism , or recombinant antigens as the immunogen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis", "immunology/immunity", "to", "infections", "microbiology/immunity", "to", "infections" ]	2010	Tick Histamine Release Factor Is Critical for Ixodes scapularis Engorgement and Transmission of the Lyme Disease Agent
Currently , there are three algorithms for screening of syphilis: traditional algorithm , reverse algorithm and European Centre for Disease Prevention and Control ( ECDC ) algorithm . To date , there is not a generally recognized diagnostic algorithm . When syphilis meets HIV , the situation is even more complex . To e...	Syphilis remains a worldwide public health concern as there has been a global increase in the incidence of syphilis . Serologic tests are still considered the mainstay of syphilis diagnosis . Currently , there are three algorithms for screening of syphilis- traditional algorithm , reverse algorithm and European Centre ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "urology", "hiv", "infections", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "applied", "mathematics", "tropical", "diseases", "microbiology", "simulation", "and", "modeling", "algorithms", "treponematoses", "bacteria...	2017	The tradition algorithm approach underestimates the prevalence of serodiagnosis of syphilis in HIV-infected individuals
Involuntary force variability below 15 Hz arises from , and is influenced by , many factors including descending neural drive , proprioceptive feedback , and mechanical properties of muscles and tendons . However , their potential interactions that give rise to the well-structured spectrum of involuntary force variabil...	Involuntary fluctuations in muscle force are an unavoidable consequence of human motor control and underlie movement execution errors . Amplification and distortion of involuntary force variability are common phenomena found in various neurological conditions and in fatigue . However , the underlying mechanisms for thi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "classical", "mechanics", "myoclonus", "pathology", "and", "laboratory", "medicine", "fatigue", "engineering", "and", "technology", "signal", "processing", "biomechanics", "noise", "reduction", "simulation", "and", "modeling", "s...	2018	Cardinal features of involuntary force variability can arise from the closed-loop control of viscoelastic afferented muscles
The cytoplasmic TRIM5α proteins of certain mammalian lineages efficiently recognize the incoming capsids of particular retroviruses and potently restrict infection in a species-specific manner . Successful retroviruses have evolved capsids that are less efficiently recognized by the TRIM5α proteins of the natural hosts...	The cytoplasmic TRIM5α restricts the replication of a broad range of retroviruses in a species-specific manner . In the present study we show that TRIM5α is more than a species barrier for retroviruses . We show that naturally occurring B30 . 2 ( SPRY ) polymorphisms affect retrovirus infection . These observations dem...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics", "virology/immunodeficiency", "viruses", "virology/animal", "models", "of", "infection", "virology/host", "antiviral", "responses" ]	2010	TRIM5α Modulates Immunodeficiency Virus Control in Rhesus Monkeys
Assembling of the membrane-bound viral replicase complexes ( VRCs ) consisting of viral- and host-encoded proteins is a key step during the replication of positive-stranded RNA viruses in the infected cells . Previous genome-wide screens with Tomato bushy stunt tombusvirus ( TBSV ) in a yeast model host have revealed t...	Replication of positive-stranded RNA viruses depends on recruitment of host proteins and cellular membranes to assemble the viral replicase complexes . Tombusviruses , small RNA viruses of plants , co-opt the cellular ESCRT ( endosomal sorting complexes required for transport ) proteins to facilitate replicase assembly...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "model", "organisms", "cell", "biology", "biology", "and", "life", "sciences", "microbiology", "molecular", "cell", "biology", "agriculture", "research", "and", "analysis", "methods" ]	2014	Noncanonical Role for the Host Vps4 AAA+ ATPase ESCRT Protein in the Formation of Tomato Bushy Stunt Virus Replicase
One of the fundamental questions in biology is how cooperative and altruistic behaviors evolved . The majority of studies seeking to identify the genes regulating these behaviors have been performed in systems where behavioral and physiological differences are relatively fixed , such as in the honey bee . During colony...	The characterization of the genomic basis for complex behaviors is one of the major goals of biological research . The genomic state of an individual results from the interplay between its internal condition ( the “nature” ) and the external environment ( the “nurture” ) , which may include the social environment . Col...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "expression", "analysis", "evolutionary", "ecology", "functional", "genomics", "genome", "evolution", "integrated", "control", "gene", "function", "genome", "analysis", "tools", "chemical", "ecology", "genome", "databases...	2013	Sociogenomics of Cooperation and Conflict during Colony Founding in the Fire Ant Solenopsis invicta
An approach combining genetic , proteomic , computational , and physiological analysis was used to define a protein network that regulates fat storage in budding yeast ( Saccharomyces cerevisiae ) . A computational analysis of this network shows that it is not scale-free , and is best approximated by the Watts-Strogatz...	We discovered a large protein network that regulates fat storage in budding yeast . This network contains 94 proteins , almost all of which bind to other proteins in the network . To understand the functions of large protein collections such as these , it will be necessary to move away from one-by-one analysis of indiv...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Experimental and Computational Analysis of a Large Protein Network That Controls Fat Storage Reveals the Design Principles of a Signaling Network
First described in humans in 1964 , reports of co-infections with dengue ( DENV ) and chikungunya ( CHIKV ) viruses are increasing , particularly after the emergence of chikungunya ( CHIK ) in the Indian Ocean in 2005–2006 due to a new variant highly transmitted by Aedes albopictus . In this geographic area , a dengue ...	Dengue ( DEN ) and chikungunya ( CHIK ) are two mosquito borne infections transmitted by Aedes mosquitoes in the tropical world . Ae . albopictus has been shown to efficiently transmit the new variant of CHIK virus ( CHIKV ) that emerged in the Indian Ocean region in 2005 . At the same time , this vector is able to sus...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Acknowledgments" ]	[ "infectious", "diseases/neglected", "tropical", "diseases" ]	2010	Orally Co-Infected Aedes albopictus from La Reunion Island, Indian Ocean, Can Deliver Both Dengue and Chikungunya Infectious Viral Particles in Their Saliva
Brucella are highly infectious bacterial pathogens responsible for a severely debilitating zoonosis called brucellosis . Half of the human population worldwide is considered to live at risk of exposure , mostly in the poorest rural areas of the world . Prompt diagnosis of brucellosis is essential to prevent complicatio...	Brucella are bacteria that mainly infect animals . They can also be transmitted to humans and cause a serious disease called brucellosis . Half the world's population is considered exposed , especially in the poorest rural areas . Experts agree that prompt identification of Brucella isolates is essential to provide app...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "ruminants", "pathogens", "tropical", "diseases", "microbiology", "vertebrates", "animals", "mammals", "brucellosis", "marine", "biology", "bacterial", "diseases", "...	2018	A MALDI-TOF MS database with broad genus coverage for species-level identification of Brucella
The function of most proteins is not determined experimentally , but is extrapolated from homologs . According to the “ortholog conjecture” , or standard model of phylogenomics , protein function changes rapidly after duplication , leading to paralogs with different functions , while orthologs retain the ancestral func...	To infer the function of an unknown gene , possibly the most effective way is to identify a well-characterized evolutionarily related gene , and assume that they have both kept their ancestral function . If several such homologs are available , all else being equal , it has long been assumed that those that diverged by...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "function", "genome", "analysis", "tools", "phylogenetics", "sequence", "analysis", "comparative", "genomics", "biology", "proteomics", "evolutionary", "systematics", "biochemistry", "genetics", "genomics", "evolutionary", "biology", "computational", "biology", "gen...	2012	Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs
Plant organ growth is controlled by inter-cell-layer communication , which thus determines the overall size of the organism . The epidermal layer interfaces with the environment and participates in both driving and restricting growth via inter-cell-layer communication . However , it remains unknown whether the epidermi...	The epidermis functions as an important interface with the environment , but in plants it is also essential for establishing and maintaining the primary plant body . Recent studies have shown that the epidermis participates in both driving and restricting plant growth via inter-cell-layer communication . However , it r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "plant", "science", "model", "organisms", "plant", "biology", "biology" ]	2013	Synthesis of Very-Long-Chain Fatty Acids in the Epidermis Controls Plant Organ Growth by Restricting Cell Proliferation
We are interested in how intragenic recombination contributes to the evolution of proteins and how this mechanism complements and enhances the diversity generated by random mutation . Experiments have revealed that proteins are highly tolerant to recombination with homologous sequences ( mutation by recombination is co...	Mutation and recombination are the primary sources of genetic variation in evolving populations . The relative benefit of these two diversification mechanisms and how they complement each other has been a long-standing question in evolutionary biology . While it is clear what types of genetic diversity these two mechan...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "evolutionary", "biology", "evolutionary", "modeling", "protein", "structure", "biology", "computational", "biology", "macromolecular", "structure", "analysis" ]	2012	Random Field Model Reveals Structure of the Protein Recombinational Landscape

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