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Tumors exploit angiogenesis , the formation of new blood vessels from pre-existing vasculature , in order to obtain nutrients required for continued growth and proliferation . Targeting factors that regulate angiogenesis , including the potent promoter vascular endothelial growth factor ( VEGF ) , is therefore an attra...	One hallmark of cancer is angiogenesis , the formation of new blood capillaries from pre-existing vessels . Angiogenesis promotes tumor growth by enabling the tumor to obtain oxygen and nutrients from the surrounding microenvironment . Cancer drugs that inhibit angiogenesis ( "anti-angiogenic therapies" ) have focused ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "cardiovascular", "physiology", "vegf", "signaling", "dose", "prediction", "methods", "endothelial", "cells", "cancer", "treatment", "basic", "cancer", "research", "biomarkers", "epithelial", "cells", "oncology", "angiogenesis", ...	2017	Mechanistic modeling quantifies the influence of tumor growth kinetics on the response to anti-angiogenic treatment
Cells respond to stressful conditions by coordinating a complex , multi-faceted response that spans many levels of physiology . Much of the response is coordinated by changes in protein phosphorylation . Although the regulators of transcriptome changes during stress are well characterized in Saccharomyces cerevisiae , ...	Cells sense and respond to stressful environments by utilizing complex signaling networks that integrate diverse signals to coordinate a multi-faceted physiological response . Much of this response is controlled by post-translational protein phosphorylation . Although many regulators that mediate changes in protein pho...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "cellular", "stress", "responses", "gene", "regulation", "protein", "interaction", "networks", "regulatory", "proteins", "cell", "processes", "signaling", "networks", "dna-binding", "proteins", "network", "analysis", "genome", "analysis", "transcription",...	2018	Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response
Recently , improvements have been made to diagnostics for gambiense sleeping sickness control but their performance remains poorly documented and may depend on specimen processing prior to examination . In a prospective study in the Democratic Republic of the Congo , we compared the diagnostic performance of several pa...	Human African trypanosomiasis or sleeping sickness still causes considerable suffering in sub-Sahara Africa . Diagnostics for this infectious disease constantly improve but their performance in terms of accuracy and reproducibility should be evaluated prior to implementation in control activities . We evaluated the dia...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "diagnostic", "medicine", "african", "trypanosomiasis", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "tropical", "diseases", "trypanosomi...	2014	Performance of Parasitological and Molecular Techniques for the Diagnosis and Surveillance of Gambiense Sleeping Sickness
Our motor commands can be exquisitely timed according to the demands of the environment , and the ability to generate rhythms of different tempos is a hallmark of musical cognition . Yet , the neuronal underpinnings behind rhythmic tapping remain elusive . Here , we found that the activity of hundreds of primate medial...	The ability to extract the regular pulse in music and to respond in synchrony to this pulse is called beat synchronization and is a natural human behavior exhibited during dancing and musical ensemble playing . A part of the brain called the medial premotor cortex has been associated with rhythmic entrainment , and yet...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusions", "Materials", "and", "methods" ]	[]	2019	The amplitude in periodic neural state trajectories underlies the tempo of rhythmic tapping
Much laboratory work has been carried out to determine the gene regulatory network ( GRN ) that results in plant cells becoming flowers instead of leaves . However , this also involves the spatial distribution of different cell types , and poses the question of whether alternative networks could produce the same set of...	Complex organisms develop following a genetic program specifying how their cells differentiate into organs with different specialized functions . Details of these mechanisms are incomplete , and aspects might not be correct . These genetic programs can be represented by simple computer programs processing input data in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "computer", "applications", "plant", "anatomy", "gene", "regulation", "plant", "physiology", "hormones", "regulator", "genes", "plant", "science", "plant", "hormones", "gene", "types", "inflorescences", "computer", "and", "information", "sciences", "gene", "expression",...	2017	The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs
The cat flea , Ctenocephalides felis , is prevalent worldwide , will parasitize animal reservoirs of plague , and is associated with human habitations in known plague foci . Despite its pervasiveness , limited information is available about the cat flea’s competence as a vector for Yersinia pestis . It is generally con...	Although plague primarily affects wild rodents , human plague outbreaks still occur periodically in some areas of the world . Yersinia pestis , the bacterial agent of plague , is transmitted by fleas . Cat fleas are abundant worldwide , regularly infest human habitations in plague endemic areas , and readily bite human...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "bacteriology", "biofilms", "invertebrates", "medicine", "and", "health", "sciences", "plagues", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "animals", "mammals", "bacterial", "diseases", "yersinia", "fleas",...	2016	Feeding Behavior Modulates Biofilm-Mediated Transmission of Yersinia pestis by the Cat Flea, Ctenocephalides felis
Apicomplexa are intracellular parasites that cause important human diseases including malaria and toxoplasmosis . During host cell infection new parasites are formed through a budding process that parcels out nuclei and organelles into multiple daughters . Budding is remarkably flexible in output and can produce two to...	Malaria , toxoplasmosis , and related diseases are caused by infection with unicellular parasites called Apicomplexa . Their name refers to the elaborate invasion machinery that occupies the apical end of the parasite cell . This apparatus allows the parasite to force its way into the cells of its host , and to deliver...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "cell", "division", "cell", "biology", "protozoology", "biology", "microbiology", "parasitology" ]	2012	Cell Division in Apicomplexan Parasites Is Organized by a Homolog of the Striated Rootlet Fiber of Algal Flagella
Recent evidence on HDAC6 function underlines its role as a key protein in the innate immune response to viral infection . However , whether HDAC6 regulates innate immunity during bacterial infection remains unexplored . To assess the role of HDAC6 in the regulation of defence mechanisms against intracellular bacteria ,...	Listeria monocytogenes ( Lm ) is a food-borne intracellular bacterium that causes listeriosis to 1 . 600 people each year , being responsible of approximately 260 deaths . This pathogen mostly affects immunocompromised individuals and pregnant women . It is particularly dangerous for the later due to its ability to pas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "death", "innate", "immune", "system", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "immune", "cells",...	2017	HDAC6 controls innate immune and autophagy responses to TLR-mediated signalling by the intracellular bacteria Listeria monocytogenes
Because species invasions are a principal driver of the human-induced biodiversity crisis , the identification of the major determinants of global invasions is a prerequisite for adopting sound conservation policies . Three major hypotheses , which are not necessarily mutually exclusive , have been proposed to explain ...	As one of the major threats to biodiversity , the detrimental consequences of biological invasions are widely recognised . Despite this , a global view of invasion patterns and their determinants is still lacking in aquatic ecosystems , reducing our ability to initiate practical actions . Here we report the global patt...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology" ]	2008	Fish Invasions in the World's River Systems: When Natural Processes Are Blurred by Human Activities
Small noncoding RNAs ( sRNAs ) play important roles in gene regulation in both prokaryotes and eukaryotes . Thus far , no sRNA has been assigned a definitive role in virulence in the major human pathogen Streptococcus pneumoniae . Based on the potential coding capacity of intergenic regions , we hypothesized that the p...	Pneumonia is a leading cause of childhood mortality worldwide , resulting in more deaths in young children than any other infectious disease . One of the leading causes of pneumonia is the human pathogen , Streptococcus pneumoniae , the causative agent of over six million infections each year in the United States . Und...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology" ]	2012	Control of Virulence by Small RNAs in Streptococcus pneumoniae
The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction . As is the case for proteins , RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling procedure . Both ar...	The importance of RNA in biology and medicine has increased immensely over the last several years , due to the discovery of a wide range of important biological processes that are under the guidance of non-coding RNA . As is the case with proteins , the function of an RNA molecule is encoded in its three-dimensional ( ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "biophysics/theory", "and", "simulation", "molecular", "biology/bioinformatics", "biophysics/rna", "structure", "mathematics/statistics", "computational", "biology/molecular", "dynamics" ]	2009	A Probabilistic Model of RNA Conformational Space
Early ante-mortem laboratory confirmation of human rabies is essential to aid patient management and institute public health measures . Few studies have highlighted the diagnostic value of antibody detection in CSF/serum in rabies , and its utility is usually undermined owing to the late seroconversion and short surviv...	Ante-mortem diagnosis of human rabies is essential for patient management and public health measures . The detection of virus specific antibodies in the CSF/serum of patients with suspected rabies is thought to have a limited diagnostic role owing to late seroconversion and short survival in rabies . We examined the di...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "clinical", "laboratory", "sciences", "immune", "physiology", "body", "fluids", "pathology", "and", "laboratory", "medicine", "nervous", "system", "pathogens", "immunology", "tropical", "diseases", "microbiology", "saliva", "viru...	2019	Utility of rabies neutralizing antibody detection in cerebrospinal fluid and serum for ante-mortem diagnosis of human rabies
We uncovered the universal statistical laws for the biomolecular recognition/binding process . We quantified the statistical energy landscapes for binding , from which we can characterize the distributions of the binding free energy ( affinity ) , the equilibrium constants , the kinetics and the specificity by explorin...	Uncovering the principles and underlying mechanisms of biomolecular recognition and molecular binding process is crucial for understanding the function and evolution , yet challenging . We meet the challenge by quantifying the statistical natures of the relevant physical variables of biomolecular recognition using the ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition
Gene loss by deletion is a common evolutionary process in bacteria , as exemplified by bacteria with small genomes that have evolved from bacteria with larger genomes by reductive processes . The driving force ( s ) for genome reduction remains unclear , and here we examined the hypothesis that gene loss is selected be...	The mechanisms and driving forces involved in reductive evolution and loss of non-used gene functions are still largely unknown . Since most deletions are thought to have a negative effect on fitness , it is thought that deletions accumulate by chance , via non-adaptive genetic drift combined with an associated underly...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "microbiology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2012	Selection-Driven Gene Loss in Bacteria
Developing organs acquire a specific three-dimensional form that ensures their normal function . Cardiac function , for example , depends upon properly shaped chambers that emerge from a primitive heart tube . The cellular mechanisms that control chamber shape are not yet understood . Here , we demonstrate that chamber...	As organs develop , they acquire a characteristic shape; the factors governing this complex process , however , are not understood . Shape may be sculpted by cell movement , cell division , or changes in cell size and shape , all of which can be influenced by the local environment . Here we investigate heart formation ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "developmental", "biology", "in", "vitro", "eukaryotes", "vertebrates", "mammals" ]	2007	Functional Modulation of Cardiac Form through Regionally Confined Cell Shape Changes
Deregulated CD8+ T cell cytotoxicity plays a central role in enhancing disease severity in several conditions . However , we have little understanding of the mechanisms by which immunopathology develops as a consequence of cytotoxicity . Using murine models of inflammation induced by the protozoan parasite leishmania ,...	Leishmaniasis is a neglected tropical disease endemic in 98 countries and approximately 1 million new cases occur each year . Disease caused by Leishmania braziliensis , the main causative agent of leishmaniasis in South America , leads to skin ulcers that are difficult to heal with drugs that target the parasites . Th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "ears", "immunology", "parasitic", "diseases", "animal", "models", "otology", "model", "organisms", "ear", "infections", "signs", "and", "symp...	2017	CD8+ T cell cytotoxicity mediates pathology in the skin by inflammasome activation and IL-1β production
Bacteria depend on efficient RNA turnover , both during homeostasis and when rapidly altering gene expression in response to changes . Nevertheless , remarkably few details are known about the rate-limiting steps in targeting and decay of RNA . The membrane-anchored endoribonuclease RNase Y is a virulence factor in Gra...	Ribonucleic acids ( RNA ) are key intermediates between the heritable genome and the expression of proteins . Thus the level of a specific RNA determines the capability of the cell to produce the corresponding protein . Bacteria maintain a very high turnover ( high production but also high decay-rate ) of RNA molecules...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation
Neorickettsia sennetsu infection is rarely recognized , with less than 100 globally reported patients over the last 50 years . The disease is thought to be contracted by eating raw fish , a staple of many South-East Asian cuisines . In 2009 , the first patient with sennetsu was identified in the Lao PDR ( Laos ) , rais...	After the rediscovery of Neorickettsia sennetsu as a possible fish-borne cause of fever in 2009 , it remained unclear to what extent this pathogen was responsible for disease in Laos and South-East Asia . The original reports from the 1960s proposed an epidemiological link between eating raw fish and sennetsu . Dishes ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Neorickettsia sennetsu as a Neglected Cause of Fever in South-East Asia
Bcl-2 family proteins including the pro-apoptotic BH3-only proteins are central regulators of apoptotic cell death . Here we show by a focused siRNA miniscreen that the synergistic action of the BH3-only proteins Bim and Bmf is required for apoptosis induced by infection with Neisseria gonorrhoeae ( Ngo ) . While Bim a...	A variety of physiological death signals , as well as pathological insults , trigger apoptosis , a genetically programmed form of cell death . Pathogens often induce host cell apoptosis to establish a successful infection . Neisseria gonorrhoeae ( Ngo ) , the etiological agent of the sexually transmitted disease gonorr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cytoskeleton", "microbiology/cellular", "microbiology", "and", "pathogenesis", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2009	Bim and Bmf Synergize To Induce Apoptosis in Neisseria Gonorrhoeae Infection
Chikungunya virus ( CHIKV ) typically causes explosive epidemics of fever , rash and polyarthralgia after its introduction into naïve populations . Since its introduction in Panama in May of 2014 , few autochthonous cases have been reported; most of them were found within limited outbreaks in Panama City in 2014 and Pu...	Chikungunya virus ( CHIKV ) is a mosquito borne pathogen that causes fever with rash and arthralgia , which are often confused with Dengue virus ( DENV ) infections . It has been reported that when CHIKV colonizes regions without previous circulation , it generally results in explosive human epidemics . In Panama , the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "panama", "animals", "alphaviruses", "viruses...	2017	Unusual pattern of chikungunya virus epidemic in the Americas, the Panamanian experience
Pregnant women , and their fetal offspring , are uniquely susceptible to Zika virus and other microbial pathogens capable of congenital fetal infection . Unavoidable exposure to Zika virus in endemic areas underscores the need for identifying at-risk individuals , and protecting expecting mothers and their fetal offspr...	Expecting mothers are uniquely susceptible to Zika virus infection that often spreads to vital tissues of the developing fetus . Since Zika virus infection in healthy non-pregnant individuals is mostly asymptomatic , a large proportion of reproductive age women that live in Zika endemic areas have been previously infec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "physiology", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "cloning", "viruses", "rna", "viruses", "mammalian", "genomics", "molecular", ...	2017	Preconceptual Zika virus asymptomatic infection protects against secondary prenatal infection
In many bacteria the rate of DNA replication is linked with cellular physiology to ensure that genome duplication is coordinated with growth . Nutrient-mediated growth rate control of DNA replication initiation has been appreciated for decades , however the mechanism ( s ) that connects these cell cycle activities has ...	DNA replication must be coordinated with cellular physiology to ensure proper genome inheritance . Model bacteria such as the soil-dwelling Bacillus subtilis can achieve a wide range of growth rates in response to nutritional and chemical signals . In order to match the rate of DNA synthesis to the rate of nutrient-med...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "gram", "positive", "bacteria", "biochemistry", "developmental", "biology", "dna", "replication", "bacterial", "genes", "genetics", "biology", "and", "life", "sciences", "dna", "microbial", "growth", "and", "development", "molecular", "genetics", "microb...	2014	Multiple Regulatory Systems Coordinate DNA Replication with Cell Growth in Bacillus subtilis
Collagen is a major component of the extracellular matrix and its integrity is essential for connective tissue and organ function . The importance of proteins involved in intracellular collagen post-translational modification , folding and transport was recently highlighted from studies on recessive forms of osteogenes...	Fibrillar collagens are major components of connective tissue extracellular matrix ( ECM ) . Among them , type I collagen is the most abundant protein in the human body and a large constituent of bone , dermis , tendon and ligament ECMs; type I collagen is also present in the stroma of other organs including heart , lu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "bonding", "medicine", "and", "health", "sciences", "chemical", "compounds", "endoplasmic", "reticulum", "cell", "processes", "organic", "compounds", "fibroblasts", "collagens", "animal", "models", "model", "organisms", "immunoprecipitation", "connective", "ti...	2016	Sc65-Null Mice Provide Evidence for a Novel Endoplasmic Reticulum Complex Regulating Collagen Lysyl Hydroxylation
Notch signaling between neighboring cells controls many cell fate decisions in metazoans both during embryogenesis and in postnatal life . Previously , we uncovered a critical role for physiological Notch signaling in suppressing osteoblast differentiation in vivo . However , the contribution of individual Notch recept...	Osteoporosis is a disease caused by disruption of the balance between bone formation and resorption resulting in a net loss of bone mass . Although anti-resorptive agents are the current mainstay of osteoporosis therapy , novel strategies to promote bone formation are critically needed for more effective prevention and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "histology", "model", "organisms", "physiology", "genetics", "biology", "anatomy", "and", "physiology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Physiological Notch Signaling Maintains Bone Homeostasis via RBPjk and Hey Upstream of NFATc1
In the malaria parasite Plasmodium falciparum , the cellular redox potential influences signaling events , antioxidant defense , and mechanisms of drug action and resistance . Until now , the real-time determination of the redox potential in malaria parasites has been limited because conventional approaches disrupt sub...	In the malaria parasite Plasmodium falciparum , cellular redox reactions play important roles not only in redox-regulatory processes and antioxidant defense but also in the mechanisms of drug action and drug resistance . The tripeptide glutathione is present in malaria parasites in millimolar concentrations and represe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Real-Time Imaging of the Intracellular Glutathione Redox Potential in the Malaria Parasite Plasmodium falciparum
Caviomorph rodents , some of the oldest Leishmania spp . hosts , are widely dispersed in Brazil . Despite both experimental and field studies having suggested that these rodents are potential reservoirs of Leishmania parasites , not more than 88 specimens were analyzed in the few studies of natural infection . Our hypo...	Leishmaniasis is a major public health problem expanding in Brazil and one of the reasons is that we still have poor knowledge of some aspects of the biology and epidemiology of Leishmania species , including the role of wild mammals . Caviomorph rodents , some of the oldest Leishmania spp . hosts , are widely disperse...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "veterinary", "parasitology", "leishmaniasis", "parasitology", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "tropical", "diseases", "prot...	2014	Distinct Leishmania Species Infecting Wild Caviomorph Rodents (Rodentia: Hystricognathi) from Brazil
Ongoing greenhouse gas emissions can modify climate processes and induce shifts in ocean temperature , pH , oxygen concentration , and productivity , which in turn could alter biological and social systems . Here , we provide a synoptic global assessment of the simultaneous changes in future ocean biogeochemical variab...	Climate change caused by human activity could damage biological and social systems . Here we gathered climate , biological , and socioeconomic data to describe some of the events by which ocean biogeochemical changes triggered by ongoing greenhouse gas emissions could cascade through marine habitats and organisms , eve...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[]	2013	Biotic and Human Vulnerability to Projected Changes in Ocean Biogeochemistry over the 21st Century
SNARE complexes are required for membrane fusion in the endomembrane system . They contain coiled-coil bundles of four helices , three ( Qa , Qb , and Qc ) from target ( t ) -SNAREs and one ( R ) from the vesicular ( v ) -SNARE . NSF/Sec18 disrupts these cis-SNARE complexes , allowing reassembly of their subunits into ...	Cellular components often travel between organelles in vesicular entities . This intracellular traffic usually involves production of a vesicle containing cargo from one organelle membrane , movement of the vesicle to its destination , and then fusion of the vesicle with the target organelle . Thus , membrane fusion is...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biology", "molecular", "cell", "biology" ]	2012	Sequential Analysis of Trans-SNARE Formation in Intracellular Membrane Fusion
Quantitative mechanistic models are valuable tools for disentangling biochemical pathways and for achieving a comprehensive understanding of biological systems . However , to be quantitative the parameters of these models have to be estimated from experimental data . In the presence of significant stochastic fluctuatio...	In this manuscript , we introduce efficient methods for parameter estimation for stochastic processes . The stochasticity of chemical reactions can influence the average behavior of the considered system . For some biological systems , a microscopic , stochastic description is computationally intractable but a macrosco...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "condensed", "matter", "physics", "simulation", "and", "modeling", "optimization", "mathematics", "statistics", "(mathematics)", "stochastic", "processes", "research", "and", "analysis", "methods", "stat", "signaling", "probability", "theory", "mesoscopic", "physics", "ap...	2016	Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion
Neuronal oscillatory activity has been reported in relation to a wide range of cognitive processes including the encoding of external stimuli , attention , and learning . Although the specific role of these oscillations has yet to be determined , it is clear that neuronal oscillations are abundant in the central nervou...	Oscillatory activity in the brain has been described in relation to many cognitive states and tasks , including the encoding of external stimuli , attention , learning and consolidation of memory . However , without tuning of synaptic weights with the preferred phase of firing the oscillatory signal may not be able to ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "learning", "medicine", "and", "health", "sciences", "action", "potentials", "nervous", "system", "population", "dynamics", "membrane", "potential", "social", "sciences", "electrophysiology", "neuroscience", "learning", "and", "memory", "synaptic", "plasticity", "cognitiv...	2016	Oscillations via Spike-Timing Dependent Plasticity in a Feed-Forward Model
A number of different genetics-based vector control methods have been proposed . Two approaches currently under development in Aedes aegypti mosquitoes are the two-locus engineered underdominance and killer-rescue gene drive systems . Each of these is theoretically capable of increasing in frequency within a population...	Vector-borne diseases represent a severe burden to both human and animal health worldwide . The methods currently being used to control a range of these diseases do not appear sufficient to address the issues at hand . As such , alternate methods for the control of vector-borne diseases are currently being investigated...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biotechnology", "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "population", "dynamics", "population", "genetics", "animals", "theoretical", "ecology", "population", "biology", "insect", "vectors", "genetic", "eng...	2018	Population dynamics of engineered underdominance and killer-rescue gene drives in the control of disease vectors
Sex ratio shifts in response to temperature are common in fish and reptiles . However , the mechanism linking temperature during early development and sex ratios has remained elusive . We show in the European sea bass ( sb ) , a fish in which temperature effects on sex ratios are maximal before the gonads form , that j...	Temperature changes during early embryonic and/or larval stages are able to modify sex ratios in fish and reptiles . However , the underlying mechanism by which temperature is able to modify the molecular pathways that developing gonads follow to become ovaries or testes is still unknown . One of the most interesting q...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "fisheries", "science", "marine", "and", "aquatic", "sciences", "genetics", "epigenetics", "biology", "dna", "modification", "morphogenesis", "marine", "biology", "genetics", "and", "genomics", "sex", "determination" ]	2011	DNA Methylation of the Gonadal Aromatase (cyp19a) Promoter Is Involved in Temperature-Dependent Sex Ratio Shifts in the European Sea Bass
The TOCA family of F-BAR–containing proteins bind to and remodel lipid bilayers via their conserved F-BAR domains , and regulate actin dynamics via their N-Wasp binding SH3 domains . Thus , these proteins are predicted to play a pivotal role in coordinating membrane traffic with actin dynamics during cell migration and...	Cells continuously remodel their shape especially during cell migration , differentiation , and tissues morphogenesis . This occurs through the dynamic reorganization of their plasma membrane and actin cytoskeleton: two processes that must therefore be intimately linked and coordinated . Molecules that sit at the cross...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "developmental", "biology/embryology", "developmental", "biology", "cell", "biology/cell", "signaling", "cell", "biology/membranes", "and", "sorting", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "cell", "biol...	2009	Requirements for F-BAR Proteins TOCA-1 and TOCA-2 in Actin Dynamics and Membrane Trafficking during Caenorhabditis elegans Oocyte Growth and Embryonic Epidermal Morphogenesis
In recent years , an increasing number of outbreaks of Dengue , Chikungunya and Zika viruses have been reported in Asia and the Americas . Monitoring virus genotype diversity is crucial to understand the emergence and spread of outbreaks , both aspects that are vital to develop effective prevention and treatment strate...	Dengue ( DENV ) , Chikungunya ( CHIKV ) and Zika ( ZIKV ) are considered major public health challenges . In addition to the epidemic caused by DENV , which has been described in many tropical countries , the introduction of CHIKV and ZIKV in these countries is a major public health concern . These arboviruses are prim...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "pathogens", "microbiology", "alphaviruses", "viruses", "phylogenetics", "data", "management", "chikungunya", "virus", "rna", "viruses", "phylogenetic", "anal...	2019	A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes
Cryptococcus neoformans is a human fungal pathogen that undergoes a dimorphic transition from a unicellular yeast to multicellular hyphae during opposite sex ( mating ) and unisexual reproduction ( same-sex mating ) . Opposite- and same-sex mating are induced by similar environmental conditions and involve many shared ...	Although sexual reproduction typically involves partners of opposite mating type ( sexuality ) , sex can occur with just one mating type and even with single individuals ( parthenogenesis , homothallism ) . For example , Cryptococcus neoformans , a fungal pathogen that causes cryptococcal meningitis , can undergo oppos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "infectious", "diseases/fungal", "infections", "genetics", "and", "genomics/gene", "function", "microbiology/microbial", "growth", "and", "development", "molecular", "biology" ]	2010	Transcription Factors Mat2 and Znf2 Operate Cellular Circuits Orchestrating Opposite- and Same-Sex Mating in Cryptococcus neoformans
Crohn's disease ( CD ) is a complex disorder resulting from the interaction of intestinal microbiota with the host immune system in genetically susceptible individuals . The largest meta-analysis of genome-wide association to date identified 71 CD–susceptibility loci in individuals of European ancestry . An important e...	Crohn's disease causes inflammation of the digestive tract resulting from the interaction of normal gut bacteria with the host immune system in genetically predisposed individuals . People of Jewish heritage have an increased risk of developing Crohn's disease compared to non-Jewish Europeans . So far , 71 genetic vari...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "epidemiology", "gastroenterology", "and", "hepatology", "inflammatory", "bowel", "disease" ]	2012	A Genome-Wide Scan of Ashkenazi Jewish Crohn's Disease Suggests Novel Susceptibility Loci
In endemic settings , diagnosis of malaria increasingly relies on the use of rapid diagnostic tests ( RDTs ) . False positivity of such RDTs is poorly documented , although it is especially relevant in those infections that resemble malaria , such as human African trypanosomiasis ( HAT ) . We therefore examined specifi...	Rapid diagnostic tests ( RDT ) for malaria are currently rolled-out as the backbone of parasite-based diagnosis , and their diagnostic accuracy is sufficiently high to substitute microscopy . One decade ago , attention has been given to occurrence of limited false positivity in a number of malaria RDTs , but false posi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "test", "evaluation", "diagnostic", "medicine", "african", "trypanosomiasis", "neglected", "tropical", "diseases", "malaria", "parasitic", "diseases" ]	2013	False Positivity of Non-Targeted Infections in Malaria Rapid Diagnostic Tests: The Case of Human African Trypanosomiasis
The formation of synapses and the proper construction of neural circuits depend on signaling pathways that regulate cytoskeletal structure and dynamics . After the mutual recognition of a growing axon and its target , multiple signaling pathways are activated that regulate cytoskeletal dynamics to determine the morphol...	Synapses are specialized junctions at which neurons communicate with target cells . To establish properly wired neuronal circuits , synapses must grow in size and strength with a high degree of accuracy . The actin cytoskeleton plays a crucial role in the formation and function of synapses , but the underlying mechanis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "cell", "biology", "synapses", "biology", "molecular", "cell", "biology", "neuroscience", "neurophysiology", "cytoskeleton" ]	2013	Drosophila cyfip Regulates Synaptic Development and Endocytosis by Suppressing Filamentous Actin Assembly
A reduction in the global burden of malaria over the past two decades has encouraged efforts for regional malaria elimination . Despite the need to target all Plasmodium species , current focus is mainly directed towards Plasmodium falciparum , and to a lesser extent P . vivax . There is a substantial lack of data on b...	The reduction in the global burden of malaria has encouraged efforts for elimination . Attempts to control and monitor transmission have mainly focused on the predominant malaria parasites Plasmodium falciparum and P . vivax . However , eliminating malaria requires the elimination of all human malaria parasites and lim...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "plasmodium", "tropical", "diseases", "plasmodium", "falciparum", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa", "protozoans", ...	2019	Persistent transmission of Plasmodium malariae and Plasmodium ovale species in an area of declining Plasmodium falciparum transmission in eastern Tanzania
DNA mutational events are increasingly being identified in autism spectrum disorder ( ASD ) , but the potential additional role of dysregulation of the epigenome in the pathogenesis of the condition remains unclear . The epigenome is of interest as a possible mediator of environmental effects during development , encod...	Older mothers have a higher than expected risk of having a child with an autism spectrum disorder ( ASD ) . The reason for this increased risk is unknown . The eggs of older mothers are more prone to abnormalities of chromosome numbers , suggesting this as one possible mechanism of the increased ASD risk . Age is also ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "population", "genetics", "departures", "from", "diploidy", "pediatrics", "bioassays", "and", "physiological", "analysis", "dna", "epigenetics", "molecular", "genetics", "epigenomics", "population", "biology",...	2014	Mosaic Epigenetic Dysregulation of Ectodermal Cells in Autism Spectrum Disorder
Novel antimalarial therapies are urgently needed for the fight against drug-resistant parasites . The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex . Computational methods can handle this complexity and allow integrative analyses of cell metabolism . In ...	Almost half of the world population is at risk of infection by malaria parasites . The rise in drug-resistant parasites requires better understanding and targeting of their metabolism . In this study , we present a genome-scale metabolic reconstruction ( iPfa ) of the deadliest malaria parasite , Plasmodium falciparum ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "parasite", "groups", "plasmodium", "tropical", "diseases", "enzymology", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa", "metabolomics", "protozoans", "metabolites", "enzyme", "metabolism", "pharma...	2017	Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks
Glutamine synthetase ( GS ) catalyzes ATP-dependent ligation of ammonia and glutamate to glutamine . Two mutations of human GS ( R324C and R341C ) were connected to congenital glutamine deficiency with severe brain malformations resulting in neonatal death . Another GS mutation ( R324S ) was identified in a neurologica...	Glutamine synthetase ( GS ) catalyzes the ATP-dependent ligation of ammonia and glutamate to glutamine , which makes the enzyme essential for human nitrogen metabolism . Three mutations in human GS , R324C , R324S , and R341C , had been identified previously that lead to a glutamine deficiency , resulting in neonatal d...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "chemical", "bonding", "chemical", "characterization", "neurochemistry", "crystal", "structure", "chemical", "compounds", "oxygen", "condensed", "matter", "physics", "neuroscience", "organic", "compounds", "simulation", "and", "modeling", "acidic", "amino", "acids", "amin...	2016	Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies
Infections during pregnancy may have serious consequences for both mother and baby . Assessment of risk factors for infections informs planning of interventions and analysis of the impact of infections on health outcomes . To describe risk factors for helminths , malaria and HIV in pregnant Ugandan women before interve...	Infections in pregnancy can cause miscarriage , stillbirth , maternal mortality , and low birth weight and have other long-term complications for mother and baby , although the full impact of many infections , particularly worm infections , is not yet fully understood . There is a high burden of infectious disease in m...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "obstetrics/pregnancy", "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/hiv", "infection", "and", "aids", "infectious", "diseases/tropical", "and", "travel-associated", "diseases" ]	2009	Risk Factors for Helminth, Malaria, and HIV Infection in Pregnancy in Entebbe, Uganda
Planar cell polarity ( PCP ) regulates cell alignment required for collective cell movement during embryonic development . This requires PCP/PCP effector proteins , some of which also play essential roles in ciliogenesis , highlighting the long-standing question of the role of the cilium in PCP . Wdpcp , a PCP effector...	Cilia are microscopic cell surface hair-like protrusions that can act as antennae to mediate cell signaling . Mutations disrupting ciliogenesis can cause many developmental anomalies associated with syndromes known as “ciliopathies . ” Some developmental defects , such as limb polydactyly , arise from disruption of cil...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Wdpcp, a PCP Protein Required for Ciliogenesis, Regulates Directional Cell Migration and Cell Polarity by Direct Modulation of the Actin Cytoskeleton
Around the world , the human-induced collapses of populations and species have triggered a sixth mass extinction crisis , with rare species often being the first to disappear . Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated , the role of rare species remain...	In ecological systems most species are rare—that is , represented by only a few individuals or restricted to particular habitats—and are vulnerable to being lost . Yet the ecological consequences of such biodiversity loss are often overlooked and remain controversial . In the best-case scenario , the functions that the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "And", "Methods" ]	[ "marine", "biology", "ecology", "biology" ]	2013	Rare Species Support Vulnerable Functions in High-Diversity Ecosystems
Chromatin Assembly Factor 1 ( CAF-1 ) is a histone chaperone that assembles acetylated histones H3/H4 onto newly synthesized DNA , allowing the de novo assembly of nucleosomes during replication . CAF-1 is an evolutionary conserved heterotrimeric protein complex . In Arabidopsis , the three CAF-1 subunits are encoded b...	Meiosis is a special cell division common in all sexually reproducing organisms . It consists of two successive rounds of chromosome segregation , preceded by a single DNA replication event . Homologous recombination is a key process that occurs during the first meiotic division . It guarantees the association of the h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Analysis of the Relationships between DNA Double-Strand Breaks, Synaptonemal Complex and Crossovers Using the Atfas1-4 Mutant
There continue to be increasing occurrences of both atomistic structure models in the PDB ( possibly reconstructed from X-ray diffraction or NMR data ) , and 3D reconstructed cryo-electron microscopy ( 3D EM ) maps ( albeit at coarser resolution ) of the same or homologous molecule or molecular assembly , deposited in ...	In recent years , advances in cryo-electron microscopy ( cryoEM ) and three-dimensional ( 3D ) image reconstruction have made it possible to determine the structures of molecular complexes , to sub-nanometer resolutions . These reconstructed 3D cryoEM maps provide a unique challenge , since the resolutions are often su...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion", "Software", "and", "Data", "Availability" ]	[]	2015	PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps
Autophagy has emerged as an important antimicrobial host defense mechanism that not only orchestrates the systemic immune response , but also functions in a cell autonomous manner to directly eliminate invading pathogens . Pathogenic bacteria such as Salmonella have evolved adaptations to protect themselves from autoph...	Salmonella enterica is a food- and water-borne pathogen that has evolved closely with vertebrate hosts . Two medically relevant serovars include S . typhimurium , which causes gastroenteritis and S . typhi , which is the causative agent of typhoid fever . Host cells can utilize a process called autophagy , normally inv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	Activation of Focal Adhesion Kinase by Salmonella Suppresses Autophagy via an Akt/mTOR Signaling Pathway and Promotes Bacterial Survival in Macrophages
In a sensitive cochlea , the basilar membrane response to transient excitation of any kind–normal acoustic or artificial intracochlear excitation–consists of not only a primary impulse but also a coda of delayed secondary responses with varying amplitudes but similar spectral content around the characteristic frequency...	The fluid-structure-electrical interaction in the cochlea enable the basilar membrane , one of the most important structures in the cochlear partition , to display different dynamic patterns depending on the frequency content of the incoming sound . Interestingly , in a healthy cochlea the motion of the basilar membran...	[ "Abstract", "Introduction", "Mathematical", "and", "Computational", "Model", "Results", "Discussion" ]	[ "acoustics", "medicine", "and", "health", "sciences", "classical", "mechanics", "engineering", "and", "technology", "ears", "lasers", "inner", "ear", "reflection", "optical", "equipment", "waves", "traveling", "waves", "sensory", "physiology", "head", "physics", "soun...	2016	The Coda of the Transient Response in a Sensitive Cochlea: A Computational Modeling Study
Modularity is a widespread property in biological systems . It implies that interactions occur mainly within groups of system elements . A modular arrangement facilitates adjustment of one module without perturbing the rest of the system . Therefore , modularity of developmental mechanisms is a major factor for evolvab...	Modular systems have performance and design advantages over non-modular systems . Thus , modularity is very important for the development of a wide range of new technological or clinical applications . Moreover , modularity is paramount to evolutionary biology since it allows adjusting one organismal function without d...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "developmental", "biology", "computer", "and", "information", "sciences", "genetic", "networks", "gene", "regulatory", "networks", "network", "analysis", "gene", "identification", "and", "analysis", "evolutionary", "processes", "genetics", "natural", "selection", "biology...	2018	On the role of sparseness in the evolution of modularity in gene regulatory networks
Urogenital schistosomiasis , chronic infection by Schistosoma haematobium , affects 112 million people worldwide . S . haematobium worm oviposition in the bladder wall leads to granulomatous inflammation , fibrosis , and egg expulsion into the urine . Despite the global impact of urogenital schistosomiasis , basic unde...	Parasitic Schistosoma haematobium worms cause urogenital schistosomiasis in 112 million people worldwide . These worms lay eggs in the bladder wall , resulting in inflammation , fibrosis ( internal scarring ) , bladder cancer , and passage of eggs into the urine . Indeed , the International Agency for Research on Cance...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "urology", "bladder", "and", "ureteric", "disorders", "immunity", "to", "infections", "immunology", "microbiology", "host-pathogen", "interaction", "parasitic", "diseases", "parasitology", "dna", "transcription", "animal", "models", "model", "organisms", "glob...	2012	Transcriptional Profiling of the Bladder in Urogenital Schistosomiasis Reveals Pathways of Inflammatory Fibrosis and Urothelial Compromise
Podoconiosis ( mossy foot ) is a neglected non-filarial elephantiasis considered to be caused by predisposition to cumulative contact of uncovered feet to irritative red clay soil of volcanic origins in the tropical regions . Data from structured observational studies on occurrence of Podoconiosis and related factors a...	Podoconiosis is a neglected disease in the tropical regions of the world considered to be caused by prolonged contact of uncovered feet to irritant particles found in red clay soil from volcanic origins . The disease presents like filarial elephantiasis . Data from observational studies from Kenya are not available . W...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "legs", "education", "sociology", "tropical", "diseases", "geographical", "locations", "limbs", "(anatomy)", "social", "sciences", "parasitic", "diseases", "filariasis", "neglected", "tropical", "diseases", "ethiopia", "lymphatic",...	2017	Soil iron and aluminium concentrations and feet hygiene as possible predictors of Podoconiosis occurrence in Kenya
Through their increased potential to be engaged and processed by dendritic cells ( DCs ) , nanovaccines consisting of Poly ( D , L-lactic-co-glycolic acid ) ( PLGA ) nanoparticles ( NPs ) loaded with both antigenic moieties and adjuvants are attractive candidates for triggering specific defense mechanisms against intra...	Leishmaniases are a wide spectrum of parasite diseases caused by different species of the genus Leishmania . Among them , visceral leishmaniasis is the most severe form of the disease affecting millions of people worldwide . Currently chemotherapeutic agents are highly toxic and suffer from extensive drug resistance . ...	[ "Abstract", "Introduction", "Methods", "Vaccination", "schedules", "with", "peptide-based", "nanovaccines", "and", "challenge", "infection", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "spleen", "immunology", "tropical", "diseases", "parasitic", "diseases", "drug", "delivery", "system", "preparation", "preventive", "medicine", "antigen", "encapsulatio...	2017	Identification of BALB/c Immune Markers Correlated with a Partial Protection to Leishmania infantum after Vaccination with a Rationally Designed Multi-epitope Cysteine Protease A Peptide-Based Nanovaccine
In Pseudomonas fluorescens Pf0-1 the availability of inorganic phosphate ( Pi ) is an environmental signal that controls biofilm formation through a cyclic dimeric GMP ( c-di-GMP ) signaling pathway . In low Pi conditions , a c-di-GMP phosphodiesterase ( PDE ) RapA is expressed , depleting cellular c-di-GMP and causing...	Bacteria can live as free swimming cells or attached to surfaces in communities called biofilms . The di-nucleotide c-di-GMP is a key cytoplasmic signal that regulates biofilm formation in a number of bacterial species . Our study , in combination with structural analysis described in the accompanying paper by Sonderma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/environmental", "microbiology", "microbiology/microbial", "growth", "and", "development", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "biochemistry/biomacromolecule-ligand", "interactions" ]	2011	A c-di-GMP Effector System Controls Cell Adhesion by Inside-Out Signaling and Surface Protein Cleavage
In Drosophila , 50 classes of olfactory receptor neurons ( ORNs ) connect to 50 class-specific and uniquely positioned glomeruli in the antennal lobe . Despite the identification of cell surface receptors regulating axon guidance , how ORN axons sort to form 50 stereotypical glomeruli remains unclear . Here we show tha...	In the human brain there are over 80 billion neurons that form approximately 100 trillion specific connections . How the brain organizes the axon terminals of these neurons into distinct synaptic units on such a large scale is largely unknown . In Drosophila , 50 classes of olfactory receptor neurons ( ORNs ) connect t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "rna", "interference", "neuroscience", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "nerve", "fibers", "epigenetics", "molecular", "biology", "techniques", "drosophila", "research"...	2018	Combinations of DIPs and Dprs control organization of olfactory receptor neuron terminals in Drosophila
Chagas disease affects about 5 million people across the world . The etiological agent , the intracellular parasite Trypanosoma cruzi ( T . cruzi ) , can be diagnosed using microscopy , serology or PCR based assays . However , each of these methods has their limitations regarding sensitivity and specificity , and thus ...	Chagas disease , caused by the parasite Trypanosoma cruzi , is a major health concern for people living in Latin America . There are no vaccines to prevent this disease and only two drugs are prescribed for treatment . Current methods to diagnose patients are not always successful and thus new methods need to be develo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion", "Conclusions" ]	[ "medicine", "infectious", "diseases", "chagas", "disease", "neglected", "tropical", "diseases", "parasitic", "diseases" ]	2014	Aptamer Based, Non-PCR, Non-Serological Detection of Chagas Disease Biomarkers in Trypanosoma cruzi Infected Mice
Hypochlorous acid ( HOCl ) is produced naturally by neutrophils and other cells to kill conventional microbes in vivo . Synthetic preparations containing HOCl can also be effective as microbial disinfectants . Here we have tested whether HOCl can also inactivate prions and other self-propagating protein amyloid seeds ....	Many serious diseases have been linked to pathogenic states of various proteins . These naturally occurring proteins can be corrupted to form aggregates such as prions and amyloids that propagate in and between tissues by acting as seeds that convert the normal form of the protein into more of the pathological form . F...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "diseases", "medicine", "and", "health", "sciences", "alloys", "chemical", "compounds", "metallurgy", "prions", "neurodegenerative", "diseases", "salts", "hypochlorites", "vertebrates", "animals", "mammals", "animal", "prion", "diseases", "stainless", "steel", ...	2016	Inactivation of Prions and Amyloid Seeds with Hypochlorous Acid
Human ageing has been predicted to be caused by the accumulation of molecular damage in cells and tissues . Somatic mitochondrial DNA ( mtDNA ) mutations have been documented in a number of ageing tissues and have been shown to be associated with cellular mitochondrial dysfunction . It is unknown whether there are sele...	Mitochondrial DNA encodes essential components of the mitochondrial respiratory chain and is strictly maternally inherited , making it vulnerable to the accumulation of deleterious mutations . To avoid this , mtDNA is subjected to a bottleneck phenomenon whereby only a small number of mtDNA molecules are passed on to t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "mutation", "heredity", "genetics", "molecular", "genetics", "biology", "human", "genetics", "population", "genetics", "genetics", "and", "genomics" ]	2012	Comparison of Mitochondrial Mutation Spectra in Ageing Human Colonic Epithelium and Disease: Absence of Evidence for Purifying Selection in Somatic Mitochondrial DNA Point Mutations
Drosophila neuroendocrine cells comprising the corpora cardiaca ( CC ) are essential for systemic glucose regulation and represent functional orthologues of vertebrate pancreatic α-cells . Although Drosophila CC cells have been regarded as developmental orthologues of pituitary gland , the genetic regulation of CC deve...	The requirement for glucose regulation is conserved in metazoans and crucial for metabolism , growth , and survival . In fruit flies and other insects , neurons secrete insulin-like hormones and neuroendocrine corpora cardiaca cells secrete adipokinetic hormone , a peptide with functional similarities to glucagon . Bot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "genetics", "and", "genomics" ]	2011	Specification of Drosophila Corpora Cardiaca Neuroendocrine Cells from Mesoderm Is Regulated by Notch Signaling
Hunchback is a bifunctional transcription factor that can activate and repress gene expression in Drosophila development . We investigated the regulatory DNA sequence features that control Hunchback function by perturbing enhancers for one of its target genes , even-skipped ( eve ) . While Hunchback directly represses ...	During development , animals express genes in distinct patterns to specify different cell types that are important for function . Enhancers are DNA sequences that generate these patterns by binding proteins that activate gene expression , repress gene expression , or both . We have learned how enhancers generate patter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "textbooks", "invertebrates", "chemical", "characterization", "rna", "interference", "education", "gene", "regulation", "sociology", "social", "sciences", "animals", "invertebrate", "genomics", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "m...	2018	Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos
Posttranslational arginylation is critical for embryogenesis , cardiovascular development , and angiogenesis , but its molecular effects and the identity of proteins arginylated in vivo are largely unknown . Here we report a global analysis of this modification on the protein level and identification of 43 proteins arg...	A common cellular mechanism for the regulation of proteins , once they have been translated from mRNA , is the addition and removal of chemical groups via enzymatic reactions . The posttranslational addition of arginyl groups is critical for the embryonic development and survival of an organism , but the molecular effe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "cell", "biology", "in", "vitro", "chemical", "biology" ]	2007	Global Analysis of Posttranslational Protein Arginylation
Trachoma , caused by Chlamydia trachomatis , remains the leading infectious cause of blindness worldwide . Persistence and progression of the resulting clinical disease appears to be an immunologically mediated process . Azithromycin , which is distributed at the community level for trachoma control , has immunomodulat...	Trachoma , caused by conjunctival infection with Chlamydia trachomatis , remains the leading infectious cause of blindness . Repeated infection during childhood can trigger prolonged inflammation , which is the main risk factor for conjunctival scarring . Azithromycin is distributed globally for trachoma control , howe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "inflammatory", "diseases", "children", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chlamydia", "trachomatis", "pathogens", "immunology", "tropical", "diseases", "microbiology", "bacterial", "diseases", "age", "groups", "signs",...	2019	Ocular immune responses, Chlamydia trachomatis infection and clinical signs of trachoma before and after azithromycin mass drug administration in a treatment naïve trachoma-endemic Tanzanian community
Signal transducer and activator of transcription 1 ( Stat1 ) is a key player in responses to interferons ( IFN ) . Mutations of Stat1 cause severe immune deficiencies in humans and mice . Here we investigate the importance of Stat1 signaling for the innate and secondary immune response to the intracellular bacterial pa...	Signal transducer and activator of transcription 1 ( Stat1 ) is an indispensable component of the cellular response to interferons ( IFN ) during immune reactions to pathogens . Stat1 deficiency leads to severe immune defects in humans and mice . The sensitivity of animals with complete Stat1 ablation to microbial path...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immune", "cells", "antigen-presenting", "cells", "immunity", "to", "infections", "immunology", "adaptive", "immunity", "gene", "expression", "t", "cells", "biology", "molecular", "biology", "immune", "response", "signal", "transduction", "monocytes", "immunity", "innat...	2012	Conditional Stat1 Ablation Reveals the Importance of Interferon Signaling for Immunity to Listeria monocytogenes Infection
Bacterial lung infections , particularly with methicillin-resistant Staphylococcus aureus ( MRSA ) , increase mortality following influenza infection , but the mechanisms remain unclear . Here we show that expression of TLR9 , a microbial DNA sensor , is increased in murine lung macrophages , dendritic cells , CD8+ T c...	Influenza-associated secondary bacterial infections , particularly with methicillin-resistant Staphylococcus aureus ( MRSA ) , are a major cause of morbidity and mortality , and better therapeutic strategies are needed . Stimulation of TLR2 has shown promise for improving health in influenza-bacteria dual-infected anim...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "influenza", "pathogens", "immunology", "microbiology", "orthomyxoviruses", "staphylococcus", "aureus", "viruses", "methicillin-resistant", "staphyloc...	2019	Influenza-induced immune suppression to methicillin-resistant Staphylococcus aureus is mediated by TLR9
The need for improved dengue vaccines remains since the only licensed vaccine , Dengvaxia , shows variable efficacy depending on the infecting dengue virus ( DENV ) type , and increases the risk of hospitalization for severe dengue in children not exposed to DENV before vaccination . Here , we developed a tetravalent d...	Dengue virus ( DENV ) is responsible for the most widespread arboviral disease affecting humans . A pre-existing suboptimal immunity to DENV is accepted as being the major risk factor for severe dengue . Thus , if vaccination does not elicit optimal DENV-specific immunity , a vaccine might , instead , increase the risk...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "dengue", "virus", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vertebrates", "animals", "mam...	2019	Detection of post-vaccination enhanced dengue virus infection in macaques: An improved model for early assessment of dengue vaccines
Glycogen metabolism commonly altered in cancer is just beginning to be understood . Phosphoglucomutase 1 ( PGM1 ) , the first enzyme in glycogenesis that catalyzes the reversible conversion between glucose 1-phosphate ( G-1-P ) and glucose 6-phosphate ( G-6-P ) , participates in both the breakdown and synthesis of glyc...	Hepatocellular carcinoma ( HCC ) is the most common type of primary liver cancer in adults . Sorafenib is the only clinically approved systemic drug for patients with advanced HCC . Identification of novel targets and biomarkers will provide new therapeutic strategies for advanced HCC and better prognostic prediction ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "forkhead", "box", "chemical", "compounds", "molecular", "probe", "techniques", "metabolic", "processes", "carcinomas", "cancers", "and", "neoplasms", "immunoblotting", "carbohydrates", "glucose", "met...	2018	Phosphoglucomutase 1 inhibits hepatocellular carcinoma progression by regulating glucose trafficking
Cancer cells have acquired mutations that alter their growth . Aneuploidy that typify cancer cells are often assumed to contribute to the abnormal growth characteristics . Here we test the idea of a link between aneuploidy and mutations allowing improved growth , using Saccharomyces cerevisiae containing a mcm4 helicas...	Aneuploidy , an abnormality in chromosome number and structure , occurs commonly in cancers and has been suggested to be required to maintain accelerated cell proliferation . However , this hypothesis remains untested as it is not possible to selectively remove the acquired aneuploidy in cells that already have altered...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics", "oncology/breast", "cancer" ]	2009	Aneuploidy and Improved Growth Are Coincident but Not Causal in a Yeast Cancer Model
In this work we studied the folding process of the hybrid-1 type human telomeric DNA G-quadruplex with solvent and ions explicitly modeled . Enabled by the powerful bias-exchange metadynamics and large-scale conventional molecular dynamic simulations , the free energy landscape of this G-DNA was obtained for the first ...	G-quadruplexes are high-order DNA/RNA structures . They are involved in the regulation of telomere maintenance , DNA replication , transcription and translation , and are also attractive drug designing targets for treating cancers and promising building blocks for molecular nanodevices . The knowledge of their formatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "biology", "and", "life", "sciences", "computational", "biology" ]	2014	Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex
Iron is an essential element for the survival of microorganisms in vitro and in vivo , acting as a cofactor of several enzymes and playing a critical role in host-parasite relationships . Leishmania ( Viannia ) braziliensis is a parasite that is widespread in the new world and considered the major etiological agent of ...	American tegumentary leishmaniasis ( ATL ) is a neglected disease that is widely distributed in the Americas . The protozoan parasite Leishmania ( Viannia ) braziliensis is one of the main causative agents of ATL , being responsible for the development of different clinical manifestations of the disease , which ranges ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Cellular Growth and Mitochondrial Ultrastructure of Leishmania (Viannia) braziliensis Promastigotes Are Affected by the Iron Chelator 2,2-Dipyridyl
The incidence of cardiac arrhythmias is known to be associated with tissue heterogeneities including fibrosis . However , the impact of microscopic structural heterogeneities on conduction in excitable tissues remains poorly understood . In this study , we investigated how acellular microheterogeneities affect macrosco...	It is well known that perturbations in the heart structure are associated with the initiation and maintenance of clinically significant cardiac arrhythmia . While previous studies have examined how single structural perturbations affect local electrical conduction , our understanding of how numerous microscopic heterog...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "velocity", "acceleration", "action", "potentials", "medicine", "and", "health", "sciences", "classical", "mechanics", "membrane", "potential", "condensed", "matter", "physics", "electricity", "fibrosis", "electrophysiology", "anisotropy", "neuroscience", "geometry", "devel...	2018	Microheterogeneity-induced conduction slowing and wavefront collisions govern macroscopic conduction behavior: A computational and experimental study
Influenza A viruses modulate host antiviral responses to promote viral growth and pathogenicity . Through viral PA-X and NS1 proteins , the virus is capable of suppressing host protein synthesis , termed “host shutoff . ” Although both proteins are known to induce general shutoff , specificity of target genes and their...	Virus infection induces a wide range of host defense responses , such as the innate immune response and inflammation . Some viruses express accessory proteins to induce general shutoff of host protein synthesis , which is one of the major viral strategies to counteract host antiviral activity and immune response . Infl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "influenza", "pathogens", "messenger", "rna", "microbiology", "orthomyxoviruses", "viruses", "virus", "effects", "on", "host", "gene", "expression", "protein", "synthesis", "rna", "...	2018	Specificity and functional interplay between influenza virus PA-X and NS1 shutoff activity
Mycobacterium ulcerans is the causative agent of Buruli ulcer , the third most common mycobacterial disease after tuberculosis and leprosy . It is an emerging infectious disease that afflicts mainly children and youths in West Africa . Little is known about the evolution and transmission mode of M . ulcerans , partiall...	Mycobacterium ulcerans is the causative agent of Buruli ulcer ( BU ) , a necrotizing skin disease and the third most common mycobacterial disease after tuberculosis and leprosy . It is an emerging infectious disease that afflicts mainly children and youths in West Africa . The disease is also found in tropical and subt...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/microbial", "evolution", "and", "genomics" ]	2009	Genomic Diversity and Evolution of Mycobacterium ulcerans Revealed by Next-Generation Sequencing
The striatum is the main input station of the basal ganglia and is strongly associated with motor and cognitive functions . Anatomical evidence suggests that individual striatal neurons are unlikely to share their inputs from the cortex . Using a biologically realistic large-scale network model of striatum and cortico-...	The striatum is the main input station of the basal ganglia and plays a crucial role in multiple motor and cognitive functions . Striatum is a recurrently connected network of GABAergic medium spiny neurons ( MSNs ) , which receive strong feedforward inhibition from the fast spiking interneurons and massive excitatory ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neural", "networks", "computational", "neuroscience", "biology", "computational", "biology", "neuroscience" ]	2011	Significance of Input Correlations in Striatal Function
The 3′ untranslated genome region ( UTR ) of arthropod-borne viruses is characterized by enriched direct repeats ( DRs ) and stem-loop structures . Despite many years of theoretical and experimental study , on-going positive selection on the 3′UTR had never been observed in ‘real-time , ’ and the role of the arbovirus ...	The 3′ untranslated genome region ( UTR ) of arbovirus ( arthropod-borne virus ) RNA genomes is characterized by enriched direct repeats ( DRs ) and stem-loop structures , which are thought to play a specific role in maintaining efficient transmission in multiple hosts . However , this hypothesis is vague and has littl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "genetics", "biology", "microbiology" ]	2013	Chikungunya Virus 3′ Untranslated Region: Adaptation to Mosquitoes and a Population Bottleneck as Major Evolutionary Forces
Mechanisms by which viruses counter innate host defense responses generally involve inhibition of one or more components of the interferon ( IFN ) system . Multiple steps in the induction and amplification of IFN signaling are targeted for inhibition by viral proteins , and many of the IFN antagonists have direct or in...	Cells respond to virus infection by inducing a pattern of gene expression regulated by interferon ( IFN ) that modulates the host immune response . In order to successfully replicate , viruses have evolved mechanisms to block the induction or function of IFN and IFN-regulated genes . Multiple proteins are activated in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/immune", "evasion", "virology/host", "antiviral", "responses", "virology" ]	2009	Rotavirus NSP1 Inhibits NFκB Activation by Inducing Proteasome-Dependent Degradation of β-TrCP: A Novel Mechanism of IFN Antagonism
Chagas disease treatment is limited by drug availability , adverse side effect profiles of available medications , and poor adherence . Adult Chagas disease patients initiating 60-days of benznidazole were randomized to weekly or twice-weekly evaluations of medication adherence and screening for adverse drug events ( A...	Treatment of Chagas disease is complicated by poor adherence and frequent adverse drug events ( ADEs ) . To determine the utility of pill counts and frequent monitoring to improve treatment completion and reduce ADEs , this study randomized Bolivian adults with chronic Chagas disease to either weekly or twice-weekly cl...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[]	2013	Improved Completion Rates and Characterization of Drug Reactions with an Intensive Chagas Disease Treatment Program in Rural Bolivia
Mapping of lymphatic filariasis ( LF ) caused by Wuchereria bancrofti largely relies on the detection of circulating antigen using ICT cards . Several studies have recently shown that this test can be cross-reactive with sera of subjects heavily infected with Loa loa and thus mapping results in loiasis endemic areas ma...	High prevalence of loiasis can confound the mapping efforts for lymphatic filariasis ( LF ) that use tests for circulating filarial antigen . In order to develop a LF mapping strategy for loiasis endemic areas , we screened day blood samples from 5 , 001 subjects residing in 50 villages in 6 health districts throughout...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "immunology", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "nematode", "infections", "filariasis", "neglected", "tropical", "diseases", "onchocerciasis", ...	2019	Mapping of lymphatic filariasis in loiasis areas: A new strategy shows no evidence for Wuchereria bancrofti endemicity in Cameroon
Ubiquitin ( Ub ) is a vital regulatory component in various cellular processes , including cellular responses to viral infection . As obligate intracellular pathogens , viruses have the capacity to manipulate the ubiquitin ( Ub ) cycle to their advantage by encoding Ub-modifying proteins including deubiquitinases ( DUB...	Deubiquitinases ( DUBs ) are enzymes , which are implicated in many cellular processes but their functions during virus infection are not well understood . We used WP1130 , a small molecule inhibitor of a subset of DUBs , as a probe to unravel the functions of DUBs during norovirus infections . We identified USP14 as a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology", "molecular", "cell", "biology" ]	2012	Antiviral Activity of a Small Molecule Deubiquitinase Inhibitor Occurs via Induction of the Unfolded Protein Response
Myotonic dystrophy type 1 ( DM1 ) is caused by an unstable CTG repeat expansion in the 3′UTR of the DM protein kinase ( DMPK ) gene . DMPK transcripts carrying CUG expansions form nuclear foci and affect splicing regulation of various RNA transcripts . Furthermore , bidirectional transcription over the DMPK gene and no...	Myotonic dystrophy type 1 ( DM1 ) is caused by the abnormal expansion of a CTG repeat located in the DM protein kinase ( DMPK ) gene . DMPK transcripts carrying CUG expansions form toxic nuclear foci that affect other RNAs . DM1 involve multiple pathogenic pathways including changes in gene expression , RNA stability a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Molecular, Physiological, and Motor Performance Defects in DMSXL Mice Carrying >1,000 CTG Repeats from the Human DM1 Locus
Blood fluke proteases play pivotal roles in the processes of invasion , nutrition acquisition , immune evasion , and other host-parasite interactions . Hundreds of genes encoding putative proteases have been identified in the recently published schistosome genomes . However , the expression profiles of these proteases ...	Parasite proteases play critical roles in host-parasite interactions and thus are considered to be potential anti-schistosomal targets . Although numerous schistosome proteases have been predicted based on recently published genomes , no systematic analysis of their expression in Schistosoma species has been performed ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "veterinary", "parasitology", "biology", "and", "life", "sciences", "parasitology", "parasite", "physiology" ]	2014	Expression Profile of the Schistosoma japonicum Degradome Reveals Differential Protease Expression Patterns and Potential Anti-schistosomal Intervention Targets
Aedes aegypti , the yellow fever mosquito , is an efficient vector of arboviruses and a convenient model system for laboratory research . Extensive linkage mapping of morphological and molecular markers localized a number of quantitative trait loci ( QTLs ) related to the mosquito's ability to transmit various pathogen...	About half of the human population is under risk of dengue infection . Because of the absence of a vaccine or drug treatment , the prevention of this disease largely relies on controlling its major vector mosquito Aedes aegypti . Availability of the complete genome sequence for this mosquito offers the potential to hel...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "biology" ]	2013	An Integrated Linkage, Chromosome, and Genome Map for the Yellow Fever Mosquito Aedes aegypti
High-throughput data generation and genome-scale stoichiometric models have greatly facilitated the comprehensive study of metabolic networks . The computation of all feasible metabolic routes with these models , given stoichiometric , thermodynamic , and steady-state constraints , provides important insights into the ...	Organisms depend on huge networks of molecular reactions for environmental sensing , information integration , gene expression , and metabolism . The discovery of general principles of network behavior is a major ambition of systems biology and of great interest to biotechnology and medicine . We present a computationa...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models
Genome reduction is typical of obligate symbionts . In cellular organelles , this reduction partly reflects transfer of ancestral bacterial genes to the host genome , but little is known about gene transfer in other obligate symbioses . Aphids harbor anciently acquired obligate mutualists , Buchnera aphidicola ( Gammap...	Bacterial lineages have repeatedly evolved intimate symbioses with eukaryotic hosts , the most famous cases being those of the cell organelles , mitochondria , and plastids . Symbiont genomes typically lose many ancestral genes , raising the question of how they function with so few genes . In organelles , part of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "...	2010	Bacterial Genes in the Aphid Genome: Absence of Functional Gene Transfer from Buchnera to Its Host
Soluble extracellular proteins usually do not enter the endogenous human leukocyte antigen ( HLA ) I–dependent presentation pathway of antigen-presenting cells , strictly impeding their applicability for the re-stimulation of protein-specific CD8+ cytotoxic T lymphocytes ( CTL ) . Here we present for the Epstein-Barr v...	CD8+ T lymphocytes ( CTL ) play a key role in the immunological control of persistent intracellular pathogens and tumors . Thus , the development of improved technologies for the monitoring and expansion of protein-specific CTL represents a major challenge in clinical immunology . CTL specifically target infected cells...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "immunology/antigen", "processing", "and", "recognition", "immunology", "immunology/immune", "response" ]	2008	Urea-Mediated Cross-Presentation of Soluble Epstein-Barr Virus BZLF1 Protein
A new theoretical survey of proteins' resistance to constant speed stretching is performed for a set of 17 134 proteins as described by a structure-based model . The proteins selected have no gaps in their structure determination and consist of no more than 250 amino acids . Our previous studies have dealt with 7510 pr...	The advances in nanotechnology have allowed for manipulation of single biomolecules and determination of their elastic properties . Titin was among the first proteins studied in this way . Its unravelling by stretching requires a 204 pN force . The resistance to stretching comes mostly from a localized region known as ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/molecular", "dynamics", "biophysics", "biophysics/theory", "and", "simulation" ]	2009	Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots
Insect cuticle or exoskeleton is an extracellular matrix formed primarily from two different structural biopolymers , chitin and protein . During each molt cycle , a new cuticle is deposited simultaneously with degradation of the inner part of the chitinous procuticle of the overlying old exoskeleton by molting fluid e...	Insect cuticle or exoskeleton is an extracellular matrix consisting of three major morphologically distinct layers , the water-proofing envelope , the protein-rich epicuticle and the chitin/protein-rich procuticle . To accommodate growth , insects must periodically replace their cuticles in a process called “molting or...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chitin", "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "animals", "membrane", "proteins", "physiological", "processes", "developmental", "biology", "pupae", "materials", "science", "epigenetics", "macromolecules", "cellular", "structures"...	2018	A chitinase with two catalytic domains is required for organization of the cuticular extracellular matrix of a beetle
Alphaviruses present serious health threats as emerging and re-emerging viruses . Venezuelan equine encephalitis virus ( VEEV ) , a New World alphavirus , can cause encephalitis in humans and horses , but there are no therapeutics for treatment . To date , compounds reported as anti-VEEV or anti-alphavirus inhibitors h...	Alphaviruses occur worldwide , causing significant diseases such as encephalitis or arthritis in humans and animals . In addition , some alphaviruses , such as VEEV , pose a biothreat due to their high infectivity and lack of available treatments . To discover small molecule inhibitors with lead development potential ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "antimicrobials", "medicine", "and", "health", "sciences", "microbiology", "clinical", "medicine", "pharmacology", "veterinary", "science", "infectious", "diseases", "veterinary", "diseases", "viral", "replication", "drug", "discovery", "biochemistry", "dru...	2014	Discovery of a Novel Compound with Anti-Venezuelan Equine Encephalitis Virus Activity That Targets the Nonstructural Protein 2
Japanese encephalitis virus ( JEV ) is a major cause of viral encephalitis in South and South-East Asia . Lack of antivirals and non-availability of affordable vaccines in these endemic areas are a major setback in combating JEV and other closely related viruses such as West Nile virus and dengue virus . Protein second...	Japanese encephalitis virus is a mosquito-borne virus , which causes encephalitis primarily in children and is a major cause of encephalitis-related deaths in South and South-East Asian countries . Although new and safe vaccines are available for use , it is neither affordable nor readily available in endemic regions ....	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biotechnology", "small", "molecules", "microbiology", "chemical", "biology", "emerging", "infectious", "diseases", "organic", "synthesis", "chemistry", "biology", "drug", "discovery", "biochemistry", "virology", "microbial", "control", "antivirals", "synthetic", "chemistry...	2013	Bispidine-Amino Acid Conjugates Act as a Novel Scaffold for the Design of Antivirals That Block Japanese Encephalitis Virus Replication
Parasitic sea lice represent a major sanitary threat to marine salmonid aquaculture , an industry accounting for 7% of world fish production . Caligus rogercresseyi is the principal sea louse species infesting farmed salmon and trout in the southern hemisphere . Most effective control of Caligus has been obtained with ...	Sea lice are the main parasites affecting farmed salmon and trout in the world . Caligus rogercresseyi is the principal sea louse species infesting farmed fish in the southern hemisphere . Successful control of these parasites has been achieved using macrocyclic lactones ( MLs ) , but resistance has emerged over time ....	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "veterinary", "science", "veterinary", "diseases", "veterinary", "parasitology", "proteins", "physiology", "protein", "structure", "biology", "and", "life", "sciences", "computational", "biology", "electrophysiology", "molecular", "biology", "parasitology", ...	2014	Identification and Functional Expression of a Glutamate- and Avermectin-Gated Chloride Channel from Caligus rogercresseyi, a Southern Hemisphere Sea Louse Affecting Farmed Fish
Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions , yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited . One main difficulty , in addition to inaccuracies in energ...	Designing new protein–ligand interactions has tremendous potential for engineering sensitive biosensors for diagnostics or new enzymes useful in biotechnology , but these applications are extremely challenging , both because of inaccuracies of the energy functions used in modeling and design , and because protein activ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
ClinicalTrials . gov clinical trial numbers ACTRN12612000814875 , ACTRN12613000565741 and ACTRN12613001040752 Malaria is associated with complex multi-factorial immune responses , due in part to the multi-stage life cycle of the Plasmodium spp . parasite which is targeted by multiple arms of the immune system , and the...	Malaria is one of the three most deadly infectious disease worldwide , together with tuberculosis and HIV . The exact mechanisms underlying effective immunity to malaria remain largely unknown and there is no reliable immune correlate of protection . Here , we take advantage of a unique experimental human infection mod...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "innate", "immune", "system", "medicine", "and", "health", "sciences", "parasite", "groups", "immune", "cells", "immune", "physiology", "cytokines", "plasmodium", "immunology", "tropical", "diseases", "parasitic", "diseases", "pa...	2016	Reduced Plasmodium Parasite Burden Associates with CD38+ CD4+ T Cells Displaying Cytolytic Potential and Impaired IFN-γ Production
Successful navigation is fundamental to the survival of nearly every animal on earth , and achieved by nervous systems of vastly different sizes and characteristics . Yet surprisingly little is known of the detailed neural circuitry from any species which can accurately represent space for navigation . Path integration...	The ability to navigate allows animals to vastly increase the action space for finding resources , mates , and to avoid predators . The benefits are many and it is commonly believed that modern brain functions have emerged from ancestral forms evolved for effective navigation . Since the time of Charles Darwin , it has...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "physiology/cognitive", "neuroscience", "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2010	Finding the Way with a Noisy Brain
Constitutive heterochromatin comprising the centromeric and telomeric parts of chromosomes includes DNA marked by high levels of methylation associated with histones modified by repressive marks . These epigenetic modifications silence transcription and ensure stable inheritance of this inert state . Although environme...	In eukaryotic cells , DNA is packaged into chromatin that is present in two different forms named euchromatin and heterochromatin . Gene-rich euchromatin is relaxed and permissive to transcription compared with heterochromatin that essentially contains transcriptionally inert non-coding repeated DNA . The silent state ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "plant", "biology/plant", "genetics", "and", "gene", "expression", "plant", "biology/plant-environment", "interactions" ]	2010	Stress-Induced Activation of Heterochromatic Transcription
In Sub-Saharan Africa , urogenital schistosomiasis remains a significant public health problem , causing 150 . 000 deaths/year with approximately 112 million cases diagnosed . The Niakhar district is a disease hotspot in central Senegal where transmission occurs seasonally with high prevalences . The aim of this study ...	Urogenital schistosomiasis represents a serious cause of morbidity and mortality in S . haematobium endemic countries . Treatment with praziquantel ( PZQ ) is effective at reducing or eliminating active infection , but does not prevent reinfection that remains a continuing problem in high-risk communities , especially ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "helminths", "malacology", "tropical", "diseases", "geographical", "locations", "ponds", "parasitic", "diseases", "animals", "urine", "gastropods", "fresh", "water", "bodies", "of...	2016	Impact of Annual Praziquantel Treatment on Urogenital Schistosomiasis in a Seasonal Transmission Focus in Central Senegal
Despite recent advances in our understanding of the pathogenesis of ectodermal dysplasias ( EDs ) , the molecular basis of many of these disorders remains unknown . In the present study , we aimed at elucidating the genetic basis of a new form of ED featuring facial dysmorphism , scalp hypotrichosis and hypodontia . Us...	Ectodermal dysplasias refer to a large group of inherited disorders characterized by developmental defects in tissues of ectodermal origin . The study of these conditions has been instrumental in the discovery of biological pathways involved in the regulation of epithelial tissue morphogenesis . In this report , throug...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "skin", "medicine", "and", "health", "sciences", "integumentary", "system", "dysplasia", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "notch", "signaling", "mutation", "signs", "and", "symptoms", "mutation", "databases", "digestive", "system", "...	2016	Mutations in TSPEAR, Encoding a Regulator of Notch Signaling, Affect Tooth and Hair Follicle Morphogenesis
Chagas disease prevention critically depends on keeping houses free of triatomine vectors . Insecticide spraying is very effective , but re-infestation of treated dwellings is commonplace . Early detection-elimination of re-infestation foci is key to long-term control; however , all available vector-detection methods h...	Triatoma infestans is the main vector of Chagas disease in southern South America . Dwelling-infesting populations are controlled through insecticide-spraying campaigns; however , dwellings are often re-infested when insecticide effects wane , and this leads to the re-establishment of disease transmission . Detecting a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry", "applied", "chemistry", "animal", "behavior", "entomology", "chemical", "biology", "chemistry", "biology", "zoology", "neuroscience", "hormones" ]	2012	Post-Control Surveillance of Triatoma infestans and Triatoma sordida with Chemically-Baited Sticky Traps
The optic nerve head is involved in many ophthalmic disorders , including common diseases such as myopia and open-angle glaucoma . Two of the most important parameters are the size of the optic disc area and the vertical cup-disc ratio ( VCDR ) . Both are highly heritable but genetically largely undetermined . We perfo...	Morphologic characteristics of the optic nerve head are involved in many ophthalmic diseases . Its size , called the optic disc area , is an important measure and has been associated with e . g . myopia and open-angle glaucoma ( OAG ) . Another important and clinical parameter of the optic disc is the vertical cup-disc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "public", "health", "and", "epidemiology", "public", "health", "and", "epidemiology/epidemiology", "ophthalmology", "genetics", "and", "genomics", "ophthalmology/glaucoma", "genetics", "and", "genomics/population", "genetics" ]	2010	A Genome-Wide Association Study of Optic Disc Parameters
Genome-wide association studies of lung cancer reported in populations of European background have identified three regions on chromosomes 5p15 . 33 , 6p21 . 33 , and 15q25 that have achieved genome-wide significance with p-values of 10−7 or lower . These studies have been performed primarily in cigarette smokers , rai...	Worldwide , approximately 15% of lung cancer cases occur among nonsmokers . Genome-wide association studies ( GWAS ) of lung cancer conducted in populations of European background have identified three regions on chromosomes 5 , 6 , and 15 that harbor genetic variants that confer risk for lung cancer . Prior studies we...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "genetics", "and", "genomics/cancer", "genetics" ]	2010	The 5p15.33 Locus Is Associated with Risk of Lung Adenocarcinoma in Never-Smoking Females in Asia
Response to Zika virus ( ZIKV ) invasion in Brazil lagged a year from its estimated February 2014 introduction , and was triggered by the occurrence of severe congenital malformations . Dengue ( DENV ) and chikungunya ( CHIKV ) invasions tend to show similar response lags . We analyzed geo-coded symptomatic case report...	Over the past decades , Aedes-borne viruses ( dengue , chikungunya , Zika ) have become a major source of morbidity within urban areas . Worldwide , public health response to these viruses is reactive to the occurrence of symptomatic cases ( a small proportion of all infections ) . Here we used geocoded passive surveil...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "viral", "transmission", "and", "infection", "pathogens", "spatial", "epidemiology", "microbiology", "census", "alphaviruses", "viruses", "research", ...	2018	Spatio-temporal coherence of dengue, chikungunya and Zika outbreaks in Merida, Mexico
The relative contribution of genetic risk factors to the progression of subclinical atherosclerosis is poorly understood . It is likely that multiple variants are implicated in the development of atherosclerosis , but the subtle genotypic and phenotypic differences are beyond the reach of the conventional case-control ...	Although cardiovascular events , such as myocardial infarction and stroke , usually occur at later ages , it is known that the atherogenic process begins much earlier in life . Detection of subclinical atherosclerosis would therefore offer the means to identify individuals who are at increased risk of developing cardio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/population", "genetics", "computer", "science/applications", "cardiovascular", "disorders/cardiovascular", "imaging", "genetics", "and", "genomics/bioinformatics", "computer", "science/numerical", "analysis", "and", "theoretical", "computing", "cardiovascu...	2010	Genetic Variants and Their Interactions in the Prediction of Increased Pre-Clinical Carotid Atherosclerosis: The Cardiovascular Risk in Young Finns Study

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