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Viral infection induces innate immunity and apoptosis . Apoptosis is an effective means to sacrifice virus-infected host cells and therefore restrict the spread of pathogens . However , the underlying mechanisms of this process are still poorly understood . Here , we show that the mitochondrial antiviral signaling prot...	The mitochondrial antiviral signaling protein ( MAVS/VISA/Cardif/IPS-1 ) is critical for the innate immune response during viral infection , and its function has been well documented in mediating type I interferon production . In this study , we revealed the essential role of MAVS in virus-induced apoptosis , independe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "signal", "transduction", "immunity", "innate", "immunity", "immunology", "host-pathogen", "interaction", "biology", "microbiology", "molecular", "cell", "biology" ]	2014	MAVS-MKK7-JNK2 Defines a Novel Apoptotic Signaling Pathway during Viral Infection
The capacity of Aedes mosquitoes to resist chemical insecticides threatens the control of major arbovirus diseases worldwide . Until alternative control tools are widely deployed , monitoring insecticide resistance levels and identifying resistance mechanisms in field mosquito populations is crucial for implementing ap...	The ability of mosquitoes to resist insecticides represents a serious threat to the prevention of arbovirus diseases such as dengue , zika and chikungunya . The detection and monitoring of the resistances developed by natural mosquito populations is essential to enabling their management in the field for as long as the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymology", "invertebrate", "genomics", "animals", "toxicology", "dna", "transcription", "enzyme", "metabolism", "molecular", "biology", "...	2017	In the hunt for genomic markers of metabolic resistance to pyrethroids in the mosquito Aedes aegypti: An integrated next-generation sequencing approach
Paracoccin is a dual-function protein of the yeast Paracoccidioides brasiliensis that has lectin properties and N-acetylglucosaminidase activities . Proteomic analysis of a paracoccin preparation from P . brasiliensis revealed that the sequence matched that of the hypothetical protein encoded by PADG-3347 of isolate Pb...	Paracoccin is a constituent of Paracoccidioides brasiliensis , a human pathogen that causes paracoccidioidomycosis , the most prevalent systemic mycosis in Latin America . Paracoccin is a dual function protein with domains for lectin and N-acetylglucosaminidase activities . Proteomic analysis of paracoccin preparation ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "medicine", "and", "health", "sciences", "immunochemistry", "pathology", "and", "laboratory", "medicine", "proteins", "immunity", "medical", "microbiology", "host-pathogen", "interactions", "biology", "and", "life", "sciences", "immunology", "recombinant", ...	2014	Recombinant Paracoccin Reproduces the Biological Properties of the Native Protein and Induces Protective Th1 Immunity against Paracoccidioides brasiliensis Infection
The single celled eukaryote Trypanosoma cruzi , a parasite transmitted by numerous species of triatomine bug in the Americas , causes Chagas disease in humans . T . cruzi generally reproduces asexually and appears to have a clonal population structure . However , two of the six major circulating genetic lineages , TcV ...	Trypanosoma cruzi is a parasite that causes Chagas disease in humans , an often fatal condition affecting at least 8 million people . The clinical outcome of Chagas disease is variable , which is probably partially attributable to genetic differences between T . cruzi strains . Differences between T . cruzi strains can...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "genetics", "biology", "microbiology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2011	Recent, Independent and Anthropogenic Origins of Trypanosoma cruzi Hybrids
Dengue virus ( DENV ) is a significant public health threat in tropical and subtropical regions of the world . A therapeutic antibody against the viral envelope ( E ) protein represents a promising immunotherapy for disease control . We generated seventeen novel mouse monoclonal antibodies ( mAbs ) with high reactivity...	Dengue virus ( DENV ) infection remains a serious health threat despite the availability of supportive care in modern medicine . Monoclonal antibodies ( mAbs ) of DENV would be powerful research tools for antiviral development , diagnosis and pathological investigations . Here we described generation and characterizati...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2012	Development of a Humanized Antibody with High Therapeutic Potential against Dengue Virus Type 2
Capnocytophaga canimorsus , a commensal bacterium of the canine oral flora , has been repeatedly isolated since 1976 from severe human infections transmitted by dog bites . Here , we show that C . canimorsus exhibits robust growth when it is in direct contact with mammalian cells , including phagocytes . This property ...	Capnocytophaga canimorsus is a commensal bacterium of dogs/cats oral flora , which causes rare but severe infections in humans that have been bitten or simply licked by a dog/cat . Fulminant septicemia and peripheral gangrene are most common symptoms . Although splenectomy has been identified as a predisposing factor ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2008	Capnocytophaga canimorsus: A Human Pathogen Feeding at the Surface of Epithelial Cells and Phagocytes
Pseudogenes are significant components of eukaryotic genomes , and some have acquired novel regulatory roles . To date , no study has characterized rice pseudogenes systematically or addressed their impact on the structure and function of the rice genome . In this genome-wide study , we have identified 11 , 956 non-tra...	Pseudogenes are “defunct” copies of protein-coding genes that have been accumulated in a genome . They have conventionally been considered the junk byproducts of genome evolution , as they cannot code for proteins due to sequence degeneration . Recent important studies , however , have discovered that a subset of them ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/comparative", "sequence", "analysis", "plant", "biology/plant", "genomes", "and", "evolution", "computational", "biology/genomics" ]	2009	Small RNAs Originated from Pseudogenes: cis- or trans-Acting?
Pediatric diarrhea can be caused by a wide variety of pathogens , from bacteria to viruses to protozoa . Pathogen prevalence is often described as seasonal , peaking annually and associated with specific weather conditions . Although many studies have described the seasonality of diarrheal disease , these studies have ...	Diarrheal disease is one of the leading causes of death among young children in the developing world . It is difficult to determine which of a wide variety of pathogens are most responsible for disease , since this differs by location and time of year . Here , we study the seasonal prevalence of several pathogens among...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "atmospheric", "science", "pathogens", "microbiology", "cryptosporidium", "reoviruses", "parasitic", "protozoans", "shigella", "viruses", "diarrhea", "seasons", "protozoans", "rna", "vi...	2019	The seasonality of diarrheal pathogens: A retrospective study of seven sites over three years
Scale up of Long Lasting Insecticide Nets ( LLINs ) has massively contributed to reduce malaria mortality across Africa . However , resistance to pyrethroid insecticides in malaria vectors threatens its continued effectiveness . Deciphering the detailed molecular basis of such resistance and designing diagnostic tools ...	Scale up of Long Lasting Insecticide Nets has massively reduced malaria mortality across Africa . However , resistance to pyrethroid insecticides in malaria vectors threatens its continued effectiveness . Here , we established that allelic variation in two CYP450s is the most important driver of pyrethroid resistance i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Allelic Variation of Cytochrome P450s Drives Resistance to Bednet Insecticides in a Major Malaria Vector
The phytohormone abscisic acid ( ABA ) is an essential part of the plant response to abiotic stressors such as drought . Upon the perception of ABA , pyrabactin resistance ( PYR ) /PYR1-like ( PYL ) /regulatory components of ABA receptor ( RCAR ) proteins interact with co-receptor protein phosphatase type 2Cs to permit...	The phytohormone ABA plays critical roles in both plant growth and development and the response to environmental stimuli . The SnRK2s are important components of the PYR/PYL-ABA-PP2C regulatory machine which activate a set of bZIP transcription factors and ion transporters . However , the regulation of SnRK2 turnover i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "enzymes", "brassica", "enzymology", "luminescent", "proteins", "model", "organisms", "plant", "science", "yellow", "fluorescent", "protein", "experimental", "organism", "systems", "seedlings", "molecular", "biology", "techniques", "plants", "extraction", "techniques", "l...	2017	SCFAtPP2-B11 modulates ABA signaling by facilitating SnRK2.3 degradation in Arabidopsis thaliana
Typhoid fevers are infections caused by the bacteria Salmonella enterica serovar Typhi ( Salmonella Typhi ) and Paratyphi A , B and C ( Salmonella Paratyphi ) . Approximately 17 . 8 million incident cases of typhoid fever occur annually , and incidence is highest in children . The accuracy of current diagnostic tests o...	Typhoid fever is an infection caused by the bacterium Salmonella Typhi . Typhoid fever is rare in developed countries but remains high in the developing world . Effective treatment is available but accurate diagnosis of typhoid fever is challenging as typhoid fever can be difficult to distinguish from other infections ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "body", "fluids", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "statistics", "metaanalysis", "immunology", "pediatrics", "bacterial", "diseases", "mathematics", "signs", "an...	2019	Comparative accuracy of typhoid diagnostic tools: A Bayesian latent-class network analysis
Stimulator of interferon genes ( STING , also known as MITA and ERIS ) is critical in protecting the host against DNA pathogen invasion . However , the molecular mechanism underlying the regulation of STING remains unclear . Here , we show that PPM1A negatively regulates antiviral signaling by targeting STING in its ph...	Innate antiviral immunity is essential for the host defense system that rapidly detects and eliminates invading viruses . STING , an endoplasmic reticulum ( ER ) -associated protein , plays important roles in the activation of type I IFN in response to DNA virus infection . Whereas excessive activation of STING can pot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	PPM1A Regulates Antiviral Signaling by Antagonizing TBK1-Mediated STING Phosphorylation and Aggregation
Portal hypertension is responsible for various complications in patients with schistosomiasis , among them intrapulmonary vascular dilations ( IPVD ) . In cirrhotic patients the presence of IPVD is a sign of poor prognosis , but in patients with hepatosplenic schistosomiasis ( HSS ) there are no studies assessing the s...	Intrapulmonary vascular dilatation ( IPVD ) is the key event in development of hepatopulmonary syndrome , an arterial oxygenation defect in patients with portal hypertension . IPVD diagnosis can be made by EchoDopplercardiography or 99mTc-macroaggregated albumin scintigraphy ( 99mTc-MAA ) , and ethiopatogeny is still u...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "gastroenterology", "and", "hepatology", "liver", "diseases", "medicine", "and", "health", "sciences" ]	2014	Intrapulmonary Vascular Dilatation Evaluated by 99mTc-MAA Scintigraphy and Its Association with Portal Hypertension in Schistosomiasis
Numerous bacterial pathogens secrete multiple effectors to modulate host cellular functions . These effectors may interfere with each other to efficiently control the infection process . Bartonellae are Gram-negative , facultative intracellular bacteria using a VirB type IV secretion system to translocate a cocktail of...	Cell migration , a fundamental feature of eukaryotic cells , plays a crucial role in mounting an effective immune response . However , several pathogens subvert the migratory properties of infected host cells to their benefit , such as using them as Trojan horses to disseminate within the host . Bartonella effector pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "gram", "negative", "bacteria", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "microbiology...	2014	A Translocated Effector Required for Bartonella Dissemination from Derma to Blood Safeguards Migratory Host Cells from Damage by Co-translocated Effectors
Interleukin ( IL ) -10 increases host susceptibility to microorganisms and is involved in intracellular persistence of bacterial pathogens . IL-10 is associated with chronic Q fever , an infectious disease due to the intracellular bacterium Coxiella burnetii . Nevertheless , accurate animal models of chronic C . burnet...	The interaction between immune system and invading bacteria is sufficient to eradicate microorganisms in the majority of bacterial infections , but the suppression of the microbicidal response leads to reactivation or chronic evolution of infections and to bacterial persistence . Coxiella burnetii , an obligate intrace...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mus", "(mouse)", "infectious", "diseases", "eubacteria" ]	2008	Persistent Coxiella burnetii Infection in Mice Overexpressing IL-10: An Efficient Model for Chronic Q Fever Pathogenesis
Candida albicans is the most frequent cause of oral fungal infections . However , the exact pathogenicity mechanisms that this fungus employs are largely unknown and many of the genes expressed during oral infection are uncharacterized . In this study we sought to functionally characterize 12 previously unknown functio...	The normally commensal yeast , Candida albicans is the leading cause of both oral and vaginal thrush , as well as life-threatening disseminated infections in the nosocomial setting . Treatment of such infections is hampered by the limited number of suitable antimycotics . Therefore , understanding how this fungus cause...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "mycology", "model", "organisms", "proteins", "oral", "medicine", "yeast", "and", "fungal", "models", "biology", "microbiology" ]	2012	The Novel Candida albicans Transporter Dur31 Is a Multi-Stage Pathogenicity Factor
Japanese encephalitis ( JE ) is the leading cause of viral encephalitis across Asia with approximately 70 , 000 cases a year and 10 , 000 to 15 , 000 deaths . Because JE incidence varies widely over time , partly due to inter-annual climate variability effects on mosquito vector abundance , it becomes more complex to a...	Japanese encephalitis ( JE ) virus is a mosquito-borne virus which is the leading cause of viral encephalitis in Asia . The cumulative attack rate for human JE cases is seemingly low ( 2-cases/105/year ) ; however , epidemics are focal and intense , being concentrated in children 1 to 15 years of age and highly cluster...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "viral", "vaccines", "infectious", "disease", "epidemiology", "flavivirus", "atmospheric", "science", "microbiology", "vaccines", "neglected", "tropical", "diseases", "infectious", "disease", "control", "japanese", "encephalitis", "climate", "change", "vaccinati...	2013	The Effect of Vaccination Coverage and Climate on Japanese Encephalitis in Sarawak, Malaysia
Experimental data from neuroscience suggest that a substantial amount of knowledge is stored in the brain in the form of probability distributions over network states and trajectories of network states . We provide a theoretical foundation for this hypothesis by showing that even very detailed models for cortical micro...	The brain has not only the capability to process sensory input , but it can also produce predictions , imaginations , and solve problems that combine learned knowledge with information about a new scenario . But although these more complex information processing capabilities lie at the heart of human intelligence , we ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Stochastic Computations in Cortical Microcircuit Models
Thymineless death ( TLD ) is a classic and enigmatic phenomenon , documented in bacterial , yeast , and human cells , whereby cells lose viability rapidly when deprived of thymine . Despite its being the essential mode of action of important chemotherapeutic agents , and despite having been studied extensively for deca...	A long-standing enigma in the fields of DNA repair and cancer chemotherapy is why it is that cells starved of the base thymine die rapidly . This process , called thymineless death ( TLD ) , is conserved in bacterial , yeast , and human cells and is the mode of action of important cancer chemotherapeutic drugs . Tumors...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/recombination", "genetics", "and", "genomics/cancer", "genetics", "molecular", "biology/dna", "repair" ]	2010	Role of RecA and the SOS Response in Thymineless Death in Escherichia coli
In this study , we used deletions at 22q13 , which represent a substantial source of human pathology ( Phelan/McDermid syndrome ) , as a model for investigating the molecular mechanisms of terminal deletions that are currently poorly understood . We characterized at the molecular level the genomic rearrangement in 44 u...	Terminal chromosome deletions are among the most commonly observed rearrangements detected by cytogenetics and may result in several well-known genetic syndromes . We used 22q13 deletions to study how these types of chromosome abnormalities arise . Children with Phelan/McDermid syndrome , caused by deletion of the term...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cytogenetic", "analysis", "chromosomal", "disorders", "genetics", "biology", "human", "genetics", "translocations", "cytogenetics", "chromosomal", "deletions", "and", "duplications", "genetics", "and", "genomics", "clinical", "genetics" ]	2011	Molecular Mechanisms Generating and Stabilizing Terminal 22q13 Deletions in 44 Subjects with Phelan/McDermid Syndrome
Variation in plasma levels of cortisol , an essential hormone in the stress response , is associated in population-based studies with cardio-metabolic , inflammatory and neuro-cognitive traits and diseases . Heritability of plasma cortisol is estimated at 30–60% but no common genetic contribution has been identified . ...	Cortisol is a steroid hormone from the adrenal glands that is essential in the response to stress . Most cortisol in blood is bound to corticosteroid binding globulin ( CBG ) . Diseases causing cortisol deficiency ( Addison's disease ) or excess ( Cushing's syndrome ) are life-threatening . Variations in plasma cortiso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "epidemiology", "endocrinology", "mental", "health", "and", "psychiatry", "metabolic", "disorders", "cardiology" ]	2014	Genome Wide Association Identifies Common Variants at the SERPINA6/SERPINA1 Locus Influencing Plasma Cortisol and Corticosteroid Binding Globulin
The Drosophila gene ald encodes the fly ortholog of mps1 , a conserved kinetochore-associated protein kinase required for the meiotic and mitotic spindle assembly checkpoints . Using live imaging , we demonstrate that oocytes lacking Ald/Mps1 ( hereafter referred to as Ald ) protein enter anaphase I immediately upon co...	Female meiosis is the process that ensures developing eggs ( called oocytes ) receive the proper complement of chromosomes . The failure to accurately segregate chromosomes results in aneuploidy , which is the leading cause of birth defects in humans . Cells contain checkpoints that help ensure proper chromosome segreg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "molecular", "biology", "drosophila", "genetics", "and", "genomics" ]	2007	The Multiple Roles of Mps1 in Drosophila Female Meiosis
The mechanism by which hepatitis C virus ( HCV ) gains entry into cells is a complex one , involving a broad range of host proteins . Entry is a critical phase of the viral lifecycle , and a potential target for therapeutic or vaccine-mediated intervention . However , the mechanics of HCV entry remain poorly understood...	Hepatitis C virus affects approximately 70 million people worldwide , resulting in a significant impact on human health . The virus initiates infection through a complex set of interactions with proteins on the surface of human cells . Here we combine experimental approaches with a new mathematical model to study the p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "binding", "cell", "physiology", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cd", "coreceptors", "viral", "transmission", "and", "infection", "hepacivirus", "pathogens", "biological", "cultures"...	2019	Building a mechanistic mathematical model of hepatitis C virus entry
Biphasic neural response properties , where the optimal stimulus for driving a neural response changes from one stimulus pattern to the opposite stimulus pattern over short periods of time , have been described in several visual areas , including lateral geniculate nucleus ( LGN ) , primary visual cortex ( V1 ) , and m...	For many neurons in the early visual brain the optimal stimulation for driving a response changes from one stimulus pattern to the opposite stimulus pattern over short periods of time . For example , many neurons in the lateral geniculate nucleus ( LGN ) respond to a bright stimulus initially but prefer a dark stimulus...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/theoretical", "neuroscience" ]	2009	Predictive Feedback Can Account for Biphasic Responses in the Lateral Geniculate Nucleus
Exposure to hepatitis C virus ( HCV ) typically results in chronic infection that leads to progressive liver disease ranging from mild inflammation to severe fibrosis and cirrhosis as well as primary liver cancer . HCV triggers innate immune signaling within the infected hepatocyte , a first step in mounting of the ada...	Hepatitis C affects nearly 200 million people worldwide . It results from the failure of the immune system to control the hepatitis C virus ( HCV ) replication and spread , leading to progressive liver disease that can culminate in fibrosis , cirrhosis and cancer . The inflammatory cells that infiltrate the diseased li...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "inflammation", "viral", "persistence", "and", "latency", "immunity", "virology", "viruses", "and", "cancer", "biology", "microbiology" ]	2013	Lymphotoxin Signaling Is Initiated by the Viral Polymerase in HCV-linked Tumorigenesis
Var genes encode the major surface antigen ( PfEMP1 ) of the blood stages of the human malaria parasite Plasmodium falciparum . Differential expression of up to 60 diverse var genes in each parasite genome underlies immune evasion . We compared the diversity of the DBLα domain of var genes sampled from 30 parasite isol...	Malaria parasites live in red blood cells of the human host for part of the life cycle , during which a family of diverse antigens known as PfEMP1 are placed on the surface . PfEMP1 variants switch by sequential expression of up to 60 var genes . This allows the parasite to evade immune detection within an individual h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "genetics", "and", "genomics", "plasmodium", "microbiology" ]	2007	Population Genomics of the Immune Evasion (var) Genes of Plasmodium falciparum
Whole genome sequencing ( WGS ) technology holds great promise as a tool for the forensic epidemiology of bacterial pathogens . It is likely to be particularly useful for studying the transmission dynamics of an observed epidemic involving a largely unsampled ‘reservoir’ host , as for bovine tuberculosis ( bTB ) in Bri...	Whole genome sequencing ( WGS ) offers the potential for unprecedented insight into infectious diseases spread at the individual-to-individual level . However , this potential can be compromised when a poorly sampled ‘reservoir’ population contributes to transmission , as strong biases in the obtained data are inevitab...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "veterinary", "diseases", "genomics", "veterinary", "epidemiology", "mathematics", "ecology", "biology", "computational", "biology", "population", "biology", "nonlinear", "dynamics", "genetics", "and", "genomics", "veterinary", "science" ]	2012	Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations
The myelination of axons is a crucial step during vertebrate central nervous system ( CNS ) development , allowing for rapid and energy efficient saltatory conduction of nerve impulses . Accordingly , the differentiation of oligodendrocytes , the myelinating cells of the CNS , and their expression of myelin genes are u...	Oligodendrocytes are a highly specialized cell type that surround axons of the vertebrate central nervous system with myelin , electrically insulating them and allowing rapid and energy-efficient propagation of nerve signals . We previously identified a protein , MYRF , that is required for the final stages of oligoden...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroglial", "development", "developmental", "biology", "developmental", "neuroscience", "molecular", "neuroscience", "neurobiology", "of", "disease", "and", "regeneration", "nucleic", "acids", "gene", "expression", "biology", "molecular", "cell", "biology", "neuroscience"...	2013	MYRF Is a Membrane-Associated Transcription Factor That Autoproteolytically Cleaves to Directly Activate Myelin Genes
As rats learn to search for multiple sources of food or water in a complex environment , they generate increasingly efficient trajectories between reward sites . Such spatial navigation capacity involves the replay of hippocampal place-cells during awake states , generating small sequences of spatially related place-ce...	As rats search for multiple sources of food in a complex environment , they generate increasingly efficient trajectories between reward sites , across multiple trials . This spatial navigation optimization behavior can be measured in the laboratory using a traveling salesperson task ( TSP ) . This likely involves the c...	[ "Abstract", "Introduction", "Material", "&", "methods", "Results", "Discussion" ]	[ "learning", "medicine", "and", "health", "sciences", "prefrontal", "cortex", "applied", "mathematics", "brain", "vertebrates", "social", "sciences", "problem", "solving", "neuroscience", "animals", "mammals", "learning", "and", "memory", "simulation", "and", "modeling",...	2019	Reservoir computing model of prefrontal cortex creates novel combinations of previous navigation sequences from hippocampal place-cell replay with spatial reward propagation
Candida albicans , the most important fungal pathogen of humans , has a unique interaction with macrophages in which phagocytosis induces a switch from the yeast to hyphal form , allowing it to escape by rupturing the immune cell . While a variety of factors induce this switch in vitro , including neutral pH , it is no...	The innate immune system represents a key barrier that fungal pathogens such as Candida albicans must overcome in order to disseminate through the host . C . albicans cells phagocytosed by macrophages initiate a complex program that involves a large-scale reprogramming of metabolism and transcription and results in the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbial", "metabolism", "mycology", "medical", "microbiology", "microbial", "pathogens", "host-pathogen", "interaction", "biology", "microbiology", "pathogenesis", "fungal", "physiology" ]	2014	Modulation of Phagosomal pH by Candida albicans Promotes Hyphal Morphogenesis and Requires Stp2p, a Regulator of Amino Acid Transport
Neisseria meningitidis is a major cause of bacterial meningitis and sepsis worldwide . Lipopolysaccharide ( LPS ) , a major component of the Gram-negative bacterial outer membrane , is sensed by mammalian cells through Toll-like receptor 4 ( TLR4 ) , resulting in activation of proinflammatory cytokine pathways . TLR4 r...	Neisseria meningitidis is a Gram-negative bacterium that can cause the life-threatening diseases meningitis and sepsis . Most of the symptoms seen in these diseases are the result of excessive stimulation of the immune system by lipopolysaccharide ( LPS ) , a major component of the outer membrane of Gram-negative bacte...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "immunology/immunity", "to", "infections", "immunology/innate", "immunity" ]	2009	Naturally Occurring Lipid A Mutants in Neisseria meningitidis from Patients with Invasive Meningococcal Disease Are Associated with Reduced Coagulopathy
As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies , new high quality draft genome sequences are published at a striking pace . With well-established methodologies , larger and more complex genomes are being tackled , including polyploid pl...	Diploid organisms , such as human beings , have two “copies” of each chromosome , whereas polyploid organisms have multiple “copies” ( we use quotes to stress that the “copies” are not identical ) . A key difference between diploid and polyploid organisms is that the “copies” tend to be less similar in polyploid organi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Simulations" ]	[]	2015	ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
DNA damages hinder the advance of replication forks because of the inability of the replicative polymerases to synthesize across most DNA lesions . Because stalled replication forks are prone to undergo DNA breakage and recombination that can lead to chromosomal rearrangements and cell death , cells possess different m...	DNA damages can lead to the stalling of the cellular replication machinery if not repaired on time , inducing DNA strand breaks , recombination that can result in gross chromosomal rearrangements , even cell death . In order to guard against this outcome , cells have evolved several precautionary mechanisms . One of th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "model", "organisms", "protein", "interactions", "dna", "replication", "nucleic", "acids", "proteins", "genetics", "yeast", "and", "fungal", "models", "dna", "biology", "saccharomyces", "cerevisiae", "molecular", "cell", "biology", "dna", "repair", "ge...	2014	Def1 Promotes the Degradation of Pol3 for Polymerase Exchange to Occur During DNA-Damage–Induced Mutagenesis in Saccharomyces cerevisiae
The failure of gene-for-gene resistance traits to provide durable and broad-spectrum resistance in an agricultural context has led to the search for genes underlying quantitative resistance in plants . Such genes have been identified in only a few cases , all for fungal or nematode resistance , and encode diverse molec...	During the evolution of plant-pathogen interactions , plants have evolved the capability to defend themselves from pathogen infection by different overlapping mechanisms . Disease resistance is constituted by an elaborate , multilayered system of defense . Among these responses , quantitative resistance is a prevalent ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	An Atypical Kinase under Balancing Selection Confers Broad-Spectrum Disease Resistance in Arabidopsis
DNA methylation is globally reprogrammed during mammalian preimplantation development , which is critical for normal development . Recent reduced representation bisulfite sequencing ( RRBS ) studies suggest that the methylome dynamics are essentially conserved between human and mouse early embryos . RRBS is known to co...	DNA methylation reprogramming after fertilization is critical for normal mammalian development . Early embryos are sensitive to environmental stresses and a number of reports have pointed out the increased risk of DNA methylation errors associated with assisted reproduction technologies . Therefore , it is very importa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "biochemistry", "developmental", "biology", "embryology", "high", "throughput", "sequencing", "molecular", "biology", "genomic", "imprinting", "embryo", "development", "genetics", "biology", "and", "life", "sciences", "dna", "epigenetics", "dna...	2014	Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development
Several models of flocking have been promoted based on simulations with qualitatively naturalistic behavior . In this paper we provide the first direct application of computational modeling methods to infer flocking behavior from experimental field data . We show that this approach is able to infer general rules for in...	The construction of mathematical models from experimental time-series data has been considered with some success in many areas of science and engineering , using the power of computer algorithms to build model structures and suitably tuning their parameters . When considering complex systems with nonlinear or collectiv...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computer", "science", "computer", "modeling", "mathematics", "applied", "mathematics", "biology", "nonlinear", "dynamics", "zoology" ]	2012	Dynamical Modeling of Collective Behavior from Pigeon Flight Data: Flock Cohesion and Dispersion
A majority of hearing defects are due to malfunction of the outer hair cells ( OHCs ) , those cells within the mammalian hearing sensor ( the cochlea ) that provide an active amplification of the incoming signal . Malformation of the hearing sensor , ototoxic drugs , acoustical trauma , infections , or the effect of ag...	The cochlea , the mammalian hearing sensor , is a formidable biophysical construct in many respects . Its task is to pick up environmental auditory information , which provides us with a sensory communication channel without which we experience great problems in our every day life . In its extreme form , the lack of he...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics/theory", "and", "simulation", "biophysics/replication", "and", "repair", "otolaryngology/audiology", "biophysics", "physics/interdisciplinary", "physics" ]	2008	Biophysical Parameters Modification Could Overcome Essential Hearing Gaps
Spatiotemporal patterns often emerge from local interactions in a self-organizing fashion . In biology , the resulting patterns are also subject to the influence of the systematic differences between the system’s constituents ( biological variability ) . This regulation of spatiotemporal patterns by biological variabil...	Pattern formation is abundant in nature—from the rich ornaments of sea shells and the diversity of animal coat patterns to the myriad of fractal structures in biology and pattern-forming colonies of bacteria . Particularly fascinating are patterns changing with time , spatiotemporal patterns , like propagating waves an...	[ "Abstract", "Introduction", "Effect", "of", "Variability:", "A", "Model", "Study", "Outlook", "Background" ]	[]	2015	Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum
Schistosomiasis is a chronic but preventable disease that affects 260 million people worldwide . In the Philippines , 860 , 000 people are afflicted with Schistosoma japonicum annually , and another 6 . 7 million live in endemic areas . The disease’s complex epidemiology as well as the influence of poverty in endemic a...	Schistosomiasis is a chronic tropical disease caused by parasitic worms of the genus Schistosoma . In the Philippines , Schistosoma japonicum afflicts over 800 , 000 people annually , and another 6 . 7 million live in endemic areas . The current national control program based on human mass treatment has been unable to ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "immunology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "parasitic", "diseases", "animals", "preventive", "medicine", "gastropods", "neglected", "tropical", "diseases", "infectious", ...	2019	Knowledge, attitudes and practices related to schistosomiasis transmission and control in Leyte, Philippines
Previous genome-wide association ( GWA ) studies have identified SNPs associated with areal bone mineral density ( aBMD ) . However , this measure is influenced by several different skeletal parameters , such as periosteal expansion , cortical bone mineral density ( BMDC ) cortical thickness , trabecular number , and t...	Previous studies that have identified genetic polymorphisms involved in bone density have used a technique that cannot differentiate between cortical and trabecular bone . We have carried out the first genome-wide association study using a bone scanning method that can differentiate between the constituent parts of bon...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "genetics", "and", "genomics/complex", "traits", "rheumatology/bone", "and", "mineral", "metabolism" ]	2010	Genome-Wide Association Meta-Analysis of Cortical Bone Mineral Density Unravels Allelic Heterogeneity at the RANKL Locus and Potential Pleiotropic Effects on Bone
Epstein-Barr virus ( EBV ) has been identified as a putative environmental trigger of multiple sclerosis ( MS ) , yet EBV's role in MS remains elusive . We utilized murine gamma herpesvirus 68 ( γHV-68 ) , the murine homolog to EBV , to examine how infection by a virus like EBV could enhance CNS autoimmunity . Mice lat...	Multiple sclerosis ( MS ) is a chronic inflammatory disease of the central nervous system ( CNS ) that leads to progressive disability . The causes of the disease are still unknown . Viral infections has been linked to MS development and Epstein-Barr virus has been shown to have a strong link to MS . Here , we use an a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immune", "cells", "multiple", "sclerosis", "antigen-presenting", "cells", "immunology", "epstein-barr", "virus", "infectious", "mononucleosis", "demyelinating", "disorders", "immunomodulation", "infectious", "diseases", "t", "cells", "immune", "response", "immu...	2012	Gammaherpesvirus Latency Accentuates EAE Pathogenesis: Relevance to Epstein-Barr Virus and Multiple Sclerosis
Schistosomiasis is a serious global problem and the second most devastating parasitic disease following malaria . Parasitic worms of the genus Schistosoma are the causative agents of schistosomiasis and infect more than 240 million people worldwide . The paucity of molecular tools to manipulate schistosome gene express...	Schistosomiasis is a global disease infecting more than 240 million people worldwide and is ranked second only to malaria in global health importance . The causative agents of human schistosomiasis are parasitic worms that ingest red blood cells and can live for decades producing hundreds of eggs daily . There is one p...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mutagenesis", "developmental", "biology", "genetic", "mutation", "molecular", "development", "gene", "expression", "genetics", "gene", "identification", "and", "analysis", "molecular", "genetics", "gene", "regulation", "biology", "molecular", "cell", "biology", "dna", ...	2013	Polyethyleneimine Mediated DNA Transfection in Schistosome Parasites and Regulation of the WNT Signaling Pathway by a Dominant-Negative SmMef2
Microbial communities carry out the majority of the biochemical activity on the planet , and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome . Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from ta...	The human body is inhabited by trillions of bacteria and other microbes , which have recently been studied in many different habitats ( including gut , mouth , skin , and urogenital ) by the Human Microbiome Project ( HMP ) . These microbial communities were assayed using high-throughput DNA sequencing , but it can be ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "microbial", "metabolism", "genomics", "functional", "genomics", "metagenomics", "biology", "computational", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
Modeling of the transmission dynamics of typhoid allows for an evaluation of the potential direct and indirect effects of vaccination; however , relevant typhoid models rooted in data have rarely been deployed . We developed a parsimonious age-structured model describing the natural history and immunity to typhoid infe...	We developed a mathematical model for the transmission dynamics of typhoid in order to evaluate the potential direct and indirect ( i . e . herd immunity ) effects of vaccination . The model was fit to data from Vellore , India and validated against the results of cluster randomized vaccine trials . We evaluated a vari...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "population", "modeling", "epidemiology", "infectious", "disease", "epidemiology", "disease", "dynamics", "population", "dynamics", "global", "health", "population", "biology", "infectious", "disease", "modeling", "biology", "infectious...	2014	Predicting the Impact of Vaccination on the Transmission Dynamics of Typhoid in South Asia: A Mathematical Modeling Study
Environmental fluctuations affect distribution , growth and abundance of diatoms in nature , with iron ( Fe ) availability playing a central role . Studies on the response of diatoms to low Fe have either utilized continuous ( 24 hr ) illumination or sampled a single time of day , missing any temporal dynamics . We pro...	Oceanic diatoms live in constantly fluctuating environments to which they must adapt in order to survive . During sunlit hours , photosynthesis occurs allowing diatoms to store energy used at night to sustain energy demands . Cellular and molecular mechanisms for regulation of phytoplankton growth are important to unde...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Conclusions", "Methods" ]	[ "invertebrates", "urea", "phytoplankton", "chemical", "compounds", "cell", "cycle", "and", "cell", "division", "plant", "cell", "biology", "cell", "processes", "chloroplasts", "animals", "organic", "compounds", "plant", "science", "mitochondria", "bioenergetics", "plant...	2016	Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation
Epithelial to mesenchymal transition ( EMT ) is an essential differentiation program during tissue morphogenesis and remodeling . EMT is induced by soluble transforming growth factor β ( TGF-β ) family members , and restricted by vascular endothelial growth factor family members . While many downstream molecular regula...	Tissue formation and remodeling requires a complex and dynamic balance of interactions between epithelial cells , which reside on the surface , and mesenchymal cells that reside in the tissue interior . During embryonic development , wound healing , and cancer , epithelial cells transform into a mesenchymal cell to for...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "vegf", "signaling", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "epithelial", "cells", "dna", "transcription", "transcription", "factors", "animal", "cells", "proteins", "gene", "expression", "biol...	2016	Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1
Gene expression analysis is generally performed on heterogeneous tissue samples consisting of multiple cell types . Current methods developed to separate heterogeneous gene expression rely on prior knowledge of the cell-type composition and/or signatures - these are not available in most public datasets . We present a ...	Gene expression microarrays are widely used to uncover biological insights . Most microarray experiments profile whole tissues containing mixtures of multiple cell-types . As such , gene expression differences between samples may be due to different cellular compositions or biological differences , highly limiting the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "signal", "processing", "biology", "genomics", "computational", "biology", "engineering" ]	2013	A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays
The parasitoid wasp Nasonia vitripennis is an emerging genetic model for functional analysis of DNA methylation . Here , we characterize genome-wide methylation at a base-pair resolution , and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects...	Insects use methylation to modulate genome function in a different manner from vertebrates . Here , we quantified the global methylation profile in a parasitic wasp species , Nasonia vitripennis , a model with some advantages over ant and honeybee for functional and genetic analyses of methylation , such as short gener...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Function and Evolution of DNA Methylation in Nasonia vitripennis
Functional brain network studies using the Blood Oxygen-Level Dependent ( BOLD ) signal from functional Magnetic Resonance Imaging ( fMRI ) are becoming increasingly prevalent in research on the neural basis of human cognition . An important problem in functional brain network analysis is to understand directed functio...	Modern cognitive neuroscience views cognition in terms of brain network function . A network is a physical system of nodes connected to each other by edges . From the network perspective , cognitive function depends on activity patterns involving the nodes and edges of functional brain networks . It is important then ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cognitive", "neuroscience", "computational", "neuroscience", "biology", "neuroscience" ]	2012	Measuring Granger Causality between Cortical Regions from Voxelwise fMRI BOLD Signals with LASSO
Nucleoside analogs ( NAs ) are used to treat numerous viral infections and cancer . They compete with endogenous nucleotides ( dNTP/NTP ) for incorporation into nascent DNA/RNA and inhibit replication by preventing subsequent primer extension . To date , an integrated mathematical model that could allow the analysis of...	Nucleoside analogs ( NAs ) represent an important drug class for the treatment of viral infections and cancer . They inhibit DNA/RNA polymerization after being incorporated into nascent DNA/RNA , which prevents primer extension . Viruses are particularly versatile and frequently develop mutations enabling them to avert...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "enzymes", "applied", "mathematics", "microbiology", "mathematical", "computing", "mathematics", "infectious", "diseases", "biology", "viral", "replication", "biochemistry", "virology", "viral", "diseases", "computational", "biology", "evolutionary", "biology" ]	2012	HIV-1 Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection
The bivalent whole-cell ( BivWC ) oral cholera vaccine ( Shanchol ) is effective in preventing cholera . However , evaluations of immune responses following vaccination with BivWC have been limited . To determine whether BivWC induces significant mucosal immune responses , we measured V . cholerae O1 antigen-specific a...	The bivalent whole-cell ( BivWC ) oral cholera vaccine ( Shanchol ) is effective in preventing cholera . Despite its increasing use as part of comprehensive cholera prevention and control efforts , evaluations of immune responses following vaccination with BivWC have been limited . In this study , we measured the devel...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "vibrio", "immunology", "tropical", "diseases", "microbiology", "vaccines", "preventive", "medicine", "bacterial", ...	2016	Antibody Secreting Cell Responses following Vaccination with Bivalent Oral Cholera Vaccine among Haitian Adults
High-throughput multi-omics studies and corresponding network analyses of multi-omic data have rapidly expanded their impact over the last 10 years . As biological features of different types ( e . g . transcripts , proteins , metabolites ) interact within cellular systems , the greatest amount of knowledge can be gain...	Inferring co-expression networks that combine multiple types of–omics data can lead to networks that are highly segregated with very few edges linking nodes of different–omics types . Here , we explored methods of improving integration in co-expression networks and found that a random forest approach , GENIE3 , was , i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "genetic", "networks", "pathology", "and", "laboratory", "medicine", "pathogens", "protein", "interaction", "networks", "microbiology", "viruses", "rna", "viruses", "network", "analysis", "genome", "analysis", ...	2019	Unified feature association networks through integration of transcriptomic and proteomic data
Two-component systems ( TCS ) represent major signal-transduction pathways for adaptation to environmental conditions , and regulate many aspects of bacterial physiology . In the whooping cough agent Bordetella pertussis , the TCS BvgAS controls the virulence regulon , and is therefore critical for pathogenicity . BvgS...	Bacteria make use of two-component transduction systems , composed of a sensor-kinase and a response regulator , to perceive environmental signals and orchestrate an appropriate response . The virulence regulon of the whooping cough agent Bordetella pertussis is controlled by the two-component system BvgAS . The sensor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Virulence Regulation with Venus Flytrap Domains: Structure and Function of the Periplasmic Moiety of the Sensor-Kinase BvgS
The capacity of pluripotent embryonic stem cells to differentiate into any cell type in the body makes them invaluable in the field of regenerative medicine . However , because of the complexity of both the core pluripotency network and the process of cell fate computation it is not yet possible to control the fate of ...	Pluripotent stem cells possess the capacity both to renew themselves indefinitely and to differentiate to any cell type in the body . Thus the ability to direct stem cell differentiation would have immense potential in regenerative medicine . There is a massive amount of biological data relevant to stem cells; here we ...	[ "Abstract", "Introduction", "Results", "Discussion", "Model" ]	[ "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "cell", "differentiation", "simulation", "and", "modeling", "developmental", "biology", "stem", "cells", "transcription", "factors", "research", "and", "analysis", "methods", "cell", "potency", "...	2017	A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells
The reticuloendotheliosis viruses ( REVs ) comprise several closely related amphotropic retroviruses isolated from birds . These viruses exhibit several highly unusual characteristics that have not so far been adequately explained , including their extremely close relationship to mammalian retroviruses , and their pres...	Retroviruses are characterized by their ability to insert a DNA copy of their genome into the chromosomes of infected cells . Occasionally , retroviruses insert into “germline” cells and are subsequently inherited as host alleles called endogenous retroviruses ( ERVs ) . Vertebrate genomes contain thousands of ERV sequ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "vaccines", "mammalogy", "viruses", "and", "cancer", "emerging", "viral", "diseases", "computational", "biology", "microbiology", "parasitology", "genome", "databases", "zoology", "veterinary", "science", "viral", "disease", "diagnosis", "sequence", "analysis", ...	2013	The Extraordinary Evolutionary History of the Reticuloendotheliosis Viruses
For nearly all life forms , perceptual systems provide access to a host of environmental cues , including the availability of food and mates as well as the presence of disease and predators . Presumably , individuals use this information to assess the current and future states of the environment and to enact appropriat...	Sensory inputs , including taste and smell , can modulate lifespan in organisms such as fruit flies and nematodes . For example , the smell of live yeast is sufficient to accelerate aging in fruit flies that are nutrient restricted . However , the sensory pathways and specific olfactory cues that modulate aging are unk...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "nutrition", "neuroscience", "developmental", "biology/aging" ]	2010	Carbon Dioxide Sensing Modulates Lifespan and Physiology in Drosophila
Different interoceptive systems must be integrated to ensure that multiple homeostatic insults evoke appropriate behavioral and physiological responses . Little is known about how this is achieved . Using C . elegans , we dissect cross-modulation between systems that monitor temperature , O2 and CO2 . CO2 is less avers...	Many animals are either attracted or repelled by carbon dioxide . We show that the way C . elegans responds to CO2 depends on the temperature it has acclimated to and the oxygen tensions it is experiencing . The effects of acclimation temperature are mediated by a temperature-sensing neuron called AFD that also respond...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. elegans
Gene regulatory networks are perhaps the most important organizational level in the cell where signals from the cell state and the outside environment are integrated in terms of activation and inhibition of genes . For the last decade , the study of such networks has been fueled by large-scale experiments and renewed a...	A cell receives signals both from its internal and external environment and responds by changing the expression of genes . In this manner the cell adjusts to heat , osmotic pressures and other circumstances during its lifetime . Over long timescales , the network of interacting genes and its regulatory actions also und...	[ "Abstract", "Introduction", "Results", "Discussion", "Model" ]	[ "computational", "biology/evolutionary", "modeling", "computational", "biology/transcriptional", "regulation" ]	2008	Evolution of Evolvability in Gene Regulatory Networks
The innate immune system is responsible for many important functions in the body including responding to infection , clearing cancerous cells , healing wounds , and removing foreign substances . Although many of these functions happen simultaneously in life , most laboratory studies of the innate immune response focus ...	In a natural setting , the innate immune system is frequently faced with multiple insults , against which it must mount overlapping inflammatory responses . We are interested in how the innate immune system deals with multiple , simultaneously occurring inflammatory insults , and if the response to one will take priori...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "motility", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "immune", "cells", "pathogens", "immunology", "microbiology", "orthomyxoviruse...	2018	Pulmonary influenza A virus infection leads to suppression of the innate immune response to dermal injury
Ligand binding sites in proteins are often localized to deeply buried cavities , inaccessible to bulk solvent . Yet , in many cases binding of cognate ligands occurs rapidly . An intriguing system is presented by the L99A cavity mutant of T4 Lysozyme ( T4L L99A ) that rapidly binds benzene ( ~106 M-1s-1 ) . Although th...	Proteins often bind ligands in buried cavities that appear to be inaccessible based on static structures . The mechanisms and pathways by which ligands reach their binding sites in such cases are , thus , often unknown . Yet , ligand recognition by occluded cavities can happen rapidly . A central question remains: How ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "chemical", "characterization", "crystal", "structure", "chemical", "compounds", "condensed", "matter", "physics", "organic", "compounds", "simulation", "and", "modeling", "protein", "structure", "crystallography", "thermodynamics", "research", "and", "analysis", "methods",...	2018	Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme
Steroid hormones regulate gene expression by interaction of their receptors with hormone responsive elements ( HREs ) and recruitment of kinases , chromatin remodeling complexes , and coregulators to their target promoters . Here we show that in breast cancer cells the BAF , but not the closely related PBAF complex , i...	In order to adapt its gene expression program to the needs of the environment , the cell must access the information stored in the DNA sequence that is tightly packaged into chromatin in the cell nucleus . How the cell manages to do it in a selective maner is still unclear . Here we show that , in breast cancer cells t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "molecular", "biology/transcription", "initiation", "and", "activation", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/epigenetics", "molecular", "biology/translational", "regulation", "molecular", ...	2009	Two Chromatin Remodeling Activities Cooperate during Activation of Hormone Responsive Promoters
Apoptosis is a tightly controlled process in mammalian cells . It is important for embryogenesis , tissue homoeostasis , and cancer treatment . Apoptosis not only induces cell death , but also leads to the release of signals that promote rapid proliferation of surrounding cells through the Phoenix Rising ( PR ) pathway...	Apoptosis , or programmed cell death , is known to be important for embryogenesis , tissue homoeostasis , and cancer treatment . Furthermore , researchers have recently observed that apoptosis may promote wound healing and tissue regeneration , and accelerate undesired solid tumor regrowth after chemotherapy/radiation ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "bioengineering", "systems", "biology", "biomedical", "engineering", "biological", "systems", "engineering", "biology", "computational", "biology", "engineering" ]	2014	Mathematical Modeling of the Phoenix Rising Pathway
Fission yeast serves as a model for how cellular polarization machinery consisting of signaling molecules and the actin and microtubule cytoskeleton regulates cell shape . In this work , we develop mathematical models to investigate how these cells maintain a tubular shape of approximately constant diameter . Many stud...	Fission yeast is a rod-shaped organism that is studied , in part , as a model for how cells develop and regulate their shape . Despite extensive work identifying effects of genetic mutations and pharmacological treatments on the shape of these cells , there is a lack of mathematical and computational models examining h...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[]	2013	Model of Fission Yeast Cell Shape Driven by Membrane-Bound Growth Factors and the Cytoskeleton
Elevated temperature induces the heat shock ( HS ) response , which modulates cell proliferation , apoptosis , the immune and inflammatory responses . However , specific mechanisms linking the HS response pathways to major cellular signaling systems are not fully understood . Here we used integrated computational and e...	Hyperthermia has been considered a promising strategy to sensitize cancer cells to treatment . As such , it might potentially increase treatment efficacy while reducing negative side effects . So far , this potential has not been fully realized . One of the major obstacles is a lack of quantitative understanding of cro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "cancer", "treatment", "immunology", "dna", "transcription", "simulation", "and", "modeling", "oncology", "developmental", "biology", "molecular"...	2018	Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level
Germ cell immortality , or transgenerational maintenance of the germ line , could be promoted by mechanisms that could occur in either mitotic or meiotic germ cells . Here we report for the first time that the GSP-2 PP1/Glc7 phosphatase promotes germ cell immortality . Small RNA-induced genome silencing is known to pro...	The germ line of an organism is considered immortal in its capacity to give rise to an unlimited number of future generations . To protect the integrity of the germ line , mechanisms act to suppress the accumulation of transgenerational damage to the genome or epigenome . Loss of germ cell immortality can result from m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "cell", "physiology", "meiosis", "rna", "interference", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna-binding", "proteins", "invertebrate", "genomics", "germ", "cells", "epigenetics", "small", "interfering...	2019	The meiotic phosphatase GSP-2/PP1 promotes germline immortality and small RNA-mediated genome silencing
Elevated proteasome activity extends lifespan in model organisms such as yeast , worms and flies . This pro-longevity effect might be mediated by improved protein homeostasis , as this protease is an integral module of the protein homeostasis network . Proteasomes also regulate cellular processes through temporal and s...	Advanced cellular age is associated with decreased efficiency of the proteostasis network . The proteasome , a protease in the cytoplasm and nuclei of eukaryotic cells , is an important component of this network . Recent studies demonstrate that increased proteasome capacity has a positive impact on longevity . The und...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Proteasomes, Sir2, and Hxk2 Form an Interconnected Aging Network That Impinges on the AMPK/Snf1-Regulated Transcriptional Repressor Mig1
Monoamine transporters ( MATs ) carry out neurotransmitter reuptake from the synaptic cleft , a key step in neurotransmission , which is targeted in the treatment of neurological disorders . Cholesterol ( CHOL ) , a major component of the synaptic plasma membrane , has been shown to exhibit a modulatory effect on MATs ...	It has been revealed that the cellular membrane is an active contributor to biological processes occurring in and across it and can regulate the function of proteins embedded within it . Cholesterol ( CHOL ) plays a key role in these effects . Notably , CHOL affects neurotransmission . Neurotransmission occurs at the s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "crystal", "structure", "molecular", "dynamics", "condensed", "matter", "physics", "simulation", "and", "modeling", "multivariate", "analysis", "mathematics", "statistics", "(mathematics)", "crystallography", "research", "and", "analysis", "methods", "lipids", "solid", "s...	2018	A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition
During spermatogenesis , interconnected haploid spermatids segregate undesired cellular contents into residual bodies ( RBs ) before detaching from RBs . It is unclear how this differentiation process is controlled to produce individual spermatids or motile spermatozoa . Here , we developed a live imaging system to vis...	Spermatogenesis is a conserved multistep process that involves mitotic proliferation of spermatogonia , meiotic division of spermatocytes , and differentiation of haploid spermatids into mature spermatozoa . During spermatid differentiation , spermatids shed unwanted cellular contents in the form of a residual body ( R...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	Distinct roles of two myosins in C. elegans spermatid differentiation
In French Guiana , cutaneous leishmaniasis is highly endemic , whereas no autochthonous case of visceral leishmaniasis have been reported so far . However , due to its proximity to Brazil which is highly endemic for visceral leishmaniasis , and the high transboundary population flow , an epidemiological challenge could...	Leishmaniasis is endemic in French Guiana under its cutaneous form where Leishmania guyanensis is the principle parasite species . Visceral leishmaniasis is much more severe , although well known in neighbouring countries ( Brazil , Suriname , Venezuela ) , it has not been known in French Guiana until now . Our study p...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "dogs", "parasitic", "protozoans", "animals", "mammals", "protozoans", "leishmania", "neglected", "tropical", "diseases", "cellular", "structures", ...	2019	Potential animal reservoirs (dogs and bats) of human visceral leishmaniasis due to Leishmania infantum in French Guiana
We investigate methods to vaccinate contact networks—i . e . removing nodes in such a way that disease spreading is hindered as much as possible—with respect to their cost-efficiency . Any real implementation of such protocols would come with costs related both to the vaccination itself , and gathering of information a...	Finding methods to identify important spreaders—and consequently protocols to identify individuals to vaccinate in targeted vaccination campaigns—is one of the most important topics of network theory . Earlier studies typically make some assumption about what information is available about the contact network that the ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "mathematical", "models", "retroviruses", "viruses", "preventive", "medicine", "immunodeficiency", "viruses", "rna", "viruses", "sexually", "t...	2017	Cost-efficient vaccination protocols for network epidemiology
Although cancers are considered stem cell diseases , mechanisms involving stem cell alterations are poorly understood . Squamous cell carcinoma ( SQCC ) is the second most common lung cancer , and its pathogenesis appears to hinge on changes in the stem cell behavior of basal cells in the bronchial airways . Basal cell...	Squamous cell carcinoma ( SQCC ) is a deadly and common form of lung cancer . How it develops from stem cells is poorly understood . SQCCs predominantly arise in bronchial epithelia , likely from basal cells , stem cells that normally generate mucinous and ciliated cells . Smoking , however , causes normally quiescent ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "keratinocytes", "medicine", "and", "health", "sciences", "dysplasia", "pathology", "and", "laboratory", "medicine", "cell", "differentiation", "epithelial", "cells", "developmental", "biology", "signs", "and", "symptoms", "stem", "cells", "infectious", "disease", "cont...	2016	SOX2 and PI3K Cooperate to Induce and Stabilize a Squamous-Committed Stem Cell Injury State during Lung Squamous Cell Carcinoma Pathogenesis
tRNA is the most highly modified class of RNA species , and modifications are found in tRNAs from all organisms that have been examined . Despite their vastly different chemical structures and their presence in different tRNAs , occurring in different locations in tRNA , the biosynthetic pathways of the majority of tRN...	Numerous studies revealed the existence of nearly 110 ribonucleoside structures incorporated as post-transcriptional modifications in tRNA , with 25–30 modifications present in any one organism . Emerging evidence points to the critical role of tRNA modifications in various cellular responses to stimuli , including tra...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity
Co-transcriptional RNA-DNA hybrids ( R loops ) cause genome instability . To prevent harmful R loop accumulation , cells have evolved specific eukaryotic factors , one being the BRCA2 double-strand break repair protein . As BRCA2 also protects stalled replication forks and is the FANCD1 member of the Fanconi Anemia ( F...	R loops are co-transcriptional RNA-DNA hybrids that can have a physiological role in transcription and replication , but also may be a major threat to genome stability . To avoid the deleterious effects of R loops , specific factors prevent their formation or facilitate their removal . The double-strand break repair fa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Fanconi Anemia Pathway Protects Genome Integrity from R-loops
Kaposi’s sarcoma ( KS ) , caused by Kaposi’s sarcoma herpesvirus ( KSHV ) , is a highly vascularised tumour of endothelial origin . KSHV infected endothelial cells show increased invasiveness and angiogenesis . Here , we report that the KSHV K15 protein , which we showed previously to contribute to KSHV-induced angioge...	Kaposi’s Sarcoma ( KS ) , etiologically linked to Kaposi’s sarcoma herpesvirus ( KSHV ) , is a tumour of endothelial origin characterised by angiogenesis and invasiveness . In vitro , KSHV infected endothelial cells display an increased invasiveness and high angiogenicity . Here we report that the KSHV protein K15 , wh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Inhibiting the Recruitment of PLCγ1 to Kaposi’s Sarcoma Herpesvirus K15 Protein Reduces the Invasiveness and Angiogenesis of Infected Endothelial Cells
Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample . As previously available phylogenetic inference tools assume that all samples are tips , they do not allow for this possibility . We have devel...	A central goal of phylogenetic analysis is to estimate evolutionary relationships and the dynamical parameters underlying the evolutionary branching process ( e . g . macroevolutionary or epidemiological parameters ) from molecular data . The statistical methods used in these analyses require that the underlying tree b...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "macroevolution", "phylogenetic", "analysis", "molecular", "biology", "evolutionary", "processes", "mathematical", "and", "statistical", "techniques", "evolutionary", "modeling", "bayesian", "method", "biology", "and", "life", "sciences", "molecular", "biology", "techniques...	2014	Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
Major histocompatibility complex ( MHC ) class I molecules determine immune responses to viral infections . These polymorphic cell-surface glycoproteins bind peptide antigens , forming ligands for cytotoxic T and natural killer cell receptors . Under pressure from rapidly evolving viruses , hominoid MHC class I molecul...	Polymorphic major histocompatibility complex ( MHC ) class I molecules activate immune responses against infection and correlate with susceptibilities to disease . In humans , longitudinal study of how disease epidemics alter MHC frequencies has not been possible . We studied chimpanzees , a species having direct equiv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Signature Patterns of MHC Diversity in Three Gombe Communities of Wild Chimpanzees Reflect Fitness in Reproduction and Immune Defense against SIVcpz
Leishmania donovani , belonging to a unicellular protozoan parasite , display the differential level of linkage-specific sialic acids on their surface . Sialic acids binding immunoglobulin-like lectins ( siglecs ) are a class of membrane-bound receptors present in the haematopoetic cell lineages interact with the linka...	Sialic acids are nine carbon sugars present on terminal cell surface glycoproteins and glycolipids . Siglec is a membrane receptor that belongs to an immunoglobulin super family present in almost all the haematopoetic cell lineages . There are 14 different types of siglecs present on human immune cells that take an act...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "cell", "binding", "cell", "physiology", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "chemical", "compounds", "sialic", "acids", "immunology", "cell", "processes", "...	2016	Leishmania donovani Utilize Sialic Acids for Binding and Phagocytosis in the Macrophages through Selective Utilization of Siglecs and Impair the Innate Immune Arm
Effective cancer treatment is crucially dependent on the identification of the biological processes that drive a tumor . However , multiple processes may be active simultaneously in a tumor . Clustering is inherently unsuitable to this task as it assigns a tumor to a single cluster . In addition , the wide availability...	In order to select effective cancer treatment , we need to determine which biological processes are active in a tumor . To this end , tumors have been quantified by high dimensional molecular measurements such as RNA sequencing and DNA copy number profiling . In order to support decision making , these measurements nee...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "breast", "tumors", "cancer", "treatment", "carcinomas", "cancers", "and", "neoplasms", "oncology", "protein", "expression", "adenocarcinomas", "molecular", "biology", "techniques", "secondary", "lung", "tumors", "research", "and...	2018	Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis
Autophagy is a physiological process for the recycling and degradation of cellular materials . Forming the autophagosome from the phagophore , a cup-shaped double-membrane vesicle , is a critical step in autophagy . The origin of the cup shape of the phagophore is poorly understood . In yeast , fusion of a small number...	Cells use autophagy to recycle and degrade a wide range of materials , from individual molecules to entire organelles . We perform simulations to study a key step in the initial stages of the autophagy pathway: how the membrane adopts the characteristic cup shape of the phagophore that then engulfs its targets . We fin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "autophagic", "cell", "death", "vesicles", "molecular", "dynamics", "built", "structures", "engineering", "and", "technology", "cell", "processes", "membrane", "fusion", "membrane", "structures", "vesicle", "fusion", "cellular", "structures", "and", "...	2017	Scaffolding the cup-shaped double membrane in autophagy
As sessile organisms , plants must cope with multiple and combined variations of signals in their environment . However , very few reports have studied the genome-wide effects of systematic signal combinations on gene expression . Here , we evaluate a high level of signal integration , by modeling genome-wide expressio...	Light ( L ) , nitrogen ( N ) , and carbon ( C ) are well known to be strong signals regulating gene expression in plants . But , so far , few reports have described their interactions on a genome scale . Here , we report the transcriptome response of the factorial combination of these three signals in leaves and roots ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-environment", "interactions", "plant", "biology/plant", "genetics", "and", "gene", "expression", "plant", "biology" ]	2009	A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis
Due to the selection pressure imposed by highly variable environmental conditions , stress sensing and regulatory response mechanisms in plants are expected to evolve rapidly . One potential source of innovation in plant stress response mechanisms is gene duplication . In this study , we examined the evolution of stres...	Plants have developed a multitude of response mechanisms to survive stressful environments . Since the environment is highly variable , these stress response mechanisms are expected to undergo frequent innovation . Duplicate genes represent a potential source for such innovation . In this paper , we explored the evolut...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/gene", "function", "plant", "biology/plant", "genetics", "and", "gene", "expression", "genetics", "and", "genomics/plant", "genomes", "and", "evolution", "plant", "biology/plant-environment", "interactions" ]	2009	Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana
Eukaryotic genomes are repetitively packaged into chromatin by nucleosomes , however they are regulated by the differences between nucleosomes , which establish various chromatin states . Local chromatin cues direct the inheritance and propagation of chromatin status via self-reinforcing epigenetic mechanisms . Replica...	Chromatin is based on a repetitive structural unit called the nucleosome . However , the regulatory properties of chromatin are mediated by the differences between nucleosomes , due to post-translational modifications or the inclusion of histone variants . These differences are maintained by inheritance through cis-act...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "genetics", "and", "genomics/gene", "expression", "molecular", "biology/centromeres", "genetics", "and", "genomics/epigenetics", "chemical", "biology/protein", "chemistry", "and", "proteomics", "molecular", "biology/chromatin", "s...	2009	The Schizosaccharomyces pombe JmjC-Protein, Msc1, Prevents H2A.Z Localization in Centromeric and Subtelomeric Chromatin Domains
Congenital T . cruzi infections involve multiple factors in which complex interactions between the parasite and the immune system of pregnant women play important roles . In this study , we used an experimental murine model of chronic infection with T . cruzi to evaluate the changes in the expression of inhibitory rece...	Chagas disease or American trypanosomiasis is a complex parasitic disease caused by the protozoan Trypanosoma cruzi . This disease that affects approximately 10 million people worldwide may be mother-to-child transmitted which is an important public health problem with great relevance in endemic and non-endemic areas a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "maternal", "health", "cd", "coreceptors", "obstetrics", "and", "gynecology", "cell", "cycle", "and", "cell", "division", "immunology", "cell", "processes", "parasitic", "diseases", "paras...	2017	Expression of inhibitory receptors and polyfunctional responses of T cells are linked to the risk of congenital transmission of T. cruzi
Infection of erythrocytes with the Plasmodium parasite causes the pathologies associated with malaria , which result in at least one million deaths annually . The rupture of infected erythrocytes triggers an inflammatory response , which is induced by parasite-derived factors that still are not fully characterized . In...	Malaria , a disease that results in more than one million deaths per year , is caused by infection with the Plasmodium parasite . Plasmodium infects erythrocytes inducing an acute inflammatory response with high fevers and elevated levels of pro-inflammatory cytokines , which contribute to the pathology of the disease ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/innate", "immunity", "microbiology/parasitology" ]	2008	Plasmodium-Induced Inflammation by Uric Acid
Insecticide resistance has the potential to compromise the enormous effort put into the control of dengue and malaria vector populations . It is therefore important to quantify the amount of selection acting on resistance alleles , their contributions to fitness in heterozygotes ( dominance ) and their initial frequenc...	The emergence and spread of insecticide resistance compromise the control of mosquito borne diseases such as dengue or malaria , which are responsible for millions of deaths every year in tropical and subtropical areas . There are currently no easily implemented methodologies to quantify the strength of selection for r...	[ "Abstract", "Introduction", "Model", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "mathematics", "biology" ]	2011	Challenges in Estimating Insecticide Selection Pressures from Mosquito Field Data
Previously , we investigated the role of the Rift Valley fever virus ( RVFV ) virulence genes NSs and NSm in mosquitoes and demonstrated that deletion of NSm significantly reduced the infection , dissemination , and transmission rates of RVFV in Aedes aegypti mosquitoes . The specific aim of this study was to further c...	Rift Valley fever virus ( RVFV ) is a mosquito-borne virus endemic to Africa . Outbreaks of RVFV have resulted in devastating morbidity and mortality in livestock and humans . A novel RVFV vaccine strain has been developed in which two virulence genes , NSs and NSm , have been deleted from the RVFV genome . Previously ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mosquitoes", "zoology", "entomology", "viral", "transmission", "and", "infection", "vector", "biology", "virology", "genetics", "host-pathogen", "interaction", "microbiology", "biology", "viral", "vectors", "viral", "replication", "gene", "function" ]	2014	Deletion of the NSm Virulence Gene of Rift Valley Fever Virus Inhibits Virus Replication in and Dissemination from the Midgut of Aedes aegypti Mosquitoes
TBX3 is a member of the T-box family of transcription factors with critical roles in development , oncogenesis , cell fate , and tissue homeostasis . TBX3 mutations in humans cause complex congenital malformations and Ulnar-mammary syndrome . Previous investigations into TBX3 function focused on its activity as a trans...	TBX3 is a protein with essential roles in development and tissue homeostasis , and is implicated in cancer pathogenesis . TBX3 mutations in humans cause a complex of birth defects called Ulnar-mammary syndrome ( UMS ) . Despite the importance of TBX3 and decades of investigation , few TBX3 partner proteins have been id...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "biochemistry", "rna", "model", "organisms", "rna", "transport", "rna", "processing", "cell", "biology", "nucleic", "acids", "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "molecular", "genetics", "m...	2014	TBX3 Regulates Splicing In Vivo: A Novel Molecular Mechanism for Ulnar-Mammary Syndrome
Collective navigation and swarming have been studied in animal groups , such as fish schools , bird flocks , bacteria , and slime molds . Computer modeling has shown that collective behavior of simple agents can result from simple interactions between the agents , which include short range repulsion , intermediate rang...	Many groups of organisms , from colonies of bacteria and social insects through schools of fish and flocks of birds to herds of mammals exhibit advanced collective navigation . Identifying the minimal features of biologically-inspired interacting agents that can lead to emergence of “intelligent” like collective naviga...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "science", "computer", "modeling", "theoretical", "biology", "biology", "computerized", "simulations" ]	2011	Smart Swarms of Bacteria-Inspired Agents with Performance Adaptable Interactions
In fungi belonging to the phylum Basidiomycota , sexual compatibility is usually determined by two genetically unlinked MAT loci , one of which encodes one or more pheromone receptors ( P/R ) and pheromone precursors , and the other comprehends at least one pair of divergently transcribed genes encoding homeodomain ( H...	Some fungi are capable of sexual reproduction without the need for a sexually compatible partner , a behavior called homothallism . For some of these fungi , it was observed that they carried in a single individual all the genes normally determining sexual identity in two distinct sexually compatible individuals , but ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "fungal", "genetics", "dna-binding", "proteins", "plasmid", "construction", "fungi", "dna", "construction", "molecular", "biology", "techniques", "fungal", "reproduction", "fungal", "sporulation", "research", "and", "analysis", "methods", "pheromone", "receptors", "mycolo...	2016	Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete
The cell intrinsic innate immune responses provide a first line of defense against viral infection , and often function by targeting cellular pathways usurped by the virus during infection . In particular , many viruses manipulate cellular lipids to form complex structures required for viral replication , many of which...	RNA viruses represent an important worldwide source of infection and disease in both humans and animals . While individual viruses have unique characteristics , some stages of infection are conserved and must be completed in order to successfully infect and grow . Viruses must undergo genome replication , protein synth...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "pathology", "drugs", "and", "devices", "immunology", "microbiology", "global", "health", "veterinary", "science", "veterinary", "medicine", "infectious", "diseases", "veterinary", "diseases", "veterinary", "microbiol...	2012	AMP-Activated Kinase Restricts Rift Valley Fever Virus Infection by Inhibiting Fatty Acid Synthesis
Most monoclonal antibodies ( mAbs ) to the influenza A virus hemagglutinin ( HA ) head domain exhibit very limited breadth of inhibitory activity due to antigenic drift in field strains . However , mAb 1F1 , isolated from a 1918 influenza pandemic survivor , inhibits select human H1 viruses ( 1918 , 1943 , 1947 , and 1...	Influenza infection kills thousands of people every year and causes major pandemics every few decades . The most lethal outbreak of influenza known was the 1918 H1N1 influenza pandemic that killed an estimated 20 to 100 million people . The 1918 virus was likely introduced into the human population from birds . We prev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "influenza", "immunology", "biology", "viral", "diseases", "immune", "response", "immunoglobulins" ]	2012	Influenza Human Monoclonal Antibody 1F1 Interacts with Three Major Antigenic Sites and Residues Mediating Human Receptor Specificity in H1N1 Viruses
The Ari peoples of Ethiopia are comprised of different occupational groups that can be distinguished genetically , with Ari Cultivators and the socially marginalised Ari Blacksmiths recently shown to have a similar level of genetic differentiation between them ( FST ≈ 0 . 023 − 0 . 04 ) as that observed among multiple ...	While it is widely recognized that DNA patterns vary across world-wide human populations , the primary features that drive these differences are less well understood . As an example , the Ari peoples of Ethiopia are presently socially divided according to occupation , with Ari Blacksmiths marginalised relative to Ari C...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference
Tsetse flies ( Glossina spp . ) vector pathogenic trypanosomes ( Trypanosoma spp . ) in sub-Saharan Africa . These parasites cause human and animal African trypanosomiases , which are debilitating diseases that inflict an enormous socio-economic burden on inhabitants of endemic regions . Current disease control strateg...	Tsetse flies transmit pathogenic African trypanosomes , which are the causative agents of socio-economically devastating human and animal African trypanosomiases . These diseases are currently controlled in large part by reducing the population size of tsetse vectors through the use of insecticides , traps and sterile ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "trypanosoma", "brucei", "bacterial", "diseases", "protozoans", "enterobacteriaceae", ...	2019	Colonization of the tsetse fly midgut with commensal Kosakonia cowanii Zambiae inhibits trypanosome infection establishment
Lymphatic filariasis ( LF ) , a global public health problem affecting approximately 120 million people worldwide , is a leading cause of disability in the developing world including the South Pacific . Despite decades of ongoing mass drug administration ( MDA ) in the region , some island nations have not yet achieved...	Aedes polynesiensis is the primary mosquito vector of lymphatic filariasis ( LF ) in the island nations of the South Pacific . Control of LF in this region of the world is difficult due to the unique biology of the mosquito vector . A proposed method to control LF in the Pacific is through the release of male mosquitoe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "entomology", "biology", "zoology" ]	2011	Male Mating Competitiveness of a Wolbachia-Introgressed Aedes polynesiensis Strain under Semi-Field Conditions
High coverage whole genome sequencing provides near complete information about genetic variation . However , other technologies can be more efficient in some settings by ( a ) reducing redundant coverage within samples and ( b ) exploiting patterns of genetic variation across samples . To characterize as many samples a...	In this work we address a series of questions prompted by the rise of next-generation sequencing as a data collection strategy for genetic studies . How does low coverage sequencing compare to traditional microarray based genotyping ? Do studies increase sensitivity by collecting both sequencing and array data ? What c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "sequencing", "genome-wide", "association", "studies", "genome", "analysis", "tools", "genomics", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics", "human", "genetics" ]	2012	Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation
Despite high rates of exposure , only 5–10% of people infected with Mycobacterium tuberculosis will develop active tuberculosis ( TB ) disease , suggesting a significant role for genetic variation in the human immune response to this infection . Here , we studied TB association and expression of 18 genes involved in th...	One third of the world population is infected with Mycobacterium tuberculosis , the bacterium that causes tuberculosis; however , only 5–10% of those infected will develop active disease . Difference in polymorphisms within genes involved in host immune response has been proposed as a plausible reason to explain this p...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "infectious", "diseases", "genetics", "and", "genomics/population", "genetics" ]	2008	Genetic Association and Expression Studies Indicate a Role of Toll-Like Receptor 8 in Pulmonary Tuberculosis
Mycobacterium tuberculosis is a hard-to-eradicate intracellular pathogen that infects one-third of the global population . It can live within macrophages owning to its ability to arrest phagolysosome biogenesis . Autophagy has recently been identified as an effective way to control the intracellular mycobacteria by enh...	microRNA-155 ( miR-155 ) plays an essential role in regulating the host immune response by post-transcriptionally repressing the expression of target genes . However , little is known regarding its activity in modulating autophagy , an important host defense mechanism against intracellular bacterial infection . Mycobac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	MicroRNA-155 Promotes Autophagy to Eliminate Intracellular Mycobacteria by Targeting Rheb
Sustainable control of soil-transmitted helminths requires a combination of chemotherapy treatment and environmental interventions , including access to safe drinking water , sufficient water for hygiene , use of clean sanitation facilities , and handwashing ( WASH ) . We quantified associations between home- , school-...	Preventive chemotherapy plays a critical role in breaking transmission of soil-transmitted helminths but it is likely that sustainable control of soil-transmitted helminths will require environmental improvements such as access to water for hygiene and hygienic sanitation , access to and use of a clean toilet facility ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "water", "resources", "education", "helminths", "sociology", "tropical", "diseases", "hookworms", "social", "sciences", "geographical", "locations", "parasitic", "dise...	2018	The associations between water and sanitation and hookworm infection using cross-sectional data from Togo's national deworming program
Novel experimental techniques reveal the simultaneous activity of larger and larger numbers of neurons . As a result there is increasing interest in the structure of cooperative – or correlated – activity in neural populations , and in the possible impact of such correlations on the neural code . A fundamental theoreti...	Is neural activity more than the sum of its individual parts ? What is the impact of cooperative , or correlated , spiking among multiple cells ? We can start addressing these questions , as rapid advances in experimental techniques allow simultaneous recordings from ever-increasing populations . However , we still lac...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "biology", "neuroscience", "probability", "theory" ]	2012	Impact of Network Structure and Cellular Response on Spike Time Correlations
Leptospirosis , a re-emerging disease of global importance caused by pathogenic Leptospira spp . , is considered the world's most widespread zoonotic disease . Rats serve as asymptomatic carriers of pathogenic Leptospira and are critical for disease spread . In such reservoir hosts , leptospires colonize the kidney , a...	Leptospirosis , caused by pathogenic Leptospira spp . , constitutes an increasing global public health threat . Humans are accidental hosts , and acquire the disease primarily from contact with water sources that have been contaminated with urine from infected animals . Rats are asymptomatic carriers of infection and a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "leptospira", "microbiology", "bacterial", "pathogens", "veterinary", "science", "animal", "models", "of", "infection", "infectious", "diseases", "veterinary", "diseases", "zoonoses", "proteins", "medical", "microbiology", "lipopro...	2014	Post-translational Modification of LipL32 during Leptospira interrogans Infection

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