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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Algorithms for comparing protein structure are frequently used for function annotation . By searching for subtle similarities among very different proteins , these algorithms can identify remote homologs with similar biological functions . In contrast , few comparison algorithms focus on specificity annotation , where ...	Proteins , the ubiquitous worker molecules of the cell , are a diverse class of molecules that perform very specific tasks . Understanding how proteins achieve specificity is a critical step towards understanding biological systems and a key prerequisite for rationally engineering new proteins . To examine electrostati...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "macromolecular", "complex", "analysis", "biochemistry", "proteins", "protein", "structure", "biology", "and", "life", "sciences", "computational", "biology", "molecular", "biology", "macromolecular", "structure", "analysis" ]	2014	VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials
Inherited neurodegenerative disorders are debilitating diseases that occur across different species . We have performed clinical , pathological and genetic studies to characterize a novel canine neurodegenerative disease present in the Lagotto Romagnolo dog breed . Affected dogs suffer from progressive cerebellar ataxi...	Neurodegenerative disorders affect millions of people worldwide . We describe a novel neurodegenerative disease in a canine model , characterized by progressive cerebellar ataxia and cellular vacuolization . Our genetic analyses identified a single nucleotide change in the autophagy-related ATG4D gene in affected dogs ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Missense Change in the ATG4D Gene Links Aberrant Autophagy to a Neurodegenerative Vacuolar Storage Disease
Although the acute manifestations of Chikungunya virus ( CHIKV ) illness are well-documented , few data exist about the long-term rheumatic outcomes of CHIKV-infected patients . We undertook between June and September 2006 a retrospective cohort study aimed at assessing the course of late rheumatic manifestations and i...	Transmitted by day-biting mosquitoes , Chikungunya virus ( CHIKV ) , causing febrile illness and joint pain , is widespread in Africa and Asia . Recent outbreaks in the Indian Ocean islands , its rapid expansion across continents , and its unusual clinical acute pattern have shed light on and brought awareness of this ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "rheumatology", "virology/emerging", "viral", "diseases", "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology/infectious", "diseases" ]	2009	Post-Epidemic Chikungunya Disease on Reunion Island: Course of Rheumatic Manifestations and Associated Factors over a 15-Month Period
Human tumors that lack telomerase maintain telomeres by alternative lengthening mechanisms . Tumors can also form in telomerase-deficient mice; however , the genetic mechanism responsible for tumor growth without telomerase is unknown . In yeast , several different recombination pathways maintain telomeres in the absen...	Telomeres shorten with each cell division and are normally maintained by telomerase . Tumor cells typically up-regulate telomerase to maintain telomeres during rapid growth; however , some tumors lack telomerase and utilize alternative mechanisms to maintain the telomeres . Studies in yeast indicate that recombination ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "molecular", "biology/dna", "replication", "molecular", "biology/recombination", "cell", "biology/cell", "growth", "and", "division", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "genomics/cancer", "genetics", "molecular", "biology/dna", "repair" ]	2009	Short Telomeres Initiate Telomere Recombination in Primary and Tumor Cells
The increasing spread of the Asian tiger mosquito , Aedes albopictus , in Europe and US raises public health concern due to the species competence to transmit several exotic human arboviruses , among which dengue , chikungunya and Zika , and urges the development of suitable modeling approach to forecast the spatial an...	The Asian tiger mosquito Aedes albopictus , originating from Asia , in the last decade has spread in many regions in Europe and US . Beside the nuisance problem causing to the citizens during the day , this species has raised public health concern , due to its strict association with humans and anthropic habitats , its...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "geographical", "locations", "animals", "reproductive", "physiology", "viruses", "mathematics", "forecasting", "statistics", "(mathematics)", "theoretical", "ecology", "...	2018	Forecasting the spatial and seasonal dynamic of Aedes albopictus oviposition activity in Albania and Balkan countries
The Brugia malayi Bm-103 and Bm-RAL-2 proteins are orthologous to Onchocerca volvulus Ov-103 and Ov-RAL-2 , and which were selected as the best candidates for the development of an O . volvulus vaccine . The B . malayi gerbil model was used to confirm the efficacy of these Ov vaccine candidates on adult worms and to de...	Onchocerciasis and Lymphatic filariasis ( LF ) are debilitating neglected tropical diseases ( NTDs ) . Practical challenges in implementation of mass drug administration ( MDA ) such as prolonged treatment regime requirements and the possible emergence of drug resistance will likely impede the elimination of these NTDs...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "graduates", "medicine", "and", "health", "sciences", "immune", "physiology", "onchocerca", "volvulus", "immunology", "alumni", "animals", "onchocerca", "vaccines", "preventive", "medicine", "brugia", "educational", "status", "vaccination", "and", "immuni...	2016	Vaccination of Gerbils with Bm-103 and Bm-RAL-2 Concurrently or as a Fusion Protein Confers Consistent and Improved Protection against Brugia malayi Infection
Repeated mass azithromycin distributions are effective in controlling the ocular strains of chlamydia that cause trachoma . However , it is unclear when treatments can be discontinued . Investigators have proposed graduating communities when the prevalence of infection identified in children decreases below a threshold...	Trachoma , the major cause of infectious blindness in the world , occurs when repeated infections of the ocular strains of Chlamydia trachomatis lead to a cascade of conjunctival scarring , in-turned eyelids and eyelashes , and eventually blindness due to corneal opacity . To reduce the prevalence of infection , the Wo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/infectious", "diseases", "mathematics/mathematical", "computing", "mathematics/statistics", "infe...	2009	When Can Antibiotic Treatments for Trachoma Be Discontinued? Graduating Communities in Three African Countries
Bacteriophage modulation of microbial populations impacts critical processes in ocean , soil , and animal ecosystems . However , the role of bacteriophages with RNA genomes ( RNA bacteriophages ) in these processes is poorly understood , in part because of the limited number of known RNA bacteriophage species . Here , ...	Bacteriophages ( viruses that infect bacteria ) can alter biological processes in numerous ecosystems . While there are numerous studies describing the role of bacteriophages with DNA genomes in these processes , the role of bacteriophages with RNA genomes ( RNA bacteriophages ) is poorly understood . This gap in knowl...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "sequencing", "techniques", "microbiology", "metagenomics", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "rna", "sequencing", "rna", "alignment", "bacteria", "microbial", "genomics", "research", "and", "analysis", "methods", "sequence", "analysis...	2016	Hyperexpansion of RNA Bacteriophage Diversity
During the suckling period , intestinal enterocytes are richly endowed with endosomes and lysosomes , which they presumably utilize for the uptake and intracellular digestion of milk proteins . By weaning , mature intestinal enterocytes replace those rich in lysosomes . We found that mouse enterocytes before weaning ex...	Intestinal digestion is very different before and after weaning . In adults , extracellular enzymes in the lumen of digestive tract digest proteins and the enterocytes lining the intestine absorb the resulting amino acids . During suckling , proteins reach the intestinal lumen intact , are taken ( endocytosed ) by ente...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "physiology", "animal", "genetics", "epithelial", "cells", "gene", "function", "animal", "models", "histology", "developmental", "biology", "model", "organisms", "molecular", "cell", "biology", "molecular", "genetics", "cellular", "structures", "and", "organelle...	2014	Mucolipin Co-deficiency Causes Accelerated Endolysosomal Vacuolation of Enterocytes and Failure-to-Thrive from Birth to Weaning
Ecological communities are undeniably diverse , both in terms of the species that compose them as well as the type of interactions that link species to each other . Despite this long recognition of the coexistence of multiple interaction types in nature , little is known about the consequences of this diversity for com...	The question of how species diversity contributes to the functioning of ecological communities has intrigued ecologists for decades , and is especially relevant in the current context of species extinctions . Ecological communities are not only diverse in terms of the species that compose them but also in terms of the ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "community", "ecology", "death", "rates", "ecological", "metrics", "biomass", "population", "metrics", "ecology", "and", "environmental", "sciences", "ecology", "food", "web", "structure", "predation", "trophic", "interactions", "biology", "and", "life", "sciences", "...	2019	Non-trophic interactions strengthen the diversity—functioning relationship in an ecological bioenergetic network model
Accurate chromosome segregation requires centromeres ( CENs ) , the DNA sequences where kinetochores form , to attach chromosomes to microtubules . In contrast to most eukaryotes , which have broad centromeres , Saccharomyces cerevisiae possesses sequence-defined point CENs . Chromatin immunoprecipitation followed by s...	Centromeres ( CENs ) are chromosomal regions essential for proper chromosome segregation through their ability to establish evolutionarily conserved protein complexes called kinetochores . During mitosis , kinetochores attach to microtubules emanating from spindle poles , thus providing the mechanism for chromosome seg...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "genome", "evolution", "chromosome", "structure", "and", "function", "centromeres", "microbiology", "mitosis", "model", "organisms", "epigenetics", "chromatin", "chromosome", "biology", "gene", "expression", "biology", "cell", "biology", "genetic...	2013	Centromere-Like Regions in the Budding Yeast Genome
Neuroblasts of the statoacoustic ganglion ( SAG ) initially form in the floor of the otic vesicle during a relatively brief developmental window . They soon delaminate and undergo a protracted phase of proliferation and migration ( transit-amplification ) . Neuroblasts eventually differentiate and extend processes bi-d...	Neurons of the statoacoustic ganglion ( SAG ) , which innervate the inner ear , are derived from neuroblasts originating from the floor of the otic vesicle . Neuroblasts quickly delaminate from the otic vesicle to form dividing progenitors , which eventually differentiate into mature neurons of the SAG . Fgf has been i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "growth", "control", "neurogenesis", "neuroscience", "cell", "differentiation", "developmental", "biology", "organism", "development", "molecular", "development", "morphogenesis", "pattern", "formation", "developmental", "neuroscience", "biology", "auditory", "system", "neura...	2012	A Spatial and Temporal Gradient of Fgf Differentially Regulates Distinct Stages of Neural Development in the Zebrafish Inner Ear
Understanding naturally acquired immune responses to Plasmodium in India is key to improving malaria surveillance and diagnostic tools . Here we describe serological profiling of immune responses at three sites in India by probing protein microarrays consisting of 515 Plasmodium vivax and 500 Plasmodium falciparum prot...	Although malaria deaths have fallen by 60% worldwide since 2000 , the disease remains a significant public health problem . India has the highest burden of malaria in the South-East Asia Region , where Plasmodium vivax and Plasmodium falciparum are its main causes . While the two major malaria parasite species co-occur...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "immune", "physiology", "plasmodium", "immunology", "tropical", "diseases", "plasmodium", "falciparum", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa", "protozoans", "antibody"...	2017	Characterizing Antibody Responses to Plasmodium vivax and Plasmodium falciparum Antigens in India Using Genome-Scale Protein Microarrays
Social network analysis methods have made it possible to test whether novel behaviors in animals spread through individual or social learning . To date , however , social network analysis of wild populations has been limited to static models that cannot precisely reflect the dynamics of learning , for instance , the im...	Chimpanzees are widely considered as the most “cultural” of all animals , despite the lack of direct evidence for the spread of novel behaviors through social learning in the wild . Here , we present a novel , dynamic network-based diffusion analysis to describe the acquisition patterns of novel tool-use behavior in th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "primatology", "mammalogy", "animal", "behavior", "zoology", "cognition", "biology", "and", "life", "sciences", "cognitive", "science", "neuroscience", "animal", "cognition" ]	2014	Social Network Analysis Shows Direct Evidence for Social Transmission of Tool Use in Wild Chimpanzees
Patterns of gene expression in cultured Trypanosoma brucei bloodstream and procyclic forms have been extensively characterized , and some comparisons have been made with trypanosomes grown to high parasitaemias in laboratory rodents . We do not know , however , to what extent these transcriptomes resemble those in infe...	Most experiments on African trypanosomes - including those designed to look for new drugs - have studied parasites either from culture , or from laboratory rodents . We are interested in comparing these parasites that grow in man and domestic animals , where the parasites generally have different nutrient concentration...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "veterinary", "science", "trypanosoma", "veterinary", "diseases", "protozoans", "zoonoses", "medicine", "and", "health", "sciences", "african", "trypanosomiasis", "gene", "expression", "genetics", "neglected", "tropical", "diseases", "biology", "...	2014	Methods to Determine the Transcriptomes of Trypanosomes in Mixtures with Mammalian Cells: The Effects of Parasite Purification and Selective cDNA Amplification
Neurocysticercosis ( NCC ) is one of the most common helminth parasitic diseases of the central nervous system ( CNS ) and the leading cause of acquired epilepsy worldwide . NCC is caused by the presence of the metacestode larvae of the tapeworm Taenia solium within brain tissues . NCC patients exhibit a long asymptoma...	Eosinophils are known to mediate a protective response against several parasitic infections . This is largely accomplished by eosinophil degranulation ( direct killing ) and modulating effective adaptive immune responses . Consequently , eosinophils can also contribute to host pathology via a bystander effect . However...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "parasitic", "diseases", "animal", "models", "model", "organisms", "research", "and", "analysis", "methods", "specimen", "preparation", "and", "treatment",...	2016	Reduced Leukocyte Infiltration in Absence of Eosinophils Correlates with Decreased Tissue Damage and Disease Susceptibility in ΔdblGATA Mice during Murine Neurocysticercosis
Mutations in the gene for muscle phosphofructo-1-kinase ( PFKM ) , a key regulatory enzyme of glycolysis , cause Type VII glycogen storage disease ( GSDVII ) . Clinical manifestations of the disease span from the severe infantile form , leading to death during childhood , to the classical form , which presents mainly w...	Type VII glycogen storage disease ( GSDVII ) , or Tarui disease , is a rare genetic disorder characterized by glycogen accumulation in skeletal muscle . The molecular cause is loss of activity of the muscle isoform of phosphofructokinase ( PFK ) , which phosphorylates fructose-6-phosphate to fructose-1 , 6-bisphosphate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "biochemistry", "pathology/pathophysiology" ]	2009	Phosphofructo-1-Kinase Deficiency Leads to a Severe Cardiac and Hematological Disorder in Addition to Skeletal Muscle Glycogenosis
Pseudomonas aeruginosa is an opportunistic human pathogen that causes infections in a variety of animal and plant hosts . Caenorhabditis elegans is a simple model with which one can identify bacterial virulence genes . Previous studies with C . elegans have shown that depending on the growth medium , P . aeruginosa pro...	The increase in hospital acquired and multi-drug resistant bacterial infections calls for an urgent development of new antimicrobials . As such , the identification and characterization of novel molecular targets involved in bacterial virulence has become a common goal for researchers . The use of non-mammalian hosts ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "microbiology" ]	2009	Caenorhabditis elegans Semi-Automated Liquid Screen Reveals a Specialized Role for the Chemotaxis Gene cheB2 in Pseudomonas aeruginosa Virulence
Mechanisms that maintain transcriptional memory through cell division are important to maintain cell identity , and sequence-specific transcription factors that remain associated with mitotic chromatin are emerging as key players in transcriptional memory propagation . Here , we show that the major transcriptional effe...	How does a cell remember what it should be after cell division ? One mechanism that is beginning to emerge is the retention of a few key regulatory proteins on the highly condensed mitotic chromatin during cell division . These proteins are called mitotic bookmarks , as they are believed to offer critical information a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "sequencing", "biochemistry", "genomics", "functional", "genomics", "molecular", "cell", "biology", "nucleic", "acids", "proteins", "chromosome", "biology", "gene", "regulation", "gene", "expression", "genetics", "dna", "molecular", "genetics", "biology", "dna...	2014	RBPJ, the Major Transcriptional Effector of Notch Signaling, Remains Associated with Chromatin throughout Mitosis, Suggesting a Role in Mitotic Bookmarking
Japanese encephalitis ( JE ) , caused by a mosquito-borne flavivirus , is endemic to the entire south-east Asian and adjoining regions . Currently no therapeutic interventions are available for JE , thereby making it one of the most dreaded encephalitides in the world . An effective way to counter the virus would be to...	Japanese encephalitis ( JE ) is caused by a flavivirus that is transmitted to humans by mosquitoes belonging to the Culex sp . The threat of JE looms over a vast geographical realm , encompassing approximately 10 billion people . The disease is feared because currently there are no specific antiviral drugs available . ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "infectious", "diseases/viral", "infections", "infectious", "diseases/neglected", "tropical", "diseases" ]	2010	Antiviral and Neuroprotective Role of Octaguanidinium Dendrimer-Conjugated Morpholino Oligomers in Japanese Encephalitis
Exposure to extreme stress can trigger the development of major depressive disorder ( MDD ) as well as post-traumatic stress disorder ( PTSD ) . The molecular mechanisms underlying the structural and functional alterations within corticolimbic brain regions , including the prefrontal cortex ( PFC ) and amygdala of indi...	Improper functioning of the brain regions known as prefrontal cortex and amygdala is associated with the development of post-traumatic stress disorder . However , little is known about the molecular mechanisms that underlie this condition . We found that the expression of a protein kinase involved in cellular responses...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Decreased SGK1 Expression and Function Contributes to Behavioral Deficits Induced by Traumatic Stress
The functional consequences of missense variants in disease genes are difficult to predict . We assessed if gene expression profiles could distinguish between BRCA1 or BRCA2 pathogenic truncating and missense mutation carriers and familial breast cancer cases whose disease was not attributable to BRCA1 or BRCA2 mutatio...	Inherited mutations in the genes BRCA1 and BRCA2 increase risk of breast cancer and contribute to a proportion of breast cancer families . However , more than half of the reported sequence alterations in BRCA1 and BRCA2 are currently of unknown clinical significance . We analysed gene expression in lymphoblastoid cell ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology/breast", "cancer", "genetics", "and", "genomics/gene", "function", "genetics", "and", "genomics/cancer", "genetics", "genetics", "and", "genomics/gene", "expression" ]	2008	BRCA1 and BRCA2 Missense Variants of High and Low Clinical Significance Influence Lymphoblastoid Cell Line Post-Irradiation Gene Expression
In order to establish infections within the mammalian host , pathogens must protect themselves against toxic reactive oxygen species produced by phagocytes of the immune system . The fungal pathogen Histoplasma capsulatum infects both neutrophils and macrophages but the mechanisms enabling Histoplasma yeasts to survive...	Histoplasma capsulatum is a fungal pathogen that is endemic to the Mississippi and Ohio River valleys . An estimated 200 , 000 infections occur annually in the United States . Histoplasma is adept at surviving within both neutrophils and macrophages , which normally kill fungal cells by producing reactive oxygen molecu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "fungi", "immune", "cells", "antigen-presenting", "cells", "immunology", "biology", "microbiology", "host-pathogen", "interaction", "pathogenesis" ]	2012	Extracellular Superoxide Dismutase Protects Histoplasma Yeast Cells from Host-Derived Oxidative Stress
Several infectious diseases and therapeutic interventions cause gut microbe dysbiosis and associated pathology . We characterised the gut microbiome of children exposed to the helminth Schistosoma haematobium pre- and post-treatment with the drug praziquantel ( PZQ ) , with the aim to compare the gut microbiome structu...	The role of the gut microbiome in host health is becoming clearer with better characterisation of the nutritional , biochemical and immunological function of the microbes . However , to date , there is a paucity of studies describing/ investigating the role of the gut microbiome in infection , pathology and acquired im...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Differences in the Faecal Microbiome in Schistosoma haematobium Infected Children vs. Uninfected Children
Vibrio vulnificus necrotizing skin and soft tissue infections ( VNSSTIs ) usually predispose patients with or without preexisting liver disease to septic shock , and then evolve to multiple organ dysfunction syndrome ( MODS ) , thus resulting in high mortality in humans . However , clinicians do not have a valid predic...	VNSSTIs have increased significantly over the last two decades , with cases now regularly reported globally . Despite advancing antibiotic and infection control practices , these infections are still highly lethal and disabling diseases . They usually predispose patients to septic shock and then evolve to liver dysfunc...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Model for End-Stage Liver Disease (MELD) Score as a Predictor and Monitor of Mortality in Patients with Vibrio vulnificus Necrotizing Skin and Soft Tissue Infections
Magnaporthe oryzae , the fungus causing rice blast disease , should contend with host innate immunity to develop invasive hyphae ( IH ) within living host cells . However , molecular strategies to establish the biotrophic interactions are largely unknown . Here , we report the biological function of a M . oryzae-specif...	Biotrophic pathogens grow inside living host cells by secreting “effector” proteins that suppress host innate immunity . Magnaporthe oryzae , which causes the most serious damage to rice , and recently also to wheat , is a hemibiotrophic fungus . During the biotrophic invasion , a host membrane-rich structure called th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "fungal", "genetics", "fungal", "structure", "cereal", "crops", "fungi", "plant", "science", "rice", "model", "organisms", "crops", "plant", "pathology", "appressoria", "plants", "research", "and", "analysis", "methods", "mycology", "grasses", "c...	2016	Magnaporthe oryzae Glycine-Rich Secretion Protein, Rbf1 Critically Participates in Pathogenicity through the Focal Formation of the Biotrophic Interfacial Complex
The question of a potential biological sexual signature in the human brain is a heavily disputed subject . In order to provide further insight into this issue , we used an evolutionary approach to identify genes with sex differences in brain expression level among primates . We reasoned that expression patterns importa...	The contribution of genetics versus environment to behavioral differences between the sexes is a fundamental question in neuroscience . We hypothesized that some differences between the sexes might be partially explained by sexually dependent gene expression differences in the brain . We further speculated that if diff...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "evolutionary", "biology/animal", "genetics", "genetics", "and", "genomics/gene", "expression", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2008	An Evolutionarily Conserved Sexual Signature in the Primate Brain
Kaposi's sarcoma ( KS ) lesions are complex mixtures of KS-associated herpesvirus ( KSHV ) -infected spindle and inflammatory cells . In order to survive the host immune responses , KSHV encodes a number of immunomodulatory proteins , including the E3 ubiquitin ligase K5 . In exploring the role of this viral protein in...	Tumor viruses have proven to be valuable tools for dissecting the molecular mechanisms of transformation and cancer progression . Kaposi's sarcoma-associated herpesvirus ( KSHV ) infection is essential in driving at least three different neoplasias , including Kaposi's sarcoma ( KS ) . Our understanding , however , of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "oncology", "cell", "biology/cell", "signaling", "cell", "biology/cell", "growth", "and", "division", "cell", "biology/membranes", "and", "sorting", "physiology", "virology/viruses", "and", "cancer" ]	2011	The MARCH Family E3 Ubiquitin Ligase K5 Alters Monocyte Metabolism and Proliferation through Receptor Tyrosine Kinase Modulation
Human neurocysticercosis ( NC ) caused by Taenia solium is a parasitic disease of the central nervous system that is endemic in many developing countries . In this study , a genetic approach using the murine intraperitoneal cysticercosis caused by the related cestode Taenia crassiceps was employed to identify host fact...	Infection with the cestode Taenia solium causes cysticercosis in humans and pigs . Neurocysticercosis is a severe manifestation of T . solium infection that constitutes an important health concern in developing countries . Studies in humans living in areas of endemic disease and in pigs experimentally infected have sug...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "complement", "system", "animal", "genetics", "neurocysticercosis", "immunology", "quantitative", "traits", "microbiology", "host-pathogen", "interaction", "parasitic", "diseases", "animal", "models", "model", "organisms", "neglected", "tropical", "diseases", "l...	2011	Identification of Loci Controlling Restriction of Parasite Growth in Experimental Taenia crassiceps Cysticercosis
India has long been thought to have more snakebites than any other country . However , inadequate hospital-based reporting has resulted in estimates of total annual snakebite mortality ranging widely from about 1 , 300 to 50 , 000 . We calculated direct estimates of snakebite mortality from a national mortality survey ...	Earlier hospital based reports estimate about 1 , 300 to 50 , 000 annual deaths from snakebites per year in India . Here , we present the first ever direct estimates from a national mortality survey of 1 . 1 million homes in 2001–03 . Full-time , non-medical field workers interviewed living respondents about all deaths...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "epidemiology", "global", "health", "public", "health" ]	2011	Snakebite Mortality in India: A Nationally Representative Mortality Survey
Vesicular trafficking has emerged as an important means by which eukaryotes modulate responses to microbial pathogens , likely by contributing to the correct localization and levels of host components necessary for effective immunity . However , considering the complexity of membrane trafficking in plants , relatively ...	Plants have developed effective mechanisms for protection against pathogens including bacteria , but if a plant is unable to induce defenses , pathogenic bacteria invade and colonize the host , which can lead to reduced yield and nutritional quality of crops . An important aspect of engineering durable crop resistance ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences" ]	2014	Loss of Arabidopsis thaliana Dynamin-Related Protein 2B Reveals Separation of Innate Immune Signaling Pathways
The immediate-early response mediates cell fate in response to a variety of extracellular stimuli and is dysregulated in many cancers . However , the specificity of the response across stimuli and cell types , and the roles of non-coding RNAs are not well understood . Using a large collection of densely-sampled time se...	Cells respond to stimuli through a set of genes that are primed for rapid activation . These genes , known as immediate-early genes ( IEGs ) , are regulated at the level of transcription of the messenger RNA , and at subsequent RNA processing levels . These rapid responders are then rapidly switched off in normal cells...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response
Clostridium difficile is a diarrheagenic pathogen associated with significant mortality and morbidity . While its glucosylating toxins are primary virulence determinants , there is increasing appreciation of important roles for non-toxin factors in C . difficile pathogenesis . Cell wall glycopolymers ( CWGs ) influence...	Clostridium difficile infection is a leading healthcare-onset bacterial disease , and its management and prevention imposes significant clinical and financial burdens worldwide . While toxins TcdA and TcdB are the primary virulence factors , there is increasing interest in , and appreciation of , non-toxin virulence fa...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "walls", "medicine", "and", "health", "sciences", "gut", "bacteria", "toxins", "pathology", "and", "laboratory", "medicine", "pathogens", "vertebrates", "animals", "mammals", "toxicology", "toxic", "agents", "cellular", "structures", "and", "organelles", "bact...	2016	A Clostridium difficile Cell Wall Glycopolymer Locus Influences Bacterial Shape, Polysaccharide Production and Virulence
While rods , cones , and intrinsically photosensitive melanopsin-containing ganglion cells ( ipRGCs ) all drive light entrainment of the master circadian pacemaker of the suprachiasmatic nucleus , recent studies have proposed that entrainment of the mouse retinal clock is exclusively mediated by a UV-sensitive photopig...	The mammalian retina contains a circadian clock that plays a crucial role in adapting retinal physiology and visual function to light/dark changes . In addition , the retina coordinates rhythmic behavior and physiology by providing visual input to the master hypothalamic clock in the suprachiasmatic nucleus through a n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "ocular", "anatomy", "social", "sciences", "light", "neuroscience", "electromagnetic", "radiation", "circadian", "oscillators", "animal", "models", "model", "organisms", "experimental", "organism", "systems", "visible", "light", ...	2019	Rods contribute to the light-induced phase shift of the retinal clock in mammals
DNA synthesis must be performed with extreme precision to maintain genomic integrity . In mammalian cells , different genomic regions are replicated at defined times , perhaps to preserve epigenetic information and cell differentiation status . However , the molecular principles that define this S phase program are unk...	Eukaryotic DNA synthesis is regulated with exquisite precision so that genomes are replicated exactly once before cell division occurs . In simple eukaryotes , chromosomal loci are preferentially replicated at specific times of S phase , in part because of their differential sensitivity to cell cycle regulators and in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "cell", "biology", "genetics", "and", "genomics/chromosome", "biology", "cell", "biology/nuclear", "structure", "and", "function" ]	2010	S Phase Progression in Human Cells Is Dictated by the Genetic Continuity of DNA Foci
Genome-wide association studies ( GWAS ) often identify disease-associated mutations in intergenic and non-coding regions of the genome . Given the high percentage of the human genome that is transcribed , we postulate that for some observed associations the disease phenotype is caused by a structural rearrangement in ...	Genome-wide association studies identify mutations in the human genome that correlate with a particular disease . It is common to find mutations associated with disease in the non-coding region of the genome . These non-coding mutations are more difficult to interpret at a molecular level , because they do not affect t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/population", "genetics" ]	2010	Disease-Associated Mutations That Alter the RNA Structural Ensemble
Rabies , a 100% fatal disease claims more than 59 , 000 human lives every year globally . One human life is lost every 15 minutes due to this deadly preventable disease . Timely initiation of post exposure prophylaxis following an animal exposure can result in 100% preventability of this fatal disease . This facility b...	Rabies is a zoonotic disease . More than 95% of human rabies deaths is dog mediated . Rabies a 100% fatal yet preventable disease; a major public health problem in most of the Asian countries including India . The reduction in human rabies deaths is possible only when our clinical fraternity are aware of WHO recommende...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "post-exposure", "prophylaxis", "tropical", "diseases", "microbiology", "geographical", "locations", "india", "vaccines", "preventive", "medicine", "viruses", "pre-exposure",...	2017	How familiar are our doctors towards Rabies prophylaxis- A study from coastal south India
The options for treating the fatal disease human African trypanosomiasis are limited to a few drugs that are toxic or facing increasing resistance . New drugs that kill the causative agents , subspecies of Trypanosoma brucei , are therefore urgently needed . Little is known about the cellular mechanisms that lead to de...	The parasite Trypanosoma brucei causes human African trypanosomiasis , which is fatal unless treated . Currently used drugs are toxic , difficult to administer , and often are no longer effective due to drug resistance . The search for new drugs is long and expensive , and determining which compounds are worth pursuing...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "biology/cellular", "death", "and", "stress", "responses", "infectious", "diseases/neglected", "tropical", "diseases", "cell", "biology/cell", "growth", "and", "division", "microbiology/parasitology", "infectious", "diseases/antimicrobials", "and", "drug", "resistance...	2010	Diverse Effects on Mitochondrial and Nuclear Functions Elicited by Drugs and Genetic Knockdowns in Bloodstream Stage Trypanosoma brucei
To understand gene function , genetic analysis uses large perturbations such as gene deletion , knockdown or over-expression . Large perturbations have drawbacks: they move the cell far from its normal working point , and can thus be masked by off-target effects or compensation by other genes . Here , we offer a comple...	Inferring the function of proteins and the role they play in cellular processes is essential for our understanding of cell biology , genetics and biology in general . Standard genetic approaches use large perturbations to cells such as gene knockout , knockdown or over expression of genes . Such methods are powerful , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "cancer", "genetics", "genomics", "functional", "genomics", "genetics", "biology", "computational", "biology", "proteomics", "gene", "function" ]	2014	Noise Genetics: Inferring Protein Function by Correlating Phenotype with Protein Levels and Localization in Individual Human Cells
A homozygous mutational change in the Ataxia-Telangiectasia and RAD3 related ( ATR ) gene was previously reported in two related families displaying Seckel Syndrome ( SS ) . Here , we provide the first identification of a Seckel Syndrome patient with mutations in ATRIP , the gene encoding ATR–Interacting Protein ( ATRI...	Seckel Syndrome ( SS ) is a rare human disorder characterised by small head circumference and delayed growth . Patients can show additional features including abnormal bone development , receding chins , sloping foreheads , and small ears . In 2003 , we identified ataxia telangiectasia and Rad3 related ( ATR ) as a cau...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetic", "mutation", "phenotypes", "heredity", "gene", "identification", "and", "analysis", "genetics", "gene", "splicing", "molecular", "genetics", "biology", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2012	Identification of the First ATRIP–Deficient Patient and Novel Mutations in ATR Define a Clinical Spectrum for ATR–ATRIP Seckel Syndrome
Recent studies in population of European ancestry have shown that 30%∼50% of heritability for human complex traits such as height and body mass index , and common diseases such as schizophrenia and rheumatoid arthritis , can be captured by common SNPs and that genetic variation attributed to chromosomes are in proporti...	The “missing heritability” problem has been intensely debated for the last few years . Possible explanations include the existence of many genetic variants each with a small effect , rare variants with large effects , and heritability being over-estimated . Previous studies using whole-genome estimation have demonstrat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics", "human", "genetics" ]	2013	Ubiquitous Polygenicity of Human Complex Traits: Genome-Wide Analysis of 49 Traits in Koreans
Mammalian prions , the pathogens that cause transmissible spongiform encephalopathies , propagate by self-perpetuating the structural information stored in the abnormally folded , aggregated conformer ( PrPSc ) of the host-encoded prion protein ( PrPC ) . To date , no structural model related to prion assembly organiza...	Prions are self-propagating assemblies with all necessary and sufficient replicative information stored in the 3D structure of the misfolded form of PrP called PrPSc . Since the emergence of the prion theory in the 80s , many attempts have been done to identify prion replicative information at molecular scale . Differe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "urea", "medicine", "and", "health", "sciences", "condensation", "chemical", "compounds", "condensed", "matter", "physics", "vertebrates", "organic", "compounds", "animals", "mammals", "materials", "science", "materials", "physics", "sedimentation", "oligomers", "material...	2017	Reversible unfolding of infectious prion assemblies reveals the existence of an oligomeric elementary brick
Estimating fine-scale recombination maps of Drosophila from population genomic data is a challenging problem , in particular because of the high background recombination rate . In this paper , a new computational method is developed to address this challenge . Through an extensive simulation study , it is demonstrated ...	Recombination is a process by which chromosomes exchange genetic material during meiosis . It is important in evolution because it provides offspring with new combinations of genes , and so estimating the rate of recombination is of fundamental importance in various population genomic inference problems . In this paper...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "stochastic", "processes", "mathematics", "statistics", "population", "genetics", "biology", "evolutionary", "biology", "statistical", "methods", "probability", "theory" ]	2012	Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster
Leptospirosis is a zoonotic disease responsible for over 1 million severe cases and 60 , 000 deaths annually . The wide range of animal hosts and complex environmental drivers of transmission make targeted interventions challenging , particularly when restricted to regression-based analyses which have limited ability t...	Leptospirosis is a zoonotic disease responsible for over 60 , 000 deaths annually and is transmitted from mammal hosts to humans through contact with infected urine . The range of possible hosts and complex environmental factors related to transmission make targeted interventions challenging . We used spatial Bayesian ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "vertebrates", "animals", "mammals", "health", "care", "bacterial", "diseases", "farms", "rural", "areas", "neglected", "tropical", "diseases", "fiji", "public", ...	2018	Predictive risk mapping of an environmentally-driven infectious disease using spatial Bayesian networks: A case study of leptospirosis in Fiji
The APOBEC3 ( A3 ) cytidine deaminases are antiretroviral proteins , whose targets include human immunodeficiency virus type-1 ( HIV-1 ) . Their incorporation into viral particles is critical for antiviral activity and is driven by interactions with the RNA molecules that are packaged into virions . However , it is unc...	Cellular intrinsic immunity constitutes a key defense against infection by viruses . The APOBEC3 ( A3 ) family of cytidine deaminases are intrinsic immune proteins that can hypermutate and destabilize retroviral genomes . For A3 proteins to exert their antiviral activity , they must be incorporated into nascent virions...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "binding", "sequencing", "techniques", "cell", "physiology", "rna-binding", "proteins", "medicine", "and", "health", "sciences", "chemical", "characterization", "pathology", "and", "laboratory", "medicine", "pathogens", "messenger", "rna", "microbiology", "viral",...	2016	The RNA Binding Specificity of Human APOBEC3 Proteins Resembles That of HIV-1 Nucleocapsid
Taste stimuli are transduced by taste buds and transmitted to the brain via afferent gustatory fibers . Renewal of taste receptor cells from actively dividing progenitors is finely tuned to maintain taste sensitivity throughout life . We show that conditional β-catenin deletion in mouse taste progenitors leads to rapid...	By remaining relatively constant throughout adult life , the sense of taste helps keep the body healthy . However , taste perception can be disrupted by various environmental factors , including cancer therapies . Here , we show that Wnt/β-catenin signaling , a pathway known to control normal tissue maintenance and ass...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taste", "buds", "medicine", "and", "health", "sciences", "gustatory", "system", "social", "sciences", "vertebrates", "mice", "neuroscience", "animals", "mammals", "cell", "differentiation", "cell", "signaling", "developmental", "biology", "tongue", "digestive", "system...	2017	β-catenin is required for taste bud cell renewal and behavioral taste perception in adult mice
Choosing valuable objects and rewarding actions is critical for survival . While such choices must be made in a way that suits the animal’s circumstances , the neural mechanisms underlying such context-appropriate behavior are unclear . To address this question , we devised a context-dependent reward-seeking task for m...	The amygdala is known to control passive fear responses ( e . g . , freezing ) , but it is unclear if it also contributes to active behaviors . To reach certain goals , we ( humans and animals ) often need to go through fearful environments . We hypothesized that the amygdala contributes to such an active behavior and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "brain", "vertebrates", "social", "sciences", "neuroscience", "animals", "mammals", "primates", "animal", "behavior", "vision", "zoology", "sensory", "physiology", "foraging", "monkeys", "emotions", "animal", "cells", "behavior",...	2018	Amygdala activity for the modulation of goal-directed behavior in emotional contexts
Ranunculus trichophyllus is an amphibious plant that produces thin and cylindrical leaves if grown under water but thick and broad leaves if grown on land . We found that such heterophylly is widely controlled by two plant hormones , abscisic acid ( ABA ) and ethylene , which control terrestrial and aquatic leaf develo...	Evolutionary adaptation into aquatic environment is widely observed in diverse clades of land plants . To understand the molecular basis behind such adaptation , we analyzed Ranunculus trichophyllus , an amphibious plant producing different leaf shape depending on the growth conditions . Aquatic leaves of this plant pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "anatomy", "stem", "anatomy", "chemical", "compounds", "plant", "growth", "and", "development", "ethylene", "brassica", "stomata", "organic", "compounds", "hormones", "developmental", "biology", "plant", "science", "model", "organisms", "plant", "hormones", "...	2018	A molecular basis behind heterophylly in an amphibious plant, Ranunculus trichophyllus
Hydrolysis of ATP by partition ATPases , although considered a key step in the segregation mechanism that assures stable inheritance of plasmids , is intrinsically very weak . The cognate centromere-binding protein ( CBP ) , together with DNA , stimulates the ATPase to hydrolyse ATP and to undertake the relocation that...	Genes enabling bacteria to survive and thrive in challenging environments are very often found on small , non-essential DNA molecules called plasmids . Many plasmids are naturally present in the cell in very few copies and so risk being lost from one of the daughter cells upon division . These plasmids elaborate a part...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Defining the Role of ATP Hydrolysis in Mitotic Segregation of Bacterial Plasmids
The emergence of American Cutaneous Leishmaniasis ( ACL ) has been associated with changes in the relationship between people and forests , leading to the view that forest ecosystems increase infection risk and subsequent proposal that deforestation could reduce re-emergence of this disease . We analyzed county-level i...	American Cutaneous Leishmaniasis emergence has been associated with changes in the interaction between people and forests . The association between outbreaks and forest clearance , higher risk for populations living close to forests , and the absence of this disease from urban settings has led to the proposal that it w...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Statistical", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "ecology/conservation", "and", "restoration", "ecology", "public", "health", "and", "epidemiology/social", "and", "behavioral", "determinants", "of", "health", "public", "health", "and", "epidemiology/global", "hea...	2008	Social Exclusion Modifies Climate and Deforestation Impacts on a Vector-Borne Disease
Lipophosphoglycan ( LPG ) is the major surface glycoconjugate of Leishmania protozoan and has an important biological role in host-parasite interactions both in the midgut epithelium of the sand fly vector and in the vertebrate macrophages . Canine leishmaniasis ( CanL ) is a chronic infectious disease predominantly ca...	Canine leishmaniasis ( CanL ) caused by Leishmania infantum is a zoonotic disease with high importance for the public health of several countries . L . infantum-infected dogs can be a domestic reservoir of the protozoan parasite for sand flies , which transmit it from dogs to humans during their blood meals . It is imp...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "vertebrates", "parasitic", "diseases", "dogs", "parasitic", "protozoans", "animals", "mammals", "protozoans", "veterinary", "diagnostics", "leishmania", "immunologic", "techniques", "veterinary", "sc...	2019	Leishmania infantum-derived lipophosphoglycan as an antigen in the accurate serodiagnosis of canine leishmaniasis
Dominant mutations of Gata4 , an essential cardiogenic transcription factor ( TF ) , were known to cause outflow tract ( OFT ) defects in both human and mouse , but the underlying molecular mechanism was not clear . In this study , Gata4 haploinsufficiency in mice was found to result in OFT defects including double out...	Gata4 is an important transcription factor that regulates the development of the heart . Human possessing a single copy of Gata4 mutation display congenital heart defects ( CHD ) , including double outlet right ventricle ( DORV ) . DORV is an alignment problem in which both the Aorta and Pulmonary Artery originate from...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "cardiovascular", "anatomy", "cardiac", "ventricles", "cell", "processes", "animal", "models", "developmental", "biology", "model", "organisms", "arteries", "experimental", "organism", "systems", "pulmonary", "arteries", "embryos",...	2019	Gata4 regulates hedgehog signaling and Gata6 expression for outflow tract development
The origin recognition complex ( ORC ) marks chromosomal sites as replication origins and is essential for replication initiation . In yeast , ORC also binds to DNA elements called silencers , where its primary function is to recruit silent information regulator ( SIR ) proteins to establish transcriptional silencing ....	Chromosomes must be replicated prior to cell division . The process of duplication of each eukaryotic chromosome starts at discrete sites called origins of replication . An evolutionarily conserved Origin Recognition Complex ( ORC ) binds origins and helps make them replication-competent . ORC also binds another class ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "replication", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/nuclear", "structure", "and", "function", "genetics", "and", "genomics/chromosome", "biology", "molecular", "biology/chromatin", "structure" ]	2009	The Origin Recognition Complex Interacts with a Subset of Metabolic Genes Tightly Linked to Origins of Replication
At blocked replication forks , homologous recombination mediates the nascent strands to switch template in order to ensure replication restart , but faulty template switches underlie genome rearrangements in cancer cells and genomic disorders . Recombination occurs within DNA packaged into chromatin that must first be ...	Obstacles to the progression of DNA replication forks can result in genome rearrangements that are often observed in cancer cells and genomic disorders . Homologous recombination is a mechanism of restarting stalled replication fork that involves synthesis of the new DNA strands switching templates to a second ( alleli...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dna", "electrophoresis", "dna", "damage", "mutation", "fungi", "dna", "replication", "dna", "epigenetics", "molecular", "genetics", "chromatin", "dna", "synthesis", "schizosaccharomyces", "homologous", "recombination", "chromosome", "biology", "schizosaccharomyces", "pombe...	2014	The Chromatin Assembly Factor 1 Promotes Rad51-Dependent Template Switches at Replication Forks by Counteracting D-Loop Disassembly by the RecQ-Type Helicase Rqh1
During the acquisition of memories , influx of Ca2+ into the postsynaptic spine through the pores of activated N-methyl-d-aspartate-type glutamate receptors triggers processes that change the strength of excitatory synapses . The pattern of Ca2+ influx during the first few seconds of activity is interpreted within the ...	Networks of neurons in the brain are connected together by specialized signaling devices called synapses . One way an active neuron relays its activity to other neurons is by releasing small amounts of chemical transmitters from its presynaptic terminals which induce electrical activity in postsynaptic neurons connecte...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry/cell", "signaling", "and", "trafficking", "structures", "cell", "biology/neuronal", "signaling", "mechanisms" ]	2010	A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II
Flowering time is a key life-history trait in the plant life cycle . Most studies to unravel the genetics of flowering time in Arabidopsis thaliana have been performed under greenhouse conditions . Here , we describe a study about the genetics of flowering time that differs from previous studies in two important ways: ...	Dissecting the genetic bases of adaptive traits is of primary importance in evolutionary biology . In this study , we combined a genome-wide association ( GWA ) study with traditional linkage mapping in order to detect the genetic bases underlying natural variation in flowering time in ecologically realistic conditions...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "plant", "biology/plant", "genomes", "and", "evolution", "ecology/evolutionary", "ecology", "evolutionary", "biology/evolutionary", "ecology", "genetics", "and", "genomics/complex", "traits", "plant", "biology/plant-environment", ...	2010	Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature
Due to the large geographical overlap of populations exposed to Zika virus ( ZIKV ) and human immunodeficiency virus ( HIV ) , understanding the disease pathogenesis of co-infection is urgently needed . This warrants the development of an animal model for HIV-ZIKV co-infection . In this study , we used adult non-pregna...	The co-infection incidence of human immunodeficiency virus ( HIV ) infection and neglected tropical infectious diseases such as Zika virus ( ZIKV ) is on the rise due to the large geographical overlap of populations exposed to both of these viruses . Thus , research on such co-infection is of particular importance . In...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "hiv", "infections", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "microbiology", "vertebrates", "animals", "mammals", "retroviruses", "viruses", "prima...	2018	SIV/SHIV-Zika co-infection does not alter disease pathogenesis in adult non-pregnant rhesus macaque model
Large-scale parallel pyrosequencing produces unprecedented quantities of sequence data . However , when generated from viral populations current mapping software is inadequate for dealing with the high levels of variation present , resulting in the potential for biased data loss . In order to apply the 454 Life Science...	Due to high data volumes , error rates , and short sequence lengths , new sequencing technologies present a new challenge for computational biology . In addition , high-depth ( or ultra-deep ) datasets , for example from pathogens , contain exceptionally large amounts of variation over short genomes or genomic regions ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "science/applications", "computational", "biology/comparative", "sequence", "analysis", "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics", "infectious", "diseases/hiv", "infection", "and", "aids", "evolutionary", ...	2010	The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach
Epigenetic control of gene transcription is critical for normal human development and cellular differentiation . While alterations of epigenetic marks such as DNA methylation have been linked to cancers and many other human diseases , interindividual epigenetic variations in normal tissues due to aging , environmental ...	The causes and extent of tissue-specific interindividual variation in human epigenomes are underappreciated and , hence , poorly characterized . We surveyed over 200 carefully annotated human tissue samples from ten anatosites at 1 , 413 CpGs for methylation alterations to appraise the nature of phenotypically , and he...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "public", "health", "and", "epidemiology/environmental", "health", "developmental", "biology/aging", "molecular", "biology/dna", "methylation", "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/population", "ge...	2009	Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context
The popularity of CRISPR-based gene editing has resulted in an abundance of tools to design CRISPR-Cas9 guides . This is also driven by the fact that designing highly specific and efficient guides is a crucial , but not trivial , task in using CRISPR for gene editing . Here , we thoroughly analyse the performance of 18...	Modern genome engineering technologies provide unprecedented methods for DNA modifications . CRISPR-based systems generate a high level of interest in the community due to their effectiveness and relative simplicity . However , the design of the guides they use to target specific regions is not trivial . Researchers ne...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome", "engineering", "engineering", "and", "technology", "synthetic", "biology", "neuroscience", "learning", "and", "memory", "crispr", "synthetic", "bioengineering", "cognition", "artificial", "intelligence", "genome", "analysis", "memory", "mammalian", "genomics", "...	2019	A benchmark of computational CRISPR-Cas9 guide design methods
Providing the neurobiological basis of information processing in higher animals , spiking neural networks must be able to learn a variety of complicated computations , including the generation of appropriate , possibly delayed reactions to inputs and the self-sustained generation of complex activity patterns , e . g . ...	Animals and humans can learn versatile computations such as the generation of complicated activity patterns to steer movements or the generation of appropriate outputs in response to inputs . Such learning must be accomplished by networks of nerve cells in the brain , which communicate with short electrical impulses , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "nervous", "system", "membrane", "potential", "social", "sciences", "electrophysiology", "neuroscience", "learning", "and", "memory", "systems", "science", "mathematics", ...	2016	Learning Universal Computations with Spikes
Signaling levels within sensory neurons must be tightly regulated to allow cells to integrate information from multiple signaling inputs and to respond to new stimuli . Herein we report a new role for the cGMP-dependent protein kinase EGL-4 in the negative regulation of G protein-coupled nociceptive chemosensory signal...	All animals rely on their ability to sense and respond to their constantly changing environments to survive . C . elegans ( small roundworms ) depend heavily upon their ability to taste and smell chemical information in their soil environment to find food and avoid danger . While similar signal transduction pathways ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "calcium", "imaging", "molecular", "neuroscience", "caenorhabditis", "elegans", "behavioral", "neuroscience", "model", "organisms", "gustatory", "system", "olfactory", "system", "genetics", "signaling", "pathways", "sensory", "systems", "biology", "neu...	2013	The C. elegans cGMP-Dependent Protein Kinase EGL-4 Regulates Nociceptive Behavioral Sensitivity
Exon junction complexes ( EJCs ) link nuclear splicing to key features of mRNA function including mRNA stability , translation , and localization . We analyzed the formation of EJCs by the spliceosome , the physiological EJC assembly machinery . We studied a comprehensive set of eIF4A3 , MAGOH , and BTZ mutants in comp...	The first step in the expression of eukaryotic protein-coding genes is transcription into a messenger RNA ( mRNA ) precursor in the nucleus . These precursor mRNAs then undergo maturation through the removal of introns in a process termed splicing . During splicing , the splicing machinery or “spliceosome” deposits a c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/mrna", "stability", "molecular", "biology/rna", "splicing", "molecular", "biology/rna-protein", "interactions" ]	2009	The Hierarchy of Exon-Junction Complex Assembly by the Spliceosome Explains Key Features of Mammalian Nonsense-Mediated mRNA Decay
Diarrheal diseases are an important cause of morbidity and mortality among children in developing countries . We aimed to study the etiology and severity of diarrhea in children living in the low-income semiarid region of Brazil . This is a cross-sectional , age-matched case-control study of diarrhea in children aged 2...	Most childhood diarrheal diseases studies focus on children from health centers or emergency hospitals that contribute to a lack of understanding of the etiology of community diarrhea . We aimed to investigate the etiology and severity of diarrheal diseases in children living in Brazil’s low-income , semiarid region co...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "giardia", "pathogens", "geographical", "locations", "microbiology", "parasitic", "protozoans", "viruses", "diarrhea", "age", "groups", "protozoans", "signs", "and", "symp...	2019	Etiology and severity of diarrheal diseases in infants at the semiarid region of Brazil: A case-control study
Enteric fever due to Salmonella Typhi ( typhoid fever ) occurs in urban areas with poor sanitation . While direct fecal-oral transmission is thought to be the predominant mode of transmission , recent evidence suggests that indirect environmental transmission may also contribute to disease spread . Data from a populati...	Typhoid fever , a serious bloodstream infection caused by the bacterium Salmonella Typhi , is commonly associated with direct , person-to-person transmission as a result of improper hygiene and unsafe food/water handling practices . Recent evidence , however , suggests that individuals may be indirectly exposed to typh...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Environmental Transmission of Typhoid Fever in an Urban Slum
Toxoplasma gondii possesses a highly polarized secretory system , which efficiently assembles de novo micronemes and rhoptries during parasite replication . These apical secretory organelles release their contents into host cells promoting parasite invasion and survival . Using a CreLox-based inducible knock-out strate...	The phylum Apicomplexa comprises a large group of obligate intracellular parasites of wide human and agricultural significance . Most notable are Plasmodium , the causative agent of malaria , and Toxoplasma gondii , one of the most common human parasites , responsible for disease of the developing fetus and immune-comp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "vesicles", "vacuoles", "parasite", "replication", "toxoplasma", "gondii", "parasitic", "cell", "cycles", "cell", "cycle", "and", "cell", "division", "cell", "processes", "parasitic", "protozoans", "parasitology", "membrane", "proteins", "developmental", "biology", "pro...	2017	Dual role of the Toxoplasma gondii clathrin adaptor AP1 in the sorting of rhoptry and microneme proteins and in parasite division
We recently showed that IL-13 or peroxisome proliferator activated receptor γ ( PPARγ ) ligands attenuate Candida albicans colonization of the gastrointestinal tract . Here , using a macrophage-specific Dectin-1 deficient mice model , we demonstrate that Dectin-1 is essential to control fungal gastrointestinal infectio...	Since the early 1980s , Candida albicans has emerged as major cause of human disease , especially among immunocompromised individuals and those with metabolic dysfunction . The main host defense mechanisms against this yeast are engulfment and the production of reactive oxygen molecules by macrophages through Dectin-1 ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/fungal", "infections", "immunology/leukocyte", "signaling", "and", "gene", "expression", "immunology/innate", "immunity" ]	2010	PPARγ Controls Dectin-1 Expression Required for Host Antifungal Defense against Candida albicans
Trypanosoma cruzi infection is controlled but not eliminated by host immunity . The T . cruzi trans-sialidase ( TS ) gene superfamily encodes immunodominant protective antigens , but expression of altered peptide ligands by different TS genes has been hypothesized to promote immunoevasion . We molecularly defined TS ep...	Chagas disease , driven by persistent infection with the intracellular protozoan parasite Trypanosoma cruzi , continues to be a major cause of morbidity and mortality in the Americas . Infections with complex pathogens induce T cell responses to a variety of proteins and epitopes in a specific and sometimes predictable...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "cell-mediated", "immunity", "parasitic", "diseases", "parasitic", "protozoans", "vaccines", "preventive", "medicine", "protozoans", "cytotoxic", "t", "cells", "vaccination", "an...	2016	Costimulatory Effects of an Immunodominant Parasite Antigen Paradoxically Prevent Induction of Optimal CD8 T Cell Protective Immunity
Flubendazole ( FBZ ) is highly efficacious against filarial nematodes after parenteral administration and presents a promising macrofilaricidal drug candidate for the elimination of onchocerciasis and other filariae . In the present study the efficacy of a newly developed bioavailable amorphous solid dispersion ( ASD )...	Onchocerciasis and lymphatic filariasis are debilitating human diseases that are caused by filarial nematodes leading to blindness and severe dermatitis ( onchocerciasis ) or lymphedema ( elephantiasis ) and hydroceles . Current mass drug administration ( MDA ) programs are restricted to the use of drugs that target th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "tropical", "diseases", "parasitic", "diseases", "nematode", "infections", "developmental", "biology", "routes", "of", "administration", "filariasis", "pharmaceutics", "drug", "administration", "neglected", "tropi...	2019	Macrofilaricidal efficacy of single and repeated oral and subcutaneous doses of flubendazole in Litomosoides sigmodontis infected jirds
Interplay between apicobasal cell polarity modules and the cytoskeleton is critical for differentiation and integrity of epithelia . However , this coordination is poorly understood at the level of gene regulation by transcription factors . Here , we establish the Drosophila activating transcription factor 3 ( atf3 ) a...	Epithelial cells form sheets and line both the outside and inside of our body . Their proper development and function require the asymmetric distribution of cellular components from the top to the bottom , known as apicobasal polarization . As loss of polarity hallmarks a majority of cancers in humans , understanding h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "invertebrates", "medicine", "and", "health", "sciences", "cloning", "animals", "cell", "differentiation", "genetic", "mapping", "cell", "polarity", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", ...	2018	Atf3 links loss of epithelial polarity to defects in cell differentiation and cytoarchitecture
Lassa fever ( LF ) , an often-fatal hemorrhagic disease caused by Lassa virus ( LASV ) , is a major public health threat in West Africa . When the violent civil conflict in Sierra Leone ( 1991 to 2002 ) ended , an international consortium assisted in restoration of the LF program at Kenema Government Hospital ( KGH ) i...	Lassa fever ( LF ) is a major public health threat in West Africa . After the violent civil conflict in Sierra Leone ( 1991 to 2002 ) ended , the LF research program at Kenema Government Hospital ( KGH ) was reestablished . Higher CFRs in LF patients were observed compared to studies conducted prior to the civil confli...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "zoonoses", "rna", "viruses", "tropical", "diseases", "(non-neglected)", "viral", "classification", "virology", "biology", "microbiology" ]	2014	Lassa Fever in Post-Conflict Sierra Leone
The Escherichia coli chromosome is organized into four macrodomains ( Ori , Ter , Right and Left ) and two non-structured regions . This organization influences the segregation of sister chromatids , the mobility of chromosomal DNA , and the cellular localization of the chromosome . The organization of the Ter and Ori ...	Chromosomes allow the genetic information to be stored , transmitted and organized inside the cell . In bacteria , chromosomes are generally circular and they are shaped and organized by several mechanisms allowing simultaneous transcription , replication and segregation . The way such fundamental processes are managed...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "chromosome", "structure", "and", "function", "cell", "cycle", "and", "cell", "division", "cell", "processes", "microbiology", "chromosome", "mapping", "bacterial", "genetics", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "micro...	2017	Long range chromosome organization in Escherichia coli: The position of the replication origin defines the non-structured regions and the Right and Left macrodomains
Chikungunya , a mosquito-borne viral , acute febrile illness ( AFI ) is associated with polyarthralgia and polyarthritis . Differentiation from other AFI is difficult due to the non-specific presentation and limited availability of diagnostics . This 3-year study identified independent clinical predictors by day post-i...	Chikungunya is an acute febrile illness ( AFI ) , caused by the chikungunya virus ( CHIKV ) , that is transmitted by mosquitoes . Patients with chikungunya exhibit joint , muscle , or bone pain , and may also have skin rash , red eyes ( conjunctiva ) , and red swollen joints ( arthritis ) . Up to 20% of cases develop l...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "dermatology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "engineering", "and", "technology", "electronics", "pathogens", "tropical", "diseases", "microbiology", "alphaviruses", "viruses"...	2019	Distinguishing patients with laboratory-confirmed chikungunya from dengue and other acute febrile illnesses, Puerto Rico, 2012–2015
Large-scale genome sequencing gained general importance for life science because functional annotation of otherwise experimentally uncharacterized sequences is made possible by the theory of biomolecular sequence homology . Historically , the paradigm of similarity of protein sequences implying common structure , funct...	Sequence homology is a fundamental principle of biology . It implies common phylogenetic ancestry of genes and , subsequently , similarity of their protein products with regard to amino acid sequence , three-dimensional structure and molecular and cellular function . Originally an esoteric concept , homology with the p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "computational", "biology/comparative", "sequence", "analysis", "biochemistry/bioinformatics", "evolutionary", "biology/bioinformatics", "computational", "biology/genomics", "computational", "biology" ]	2010	More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology
Amebic colitis , caused by intestinal infection with the parasite , Entamoeba histolytica , is a common cause of diarrhea worldwide . Fulminant amebic colitis is the most devastating complication of this infection , associated with both high mortality and morbidity . We conducted a review of the English literature to d...	Entamoeba histolytica is one of the most important enteric pathogens affecting people worldwide , causing the diarrheal disease amebic colitis . Fulminant amebic colitis is an uncommon but life threatening complication that may ensue . High rates of colonization with E . histolytica burden many developing countries , a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "trophozoites", "medicine", "and", "health", "sciences", "parasite", "groups", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "corticosteroid", "therapy", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "colitis", "amebiasis", "a...	2016	Fulminant Amebic Colitis after Corticosteroid Therapy: A Systematic Review
Membrane fusion is essential for entry of the biomedically-important paramyxoviruses into their host cells ( viral-cell fusion ) , and for syncytia formation ( cell-cell fusion ) , often induced by paramyxoviral infections [e . g . those of the deadly Nipah virus ( NiV ) ] . For most paramyxoviruses , membrane fusion r...	The medically-important Paramyxovirus family includes the deadly Nipah virus ( NiV ) . After paramyxoviruses attach to a receptor at a cell surface , fusion between viral and cellular membranes must occur before the virus genetic material can enter the cell and replication of the virus inside the cell can begin . For m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Unraveling a Three-Step Spatiotemporal Mechanism of Triggering of Receptor-Induced Nipah Virus Fusion and Cell Entry
Secondary metabolites are produced by numerous organisms and can either be beneficial , benign , or harmful to humans . Genes involved in the synthesis and transport of these secondary metabolites are frequently found in gene clusters , which are often coordinately regulated , being almost exclusively dependent on tran...	Fungal infections cause severe problems for immune-compromised individuals . Current antifungal treatment is problematic , as some therapies are toxic to humans and others are not highly effective . These fungal infections also burden hospitals , as costs to treat and prevent such disease runs high . Aspergillus fumiga...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "screens", "gene", "identification", "and", "analysis", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "gene", "function" ]	2014	A Novel C2H2 Transcription Factor that Regulates gliA Expression Interdependently with GliZ in Aspergillus fumigatus
Streptococcus pyogenes ( Group A Streptococcus , GAS ) is an important human commensal that occasionally causes localized infections and less frequently causes severe invasive disease with high mortality rates . How GAS regulates expression of factors used to colonize the host and avoid immune responses remains poorly ...	Group A Streptococcus ( GAS , Streptococcus pyogenes ) is a pathogen responsible for a wide variety of diseases including pharyngitis and toxic shock , but is also commonly carried in the human population asymptomatically . What causes the switch between carrier and pathogenic states remains poorly understood . Cell-to...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "bacteriology", "streptococci", "second", "messenger", "system", "mechanisms", "of", "signal", "transduction", "microbiology", "signaling", "in", "selected", "disciplines", "feeback", "regulation", "dna", "transcription", "crosstalk", "developmental", "signaling", "signalin...	2011	Two Group A Streptococcal Peptide Pheromones Act through Opposing Rgg Regulators to Control Biofilm Development
The Group A Streptococcus remains a significant human pathogen causing a wide array of disease ranging from self-limiting to life-threatening invasive infections . Epithelium ( skin or throat ) colonization with progression to the subepithelial tissues is the common step in all GAS infections . Here , we used transposo...	The WHO ranks the Group A Streptococcus ( GAS ) in the top 10 leading causes of morbidity and mortality from infectious diseases worldwide . GAS is a strict human pathogen causing both benign superficial infections as well as life-threatening invasive diseases . All GAS infections begin by colonization of an epithelium...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "dermatology", "medicine", "and", "health", "sciences", "population", "genetics", "genomic", "library", "screening", "group", "a", "streptococcal", "infection", "gene", "pool", "bacterial", "diseases", "skin", "infections", "mammalian", "genomics", "molecular", "biology...	2017	Genome-wide discovery of novel M1T1 group A streptococcal determinants important for fitness and virulence during soft-tissue infection
Human β-defensins ( hBD ) are antimicrobial peptides that curb microbial activity . Although hBD's are primarily expressed by epithelial cells , we show that human platelets express hBD-1 that has both predicted and novel antibacterial activities . We observed that activated platelets surround Staphylococcus aureus ( S...	Platelets are small cells in the bloodstream whose primary function is to stop bleeding . In addition to their clotting functions , we show that human platelets stall bacterial growth . This inhibitory property of platelets is due to β-defensin 1 , a small antimicrobial protein that kills bacteria . β-defensin 1 also i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "platelets", "immunology", "biology", "hematology", "immune", "response" ]	2011	Novel Anti-bacterial Activities of β-defensin 1 in Human Platelets: Suppression of Pathogen Growth and Signaling of Neutrophil Extracellular Trap Formation
The oxidative phosphorylation ( OxPhos ) pathway is responsible for most aerobic ATP production and is the only pathway with both nuclear and mitochondrial encoded proteins . The importance of the interactions between these two genomes has recently received more attention because of their potential evolutionary effects...	Maintaining two distinct mitochondrial haplotypes with functionally important nucleotide variations in a single population is difficult . If interactions with the mitochondria affect the nuclear genome such that some alleles are more advantageous when they occur with a specific mitochondrial genome , then there is an a...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Conclusion", "Materials", "and", "methods" ]	[ "alleles", "invertebrate", "genomics", "genetic", "mapping", "mitochondria", "bioenergetics", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "sequence", "analysis", "genomics", "sequence", "alignment", "bioinformatics", "genetic", ...	2017	Evolved genetic and phenotypic differences due to mitochondrial-nuclear interactions
The recent availability of whole-genome scale data sets that investigate complementary and diverse aspects of transcriptional regulation has spawned an increased need for new and effective computational approaches to analyze and integrate these large scale assays . Here , we propose a novel algorithm , based on random ...	Transcriptional regulation , one of the most complex and intriguing processes in living cells , drives essential downstream cellular processes such as development , proliferation and differentiation . It gives rise to the versatility and flexibility that allows cells to determine their actions and states in response to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/sequence", "motif", "analysis", "genetics", "and", "genomics/gene", "expression", "computational", "biology/transcriptional", "regulation", "computational", "biology/genomics", "genetics", "and", "genomics/bioinformatics" ]	2009	Identification of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests
Snakebite is a major public health problem in agricultural communities in the tropics leading to acute local and systemic impairments with resultant disabilities . Snakebite related long-term musculoskeletal disabilities have been a neglected area of research . We conducted a population-based , cross-sectional study in...	Snakebite is a neglected tropical disease mainly affecting rural agricultural communities in tropical and subtropical countries . The acute effects of snake envenoming have been widely studied and well characterized , but the long-term sequelae remain poorly characterized . Given the known acute effects of snake venom ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "disabilities", "tropical", "diseases", "fingers", "vertebrates", "limbs", "(anatomy)", "animals", "biomechanics", "biological", "locomotion", "cobras", "reptiles", "neglected", "tropical", "diseases", "snakebite", "public", "and",...	2016	Chronic Musculoskeletal Disabilities following Snake Envenoming in Sri Lanka: A Population-Based Study
In the search for new drug targets , we evaluated the biotin synthetic pathway of Mycobacterium tuberculosis ( Mtb ) and constructed an Mtb mutant lacking the biotin biosynthetic enzyme 7 , 8-diaminopelargonic acid synthase , BioA . In biotin-free synthetic media , ΔbioA did not produce wild-type levels of biotinylated...	We evaluated the biotin synthetic pathway of Mycobacterium tuberculosis ( Mtb ) as a new drug target by first generating an Mtb deletion mutant , ΔbioA , in which the biotin biosynthetic enzyme 7 , 8-diaminopelargonic acid synthase ( BioA ) has been inactivated . This mutant grew in the presence of biotin or des-thiobi...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "bacteriology", "genetic", "mutation", "gene", "regulation", "microbiology", "host-pathogen", "interaction", "gene", "function", "molecular", "genetics", "microbial", "physiology", "biology", "drug", "discovery", "mutagenesis", "biochemistry", "bacterial", "physiology", "nu...	2011	Evaluating the Sensitivity of Mycobacterium tuberculosis to Biotin Deprivation Using Regulated Gene Expression
Survival analysis represents an important outcome measure in clinical research and clinical trials; further , survival ranking may offer additional advantages in clinical trials . In this study , we developed GuanRank , a non-parametric ranking-based technique to transform patients' survival data into a linear space of...	We present a novel rank-based algorithm that outputs the survival likelihood of the ALS patients from the survival data . This novel method enabled us to adopt commonplace machine learning base-learners in survival analysis of ALS and provided insight into the disease .	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "machine", "learning", "algorithms", "medicine", "and", "health", "sciences", "clinical", "research", "design", "neurodegenerative", "diseases", "applied", "mathematics", "amyotrophic", "lateral", "sclerosis", "simulation", "and", "modeling", "algorithms", "research", "de...	2017	Complete hazard ranking to analyze right-censored data: An ALS survival study
Karrikins are smoke-derived compounds presumed to mimic endogenous signalling molecules ( KAI2-ligand , KL ) , whose signalling pathway is closely related to that of strigolactones ( SLs ) , important regulators of plant development . Both karrikins/KLs and SLs are perceived by closely related α/β hydrolase receptors (...	Karrikins are plant signaling compounds from smoke , which induce germination of fire-following plants . They likely mimic endogenous plant hormones ( KAI2-ligand , KL ) , because Arabidopsis karrikin receptor mutants display shoot developmental phenotypes . Perception of karrikins/KL is very similar to that of another...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "stereoisomers", "chemical", "compounds", "plant", "growth", "and", "development", "lateral", "roots", "brassica", "isomerism", "root", "hairs", "developmental", "biology", "plant", "science", "model", "organisms", "organism", "development", "develop...	2019	SMAX1/SMXL2 regulate root and root hair development downstream of KAI2-mediated signalling in Arabidopsis
Strongyloides stercoralis is an intestinal nematode unique in its ability to replicate in the human host , allowing ongoing cycles of autoinfection , persisting for decades within the same host . Although usually asymptomatic , overwhelming infections can occur in Strongyloides and HTLV-1 co-infected individuals ( SS/H...	Strongyloidiasis is a parasitic infection found worldwide in warm , moist climates . In most people , Strongyloides causes a mild and chronic infection with few symptoms . However , some patients , including those infected with the Human T Lymphotrophic Virus 1 ( HTLV-1 ) , can get uncontrolled disease called hyperinfe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "invertebrates", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "biopsy", "pathogens", "immunology", "microbiology", "parasitic", "diseases", "animals", "surgical", "and", "invasive", "medical"...	2019	Regulatory T cells and IgE expression in duodenal mucosa of Strongyloides stercoralis and human T lymphotropic virus type 1 co-infected patients
There has been extensive debate over whether certain classes of genes are more likely than others to contain the causal variants responsible for phenotypic differences in complex traits between individuals . One hypothesis states that input/output genes positioned in signal transduction bottlenecks are more likely than...	Distinguishing the small number of genetic variants that impact phenotypes from the huge number of innocuous variants within an individual's genome is a difficult problem . Several hypotheses concerning the location of causal variants have been put forward based on the fact that genes are often organized into signaling...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genomics", "phenotypes", "gene", "regulatory", "networks", "heredity", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "quantitative", "traits", "computational", "biology", "genetic", "linkage", "complex", "traits" ]	2014	Causal Variation in Yeast Sporulation Tends to Reside in a Pathway Bottleneck
As one of the largest protein families , protein kinases ( PKs ) regulate nearly all processes within the cell and are considered important drug targets . Much research has been conducted on inhibitors for PKs , leading to a wealth of compounds that target PKs that have potential to be lead anthelmintic drugs . Identif...	Parasitic nematode infection is a large global health and economic problem , infecting around 2 billion people and costing $100 billion in crops and livestock . People in developing countries often live on one dollar per day , so treatments cannot be expensive , therefore using pre-existing drugs as lead compounds prov...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "parasite", "groups", "signaling", "networks", "microbiology", "parasitology", "pest", "control", "sequence", "analysis", "comparative", "genomics", "biology", "agriculture", "pesticides", "genomics", "computational", "biology", "genetics...	2013	Using Existing Drugs as Leads for Broad Spectrum Anthelmintics Targeting Protein Kinases
Sexual transmission of human immunodeficiency virus type 1 ( HIV-1 ) most often results from productive infection by a single transmitted/founder ( T/F ) virus , indicating a stringent mucosal bottleneck . Understanding the viral traits that overcome this bottleneck could have important implications for HIV-1 vaccine d...	Most new HIV-1 infections worldwide are caused by the sexual transmission of subtype C viruses , which are prevalent in Asia and southern Africa . While chronically infected individuals harbor a genetically diverse set of viruses , most new infections are established by single variants , termed transmitted/founder ( T/...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunodeficiency", "viruses", "viral", "entry", "viral", "transmission", "and", "infection", "virology", "biology", "microbiology" ]	2012	Transmitted/Founder and Chronic Subtype C HIV-1 Use CD4 and CCR5 Receptors with Equal Efficiency and Are Not Inhibited by Blocking the Integrin α4β7
The control of transposable element ( TE ) activity in germ cells provides genome integrity over generations . A distinct small RNA–mediated pathway utilizing Piwi-interacting RNAs ( piRNAs ) suppresses TE expression in gonads of metazoans . In the fly , primary piRNAs derive from so-called piRNA clusters , which are e...	Silencing of transposable elements ( TEs ) in germ cells depends on a distinct class of small RNAs , Piwi-interacting RNAs ( piRNAs ) . TE repression is provided by piRNAs derived from large heterochromatic loci enriched in fragmented TE copies , so-called piRNA clusters . According to the current model , individual TE...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "germ", "cells", "animal", "models", "genome", "sequencing", "transposons", "model", "organisms", "rna", "interference", "gene", "expression", "genetics", "epigenetics", "comparative", "genomics", "biology", "genomics", "molecular", "cell", "biology", "cellular", "types...	2014	Euchromatic Transposon Insertions Trigger Production of Novel Pi- and Endo-siRNAs at the Target Sites in the Drosophila Germline
Dengue is the most prevalent human arbovirus disease worldwide . Dengue virus ( DENV ) infection causes syndromes varying from self-limiting febrile illness to severe dengue . Although dengue pathophysiology is not completely understood , it is widely accepted that increased inflammation plays important roles in dengue...	Dengue is the most frequent hemorrhagic viral disease and re-emergent infection in the world . Recent decades were marked by a progressive global expansion of the infection including a higher frequency of severe dengue . Currently there is no effective vaccinal coverage or specific therapies , while efforts aimed at ve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "motility", "medicine", "and", "health", "sciences", "body", "fluids", "tropical", "diseases", "platelet", "activation", "dna-binding", "proteins", "platelets", "neglected", "tropical", "diseases", "infectious", "diseases", "animal", "cells", ...	2017	Platelet proteome reveals novel pathways of platelet activation and platelet-mediated immunoregulation in dengue
An important determinant of disease following Streptococcus pneumoniae ( pneumococcus ) lung infection is pulmonary inflammation mediated by polymorphonuclear leukocytes ( PMNs ) . We found that upon intratracheal challenge of mice , recruitment of PMNs into the lungs within the first 3 hours coincided with decreased p...	Despite the presence of vaccines and antibiotic therapies , invasive Streptococcus pneumoniae ( pneumococcus ) infections , such as pneumonia , bacteremia and meningitis , remain a leading cause of mortality and morbidity worldwide . Understanding the host factors that influence the outcome of S . pneumoniae infection ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	Extracellular Adenosine Protects against Streptococcus pneumoniae Lung Infection by Regulating Pulmonary Neutrophil Recruitment
In Amazonian Peru , the primary malaria vector , Nyssorhynchus darlingi ( formerly Anopheles darlingi ) , is difficult to target using standard vector control methods because it mainly feeds and rests outdoors . Larval source management could be a useful supplementary intervention , but to determine its feasibility , m...	The standard methods used to combat mosquitoes that transmit malaria , long-lasting insecticide treated nets and indoor residual spraying , target mosquitoes that bite people indoors and rest indoors after biting . In Amazonian Peru , the major malaria vector , Nyssorhynchus darlingi ( formerly Anopheles darlingi ) , i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "microbiome", "tropical", "diseases", "microbiology", "ponds", "parasitic", "diseases", "animals", "developmental", "biology", "habitats", "bodies", "of", "water", "...	2019	Malaria vector species in Amazonian Peru co-occur in larval habitats but have distinct larval microbial communities
Ebolavirus belongs to the family filoviridae and causes severe hemorrhagic fever in humans with 50–90% lethality . Detailed understanding of how the viruses attach to and enter new host cells is critical to development of medical interventions . The virus displays a trimeric glycoprotein ( GP1 , 2 ) on its surface that...	Ebolavirus causes often fatal hemorrhagic fever in humans and nonhuman primates . During infection , the virus is internalized into the low pH endosomes prior to the delivery of viral RNA to the infected cell . Cleavage by endosomal cathepsins of the heavily glycosylated mucin-like domain and glycan cap from the ebolav...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "biochemistry", "protein", "interactions", "proteins", "protein", "structure", "structural", "proteins", "immunology", "biology", "glycoproteins", "glycobiology" ]	2011	Ebola Virus Glycoprotein Needs an Additional Trigger, beyond Proteolytic Priming for Membrane Fusion
HIV/SIV infections break down the integrity of the gastrointestinal mucosa and lead to chronic immune activation and associated disease progression . Innate lymphoid cells ( ILCs ) , distinguishable by high expression of NKp44 and RORγt , play key roles in mucosal defense and homeostasis , but are depleted from gastroi...	HIV-1 has long been shown to deplete CD4+ T cells and disrupt barrier integrity in the gastrointestinal tract , but effects on other subpopulations of lymphocytes are less well described . A recently identified subpopulation of mucosa-restricted cells , termed innate lymphoid cells ( ILCs ) is thought to play critical ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunopathology", "infectious", "diseases", "infectious", "disease", "immunology", "medicine", "and", "health", "sciences", "hiv", "infections", "clinical", "immunology", "population", "modeling", "aids", "immunology", "biology", "and", "life", "sciences", "infectious", ...	2014	Hypercytotoxicity and Rapid Loss of NKp44+ Innate Lymphoid Cells during Acute SIV Infection
Left ventricular non-compaction ( LVNC ) is a rare cardiomyopathy associated with a hypertrabeculated phenotype and a large spectrum of symptoms . It is still unclear whether LVNC results from a defect of ventricular trabeculae development and the mechanistic basis that underlies the varying severity of this pathology ...	During fetal heart morphogenesis , formation of the mature ventricular wall requires coordinated compaction of the inner trabecular layer and growth of the outer layer of myocardium . Arrested trabecular development has been implicated in the pathogenesis of hypertrabeculation associated with ventricular non-compaction...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "cardiovascular", "anatomy", "cardiac", "ventricles", "fibrosis", "magnetic", "resonance", "imaging", "animal", "models", "developmental", "biology", "electrocardiography", "model", "organisms", "experiment...	2018	Deletion of Nkx2-5 in trabecular myocardium reveals the developmental origins of pathological heterogeneity associated with ventricular non-compaction cardiomyopathy
Upon infection , B-lymphocytes expressing antibodies specific for the intruding pathogen develop clonal responses triggered by pathogen recognition via the B-cell receptor . The constant region of antibodies produced by such responding clones dictates their functional properties . In teleost fish , the clonal structure...	In humans and mice , a broad and robust antibody response is the most effective system of defense against pathogens . While all vertebrates but the most ancient use an antibody system , it remains unknown if the clonal selection rules are conserved across vertebrates . Using high-throughput sequencing and antibody repe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "adaptive", "immunity", "immunity", "immune", "defense", "immunology", "biology", "immunity", "to", "infections", "immune", "response", "immunoglobulins" ]	2013	Teleost Fish Mount Complex Clonal IgM and IgT Responses in Spleen upon Systemic Viral Infection
Prior research has identified the lateral occipital complex ( LOC ) as a critical cortical region for the representation of object shape in humans . However , little is known about the nature of the representations contained in the LOC and their relationship to the perceptual experience of shape . We used human functio...	As early as 1031 a . d . , the Arab scholar Ibn al-Haytham suggested that visual experience was not veridical , but inherently subjective . During the last few decades , this observation has given rise to one of the core questions in visual neuroscience: how does the subjective experience of visual stimuli relate to th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience" ]	2008	Multivariate Patterns in Object-Selective Cortex Dissociate Perceptual and Physical Shape Similarity
Chorioallantoic branching morphogenesis is a key milestone during placental development , creating the large surface area for nutrient and gas exchange , and is therefore critical for the success of term pregnancy . Several Wnt pathway molecules have been shown to regulate placental development . However , it remains l...	Abnormal placental development during pregnancy is associated with conditions such as preeclampsia , intrauterine growth restriction , and even fetal death in humans . Here we focus on the earliest steps of placenta formation , which involves the development of the labyrinthine layer , a specialized epithelium that sit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "biology" ]	2013	A Positive Feedback Loop Involving Gcm1 and Fzd5 Directs Chorionic Branching Morphogenesis in the Placenta

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