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In January 2010 two groups independently published the observation that the depletion of CD8+ cells in SIV-infected macaques had no detectable impact on the lifespan of productively infected cells . This unexpected observation led the authors to suggest that CD8+ T cells control SIV viraemia via non-lytic mechanisms . ...	Several studies have shown a role for CD8+ T cells in controlling SIV-infection . However , early last year two groups independently showed that depletion of CD8+ lymphocytes did not result in a measurable increase in the lifespan of productively infected cells , suggesting that direct cell killing may not be the major...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "immune", "cells", "theoretical", "biology", "hiv", "t", "cells", "immunology", "biology", "viral", "diseases", "immune", "response" ]	2011	Why Don't CD8+ T Cells Reduce the Lifespan of SIV-Infected Cells In Vivo?
An estimated 50 million dengue virus ( DENV ) infections occur annually and more than forty percent of the human population is currently at risk of developing dengue fever ( DF ) or dengue hemorrhagic fever ( DHF ) . Despite the prevalence and potential severity of DF and DHF , there are no approved vaccines or antivir...	Dengue virus ( DENV ) is the leading cause of mosquito-borne viral illness and death in humans . At present , there are no vaccines and no specific antiviral therapeutics to prevent or treat DENV infections . We previously described that the NS5 protein of DENV inhibits type I interferon signaling in virus-infected cel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "global", "health", "immunology", "biology", "microbiology", "public", "health" ]	2013	Dengue Virus Co-opts UBR4 to Degrade STAT2 and Antagonize Type I Interferon Signaling
In the hierarchy of cellular targets damaged by ionizing radiation ( IR ) , classical models of radiation toxicity place DNA at the top . Yet , many prokaryotes are killed by doses of IR that cause little DNA damage . Here we have probed the nature of Mn-facilitated IR resistance in Deinococcus radiodurans , which toge...	One original goal of radiobiology was to explain why cells are so sensitive to ionizing radiation ( IR ) . Early studies in bacteria incriminated DNA as the principal radiosensitive target , an assertion that remains central to modern radiation toxicity models . More recently , the emphasis has shifted to understanding...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "physiology", "microbiology", "chemical", "biology", "molecular", "biology", "eubacteria" ]	2007	Protein Oxidation Implicated as the Primary Determinant of Bacterial Radioresistance
Intron number varies considerably among genomes , but despite their fundamental importance , the mutational mechanisms and evolutionary processes underlying the expansion of intron number remain unknown . Here we show that Drosophila , in contrast to most eukaryotic lineages , is still undergoing a dramatic rate of int...	The surprising observation 30 years ago that genes are interrupted by non-coding introns changed our view of gene architecture . Intron number varies dramatically among species; ranging from nine introns/gene in humans to less than one in some simple eukyarotes . Here we ask where new introns come from and how they are...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "genetics", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics" ]	2010	Nonsense-Mediated Decay Enables Intron Gain in Drosophila
Clusters of differentiated cells contributing to organ structures retain the potential to re-enter the cell cycle and replace cells lost during development or upon damage . To do so , they must be designated spatially and respond to proper activation cues . Here we show that in the case of Drosophila differentiated lar...	An important feature of organs is their ability to maintain their structure and function in spite of natural or accidental cell loss . This capacity is often sustained by so-called stem cells , which are able to provide new cells of the different types in the organ . In addition , some specialized cells , known as facu...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "respiratory", "system", "model", ...	2016	Snoo and Dpp Act as Spatial and Temporal Regulators Respectively of Adult Progenitor Cells in the Drosophila Trachea
We examined recurrent Buruli ulcer cases following treatment and assumed cure in a large cohort of Australian patients living in an endemic area . We report that while the recurrence rate was low ( 2 . 81 cases/year/1000 population ) , it remained similar to the estimated risk of primary infection within the general po...	Mycobacterium ulcerans ( M . ulcerans ) causes a necrotising infection of skin and soft-tissue known as Buruli ulcer . Since the regular use of antibiotics for Buruli ulcer treatment in Australian populations was introduced at the turn of the century , treatment success rates have been very high . However there is no i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "antimicrobials", "sequencing", "techniques", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "drugs", "tropical", "diseases", "microbiology", "genome", "sequencing", "bacterial", "diseases", "signs", "and", "symptoms", "ulcers", "...	2018	Low incidence of recurrent Buruli ulcers in treated Australian patients living in an endemic region
Zika virus was reported in the rainforest city of Iquitos , Peru in 2016 . The potential associations between Zika and fetal neurological disorders were reported extensively in the media regarding neighboring Brazil , and led to great concern about the impact Zika could have on people’s health in Iquitos when it arrive...	Zika virus is an arthropod-borne viral disease that has recently caused epidemics in many Latin American countries and is associated with adverse neurologic outcomes and fetal complications . Although the infection is typically mosquito-transmitted , infection is also possible via sexual transmission . This study uses ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "health", "promotion", "medicine", "and", "health", "sciences", "zika", "fever", "microcephaly", "pathology", "and", "laboratory", "medicine", "maternal", "health", "obstetrics", "and", "gynecology", "pathogens", "tropical", "diseases", "microbiology", "health", "care",...	2018	“Zika is everywhere”: A qualitative exploration of knowledge, attitudes and practices towards Zika virus among women of reproductive age in Iquitos, Peru
Biological systems are subject to inherent stochasticity . Nevertheless , development is remarkably robust , ensuring the consistency of key phenotypic traits such as correct cell numbers in a certain tissue . It is currently unclear which genes modulate phenotypic variability , what their relationship is to core compo...	Organisms are exposed to both internal and external perturbations in every molecular process they go through , and robustness—the ability to maintain their systems unchanged—is crucial for their development and survival . However , the processes that keep the variability of cells as low as possible are barely known . T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "rna", "interference", "cell", "division", "analysis", "caenorhabditis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "green", "fluorescent", "protein", "neuroscience", "animals", "animal", "models", "caenorhabditis", "elegans", "lum...	2017	Stochastic loss and gain of symmetric divisions in the C. elegans epidermis perturbs robustness of stem cell number
Group C orthobunyaviruses are single-stranded RNA viruses found in both South and North America . Until very recently , and despite their status as important vector-borne human pathogens , no Group C whole genome sequences containing all three segments were available in public databases . Here we report a Group C ortho...	Arthropod-borne viruses remain a significant cause of human and domestic animal disease and new viruses are constantly being discovered . RNA virus discovery and assembly remains a challenge due to highly polymorphic genomes , current lack of breadth and depth of publicly available viral genomes , and confounding facto...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "animals", "sequence", "assembly", "tools", "mammals", "viruses", "genomic", ...	2016	Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru
Related organisms typically rely on orthologous regulatory proteins to respond to a given signal . However , the extent to which ( or even if ) the targets of shared regulatory proteins are maintained across species has remained largely unknown . This question is of particular significance in bacteria due to the widesp...	Organisms often respond to environmental cues by modifying the patterns of expression of multiple genes . Related species typically rely on orthologous DNA-binding regulatory proteins to orchestrate the response to a given stimulus . However , it is unclear whether different organisms express similar or rather distinct...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics" ]	2009	Evolution of a Bacterial Regulon Controlling Virulence and Mg2+ Homeostasis
Mathematical modeling of behavioral sequences yields insight into the rules and mechanisms underlying sequence generation . Grooming in Drosophila melanogaster is characterized by repeated execution of distinct , stereotyped actions in variable order . Experiments demonstrate that , following stimulation by an irritant...	Analysis of temporally rich behavioral sequences provides a quantitative description of the rules underlying their generation . Drosophila melanogaster grooming behavior consists of many complex sequences involving repetitions of well-characterized actions . In this paper , we leverage advances in machine vision to aut...	[ "Abstract", "Introduction", "Methods", "and", "models", "Results", "Discussion" ]	[ "invertebrates", "linguistics", "medicine", "and", "health", "sciences", "abdomen", "markov", "models", "nervous", "system", "social", "sciences", "mathematical", "models", "neuroscience", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", ...	2019	Drosophila melanogaster grooming possesses syntax with distinct rules at different temporal scales
Cooperation is ubiquitous across all levels of biological systems ranging from microbial communities to human societies . It , however , seemingly contradicts the evolutionary theory , since cooperators are exploited by free-riders and thus are disfavored by natural selection . Many studies based on evolutionary game t...	Evolutionary dynamics on networks are key for biological and social evolution . Typically , the clustering mutants on networks can dramatically alter the direction of selection . Previous studies on the assortment of mutants assume that individuals interact in a frequency-dependent way . It is hard to tell how assortme...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "recreation", "organismal", "evolution", "markov", "models", "statistics", "applied", "mathematics", "microbiology", "social", "sciences", "simulation", "and", "modeling", "algorithms", "mathematics", "network", "analysis", "microbial", "evolution", "population", "biology",...	2019	Close spatial arrangement of mutants favors and disfavors fixation
Frequency tuning and phase-locking are two fundamental properties generated in the cochlea , enabling but also limiting the coding of sounds by the auditory nerve ( AN ) . In humans , these limits are unknown , but high resolution has been postulated for both properties . Electrophysiological recordings from the AN of ...	The coding of sounds by the cochlea depends on two primary properties: frequency selectivity , which refers to the ability to separate sounds into their different frequency components , and phase-locking , which refers to the neural coding of the temporal waveform of these components . These properties have been well c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chinchillas", "medicine", "and", "health", "sciences", "ears", "vertebrates", "neuroscience", "animals", "mammals", "primates", "animal", "models", "inner", "ear", "computational", "neuroscience", "experimental", "organism", "systems", "nerve", "fibers", "coding", "mec...	2018	High-resolution frequency tuning but not temporal coding in the human cochlea
The complex host-pathogen interplay involves the recognition of the pathogen by the host's innate immune system and countermeasures taken by the pathogen . Detection of invading bacteria by the host leads to rapid activation of the transcription factor NF-κB , followed by inflammation and eradication of the intruders ....	The innate immune system senses intruding pathogens and in response , mounts an inflammatory reaction . Essential for this response is the activation of the transcription factor NF-κB , which mediates reprogramming of gene expression in the host . The bacteria Escherichia coli is usually a non-pathogenic resident of ou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immune", "response", "microbiology/innate", "immunity" ]	2010	The Type III Secretion Effector NleE Inhibits NF-κB Activation
Drosophila melanogaster Held Out Wings ( HOW ) is a conserved RNA–binding protein ( RBP ) belonging to the STAR family , whose closest mammalian ortholog Quaking ( QKI ) has been implicated in embryonic development and nervous system myelination . The HOW RBP modulates a variety of developmental processes by controllin...	Somatic muscles are huge cells that feature highly organized sarcomeric architecture , whose formation and maintenance are not fully understood . Multiple signals play a role in these cells , including the highly conserved MAPK/ERK pathway , which often serves as a cue for cellular proliferation or differentiation . In...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "anatomy", "and", "physiology", "signaling", "in", "selected", "disciplines", "muscle", "animal", "models", "developmental", "biology", "model", "organisms", "molecular", "development", "musculoskeletal", "system", "signaling", "in", "cellular", "processes", "gene", "ex...	2012	Phosphorylation of the Drosophila melanogaster RNA–Binding Protein HOW by MAPK/ERK Enhances Its Dimerization and Activity
Cochlear outer hair cells ( OHCs ) are fast biological motors that serve to enhance the vibration of the organ of Corti and increase the sensitivity of the inner ear to sound . Exactly how OHCs produce useful mechanical power at auditory frequencies , given their intrinsic biophysical properties , has been a subject of...	The sense of hearing is exquisitely sensitive to quiet sounds due to active mechanical amplification of sound-induced vibrations by hair cells within the inner ear . In mammals , the amplification is due to the motor action of “outer hair cells” that feed mechanical power into the cochlea . How outer hair cells are abl...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "physiology/sensory", "systems", "neuroscience/sensory", "systems", "computational", "biology" ]	2009	Power Efficiency of Outer Hair Cell Somatic Electromotility
Tapeworms of the order Diphyllobothriidea are parasites of tetrapods and several species may infect man and cause neglected human disease called diphyllobothriosis . Identification of human-infecting diphyllobothriid cestodes is difficult because of their morphological uniformity , which concerns also their eggs in sto...	More than 2 , 000 eggs of 8 species of diphyllobothriid cestodes infecting humans were compared . Combination of morphometrical and ultrastructural ( surface morphology ) data made it possible to distinguish all species .	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "cestodes", "light", "microscopy", "parasitic", "diseases", "animals", "morphometry", "microscopy", "fresh", "water", "research", "facilities", "research", "and", "an...	2016	Eggs as a Suitable Tool for Species Diagnosis of Causative Agents of Human Diphyllobothriosis (Cestoda)
Mutations in the human Zip4 gene cause acrodermatitis enteropathica , a rare , pseudo-dominant , lethal genetic disorder . We created a tamoxifen-inducible , enterocyte-specific knockout of this gene in mice which mimics this human disorder . We found that the enterocyte Zip4 gene in mice is essential throughout life ,...	Loss-of-function of the zinc transporter ZIP4 in the mouse intestine mimics the lethal human disease acrodermatitis enteropathica . This is a rare disease in humans that is not well understood . Our studies demonstrate the paramount importance of ZIP4 in the intestine in this disease and reveal that a root cause of let...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "small", "intestine", "cellular", "stress", "responses", "animal", "genetics", "genetic", "mutation", "anatomy", "and", "physiology", "gene", "function", "animal", "models", "genetics", "of", "disease", "physiological", "processes", "immunochemistry", "model...	2012	A Mouse Model of Acrodermatitis Enteropathica: Loss of Intestine Zinc Transporter ZIP4 (Slc39a4) Disrupts the Stem Cell Niche and Intestine Integrity
Repetitive DNA elements are mutational hotspots in the genome , and their instability is linked to various neurological disorders and cancers . Although it is known that expanded trinucleotide repeats can interfere with DNA replication and repair , the cellular response to these events has not been characterized . Here...	Expansion of a CAG/CTG trinucleotide repeat is the causative mutation for multiple neurodegenerative diseases , including Huntington's disease , myotonic dystrophy , and multiple types of spinocerebellar ataxias . Two reasons for the cell death that occurs in these diseases are toxicity of the repeat-containing RNA and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/neuromuscular", "diseases", "molecular", "biology/dna", "replication", "molecular", "biology/recombination", "genetics", "and", "genomics/disease", "models", "molecular", "biology/dna", "repair" ]	2011	Expanded CAG/CTG Repeat DNA Induces a Checkpoint Response That Impacts Cell Proliferation in Saccharomyces cerevisiae
Evolutionary adaptation to a constant environment is often accompanied by specialization and a reduction of fitness in other environments . We assayed the ability of the Lenski Escherichia coli populations to grow on a range of carbon sources after 50 , 000 generations of adaptation on glucose . Using direct measuremen...	Adaptation to a single constant environment is commonly expected to result in decreased performance in alternative conditions , or specialization . It has been proposed that , rather than occurring through the neutral accumulation of mutations in unused alternative pathways , this happens because loss of these pathways...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "organismal", "evolution", "microbial", "metabolism", "microbial", "mutation", "population", "genetics", "metabolic", "networks", "microbiology", "bacterial", "biochemistry", "escherichia", "coli", "parallel", "evolution", "mutation", "prokaryotic", "models", ...	2014	Metabolic Erosion Primarily Through Mutation Accumulation, and Not Tradeoffs, Drives Limited Evolution of Substrate Specificity in Escherichia coli
In the life sciences , many measurement methods yield only the relative abundances of different components in a sample . With such relative—or compositional—data , differential expression needs careful interpretation , and correlation—a statistical workhorse for analyzing pairwise relationships—is an inappropriate meas...	Relative abundance data is common in the life sciences , but appreciation that it needs special analysis and interpretation is scarce . Correlation is popular as a statistical measure of pairwise association but should not be used on data that carry only relative information . Using timecourse yeast gene expression dat...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Proportionality: A Valid Alternative to Correlation for Relative Data
MicroRNAs ( miRNAs ) and small nucleolar RNAs ( snoRNAs ) are two classes of small non-coding regulatory RNAs , which have been much investigated in recent years . While their respective functions in the cell are distinct , they share interesting genomic similarities , and recent sequencing projects have identified pro...	The major functions known for RNA were long believed to be either messenger RNAs , which function as intermediates between genes and proteins , or ribosomal RNAs and transfer RNAs which carry out the translation process . In recent years , however , newly discovered classes of small RNAs have been shown to play importa...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "biology/rna-protein", "interactions", "evolutionary", "biology/genomics", "evolutionary", "biology/bioinformatics", "computational", "biology/genomics", "genetics", "and", "genomics/bioinformatics" ]	2009	Human miRNA Precursors with Box H/ACA snoRNA Features
Pseudomonas aeruginosa is a Gram-negative pathogen that can lead to severe infection associated with lung injury and high mortality . The interleukin ( IL ) -36 cytokines ( IL-36α , IL-36β and IL-36γ ) are newly described IL-1 like family cytokines that promote inflammatory response via binding to the IL-36 receptor ( ...	Pneumonia caused by Pseudomonas aeruginosa is a serious infection resulting in significant lung injury and mortality in susceptible hosts . The first line of defense in P . aeruginosa lung infection are neutrophils and macrophages , which play a pivotal role in the rapid clearance of pathogens from the lung . However ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "immune", "cells", "pathogens", "immunology", "microbiology", "pulmon...	2017	Interleukin-36γ and IL-36 receptor signaling mediate impaired host immunity and lung injury in cytotoxic Pseudomonas aeruginosa pulmonary infection: Role of prostaglandin E2
Four dengue virus serotypes ( DENV1-4 ) circulate globally , causing more human illness than any other arthropod-borne virus . Dengue can present as a range of clinical manifestations from undifferentiated fever to Dengue Fever to severe , life-threatening syndromes . However , most DENV infections are inapparent . Yet...	The four serotypes of the mosquito-borne dengue virus ( DENV ) infect an estimated 100 million humans annually , resulting in tens of millions of dengue cases and hundreds of thousands of cases of severe disease . However , infection with DENV does not always lead to clinical signs , and a large proportion of DENV infe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "infectious", "disease", "epidemiology", "epidemiology", "dengue", "fever", "neglected", "tropical", "diseases" ]	2013	Symptomatic Versus Inapparent Outcome in Repeat Dengue Virus Infections Is Influenced by the Time Interval between Infections and Study Year
Intercellular communication is critical for the survival of unicellular organisms as well as for the development and function of multicellular tissues . Cell-to-cell signaling is also required to develop the interconnected mycelial network characteristic of filamentous fungi and is a prerequisite for symbiotic and path...	Appropriate cellular responses to external stimuli depend on the highly orchestrated activity of interconnected signaling cascades . One crucial level of control arises from the formation of discrete complexes through scaffold proteins that bind multiple components of a given pathway . Central for our understanding of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mitogenic", "signaling", "fungal", "genetics", "microbiology", "fungi", "mapk", "signaling", "cascades", "protein", "kinase", "signaling", "cascade", "mycology", "ascomycetes", "molds", "(fungi)", "fungal", "biochemistry", "signal", "transduction", "cell", "biology", "...	2014	Fungal Communication Requires the MAK-2 Pathway Elements STE-20 and RAS-2, the NRC-1 Adapter STE-50 and the MAP Kinase Scaffold HAM-5
Little is known about the protective role of inflammatory processes in modulating lipid metabolism in infection . Here we report an intimate link between the innate immune response to infection and regulation of the sterol metabolic network characterized by down-regulation of sterol biosynthesis by an interferon regula...	Currently , little is known about the crosstalk between the body's immune and metabolic systems that occurs after viral infection . This work uncovers a previously unappreciated physiological role for the cholesterol-metabolic pathway in protecting against infection that involves a molecular link with the protein inter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "virology", "computational", "biology/systems", "biology", "immunology/innate", "immunity" ]	2011	Host Defense against Viral Infection Involves Interferon Mediated Down-Regulation of Sterol Biosynthesis
The recommended strategy for control of schistosomiasis is preventive chemotherapy with praziquantel ( PZQ ) . Pre-school children ( PSC ) are excluded from population treatment programs . In high endemic areas , these children are also at risk , and require treatment with PZQ . The Government of Kenya initiated the Na...	Control of schistosome infections is through treatment of infected people with a single dose of the anti-helminth drug praziquantel ( PZQ ) which is safe , highly efficacious , and can reverse schistosome-related morbidity particularly in the early stages of disease progression . However pre-school children are normall...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "schistosoma", "invertebrates", "children", "medicine", "and", "health", "sciences", "body", "fluids", "clinical", "research", "design", "education", "helminths", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "parasitic", "disease...	2018	Safety, efficacy and acceptability of praziquantel in the treatment of Schistosoma haematobium in pre-school children of Kwale County, Kenya
Infections with monkeypox , cowpox and weaponized variola virus remain a threat to the increasingly unvaccinated human population , but little is known about their mechanisms of virulence and immune evasion . We now demonstrate that B22 proteins , encoded by the largest genes of these viruses , render human T cells unr...	We discovered that the largest gene in the genome of monkeypox viruses and several related viruses , including the virus causing smallpox , but not vaccine strains , encode a protein ( B22 ) that renders the cellular immune system non-responsive . A particularly novel aspect of this work is that B22 proteins directly d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "immunology" ]	2014	T Cell Inactivation by Poxviral B22 Family Proteins Increases Viral Virulence
S-adenosylmethionine ( SAM ) is a donor which provides the methyl groups for histone or nucleic acid modification and phosphatidylcholine production . SAM is hypothesized to link metabolism and chromatin modification , however , its role in acute gene regulation is poorly understood . We recently found that Caenorhabdi...	Animals respond to stress by activating suites of protective genes . A specific metabolite , S-adenosylmethionine ( SAM ) , influences how these genes are activated in a variety of stress conditions . SAM is produced by the 1-carbon cycle and is the major donor for methylation reactions . Thus , SAM is used in the modi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "classical", "mechanics", "pathology", "and", "laboratory", "medicine", "caenorhabditis", "gene", "regulation", "pathogens", "enzymes", "microbiology", "enzymology", "mechanical", "stress", "...	2018	Stress-responsive and metabolic gene regulation are altered in low S-adenosylmethionine
The human cytomegalovirus ( hCMV ) major immediate-early 1 protein ( IE1 ) is best known for activating transcription to facilitate viral replication . Here we present transcriptome data indicating that IE1 is as significant a repressor as it is an activator of host gene expression . Human cells induced to express IE1 ...	Our previous work has shown that the human cytomegalovirus ( hCMV ) major immediate-early 1 protein ( IE1 ) modulates host cell signaling pathways involving proteins of the signal transducer and activator of transcription ( STAT ) family . IE1 has also long been known to facilitate viral replication by activating trans...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "immunology", "microbiology", "viruses", "developmental", "biolo...	2016	Human Cytomegalovirus Immediate-Early 1 Protein Rewires Upstream STAT3 to Downstream STAT1 Signaling Switching an IL6-Type to an IFNγ-Like Response
The cooperative developmental system of the social amoeba Dictyostelium discoideum is susceptible to exploitation by cheaters—strains that make more than their fair share of spores in chimerae . Laboratory screens in Dictyostelium have shown that the genetic potential for facultative cheating is high , and field survey...	Cooperative systems are susceptible to exploitation by cheaters who enjoy the benefits of cooperation without paying the costs . Such conflict is seen in biological systems at every level from individual genes within a cell to individuals within societies . The social amoebae Dictyostelium discoideum have a unique coop...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/cell", "differentiation", "developmental", "biology/developmental", "evolution", "evolutionary", "biology/developmental", "evolution" ]	2010	Cheating by Exploitation of Developmental Prestalk Patterning in Dictyostelium discoideum
Evaluating the effectiveness of malaria control interventions on the basis of their impact on transmission as well as impact on morbidity and mortality is becoming increasingly important as countries consider pre-elimination and elimination as well as disease control . Data on prevalence and transmission are traditiona...	While malaria is still a major public health problem in many parts of the world , control programs have greatly reduced the burden of disease in recent years and many countries are now considering the goal of elimination . Unfortunately , malaria transmission becomes more difficult to measure when it is low because tra...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "and", "information", "sciences", "medicine", "and", "health", "sciences", "population", "modeling", "biology", "and", "life", "sciences", "infectious", "disease", "modeling", "computational", "biology", "computerized", "simulations", "malaria", "parasitic", ...	2014	Seasonally Dependent Relationships between Indicators of Malaria Transmission and Disease Provided by Mathematical Model Simulations
Tetherin ( Bst2/CD317/HM1 . 24 ) is an interferon-induced antiviral host protein that inhibits the release of many enveloped viruses by tethering virions to the cell surface . The HIV-1 accessory protein , Vpu , antagonizes Tetherin through a variety of proposed mechanisms , including surface downregulation and degrada...	At the cell surface , HIV-1 particles are assembled and then released to infect new cells . However , an anti-viral host restriction factor , Tetherin , can tether outgoing virions to the infected cell surface , preventing their dissemination . HIV-1 overcomes this block through the expression of the viral accessory pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "biology", "microbiology" ]	2013	Vpu Binds Directly to Tetherin and Displaces It from Nascent Virions
Multicellular differentiated organisms are composed of cells that begin by developing from a single pluripotent germ cell . In many organisms , a proportion of cells differentiate into specialized somatic cells . Whether these cells lose their pluripotency or are able to reverse their differentiated state has important...	The evolution of multicellularity is one of the most fascinating topics of evolutionary biology . Without multicellularity the incredible diversity of extant life would not be possible . In many multicellular organisms with specialized cells , some cell types become terminally differentiated ( somatic cells ) and lose ...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "organismal", "evolution", "theoretical", "biology", "microbial", "evolution", "biology", "evolutionary", "biology", "microbiology", "evolutionary", "theory", "evolutionary", "developmental", "biology" ]	2012	Differences in Cell Division Rates Drive the Evolution of Terminal Differentiation in Microbes
Pre–mRNAs are often processed in complex patterns in tissue-specific manners to produce a variety of protein isoforms from single genes . However , mechanisms orchestrating the processing of the entire transcript are not well understood . Muscle-specific alternative pre–mRNA processing of the unc-60 gene in Caenorhabdi...	Muscle is a specialized organ with specialized contractile apparatuses . A number of genes encoding contractile apparatus-related proteins undergo muscle-specific pre–mRNA processing . However , the molecular mechanisms and consequences of muscle-specific alternative pre–mRNA processing remain largely unknown . In this...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "interference", "gene", "function", "gene", "expression", "muscle", "fibers", "biology", "molecular", "biology", "rna", "rna", "processing", "cell", "biology", "nucleic", "acids", "genetic", "screens", "genetics", "cellular", "types", "molecular", "cell", "bi...	2012	Muscle-Specific Splicing Factors ASD-2 and SUP-12 Cooperatively Switch Alternative Pre-mRNA Processing Patterns of the ADF/Cofilin Gene in Caenorhabditis elegans
The dendritic tree contributes significantly to the elementary computations a neuron performs while converting its synaptic inputs into action potential output . Traditionally , these computations have been characterized as both temporally and spatially localized . Under this localist account , neurons compute near-ins...	A central issue in biology is how local processes yield global consequences . This is especially relevant for neurons since these spatially extended cells process local synaptic inputs to generate global action potential output . The dendritic tree of a neuron , which receives most of the inputs , expresses ion channel...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/neuronal", "signaling", "mechanisms", "neuroscience/neuronal", "and", "glial", "cell", "biology", "neuroscience/theoretical", "neuroscience" ]	2009	The Role of Ongoing Dendritic Oscillations in Single-Neuron Dynamics
Accurate estimates of mutation rates provide critical information to analyze genome evolution and organism fitness . We used whole-genome DNA sequencing , pulse-field gel electrophoresis , and comparative genome hybridization to determine mutation rates in diploid vegetative and meiotic mutation accumulation lines of S...	Mutations result from errors that occur during DNA metabolism . They provide the raw materials for evolution , can affect organism fitness , and have been shown to accumulate in organisms during asexual growth . During a sexual life cycle , mutations can be removed by recombination and mating . While such removal is th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "replication", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "molecular", "biology/recombination", "molecular", "biology/chromosome", "structure", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "g...	2010	The Baker's Yeast Diploid Genome Is Remarkably Stable in Vegetative Growth and Meiosis
MicroRNAs are universal post-transcriptional regulators in genomes . They have the ability of buffering gene expressional programs , contributing to robustness of biological systems and playing important roles in development , physiology and diseases . Here , we identified a microRNA , miR-125a , as a positive regulato...	MicroRNAs are critical epigenetic modulators in development , physiology and disease processes . Many miRNAs are involved in immune cell development and function , like miR-150 for B cells , miR-181a for T cells . However , studies of miRNAs involvement in granulocyte development and function and related diseases are s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "gene", "regulation", "immunology", "bone", "marrow", "cells", "animal", "models", "micrornas", "model", "organisms", "granulocytes", "experimental", "organism", "system...	2017	MiR-125a Is a critical modulator for neutrophil development
Sensory representations are not only sparse , but often overcomplete: coding units significantly outnumber the input units . For models of neural coding this overcompleteness poses a computational challenge for shaping the signal processing channels as well as for using the large and sparse representations in an effici...	Neural systems favor overcomplete sparse codes in which the number of potential output neurons may exceed the number of input neurons , but only a small subset of neurons become actually active . We argue that efficient use of such large dimensional overcomplete sparse codes requires structural sparsity by controlling ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "neuroscience", "biology", "sensory", "systems", "neuroscience" ]	2012	Efficient Sparse Coding in Early Sensory Processing: Lessons from Signal Recovery
Trypanosoma evansi is the parasite causing surra , a form of trypanosomiasis in camels and other livestock , and a serious economic burden in Kenya and many other parts of the world . Trypanosoma evansi transmission can be sustained mechanically by tabanid and Stomoxys biting flies , whereas the closely related African...	Trypanosoma evansi is an important pathogen of the camel and other livestock where it is a causative agent of surra ( an economically burdensome disease ) . The T . evansi is found in Kenya and the rest of the world . This study indicates that T . evansi originated recently from multiple Trypanosoma brucei strains from...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion", "Conclusions", "and", "future", "directions" ]	[ "parasite", "evolution", "vertebrates", "parasitic", "protozoans", "mammals", "animals", "parasitology", "organisms", "trypanosoma", "brucei", "protozoans", "molecular", "biology", "techniques", "cellular", "structures", "and", "organelles", "research", "and", "analysis", ...	2017	Multiple evolutionary origins of Trypanosoma evansi in Kenya
Vibrations through substrates are an important source of information for diverse organisms , from nematodes to elephants . The fundamental challenge for small animals using vibrational communication is to move their limited mass fast enough to provide sufficient kinetic energy for effective information transfer through...	Animals use substrate-borne vibrations for eavesdropping and communication over an immense range of body size—from elephants to nematodes . Vibrational communication is especially challenging for small animals because of the high mechanical power that is needed to transmit information effectively over extended distance...	[ "Abstract", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "classical", "mechanics", "abdomen", "diagnostic", "radiology", "vibration", "social", "sciences", "electromagnetic", "radiation", "muscle", "contraction", "mechanical", "energy", "animal", "behavior", "synchrotron", "radiation", "...	2019	Planthopper bugs use a fast, cyclic elastic recoil mechanism for effective vibrational communication at small body size
Kernel row number ( KRN ) is an important component of yield during the domestication and improvement of maize and controlled by quantitative trait loci ( QTL ) . Here , we fine-mapped a major KRN QTL , KRN4 , which can enhance grain productivity by increasing KRN per ear . We found that a ~3-Kb intergenic region about...	Maize ( Zea mays L . ) is one of the world's most important sources of calories for humans . With an expanding global population , the demands for maize-derived food , feed , and fuel are rapidly increasing . To meet these needs , geneticists and breeders are facing the challenge of enhancing grain yield through geneti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	KRN4 Controls Quantitative Variation in Maize Kernel Row Number
Among Chagas disease triatomine vectors , the largest genus , Triatoma , includes species of high public health interest . Triatoma dimidiata , the main vector throughout Central America and up to Ecuador , presents extensive phenotypic , genotypic , and behavioral diversity in sylvatic , peridomestic and domestic habi...	Chagas disease is a serious parasitic disease of Latin America . Human contamination in poor rural or periurban areas is mainly attributed to haematophagous triatomine insects . Triatoma includes important vector species , as T . dimidiata in Central and Meso-America . DNA sequences , phylogenetic methods and genetic v...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "evolutionary", "biology/animal", "genetics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "infectious", "diseases/neglected", "tropical", "diseases", "molecular", "biology/molecular", "evolution", "infectious", "diseases/protozoal", "infections", "in...	2008	Phylogeography and Genetic Variation of Triatoma dimidiata, the Main Chagas Disease Vector in Central America, and Its Position within the Genus Triatoma
Recent studies have shown that exposure to some nutritional supplements and chemicals in utero can affect the epigenome of the developing mouse embryo , resulting in adult disease . Our hypothesis is that epigenetics is also involved in the gestational programming of adult phenotype by alcohol . We have developed a mod...	In humans it has been known for some time that exposure to environmental insults during pregnancy can harm a developing fetus and have life-long effects on the individual's health . A well known example is fetal alcohol syndrome , where the children of mothers that consume large amounts of alcohol during pregnancy exhi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/disease", "models", "molecular", "biology/dna", "methylation", "genetics", "and", "genomics/epigenetics", "developmental", "biology/developmental", ...	2010	Maternal Ethanol Consumption Alters the Epigenotype and the Phenotype of Offspring in a Mouse Model
We recently showed that the exocytosis regulator Synaptotagmin ( Syt ) V is recruited to the nascent phagosome and remains associated throughout the maturation process . In this study , we investigated the possibility that Syt V plays a role in regulating interactions between the phagosome and the endocytic organelles ...	Upon their internalization by macrophages , Leishmania donovani promastigotes inhibit phagolysosome biogenesis . This inhibition is mediated by the virulence glycolipid lipophosphoglycan ( LPG ) , attached to the promastigote surface . We recently showed that the exocytosis regulator Synaptotagmin ( Syt ) V controls ea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/leukocyte", "development", "immunology/innate", "immunity", "cell", "biology/membranes", "and", "sorting", "infectious", "diseases/protozoal", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2009	The Leishmania donovani Lipophosphoglycan Excludes the Vesicular Proton-ATPase from Phagosomes by Impairing the Recruitment of Synaptotagmin V
Poxviruses include medically important human pathogens , yet little is known about the specific cellular factors essential for their replication . To identify genes essential for poxvirus infection , we used high-throughput RNA interference to screen the Drosophila kinome for factors required for vaccinia infection . W...	Entry is a vital step in establishing viral infection , providing a potential therapeutic target . Many viruses co-op one of the various cellular endocytic routes for entry , making the host factors that contribute to these processes essential for efficient infection . In particular , vaccinia , the prototypical poxvir...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/microbial", "growth", "and", "development", "infectious", "diseases/viral", "infections", "virology/host", "invasion", "and", "cell", "entry", "genetics", "and", "genomics/functional", "genomics" ]	2010	A Kinome RNAi Screen Identified AMPK as Promoting Poxvirus Entry through the Control of Actin Dynamics
Malaria symptoms occur during Plasmodium falciparum development into red blood cells . During this process , the parasites make substantial modifications to the host cell in order to facilitate nutrient uptake and aid in parasite metabolism . One significant alteration that is required for parasite development is the e...	By replicating within red blood cells malaria parasites are largely hidden from immune recognition , but within mature erythrocytes nutrients are limiting and accumulation of potentially hazardous metabolic end products can rapidly become critical . In order to survive within red blood cells malaria parasites , therefo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "plasmodium", "physiology", "microbiology", "eukaryotes", "homo", "(human)" ]	2008	Plasmodium falciparum Regulatory Subunit of cAMP-Dependent PKA and Anion Channel Conductance
Formerly known as the Malaysian hunter gatherers , the Negrito Orang Asli ( OA ) were heavily dependent on the forest for sustenance and early studies indicated high prevalence of intestinal parasitism . Initiation of a redevelopment program in the 1970s aimed to demarginalize the OA was expected to reduce soil transmi...	Pattern of diseases in a community are associated with changes of culture , socio-economic and environmental conditions . In Malaysia , while transition towards modernity by socio-economic development has shown significant reduction in intestinal parasitism in the general population , no significant difference was obse...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "water", "resources", "helminths", "tropical", "diseases", "hookworms", "parasitic", "diseases", "animals", "physiological", "processes", "ascaris", "ascaris", "lumbri...	2019	Prevalence, intensity and associated risk factors of soil transmitted helminth infections: A comparison between Negritos (indigenous) in inland jungle and those in resettlement at town peripheries
Begomoviruses are exclusively transmitted by whiteflies in a persistent circulative manner and cause considerable economic losses to crop production worldwide . Previous studies have shown that begomoviruses accumulate in vesicle-like structures in whitefly midgut cells and that clathrin-mediated endocytosis is respons...	Many plant viruses are vectored by insects in a persistent circulative manner . In this process , the transport of virus from the gut lumen into the hemolymph of the vector is an important step . Identification of vector components involved in this transport process could lead to new strategies to combat virus spread ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "vesicles", "cell", "processes", "microbiology", "viral", "structure", "epithelial", "cells", "golgi", "apparatus", "plants", "cellular", "structures", "and", "organelles", "endosomes", "animal", "cells", "proteins", "biological"...	2018	Intracellular trafficking of begomoviruses in the midgut cells of their insect vector
Noma is a spreading and fulminant disease believed to be native to Sub-Saharan Africa over the last decade and associated with low socioeconomic status of citizens of the region . Within this noma belt , most epidemiological reports regarding the disease have emanated from the north western region of Nigeria . However ...	Noma , a devouring disease of the orofacial complex , is commonly associated with poverty and impoverished regions of the world especially Sub-Saharan Africa termed the noma belt region of the world . With more reports advocating for full inclusion of noma in the WHO Neglected Tropical Diseases ( NTDs ) program , the a...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusions", "and", "recommendations" ]	[ "medicine", "and", "health", "sciences", "face", "niger", "tropical", "diseases", "geographical", "locations", "surgical", "and", "invasive", "medical", "procedures", "health", "care", "bacterial", "diseases", "neglected", "tropical", "diseases", "africa", "veterinary",...	2019	Estimated incidence and Prevalence of noma in north central Nigeria, 2010–2018: A retrospective study
Cohesin is crucial for proper chromosome segregation but also regulates gene transcription and organism development by poorly understood mechanisms . Using genome-wide assays in Drosophila developing wings and cultured cells , we find that cohesin functionally interacts with Polycomb group ( PcG ) silencing proteins at...	An important task for the cohesin protein complex that binds chromosomes is to ensure equal distribution of chromosomes into the daughter cells when a cell divides . Small changes in cohesin activity , however , can alter gene activity without affecting chromosome distribution , and disrupt physical and mental developm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "animal", "genetics", "functional", "genomics", "gene", "regulation", "dna", "transcription", "histone", "modification", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "molecular", "genetics", "epigenetics", "ep...	2013	Cohesin and Polycomb Proteins Functionally Interact to Control Transcription at Silenced and Active Genes
Timbre is the attribute of sound that allows humans and other animals to distinguish among different sound sources . Studies based on psychophysical judgments of musical timbre , ecological analyses of sound's physical characteristics as well as machine learning approaches have all suggested that timbre is a multifacet...	Music is a complex acoustic experience that we often take for granted . Whether sitting at a symphony hall or enjoying a melody over earphones , we have no difficulty identifying the instruments playing , following various beats , or simply distinguishing a flute from an oboe . Our brains rely on a number of sound attr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "auditory", "system", "computational", "neuroscience", "psychoacoustics", "biology", "sensory", "systems", "sensory", "perception", "neuroscience" ]	2012	Music in Our Ears: The Biological Bases of Musical Timbre Perception
Rickettsial agents are sensed by pattern recognition receptors but lack pathogen-associated molecular patterns commonly observed in facultative intracellular bacteria . Due to these molecular features , the order Rickettsiales can be used to uncover broader principles of bacterial immunity . Here , we used the bacteriu...	Elimination of bacteria is orchestrated by the immune system . Intracellular bacteria are generally recognized by cytosolic molecules named Nod-like receptors ( NLRs ) . One such protein scaffold that senses needle-like structures and globular proteins , namely , the bacterial type III secretion ( T3SS ) and flagellin ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "pathogens", "immunology", "biological", "cultures", "microbiology", "immunoblo...	2016	The Prostaglandin E2-EP3 Receptor Axis Regulates Anaplasma phagocytophilum-Mediated NLRC4 Inflammasome Activation
Vaccinia virus ( VACV ) is the prototypic orthopoxvirus and the vaccine used to eradicate smallpox . Here we show that VACV strain Western Reserve protein 169 is a cytoplasmic polypeptide expressed early during infection that is excluded from virus factories and inhibits the initiation of cap-dependent and cap-independ...	Long after smallpox was eradicated by vaccination with vaccinia virus , the study of this virus continues to reveal novel aspects of the interactions between a virus and the host in which it replicates . In this work we investigated the function of a previously uncharacterized VACV protein , called 169 . The results sh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Inhibition of Translation Initiation by Protein 169: A Vaccinia Virus Strategy to Suppress Innate and Adaptive Immunity and Alter Virus Virulence
Inactivation of the Rb tumor suppressor can lead to increased cell proliferation or cell death depending on specific cellular context . Therefore , identification of the interacting pathways that modulate the effect of Rb loss will provide novel insights into the roles of Rb in cancer development and promote new therap...	Inactivation of Rb tumor suppressor is common in cancers . Therefore , identification of genes and pathways that are synthetic lethal with Rb will provide new insights into the role of Rb in cancer development and promote the development of novel therapeutic approaches . Here we identified a novel synthetic lethal inte...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "developmental", "biology", "medicine", "and", "health", "sciences", "cell", "biology", "genetics", "biology", "and", "life", "sciences", "molecular", "cell", "biology" ]	2014	Hyperactivated Wnt Signaling Induces Synthetic Lethal Interaction with Rb Inactivation by Elevating TORC1 Activities
Dengue is a fast spreading mosquito-borne disease that affects more than half of the population worldwide . An unprecedented outbreak happened in Guangzhou , China in 2014 , which contributed 52 percent of all dengue cases that occurred in mainland China between 1990 and 2015 . Our previous analysis , based on a determ...	An unprecedented dengue outbreak occurred in Guangzhou , 2014 , with 38 , 036 reported cases in contrast to 73 , 179 cases in all of mainland China from 1990 to 2015 . In an earlier analysis using a deterministic model , we concluded the early timing of local transmission to be the most important determinant of this ou...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "demography", "china", "atmospheric", "science", "pathogens", "geographical", "locations", "microbiology", "animals", "viruses", ...	2017	The interplay of climate, intervention and imported cases as determinants of the 2014 dengue outbreak in Guangzhou
Cell type-specific modifications of conventional endosomal trafficking pathways lead to the formation of lysosome-related organelles ( LROs ) . C . elegans gut granules are intestinally restricted LROs that coexist with conventional degradative lysosomes . The formation of gut granules requires the Rab32 family member ...	Lysosome-related organelles represent a diverse collection of intracellular compartments that have important physiological functions . In mammals they include melanosomes , key sites of pigment synthesis , and platelet dense granules , which play important roles in blood clotting . Defects in the pathways that direct t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "lysosomes", "caenorhabditis", "light", "microscopy", "animals", "animal", "models", "developmental", "biology", "guanine", "nucleotide", "exchange", "factors", "caenorhabditis", "elegans", "model", "organisms", "m...	2018	Function and regulation of the Caenorhabditis elegans Rab32 family member GLO-1 in lysosome-related organelle biogenesis
A recent paper of B . Naundorf et al . described an intriguing negative correlation between variability of the onset potential at which an action potential occurs ( the onset span ) and the rapidity of action potential initiation ( the onset rapidity ) . This correlation was demonstrated in numerical simulations of the...	In 1952 , Hodgkin and Huxley described the underlying mechanism for the firing of action potentials through which information is propagated in the nervous system . Hodgkin and Huxley's model relies on the opening and closing of channels , selectively allowing ions to move across the membrane . In the original picture ,...	[ "Abstract", "Introduction", "Model", "Results/Discussion" ]	[ "mathematics", "biophysics/theory", "and", "simulation", "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2009	Action Potential Initiation in the Hodgkin-Huxley Model
Mycobacterium ulcerans , the causative agent of Buruli ulcer ( BU ) , is unique among human pathogens in its capacity to produce a polyketide-derived macrolide called mycolactone , making this molecule an attractive candidate target for diagnosis and disease monitoring . Whether mycolactone diffuses from ulcerated lesi...	Mycolactone is a diffusible cytotoxin produced by Mycobacterium ulcerans , the causative agent of the skin disease Buruli ulcer . In a previous study using animal models , we reported that mycolactone released by cutaneous foci of infection gains access to the peripheral blood . Here we investigated whether mycolactone...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2011	Mycolactone Diffuses into the Peripheral Blood of Buruli Ulcer Patients - Implications for Diagnosis and Disease Monitoring
Efforts to control the spread of Buruli ulcer – an emerging ulcerative skin infection caused by Mycobacterium ulcerans - have been hampered by our poor understanding of reservoirs and transmission . To help address this issue , we compared whole genomes from 18 clinical M . ulcerans isolates from a 30km2 region within ...	In this study we use the power of whole genome sequence comparisons to track the spread of Mycobacterium ulcerans , the causative agent of Buruli ulcer , through several villages in the Ashanti region of Ghana , providing new insights on the behaviour of this enigmatic and emerging pathogen .	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Whole Genome Comparisons Suggest Random Distribution of Mycobacterium ulcerans Genotypes in a Buruli Ulcer Endemic Region of Ghana
Immune senescence , defined as the age-associated dysregulation and dysfunction of the immune system , is characterised by impaired protective immunity and decreased efficacy of vaccines . Recent clinical , epidemiological and immunological studies suggest that Cytomegalovirus ( CMV ) infection may be associated with a...	Cytomegalovirus ( CMV ) persistently infects 50–90% of the human population . After primary infection , constant immune surveillance is required to prevent CMV-related disease . During ageing , increasing T cell resources are expended to keep CMV under control . Recent human studies have suggested that this investment ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunizations", "medicine", "infectious", "diseases", "immune", "cells", "aging", "and", "immunity", "immunity", "t", "cells", "immunity", "to", "infections", "immunology", "biology", "viral", "diseases", "cytomegalovirus", "infection" ]	2012	Immune Senescence: Relative Contributions of Age and Cytomegalovirus Infection
Spatial navigation requires the processing of complex , disparate and often ambiguous sensory data . The neurocomputations underpinning this vital ability remain poorly understood . Controversy remains as to whether multimodal sensory information must be combined into a unified representation , consistent with Tolman's...	Do animals need “cognitive maps“ ? One of the main difficulties in answering this question is finding a definitive scenario where having and not having a “cognitive map“ result in measurably different outcomes . Many key predictions made by models involving some sort of “cognitive map“ can also be replicated by models ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biology", "neuroscience" ]	2012	Maintaining a Cognitive Map in Darkness: The Need to Fuse Boundary Knowledge with Path Integration
Charcot-Marie-Tooth disease ( CMT ) represents a family of related sensorimotor neuropathies . We studied a large family from a rural eastern Canadian community , with multiple individuals suffering from a condition clinically most similar to autosomal recessive axonal CMT , or AR-CMT2 . Homozygosity mapping with high-...	Sensory motor neuropathies are diseases of the peripheral nervous system , involving primarily the nerves which control our muscles . These can result from either genetic or non-genetic causes , with genetic causes usually referred to as Charcot-Marie-Tooth ( CMT ) disease after the three clinicians who first described...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/peripheral", "neuropathies", "developmental", "biology/neurodevelopment", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/medical", "genetics" ]	2010	Mutation in the Gene Encoding Ubiquitin Ligase LRSAM1 in Patients with Charcot-Marie-Tooth Disease
Cryptosporidium infection causes gastrointestinal disease and has a worldwide distribution . The highest burden is in developing countries . We sought to conduct a systematic review and meta-analysis to identify Cryptosporidium risk factors in Low and Middle Income countries ( LMICs ) . Medline Ovid and Scopus database...	Cryptosporidium is a parasite that causes diarrhoea and is transmitted through faecal contamination of water and food . Though it occurs in developed nations , it is much more prevalent in developing countries and is associated with high mortality in children under 2 years old . In this review , we looked at published ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "neonatology", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "water", "resources", "pathology", "and", "laboratory", "medicine", "maternal", "health", "cryptosporidium", "parasitic", "diseases", "parasitic", "protozoans", "pediatr...	2018	Risk factors for Cryptosporidium infection in low and middle income countries: A systematic review and meta-analysis
Schistosomiasis is one of the most important parasitic diseases worldwide , second only to malaria . Schistosomes exhibit an exceptional reproductive biology since the sexual maturation of the female , which includes the differentiation of the reproductive organs , is controlled by pairing . Pathogenicity originates fr...	As a neglected disease , schistosomiasis is still an enormous problem in the tropics and subtropics . Since the 1980s , Praziquantel ( PZQ ) has been the drug of choice but can be anticipated to lose efficacy in the future due to emerging resistance . Alternative drugs or efficient vaccines are still lacking , strength...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "functional", "genomics", "gene", "regulation", "cell", "differentiation", "parasitology", "gene", "function", "germ", "cells", "developmental", "biology", "organism", "development", "stem", "cells", "molecular", "development", "neglected", "tropical", "diseas...	2013	Whole-Organ Isolation Approach as a Basis for Tissue-Specific Analyses in Schistosoma mansoni
Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution . Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains ( PMDs ) and highly methylated domains ( HMDs ) wi...	The placenta is vital for the proper development of the fetus , not only facilitating the exchange of nutrients , oxygen , and waste between the mother and the fetus but also acting as an interface to the maternal immune system and regulating fetal growth by excreting hormones and growth factors . DNA methylation is im...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas
What role does attention play in ensuring the temporal precision of visual perception ? Behavioural studies have investigated feature selection and binding in time using fleeting sequences of stimuli in the Rapid Serial Visual Presentation ( RSVP ) paradigm , and found that temporal accuracy is reduced when attentional...	Our visual system keeps pace with a rapidly changing stream of information as we view the natural world . To do so , it uses a strongly regulated system of attentional filters to constrain which visual stimuli are permitted to be fully processed to the level of conscious awareness . This article explores what happens w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/cognitive", "neuroscience", "neuroscience/theoretical", "neuroscience" ]	2009	Attention Increases the Temporal Precision of Conscious Perception: Verifying the Neural-ST2 Model
Sporothrix schenckii and associated species are agents of human and animal sporotrichosis that cause large sapronoses and zoonoses worldwide . Epidemiological surveillance has highlighted an overwhelming occurrence of the highly pathogenic fungus Sporothrix brasiliensis during feline outbreaks , leading to massive tran...	Sporotrichosis is a neglected fungal disease of humans and animals that remains a serious public-health problem . Sporothrix infections persist in cats , leading to continued transmission via cat-to-cat and cat-to-human contact . Cats are the major source of transmission of Sporothrix brasiliensis to the human populati...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Proteomics-Based Characterization of the Humoral Immune Response in Sporotrichosis: Toward Discovery of Potential Diagnostic and Vaccine Antigens
CDH11 gene copy number and expression are frequently lost in human retinoblastomas and in retinoblastomas arising in TAg-RB mice . To determine the effect of Cdh11 loss in tumorigenesis , we crossed Cdh11 null mice with TAg-RB mice . Loss of Cdh11 had no gross morphological effect on the developing retina of Cdh11 knoc...	Despite over two decades since loss of RB1 was implicated in initiating retinoblastoma , the unique tissue specificity of this process remains puzzling . Indeed , functional loss of both alleles of the RB1 tumor suppressor gene results in >40 , 000-fold increase in predisposition to retinal cancer during childhood , wh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/neuronal", "and", "glial", "cell", "biology", "oncology", "ophthalmology/pediatric", "ophthalmology", "cell", "biology/cell", "signaling", "cell", "biology/cell", "growth", "and", "division", "developmental", "biology/cell", "differentiation", "cell", "biol...	2010	Cdh11 Acts as a Tumor Suppressor in a Murine Retinoblastoma Model by Facilitating Tumor Cell Death
CD8+ T-cell responses exert strong suppressive pressure on HIV replication and select for viral escape mutations . Some of these major histocompatibility complex class I ( MHC-I ) -associated mutations result in reduction of in vitro viral replicative capacity . While these mutations can revert after viral transmission...	CD8+ T-cell responses exert considerable control over replication of HIV and select for viral escape mutations . Recent studies have suggested that these major histocompatibility complex class I ( MHC-I ) -associated mutations accumulate in populations and make viruses less pathogenic in vitro . Other studies have show...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "microbial", "mutation", "immune", "cells", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "immunology", "microbiology", "vertebrates", "animals", "mammal...	2017	In vivo virulence of MHC-adapted AIDS virus serially-passaged through MHC-mismatched hosts
With the advent of subgenomic hepatitis C virus ( HCV ) replicons , studies of the intracellular steps of the viral replication cycle became possible . These RNAs are capable of self-amplification in cultured human hepatoma cells , but save for the genotype 2a isolate JFH-1 , efficient replication of these HCV RNAs req...	The hepatitis C virus ( HCV ) is a major cause of acute and chronic liver disease . Unusual for a positive strand RNA virus , HCV has the high propensity to establish persistent infection , which increases the risk for liver cirrhosis and hepatocellular carcinoma . No selective therapy is available thus far and its dev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "virology/viral", "replication", "and", "gene", "regulation", "virology" ]	2009	Production of Infectious Genotype 1b Virus Particles in Cell Culture and Impairment by Replication Enhancing Mutations
Microtubules are long filamentous hollow cylinders whose surfaces form lattice structures of αβ-tubulin heterodimers . They perform multiple physiological roles in eukaryotic cells and are targets for therapeutic interventions . In our study , we carried out all-atom molecular dynamics simulations for arbitrarily long ...	The molecular machinery of chromosome segregation during cell division is one of the most sophisticated molecular biology mechanisms employing the interplay of different proteins and forces . The long filamentous tube-shaped microtubule structure is a central player in chromosome segregation and cell division , making ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly
Human gammaherpesviruses are associated with malignancies in HIV infected individuals; in macaques used in non-human primate models of HIV infection , gammaherpesvirus infections also occur . Limited data on prevalence and tumorigenicity of macaque gammaherpesviruses , mostly cross-sectional analyses of small series , ...	Human gammaherpesviruses cause malignancies in HIV infected persons; in SIV infected macaques , gammaherpesvirus infections also occur . To understand the potential role of the rhesus gammaherpesviruses , RRV , RFHV and RLCV in cancers occurring in monkeys during SIV and SHIV studies spanning the last 15 years , we dev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "hiv", "infections", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "microbiology", "vertebrates", "cancers", "and", "neoplasms", "animals", "mammals", "retroviruses", "vir...	2018	Gammaherpesvirus infection and malignant disease in rhesus macaques experimentally infected with SIV or SHIV
Plant pathogenic fungi cause massive yield losses and affect both quality and safety of food and feed produced from infected plants . The main objective of plant pathogenic fungi is to get access to the organic carbon sources of their carbon-autotrophic hosts . However , the chemical nature of the carbon source ( s ) a...	The plant parasitic fungus Ustilago maydis is a biotrophic pathogen that depends on live plant tissue for development . It is highly adapted to maize ( Zea mays ) , where it causes the corn smut disease . Fungal cells growing within the plant apoplast are surrounded by the host plasma membrane at all growth stages , th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "plant", "biology/agricultural", "biotechnology", "plant", "biology" ]	2010	A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis
Replicating chromatin involves disruption of histone-DNA contacts and subsequent reassembly of maternal histones on the new daughter genomes . In bulk , maternal histones are randomly segregated to the two daughters , but little is known about the fine details of this process: do maternal histones re-assemble at prefer...	It is widely believed that chromatin , the nucleoprotein packaged state of eukaryotic genomes , can carry epigenetic information and thus transmit gene expression patterns to replicating cells . However , the inheritance of genomic packaging status is subject to mechanistic challenges that do not confront the inheritan...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "genetics", "biology", "genomics", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2011	Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast
The country of Kiribati is a small Pacific island nation which had a new case detection rate of 191 per 100 , 000 in 2016 , and is one of the few countries yet to reach the WHO leprosy elimination goal . Chemoprophylaxis of household contacts of new cases , or to the whole population in a highly endemic areas have been...	Leprosy rates in Kiribati are some of the highest in the world and it is one of the few countries yet to reach the World Health Organization leprosy elimination goal of a prevalence of less than one case per 10 , 000 population . The greatest burden is in the capital South Tarawa and the connected islet of Betio . Inte...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "medicine", "and", "health", "sciences", "landforms", "dose", "prediction", "methods", "topography", "tropical", "diseases", "geographical", "locations", "bacterial", "diseases", "pharmaceutics", "kiribati", "neglected", "tropical", "diseases", "islands", ...	2019	Predicting the impact of household contact and mass chemoprophylaxis on future new leprosy cases in South Tarawa, Kiribati: A modelling study
The standard view in biology is that all animals , from bumblebees to human beings , face a trade-off between speed and accuracy as they search for resources and mates , and attempt to avoid predators . For example , the more time a forager spends out of cover gathering information about potential food sources the more...	Efficient decision-making is vital to the lives of all animals , but the underlying principles of how they achieve this are not yet fully understood . Researchers studying decision-making have generally assumed that animals balance a two-way trade-off between speed and accuracy: the more time they spend gathering infor...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "psychology", "animal", "behavior", "zoology", "ecology", "cognition", "decision", "making", "behavior", "biology", "and", "life", "sciences", "cognitive", "science", "neuroscience", "behavioral", "ecology" ]	2014	An Extra Dimension to Decision-Making in Animals: The Three-way Trade-off between Speed, Effort per-Unit-Time and Accuracy
Meta-analysis of multiple genome-wide association studies ( GWAS ) has become an effective approach for detecting single nucleotide polymorphism ( SNP ) associations with complex traits . However , it is difficult to integrate the readily accessible SNP-level summary statistics from a meta-analysis into more powerful m...	As GWAS continue to grow in sample size , it is evident that these studies need to be utilized more effectively for detecting individual susceptibility variants , and more importantly , to provide insight into global genetic architecture of complex traits . Towards this goal , identifying association with respect to a ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "variant", "genotypes", "carcinomas", "cancers", "and", "neoplasms", "gastrointestinal", "tumors", "liver", "diseases", "genetic", "mapping", "epidemiological", "methods", "and", "statistics...	2016	A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations
Defining master transcription factors governing somatic and cancer stem cell identity is an important goal . Here we show that the Oct4 paralog Oct1 , a transcription factor implicated in stress responses , metabolic control , and poised transcription states , regulates normal and pathologic stem cell function . Oct1HI...	Understanding the mechanisms that control stem cell function is a fundamental prerequisite both for the full application of stem cells to regenerative medicine and for a full understanding of the relationship between stem cells and cancer . In this study we show that a transcription factor known as Oct1 is a central re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "gene", "expression", "genetics", "biology", "molecular", "biology", "genetics", "and", "genomics", "dna", "transcription", "gene", "function" ]	2012	Transcription Factor Oct1 Is a Somatic and Cancer Stem Cell Determinant
WAGR syndrome is characterized by Wilm’s tumor , aniridia , genitourinary abnormalities and intellectual disabilities . WAGR is caused by a chromosomal deletion that includes the PAX6 , WT1 and PRRG4 genes . PRRG4 is proposed to contribute to the autistic symptoms of WAGR syndrome , but the molecular function of PRRG4 ...	Mutants for the fruit fly commmissureless gene ( comm ) dramatically lack connections between the left and right hand sides of the nervous system . This is due to a failure to prevent Robo receptors from reaching the cell surface , where they guide growing axons away from the CNS midline . Comm proteins are not thought...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "nervous", "system", "pervasive", "developmental", "disorders", "autism", "social", "sciences", "neuroscience", "animals", "developmental", "psychology", "animal", "models", "membrane", "proteins", "developmental", ...	2017	The WAGR syndrome gene PRRG4 is a functional homologue of the commissureless axon guidance gene
Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to changing environments . We assessed variation in genome-wide gene expression and four fitness-related phenotypes of an outbred Drosophila melanogaster population under 20 different physiological , social , nutrition...	Unlike Mendelian traits , where the genotype allows a direct prediction of the phenotype , predicting phenotypic values is not straightforward for complex traits , which arise from multiple segregating genes and their interactions with the environment . Here , a single genotype can often express different phenotypes in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "genomics", "genetics", "and", "genomics" ]	2012	Phenotypic Plasticity of the Drosophila Transcriptome
Sensory information about the outside world is encoded by neurons in sequences of discrete , identical pulses termed action potentials or spikes . There is persistent controversy about the extent to which the precise timing of these spikes is relevant to the function of the brain . We revisit this issue , using the mot...	Neurons communicate by means of stereotyped pulses , called action potentials or spikes , and a central issue in systems neuroscience is to understand this neural coding . Here we study how sensory information is encoded in sequences of spikes , using a combination of novel theoretical and experimental techniques . Wit...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics/statistics", "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems" ]	2008	Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution
Translation of mRNA sequences into proteins typically starts at an AUG triplet . In rare cases , translation may also start at alternative non–AUG codons located in the annotated 5’ UTR which leads to an increased regulatory complexity . Since ribosome profiling detects translational start sites at the nucleotide level...	Ribosome profiling data and mRNA sequence features can be used to build reliable classification models with accuracies of about 80% for start codon and open reading frame prediction in human . All predicted start sites of one transcript are postulated to have the potential to initiate translation . They could , for exa...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "messenger", "rna", "mathematics", "forecasting", "statistics", "(mathematics)", "untranslated", "regions", "molecular", "biology", "techniques", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "translatio...	2016	PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse
Clonorchis sinensis infection elicits hepatic inflammation , which can lead to cholangitis , periductal hepatic fibrosis , liver cirrhosis , and even cholangiocarcinoma . Hepatic macrophages are an intrinsic element of both innate and acquired immunity . This study was conducted to demonstrate the dynamics of hepatic m...	Infection with Clonorchis sinensis is a major public health problem in Asia , resulting in loss of liver function and chronic liver diseases , including cancers . However , to the best of our knowledge , the immune response to fluke infection in the liver has not been systematically investigated . Here , we demonstrate...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "biliary", "system", "invertebrates", "cell", "motility", "innate", "immune", "system", "medicine", "and", "health", "sciences", "liver", "immune", "cells", "immune", "physiology", "cytokines", "helminths", "immunology", "fibrosis", "parasitic", "dis...	2017	Clonorchis sinensis antigens alter hepatic macrophage polarization in vitro and in vivo
The host protein CPSF6 possesses a domain that can interact with the HIV-1 capsid ( CA ) protein . CPSF6 has been implicated in regulating HIV-1 nuclear entry . However , its functional significance for HIV-1 replication has yet to be firmly established . Here we provide evidence for two divergent functions of CPSF6 fo...	The viral capsid ( CA ) protein of HIV-1 determines both the ability to infect non-dividing cells and the utilization of host factors implicated in nuclear entry . Understanding how CA controls these two properties is critical . CPSF6 , a CA-interacting host protein , may be important for these properties but its preci...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunodeficiency", "viruses", "viral", "preintegration", "complex", "mechanisms", "of", "resistance", "and", "susceptibility", "viral", "immune", "evasion", "virology", "biology", "microbiology", "viral", "replication", "viral", "evolution" ]	2014	In Vivo Functions of CPSF6 for HIV-1 as Revealed by HIV-1 Capsid Evolution in HLA-B27-Positive Subjects
HIV-1 subtype B replication in the CNS can occur in CD4+ T cells or macrophages/microglia in adults . However , little is known about CNS infection in children or the ability of subtype C HIV-1 to evolve macrophage-tropic variants . In this study , we examined HIV-1 variants in ART-naïve children aged three years or yo...	Genetically compartmentalized human immunodeficiency virus type 1 ( HIV-1 ) subtype B populations can be variably detected in the cerebrospinal fluid ( CSF ) of adults . Compartmentalization is indicative of local CNS replication , and late in disease is linked to HIV-associated dementia ( HAD ) . Compartmentalized vir...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neuroinvasiveness", "viral", "transmission", "and", "infection", "microbiology", "immunodeficiency", "viruses", "neurovirulence", "infectious", "diseases", "infectious", "diseases", "of", "the", "nervous", "system", "viral", "entry", "biology", "pathogenesis", ...	2012	Central Nervous System Compartmentalization of HIV-1 Subtype C Variants Early and Late in Infection in Young Children
Rift Valley fever virus ( RVFV ) ( genus Phlebovirus , family Bunyaviridae ) is an arbovirus that causes severe disease in humans and livestock in sub-Saharan African countries . Although the MP-12 strain of RVFV is a live attenuated vaccine candidate , neuroinvasiveness and neurovirulence of MP-12 in mice may be a con...	Rift Valley fever virus ( RVFV ) is a mosquito-borne zoonotic pathogen , which causes febrile illness , encephalitis and fatal hemorrhagic fever in humans and severe hepatic disease with high mortality and spontaneous abortion rates in ruminants . RVFV is endemic to the African continent . Because many different mosqui...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "viral", "vaccines", "viral", "entry", "rift", "valley", "fever", "zoonoses", "veterinary", "diseases", "viral", "transmission", "and", "infection", "zoonotic", "diseases", "virology", "biology", "microbiology", "viral", "diseases",...	2014	Development of a Novel, Single-Cycle Replicable Rift Valley Fever Vaccine
The matrix ( MA ) domain of HIV-1 Gag plays key roles in membrane targeting of Gag , and envelope ( Env ) glycoprotein incorporation into virions . Although a trimeric MA structure has been available since 1996 , evidence for functional MA trimers has been elusive . The mechanism of HIV-1 Env recruitment into virions l...	One of the enduring problems in HIV-1 research is the mechanism of incorporation of the viral envelope ( Env ) glycoprotein into viral particles . Several models have been proposed ranging from an entirely passive process to a requirement for binding of Env by the matrix ( MA ) domain of the Gag precursor polyprotein ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Global Rescue of Defects in HIV-1 Envelope Glycoprotein Incorporation: Implications for Matrix Structure
Background: Calodium hepaticum ( syn . Capillaria hepatica ) is a worldwide helminth parasite of which several aspects of transmission still remain unclear . In the Amazon region , the mechanism of transmission based on the ingestion of eggs present in the liver of wild mammals has been suggested as the cause of the sp...	The zoonotic parasite Calodium hepaticum is the causative agent of rarely reported liver disease ( hepatic calodiasis ) and spurious infections in humans . In spurious infections eggs of this parasite are excreted in the stools without causing disease . It has been suggested that the cause of this type of infection in ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "soil-transmitted", "helminths", "epidemiology", "environmental", "epidemiology", "infectious", "disease", "epidemiology", "neglected", "tropical", "diseases", "parasitic", "diseases", "helminth"...	2012	Calodium hepaticum: Household Clustering Transmission and the Finding of a Source of Human Spurious Infection in a Community of the Amazon Region
Placental malaria ( PM ) can lead to poor neonatal outcomes , including low birthweight due to fetal growth restriction ( FGR ) , especially when associated with local inflammation ( intervillositis or IV ) . The pathogenesis of PM-associated FGR is largely unknown , but in idiopathic FGR , impaired transplacental amin...	Malaria infection during pregnancy can cause fetal growth restriction and low birthweight associated with high infant mortality and morbidity rates . The pathogenesis of fetal growth restriction in placental malaria is largely unknown , but in other pathological pregnancies , impaired transplacental amino acid transpor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "obstetrics", "and", "gynecology", "pregnancy", "obstetrics", "biology", "microbiology", "host-pathogen", "interaction", "parasitic", "diseases", "malaria", "pathogenesis" ]	2013	Plasmodium falciparum Malaria Elicits Inflammatory Responses that Dysregulate Placental Amino Acid Transport
Mitogen-activated protein kinase ( MAPK ) and PUF ( for Pumilio and FBF [fem-3 binding factor] ) RNA-binding proteins control many cellular processes critical for animal development and tissue homeostasis . In the present work , we report that PUF proteins act directly on MAPK/ERK-encoding mRNAs to downregulate their e...	The mitogen-activated protein ( MAP ) kinase ( MAPK ) enzyme is crucial for regulation of both stem cell maintenance and tumorigenesis . Two conserved controls of MAPK include its activation by RAS signaling and a kinase cascade as well as its inactivation by MAPK phosphatases ( MKPs ) . We identify a third mode of con...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "molecular", "biology", "caenorhabditis", "homo", "(human)" ]	2007	Conserved Regulation of MAP Kinase Expression by PUF RNA-Binding Proteins
Accurate and accessible diagnosis is key for the control of visceral leishmaniasis ( VL ) . Yet , current diagnostic tests for VL have severe limitations: they are invasive or not suitable as point of care ( POC ) test or their performance is suboptimal in East Africa . We analysed the antigens in the VL serodiagnostic...	Visceral leishmaniasis is a potentially fatal disease that affects more than 20 000 people every year . Its diagnosis is difficult since the clinical symptoms are not specific and the existing diagnostic tests are not useful in limited resource countries or they a not accurate enough in East Africa . In this review we ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "chemical", "compounds", "immunology", "tropical", "diseases", "microbiology", "carbohydrates", "parasitic", "diseases", "organic", "compounds", "parasitic", "protozoans", "pro...	2019	Systematic review on antigens for serodiagnosis of visceral leishmaniasis, with a focus on East Africa
Schistosomiasis remains an important public health issue in China and worldwide . Oncomelania hupensis is the unique intermediate host of schistosoma japonicum , and its change influences the distribution of S . japonica . The Three Gorges Dam ( TGD ) has substantially changed the ecology and environment in the Dongtin...	Oncomelania hupensis , an amphibious animal , is the unique intermediate host of schistosoma japonicum . Three Gorges Dam ( TGD ) is a tremendous hydrological project , and it influences the survival of animals downstream . It is studied for several reasons . First , schistosomiasis is still a world-wide parasitic dise...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Three Gorges Dam: Impact of Water Level Changes on the Density of Schistosome-Transmitting Snail Oncomelania hupensis in Dongting Lake Area, China
The MORC family of GHKL ATPases are an enigmatic class of proteins with diverse chromatin related functions . In Arabidopsis , AtMORC1 , AtMORC2 , and AtMORC6 act together in heterodimeric complexes to mediate transcriptional silencing of methylated DNA elements . Here , we studied Arabidopsis AtMORC4 and AtMORC7 . We ...	Keeping selfish genetic elements–such as transposons–silent , while maintaining access to genes , is a fundamental challenge for eukaryotes . Different pathways frequently converge in order to identify transposons and maintain their repression , and in Arabidopsis thaliana , transposons are marked with DNA methylation ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "nuclear", "staining", "brassica", "dna", "transcription", "model", "organisms", "genetic", "elements", "epigenetics", "dna", "plants", "dna", "methylation", "chromatin", "arabidopsis", "thaliana", "research", "and", "analysis", "methods", "specimen", "preparation", "an...	2016	Arabidopsis AtMORC4 and AtMORC7 Form Nuclear Bodies and Repress a Large Number of Protein-Coding Genes
The expression of protein-coding genes requires the selective role of many transcription factors , whose coordinated actions remain poorly understood . To further grasp the molecular mechanisms that govern transcription , we focused our attention on the general transcription factor TFIIH , which gives rise , once mutat...	In eukaryotes , the expression of genes encoding proteins requires the action of hundreds of factors , together with the RNA polymerase II . While these factors are timely and selectively required for the expression of a given gene , little is known about their partnership upon gene expression . Our results reveal a co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "disorders", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "genetics", "of", "disease", "dna", "transcription" ]	2014	Dynamic Partnership between TFIIH, PGC-1α and SIRT1 Is Impaired in Trichothiodystrophy
Cardiovascular diseases ( CVD ) and type 2 diabetes ( T2D ) are closely interrelated complex diseases likely sharing overlapping pathogenesis driven by aberrant activities in gene networks . However , the molecular circuitries underlying the pathogenic commonalities remain poorly understood . We sought to identify the ...	Cardiovascular disease ( CVD ) and type 2 diabetes ( T2D ) are two tightly interrelated diseases that are leading epidemics and causes of deaths around the world . Elucidating the mechanistic connections between the two diseases will offer critical insights for the development of novel therapeutic avenues to target bot...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "genetic", "networks", "cardiovascular", "medicine", "animal", "models", "diabetes", "mellitus", "model", "organisms", "endocrine", "disorders", "network", "analysis", "genome", "analysis", ...	2017	Shared genetic regulatory networks for cardiovascular disease and type 2 diabetes in multiple populations of diverse ethnicities in the United States
Most DNA viruses replicate in the cell nucleus , although the specific sites of virion assembly are as yet poorly defined . Electron microscopy on freeze-substituted , plastic-embedded sections of murine polyomavirus ( PyV ) -infected 3T3 mouse fibroblasts or mouse embryonic fibroblasts ( MEFs ) revealed tubular struct...	Polyomaviruses are infectious pathogens of mammals and birds that have been linked to the development of cancers in their hosts . Members of the polyomavirus family are associated with human disease , such as JCV and BKV , and over the past few years , several more human polyomaviruses ( WUV , KIV and MCV ) have been d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "biology", "microbiology", "viral", "replication", "viral", "structure" ]	2012	Virion Assembly Factories in the Nucleus of Polyomavirus-Infected Cells
Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions . Little attention , however , has focused on the evolutionary impact of lineage-specific gene loss . Here , we show that identifying lineage-specific gene loss after genome duplication is important for understanding th...	Gene duplication may facilitate the acquisition of genetic diversity . Little is known , however , about the impact of gene loss on the functions of surviving genes . When a gene is lost , can other closely related genes evolve to perform the functions of the lost gene ? Answering this question can be difficult because...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "developmental", "biology/developmental", "evolution", "developmental", "biology/pattern", "formation", "genetics", "and", "genomics/gene", "function",...	2009	Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes
Only a few studies have investigated the potential of using geotagged social media data for predicting the patterns of spatio-temporal spread of vector-borne diseases . We herein demonstrated the role of human mobility in the intra-urban spread of dengue by weighting local incidence data with geo-tagged Twitter data as...	Recent studies have shown that Twitter can be utilized as a tool for health research , and aggregated large-scale social media data can indicate the risk of infectious disease in real-time with high accuracy and at low cost . However , most of these studies relied primarily on content analysis or text mining , while on...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2019	A combination of incidence data and mobility proxies from social media predicts the intra-urban spread of dengue in Yogyakarta, Indonesia
The use of internet search data has been demonstrated to be effective at predicting influenza incidence . This approach may be more successful for dengue which has large variation in annual incidence and a more distinctive clinical presentation and mode of transmission . We gathered freely-available dengue incidence da...	Improvements in surveillance , prediction of outbreaks and the monitoring of the epidemiology of dengue virus in countries with underdeveloped surveillance systems are of great importance to ministries of health and other public health decision makers who are often constrained by budget or man-power . Google Flu Trends...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "mathematics", "epidemiology", "statistics", "infectious", "disease", "epidemiology", "global", "health", "dengue", "viral", "diseases", "neglected", "tropical", "diseases", "public", "health...	2011	Prediction of Dengue Incidence Using Search Query Surveillance

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