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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Understanding how silent genes can be competent for activation provides insight into development as well as cellular reprogramming and pathogenesis . We performed genomic location analysis of the pioneer transcription factor FoxA in the adult mouse liver and found that about one-third of the FoxA bound sites are near s...	FoxA transcriptional regulatory proteins are “pioneer factors” that engage silent genes , helping to endow the competence for activation . About a third of the DNA sites we found to be occupied by FoxA in the adult liver are at genes that are silent . Analysis of transcription factor binding motifs near the FoxA sites ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development
Homeostatic proliferation ensures the longevity of central memory T-cells by inducing cell proliferation in the absence of cellular differentiation or activation . This process is governed mainly by IL-7 . Central memory T-cells can also be stimulated via engagement of the T-cell receptor , leading to cell proliferatio...	HIV-1 latently infected cells are considered the last barrier towards viral eradication and cure . However , the low number of latently infected cells found in patients makes studies extremely difficult . Here , using a model of primary CD4 T-cells we study the behavior of latently infected central memory T cells when ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "immunodeficiency", "viruses", "immune", "cells", "cytokines", "viral", "persistence", "and", "latency", "virology", "t", "cells", "immunology", "biology", "microbiology", "immune", "system" ]	2011	Homeostatic Proliferation Fails to Efficiently Reactivate HIV-1 Latently Infected Central Memory CD4+ T Cells
Although sex chromosome meiotic drive has been observed in a variety of species for over 50 years , the genes causing drive are only known in a few cases , and none of these cases cause distorted sex-ratios in nature . In stalk-eyed flies ( Teleopsis dalmanni ) , driving X chromosomes are commonly found at frequencies ...	Sex chromosome meiotic drive causes changes in the sex-ratios of natural populations , and may even lead to extinction if the driving element reaches high frequency . However , very little is known about the genes that cause sex-ratio drive , and no causal gene has been identified in a species that consistently exhibit...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "expression", "analysis", "genomics", "genome", "evolution", "genome", "analysis", "transcriptome", "analysis", "genetics", "biology", "and", "life", "sciences", "computational", "biology", "evolutionary", "biology", "evolutionary", "genetics" ]	2014	Meiotic Drive Impacts Expression and Evolution of X-Linked Genes in Stalk-Eyed Flies
Persistent viral infections are simultaneously associated with chronic inflammation and highly potent immunosuppressive programs mediated by IL-10 and PDL1 that attenuate antiviral T cell responses . Inhibiting these suppressive signals enhances T cell function to control persistent infection; yet , the underlying sign...	Persistent virus infections induce host derived immunosuppressive factors that attenuate the immune response and prevent control of infection . Although the mechanisms of T cell exhaustion are being defined , we know surprisingly little about the underlying mechanisms that induce the immunosuppressive state and the ori...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Type I and Type II Interferon Coordinately Regulate Suppressive Dendritic Cell Fate and Function during Viral Persistence
Recent studies suggest that environmental changes may tip the balance between interacting species , leading to the extinction of one or more species . While it is recognized that evolution will play a role in determining how environmental changes directly affect species , the interactions among species force us to cons...	Recent studies suggest that environmental changes may tip the balance between species that interact with each other , leading to the extinction of one or more species . While it is recognized that evolution will alter the way environmental changes directly affect individual species , the interactions between species fo...	[ "Abstract", "Introduction", "Modeling", "Coevolution", "Results", "Discussion" ]	[]	2013	Coevolution and the Effects of Climate Change on Interacting Species
In Parkinson’s disease , an increase in beta oscillations within the basal ganglia nuclei has been shown to be associated with difficulty in movement initiation . An important role in the generation of these oscillations is thought to be played by the motor cortex and by a network composed of the subthalamic nucleus ( ...	The collective firing of neurons is an essential mechanism for communicating information in the brain . However , in Parkinson’s disease there is a disruption of healthy brain dynamics , which interrupts the processing of normal movement . In particular , the neurons become overly synchronized and produce abnormally la...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[]	2015	Computational Models Describing Possible Mechanisms for Generation of Excessive Beta Oscillations in Parkinson’s Disease
KSHV envelope glycoproteins interact with cell surface heparan sulfate and integrins , and activate FAK , Src , PI3-K , c-Cbl , and Rho-GTPase signal molecules in human microvascular dermal endothelial ( HMVEC-d ) cells . c-Cbl mediates the translocation of virus bound α3β1 and αVβ3 integrins into lipid rafts ( LRs ) ,...	KSHV infection of endothelial cells in humans leads into the development of Kaposi's sarcoma ( KS ) . Hence , understanding of in vitro KSHV entry in endothelial cells is critical to develop strategies to control KSHV infection and KS . The de novo KSHV infection of endothelial HMVEC-d cells is initiated by its attachm...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology", "microbial", "pathogens", "microbial", "control", "host-pathogen", "interaction", "viral", "replication", "complex", "biology", "microbiology", "viral", "replication", "pathogenesis" ]	2014	CIB1 Synergizes with EphrinA2 to Regulate Kaposi's Sarcoma-Associated Herpesvirus Macropinocytic Entry in Human Microvascular Dermal Endothelial Cells
Circadian rhythms in transcription are generated by rhythmic abundances and DNA binding activities of transcription factors . Propagation of rhythms to transcriptional initiation involves the core promoter , its chromatin state , and the basal transcription machinery . Here , I characterize core promoters and chromatin...	Circadian rhythms switch gene expression on and off with a daily rhythm in most tissues in mammals and other animals . Typically , thousands of genes are affected , and the functions of these rhythms include preparing and adjusting various physiological functions in tissues to meet time-of-day dependent requirements op...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "gene", "regulation", "messenger", "rna", "animals", "dna", "transcription", "circadian", "oscillators", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "chronobiology", "epigenetics", "dna", "chromatin", "drosophila", "promoter", ...	2016	Linking Core Promoter Classes to Circadian Transcription
Leptospirosis is an important but largely under-recognized public health problem in the tropics . Establishment of highly sensitive and specific laboratory diagnosis is essential to reveal the magnitude of problem and to improve treatment . This study aimed to evaluate the diagnostic accuracy of a recombinant LigA prot...	Leptospirosis is an important but largely under-recognized public health problem in the tropics . A sensitive , specific and practical point-of-care laboratory test is needed to improve clinical management in resource-limited settings . We developed a recombinant LigA protein based IgM assay ( IgM ELISA ) and evaluated...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Diagnostic Accuracy of Recombinant Immunoglobulin-like Protein A-Based IgM ELISA for the Early Diagnosis of Leptospirosis in the Philippines
Sequence data arising from an increasing number of partial and complete genome projects is revealing the presence of the polyketide synthase ( PKS ) family of genes not only in microbes and fungi but also in plants and other eukaryotes . PKSs are huge multifunctional megasynthases that use a variety of biosynthetic par...	Polyketide synthases ( PKSs ) form a large family of multifunctional proteins involved in the biosynthesis of diverse classes of therapeutically important natural products . These enzymes biosynthesize natural products with enormous diversity in chemical structures by combinatorial use of a limited number of catalytic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry/molecular", "evolution", "computational", "biology/macromolecular", "structure", "analysis", "biochemistry", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "computational", "biology/sequence", "motif", "analysis", "computational", "biology/...	2009	Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis
From ants to humans , the timing of many animal behaviors comes in bursts of activity separated by long periods of inactivity . Recently , mathematical modeling has shown that simple algorithms of priority-driven behavioral choice can result in bursty behavior . To experimentally test this link between decision-making ...	It has long been observed that animal movement tends to come in bursts of activity . This has been seen in many animal species , ranging from small insects to even human activity patterns . The underlying mechanisms remain unknown , but recently a mathematical model showed that it could be due to priority-driven choice...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "nervous", "system", "components", "drosophila", "melanogaster", "model", "organisms", "cognitive", "neuroscience", "behavioral", "neuroscience", "decision", "making", "physiology", "biology", "anatomy", "and", "physiology", "neurological", "system", "...	2011	The Origin of Behavioral Bursts in Decision-Making Circuitry
Small RNAs ( sRNAs ) can operate as regulatory agents to control protein expression by interaction with the 5′ untranslated region of the mRNA . We have developed a physicochemical framework , relying on base pair interaction energies , to design multi-state sRNA devices by solving an optimization problem with an objec...	Is our current knowledge of in vivo RNA-RNA interactions and thermodynamics enough to perform the unsupervised computational design of fully synthetic sequences encoding functional RNAs in living cells ? Recent work gave a positive answer for the challenging problem of designing activating riboregulators . This was don...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "rna", "nucleic", "acids", "synthetic", "biology", "biology", "computational", "biology", "biophysics" ]	2013	Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization
Globally , trachoma is the leading cause of infectious blindness and Australia is the only developed country with endemic trachoma . It is found in remote Indigenous communities burdened with poverty , overcrowding and poor hygiene . Lack of culturally appropriate health promotion , a small trachoma workforce and lack ...	Australia is the only high-income nation with endemic trachoma . It is prevalent in remote Indigenous communities , although it was eliminated from wider society in Australia over one hundred years ago . Trachoma elimination across vast areas of remote Australia is an enormous challenge . Community members are highly m...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Strengths", "and", "limitations", "Conclusion" ]	[ "health", "promotion", "children", "medicine", "and", "health", "sciences", "face", "education", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "australia", "health", "care", "bacterial", "diseases", "age", "groups", "eye", "di...	2017	The impact of health promotion on trachoma knowledge, attitudes and practice (KAP) of staff in three work settings in remote Indigenous communities in the Northern Territory
We investigate the dynamics of a deterministic finite-sized network of synaptically coupled spiking neurons and present a formalism for computing the network statistics in a perturbative expansion . The small parameter for the expansion is the inverse number of neurons in the network . The network dynamics are fully ch...	One avenue towards understanding how the brain functions is to create computational and mathematical models . However , a human brain has on the order of a hundred billion neurons with a quadrillion synaptic connections . Each neuron is a complex cell comprised of multiple compartments hosting a myriad of ions , protei...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "statistical", "mechanics", "neural", "networks", "computational", "neuroscience", "biophysics", "theory", "biology", "biophysics", "neuroscience" ]	2013	Dynamic Finite Size Effects in Spiking Neural Networks
For scientists working on gonochoric organisms , determining sex can be crucial for many biological questions and experimental studies , such as crossbreeding , but it can also be a challenging task , particularly when no sexual dimorphism is visible or cannot be directly observed . In metazoan parasites of the genus S...	Current global changes ( environmental and anthropogenic ) are expected to promote the spread and transmission of infectious diseases . One of the direct consequences of such changes is the modification of the geographical distribution of species , enabling natural hybridization . Such hybridization is already known to...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "helminths", "parasitic", "diseases", "invertebrate", "genomics", "animals", "genomic", "library", "construction", "organisms", "genome", "analysis", "dn...	2016	A Genome Wide Comparison to Identify Markers to Differentiate the Sex of Larval Stages of Schistosoma haematobium, Schistosoma bovis and their Respective Hybrids
Circadian rhythms are generated by interlocked transcriptional-translational negative feedback loops ( TTFLs ) , the molecular process implemented within a cell . The contributions , weighting and balancing between the multiple feedback loops remain debated . Dissociated , free-running dynamics in the expression of dis...	Circadian clocks are endogenous pacemakers that generate gene expression oscillations with a period of approximately 24h . They enable an organism to anticipate daily changes in light and temperature and allow to align physiological properties to the most beneficial time around the solar day . The suprachiasmatic nucle...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "light", "neuroscience", "electromagnetic", "radiation", "circadian", "oscillators", "chronobiology", "crystallographic", "techniques", "research", "and", "analysis", "methods", "animal", "cells", "gene", "expression", "luminescence", "light", "pulses", "physics", "biochemi...	2019	Weak coupling between intracellular feedback loops explains dissociation of clock gene dynamics
Sex chromosomes originated from autosomes but have evolved a highly specialized chromatin structure . Drosophila Y chromosomes are composed entirely of silent heterochromatin , while male X chromosomes have highly accessible chromatin and are hypertranscribed as a result of dosage compensation . Here , we dissect the m...	Sex chromosomes differ from non-sex chromosomes ( “autosomes” ) at the genomic , transcriptomic , and epigenomic level , yet the X and Y share a common evolutionary origin . The Drosophila Y chromosome is gene-poor and associated with a compact and transcriptionally inactive form of genetic material called heterochroma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Epigenome of Evolving Drosophila Neo-Sex Chromosomes: Dosage Compensation and Heterochromatin Formation
Because of their nuclear dimorphism , ciliates provide a unique opportunity to study the role of non-coding RNAs ( ncRNAs ) in the communication between germline and somatic lineages . In these unicellular eukaryotes , a new somatic nucleus develops at each sexual cycle from a copy of the zygotic ( germline ) nucleus ,...	Paramecium tetraurelia provides an excellent model for studying the mechanisms involved in the production of non-coding transcripts and their mode of action . Different types of non-coding RNAs ( ncRNAs ) were shown to be implicated in the programmed DNA elimination process that occurs in this organism . At each sexual...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements
New tools are required for the diagnosis of pre-symptomatic leprosy towards further reduction of disease burden and its associated reactions . To address this need , two new skin test antigens were developed to assess safety and efficacy in human trials . A Phase I safety trial was first conducted in a non-endemic regi...	Clinically useful skin test reagents should be safe and sufficiently sensitive to detect infection prior to physical manifestations of leprosy disease . While in these small scale human studies , leprosy reagents were safe for use in humans , they failed in respect of sensitivity at a rate of 20–25% in the key indicato...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "research", "design", "infectious", "diseases", "medicine", "and", "health", "sciences", "clinical", "research", "design", "biology", "and", "life", "sciences", "microbiology", "research", "and", "analysis", "methods" ]	2014	Safety and Efficacy Assessment of Two New Leprosy Skin Test Antigens: Randomized Double Blind Clinical Study
Lassa virus ( LASV ) is the causative agent of Lassa Fever and is responsible for several hundred thousand infections and thousands of deaths annually in West Africa . LASV and the non-pathogenic Mopeia virus ( MOPV ) are both rodent-borne African arenaviruses . A live attenuated reassortant of MOPV and LASV , designat...	The virulent Lassa fever virus ( LASV ) and the non-pathogenic Mopeia virus ( MOPV ) infect rodents and , incidentally , people in West Africa . The mechanism of LASV damage in human beings is unclear . There is no licensed Lassa fever vaccine and therapeutic intervention is usually too late . The ML29 vaccine candidat...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "medicine", "infectious", "diseases", "viral", "hemorrhagic", "fevers", "gene", "expression", "neglected", "tropical", "diseases", "biology", "microbiology", "molecular", "cell", "biology" ]	2013	Transcriptome Analysis of Human Peripheral Blood Mononuclear Cells Exposed to Lassa Virus and to the Attenuated Mopeia/Lassa Reassortant 29 (ML29), a Vaccine Candidate
We introduce a novel dynamic model of stem cell and tissue organisation in murine intestinal crypts . Integrating the molecular , cellular and tissue level of description , this model links a broad spectrum of experimental observations encompassing spatially confined cell proliferation , directed cell migration , multi...	In the murine small intestine there are more than a million organized groups of proliferating cells , the crypts , each of which contains about 250–300 cells . About 60% of these cells are in rapid cycle . The functional stem cells of this tissue have been demonstrated to reside at defined positions at the lower third ...	[ "Abstract", "Introduction", "Discussion", "Materials", "and", "Methods" ]	[ "gastroenterology", "and", "hepatology/gastrointestinal", "cancers", "cell", "biology/cell", "signaling", "cell", "biology/cell", "growth", "and", "division", "biophysics/theory", "and", "simulation", "cell", "biology/cell", "adhesion", "gastroenterology", "and", "hepatology/...	2011	A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt
Total white blood cell ( WBC ) and neutrophil counts are lower among individuals of African descent due to the common African-derived “null” variant of the Duffy Antigen Receptor for Chemokines ( DARC ) gene . Additional common genetic polymorphisms were recently associated with total WBC and WBC sub-type levels in Eur...	Although recent genome-wide association studies have identified common genetic variants associated with total white blood cell ( WBC ) and WBC sub-type counts in European and Japanese ancestry populations , whether these or other loci account for differences in WBC count among African Americans is unknown . By examinin...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "genetics", "genetics", "and", "genomics", "biology", "hematology", "clinical", "genetics" ]	2011	Genome-Wide Association Study of White Blood Cell Count in 16,388 African Americans: the Continental Origins and Genetic Epidemiology Network (COGENT)
As the reality of eliminating human African trypanosomiasis ( HAT ) by 2020 draws closer , the need to detect and identify the remaining areas of transmission increases . Here , we have explored the feasibility of using commercially available LAMP kits , designed to detect the Trypanozoon group of trypanosomes , as a x...	Recent control efforts have reduced the global incidence of Gambiense human African trypanosomiasis ( HAT ) to <5 , 000 cases per year , strengthening the prospect of eliminating the disease as a public health problem by 2020 . To meet this goal , new methods for identifying transmission must be explored to provide a c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "african", "trypanosomiasis", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "animals", "glossina", "protozoans", "neglected", "tropical", "diseases", "molecular", "bi...	2016	Illuminating the Prevalence of Trypanosoma brucei s.l. in Glossina Using LAMP as a Tool for Xenomonitoring
Protein kinases are key signaling enzymes that catalyze the transfer of γ-phosphate from an ATP molecule to a phospho-accepting residue in the substrate . Unraveling the molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor is important for understanding kinase sp...	Protein kinases are key signaling enzymes and major drug targets that catalyze the transfer of phosphate group to a phospho-accepting residue in the substrate . Unraveling molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor ( substrate consensus sequence , SCS )...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "empirical", "methods", "computer", "applications", "computer", "science", "computational", "chemistry", "protein", "structure", "chemistry", "biology", "computational", "biology", "computer-aided", "design", "macromolecular", "structure", "analysis" ]	2011	Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping
Structure and dynamics of voltage-gated ion channels , in particular the motion of the S4 helix , is a highly interesting and hotly debated topic in current membrane protein research . It has critical implications for insertion and stabilization of membrane proteins as well as for finding how transitions occur in membr...	Proteins that transport ions across the cellular membrane are essential for cellular life . The proteins conducting positively charged potassium ions are key players in heart beat and nerve impulse generation because they are regulating the electrical excitability of the cell ( together with proteins transporting other...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics/macromolecular", "assemblies", "and", "machines", "biophysics/protein", "folding", "biophysics/theory", "and", "simulation", "cell", "biology/neuronal", "signaling", "mechanisms", "biophysics/membrane", "proteins", "and", "energy", "transduction" ]	2009	Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel
The pathogenic fungus Candida albicans can undergo phenotypic switching between two heritable states: white and opaque . This phenotypic plasticity facilitates its colonization in distinct host niches . The master regulator WOR1 is exclusively expressed in opaque phase cells . Positive feedback regulation by Wor1 on th...	The opportunistic fungal pathogen Candida albicans is a common member of the human gut microbiota , but can also cause serious infections in immune-compromised individuals . Morphological plasticity is essential for its ability to adapt to and colonize a varied array of diverse host niches . One such morphological cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "bonding", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "gene", "regulation", "pathogens", "microbiology", "organic", "compounds", "plasmid", "construction", "regulator", "genes", "fungi", "p...	2018	Wor1 establishes opaque cell fate through inhibition of the general co-repressor Tup1 in Candida albicans
Antigenic drift in the influenza A virus hemagglutinin ( HA ) is responsible for seasonal reformulation of influenza vaccines . Here , we address an important and largely overlooked issue in antigenic drift: how does the number and location of glycosylation sites affect HA evolution in man ? We analyzed the glycosylati...	Influenza A virus is highly susceptible to neutralizing antibodies specific for the viral hemagglutinin glycoprotein ( HA ) , and is easily controlled by standard vaccines . Influenza A virus remains an important human pathogen , however , due to its ability to rapidly evade antibody responses . This process , termed a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "virology/virus", "evolution", "and", "symbiosis", "virology", "computational", "biology/evolutionary", "modeling", "infectious", "diseases/viral", "infections", "virology/immune", "evasion" ]	2010	Glycosylation Focuses Sequence Variation in the Influenza A Virus H1 Hemagglutinin Globular Domain
Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function . However , much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcript...	The eukaryotic genome is organized in a highly dynamic structure called chromatin . Access to DNA in the context of chromatin is granted by enzymatic activities that use the energy of hydrolysis of ATP to slide or covalently modify nucleosomes . ISWI is an evolutionarily conserved nucleosome-sliding factor that plays e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics" ]	2008	Genetic Identification of a Network of Factors that Functionally Interact with the Nucleosome Remodeling ATPase ISWI
Infection with equid herpesvirus type 1 ( EHV-1 ) leads to respiratory disease , abortion , and neurologic disorders in horses . Molecular epidemiology studies have demonstrated that a single nucleotide polymorphism resulting in an amino acid variation of the EHV-1 DNA polymerase ( N752/D752 ) is significantly associat...	Equid herpesvirus type 1 ( EHV-1 ) , a close relative of varicella-zoster virus and herpes simplex virus of humans , is spread by aerosol and is the causative agent of the most common neurologic disease of horses . Outbreaks of the neurologic form of EHV-1 can be devastating to individual animals and entire herds , and...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "mammals", "virology" ]	2007	A Point Mutation in a Herpesvirus Polymerase Determines Neuropathogenicity
The discovery that somatic cells are reprogrammable to pluripotency by ectopic expression of a small subset of transcription factors has created great potential for the development of broadly applicable stem-cell-based therapies . One of the concerns regarding the safe use of induced pluripotent stem cells ( iPSCs ) in...	iPSC technology has the potential to revolutionize stem-cell based regenerative medicine and would also allow for the production of patient-specific cells for disease modeling and drug discovery . One of the primary safety concerns of iPSCs is genetic instability , which is associated with cancer and various other dise...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "aneuploidy", "stem", "cells", "induced", "pluripotent", "stem", "cells", "chromosomal", "disorders", "genetics", "biology", "human", "genetics", "genetics", "and", "genomics" ]	2012	Reprogramming to Pluripotency Can Conceal Somatic Cell Chromosomal Instability
Recent experimental and theoretical efforts have highlighted the fact that binding of transcription factors to DNA can be more accurately described by continuous measures of their binding affinities , rather than a discrete description in terms of binding sites . While the binding affinities can be predicted from a phy...	The binding of proteins to DNA is a key molecular mechanism , which can regulate the expression of genes in response to different cellular and environmental conditions . The extensive research on gene regulation has generated binding models for many transcription factors , but the prediction of new binding sites is sti...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computational", "biology/transcriptional", "regulation", "genetics", "and", "genomics/bioinformatics", "computational", "biology" ]	2008	Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions
Giardia duodenalis is a widespread intestinal protozoan of both humans and mammals . To date , few epidemiological studies have assessed the potential and importance of zoonotic transmission; and the human giardiasis burden attributable to G . duodenalis of animal origin is unclear . No information about occurrence and...	Giardiasis is a kind of zoonotic disease with global distribution . Due to the great number of asymptomatic giardiasis cases , human giardiasis is often underreported . The sources of infection of giardiasis are feces of humans and mammals with the pathogen being transmitted by the fecal-oral route . In this study , we...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "veterinary", "diseases", "veterinary", "parasitology", "giardiasis", "zoonotic", "diseases", "biology", "microbiology", "zoology", "parasitic", "diseases", "veterinary", "science", "parasitology" ]	2012	Genetic Characterizations of Giardia duodenalis in Sheep and Goats in Heilongjiang Province, China and Possibility of Zoonotic Transmission
The phylum Apicomplexa comprises a group of obligate intracellular parasites of broad medical and agricultural significance , including Toxoplasma gondii and the malaria-causing Plasmodium spp . Key to their parasitic lifestyle is the need to egress from an infected cell , actively move through tissue , and reinvade an...	The phylum Apicomplexa includes a number of medically and agriculturally relevant parasites . These include the Plasmodium species , agents of malaria and estimated to cause over 1 million deaths per year , and Toxoplasma gondii , which infects 30–80% of any human population . These parasites rely on a unique form of a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parastic", "protozoans", "protein", "kinase", "signaling", "cascade", "signal", "transduction", "molecular", "cell", "biology", "toxoplasma", "gondii", "parasitology", "protozoology", "biology", "microbiology", "signaling", "pathways", "signaling", "cascades" ]	2012	TgCDPK3 Regulates Calcium-Dependent Egress of Toxoplasma gondii from Host Cells
The semidominant Danforth's short tail ( Sd ) mutation arose spontaneously in the 1920s . The homozygous Sd phenotype includes severe malformations of the axial skeleton with an absent tail , kidney agenesis , anal atresia , and persistent cloaca . The Sd mutant phenotype mirrors features seen in human caudal malformat...	Birth defects are the leading cause of infant mortality in the United States , accounting for 1 in 5 infant deaths annually . Birth defects that affect development of the caudal portion of the embryo can include malformations of the spine , such as spina bifida , and malformations of the kidneys and lower gastrointesti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "retrotransposons", "dna", "transcription", "animal", "models", "genome", "sequencing", "developmental", "biology", "model", "organisms", "molecular", "genetics", "embryology", "transposons", "gene", "expression", "biology", "molecular", "biology", "gene", "identification",...	2013	Next-Generation Sequencing Identifies the Danforth's Short Tail Mouse Mutation as a Retrotransposon Insertion Affecting Ptf1a Expression
Emerging infectious diseases are often the result of a host shift , where the pathogen originates from a different host species . Virulence—the harm a pathogen does to its host—can be extremely high following a host shift ( for example Ebola , HIV , and SARs ) , while other host shifts may go undetected as they cause f...	Many emerging infectious diseases are the result of a host shift , with the pathogen jumping into the new host from another species . Virulence—the harm a pathogen does to its host—can be extremely high following a host shift ( for example HIV , SARs and Ebola ) , while other host shifts may go undetected as they cause...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	The Causes and Consequences of Changes in Virulence following Pathogen Host Shifts
Eukaryotic nuclei contain regions of differentially staining chromatin ( heterochromatin ) , which remain condensed throughout the cell cycle and are largely transcriptionally silent . RNAi knockdown of the highly conserved heterochromatin protein HP1 in Drosophila was previously shown to preferentially reduce male via...	Eukaryotic genomes are organized into two distinct classes of chromatin , euchromatin and heterochromatin . The former is less condensed to enable transcription , whereas heterochromatin , which is marked by Heterochromatin Protein 1 ( HP1 ) , remains compact and mostly transcriptionally silent throughout the cell cycl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2011	Cooperative and Antagonistic Contributions of Two Heterochromatin Proteins to Transcriptional Regulation of the Drosophila Sex Determination Decision
Cyclic nucleotide-gated ( CNG ) ion channels are nonselective cation channels , essential for visual and olfactory sensory transduction . Although the channels include voltage-sensor domains ( VSDs ) , their conductance is thought to be independent of the membrane potential , and their gating regulated by cytosolic cyc...	Cyclic nucleotide-gated ( CNG ) channels mediate the passage of cations through the cytoplasmic membrane . They are involved in sensory transduction and cellular development in the rod and cone photoreceptors , as well as in brain , kidney , heart and other cells , and are linked to achromatopsia and other rare genetic...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "modeling", "biology", "and", "life", "sciences", "computational", "biology", "biophysics", "biophysical", "simulations" ]	2014	Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel
Chromatin in sperm is different from that in other cells , with most of the genome packaged by protamines not nucleosomes . Nucleosomes are , however , retained at some genomic sites , where they have the potential to transmit paternal epigenetic information . It is not understood how this retention is specified . Here...	In most cells , DNA is packaged by protein complexes called nucleosomes . In sperm , however , nucleosomes are only retained at a small fraction of the genome , particularly at the start sites of genes . In this work , we show that the sites at which nucleosomes are retained in sperm are specified by variation in the b...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "epigenetics", "biology", "genomics", "genetics", "and", "genomics" ]	2011	Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome
The emergence of microbial antibiotic resistance is a global health threat . In clinical settings , the key to controlling spread of resistant strains is accurate and rapid detection . As traditional culture-based methods are time consuming , genetic approaches have recently been developed for this task . The detection...	One of the major health threats of 21st century is emergence of antibiotic resistance . To manage its human health and economic impact , efforts are made to develop novel diagnostic tools that rapidly detect resistant strains in clinical settings . In our study , we employed a range of powerful machine learning tools t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "taxonomy", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "statistics", "drugs", "microbiology", "decision", "tree", "learning", "decision", "analysis", "antibiotic", "resistance", "phylogenetics", "data", "management", "ma...	2018	Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data
Numerous genetic association studies have implicated the KIAA0319 gene on human chromosome 6p22 in dyslexia susceptibility . The causative variant ( s ) remains unknown but may modulate gene expression , given that ( 1 ) a dyslexia-associated haplotype has been implicated in the reduced expression of KIAA0319 , and ( 2...	Dyslexia , or reading disability , is a common disorder caused by both genetic and environmental factors . Genetic studies have implicated a number of genes as candidates for playing a role in dyslexia . We functionally characterized one such gene ( KIAA0319 ) to identify variant ( s ) that might affect gene expression...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/genetics", "of", "disease", "neurological", "disorders/neurogenetics" ]	2009	A Common Variant Associated with Dyslexia Reduces Expression of the KIAA0319 Gene
Terrestrial arthropods , including insects , commonly harbor maternally inherited intracellular symbionts that confer benefits to the host or manipulate host reproduction to favor infected female progeny . These symbionts may be especially vulnerable to thermal stress , potentially leading to destabilization of the sym...	Insects often harbor heritable symbiotic bacteria that infect their cells and/or bodily fluids . These heritable bacteria are passed from mother to offspring and can have substantial effects on host insect biology , and include bacteria like Cardinium that cause mating incompatibilities between symbiont-infected and un...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "bacteriophages", "symbiosis", "manufacturing", "processes", "parasitic", "diseases", "wolbachia", "germ", "cells", "viruses", "developmental", "biology", "pupae", "heat", "treatment", "bacteria"...	2019	Exposure to opposing temperature extremes causes comparable effects on Cardinium density but contrasting effects on Cardinium-induced cytoplasmic incompatibility
Currently , information on species-specific hookworm infection is unavailable in Malaysia and is restricted worldwide due to limited application of molecular diagnostic tools . Given the importance of accurate identification of hookworms , this study was conducted as part of an ongoing molecular epidemiological investi...	Parasitic zoonoses pose a continuing public health problem , especially in endemic developing countries where the majority of populations live in poor , overcrowded conditions , lack education , and practice poor standards of hygiene and improper sanitary disposal of feces . Close contact with domestic animals such as ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "veterinary", "science" ]	2012	Epidemiological and Genetic Data Supporting the Transmission of Ancylostoma ceylanicum among Human and Domestic Animals
A common theme across multiple fungal pathogens is their ability to impair the establishment of a protective immune response . Although early inflammation is beneficial in containing the infection , an uncontrolled inflammatory response is detrimental and may eventually oppose disease eradication . Chromoblastomycosis ...	Pathogenic fungi often present two distinct forms , which are correlated to the host’s inflammatory response and eventual disease outcome . Chromoblastomycosis is a fungal disease occurring especially in tropical areas , and it is most often caused by the dimorphic fungus Fonsecaea pedrosoi . Although it is not a notif...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "inflammatory", "diseases", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "fungal", "genetics", "pathogens", "immunology", ...	2017	Modulation of the immune response by Fonsecaea pedrosoi morphotypes in the course of experimental chromoblastomycosis and their role on inflammatory response chronicity
Shigella infections are a public health problem in developing and transitional countries because of high transmissibility , severity of clinical disease , widespread antibiotic resistance and lack of a licensed vaccine . Whereas Shigellae are known to be transmitted primarily by direct fecal-oral contact and less commo...	Whereas previous researchers have noted that seasonal peaks in the numbers of houseflies and patients suffering from Shigella diarrheal infection seemed to coincide , this is the first research to quantify the association using time-series statistical methods . The results show that houseflies could account for approxi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "shigellosis", "infections", "infectious", "disease", "epidemiology", "pediatrics", "bacterial", "diseases", "clinical", "epidemiology", "global", "health", "infectious", "disease", "control", "infectious", "diseases", "disease", "ecology", "epidemiology", "trav...	2013	Housefly Population Density Correlates with Shigellosis among Children in Mirzapur, Bangladesh: A Time Series Analysis
The first meiotic division reduces genome ploidy . This requires pairing of homologous chromosomes into bivalents that can be bi-oriented within the spindle during prometaphase I . Thereafter , pairing is abolished during late metaphase I , and univalents are segregated apart onto opposite spindle poles during anaphase...	Meiosis is a special cell division that occurs in two steps , meiosis I and II . It converts diploid into haploid cells which can be used as gametes for sexual reproduction where two gametes from opposite sexes , a sperm and an oocyte , fuse to generate the zygote , the first diploid cell of the next generation . Befor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "meiosis", "homologous", "chromosomes", "spermatocytes", "chromosome", "structure", "and", "function", "anaphase", "cell", "cycle", "and", "cell", "division", "cell", "processes", "germ", "cells", "mitosis", "sperm", "spermatids", "sex", "chromosomes", "animal", "cell...	2019	MNM and SNM maintain but do not establish achiasmate homolog conjunction during Drosophila male meiosis
A high-frequency , subthreshold resonance in the guinea pig medial superior olive ( MSO ) was recently linked to the efficient extraction of spatial cues from the fine structure of acoustic stimuli . We report here that MSO neurons in gerbil also have resonant properties and , based on our whole-cell recordings and com...	Principal neurons of the medial superior olive ( MSO ) are fast and precise coincidence detectors involved in the neuronal computation of sound localization . We show that they exhibit resonance properties in vitro , responding to small oscillatory inputs , maximally at preferred frequencies . Their resonant frequencie...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "resonance", "frequency", "action", "potentials", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "signal", "processing", "membrane", "potential", "electrophysiology", "neuroscience", "signal", "filtering", "systems", "science", "mathematics", ...	2016	High-Frequency Resonance in the Gerbil Medial Superior Olive
Sensory information is encoded in the response of neuronal populations . How might this information be decoded by downstream neurons ? Here we analyzed the responses of simultaneously recorded barrel cortex neurons to sinusoidal vibrations of varying amplitudes preceded by three adapting stimuli of 0 , 6 and 12 µm in a...	In the natural environment , animals are constantly exposed to sensory stimulation . A key question in systems neuroscience is how attributes of a sensory stimulus can be “read out” from the activity of a population of brain cells . We chose to investigate this question in the whisker-mediated touch system of rats beca...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "neuroscience", "sensory", "systems", "biology", "neuroscience", "coding", "mechanisms" ]	2014	Population Decoding in Rat Barrel Cortex: Optimizing the Linear Readout of Correlated Population Responses
A critical step on the way to understanding a sensory system is the analysis of the input it receives . In this work we examine the statistics of natural complex echoes , focusing on vegetation echoes . Vegetation echoes constitute a major part of the sensory world of more than 800 species of echolocating bats and play...	More than 800 species of bats perceive their surroundings through echolocation . They emit ultrasonic pulses and analyze the information conveyed in the echoes returning from objects in their surroundings . This enables bats to orient in space , to acquire food and to perfectly function in complete darkness . In the ab...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/sensory", "systems" ]	2009	What a Plant Sounds Like: The Statistics of Vegetation Echoes as Received by Echolocating Bats
Fungal pathogens of humans require molecular oxygen for several essential biochemical reactions , yet virtually nothing is known about how they adapt to the relatively hypoxic environment of infected tissues . We isolated mutants defective in growth under hypoxic conditions , but normal for growth in normoxic condition...	Opportunistic environmental pathogens adapt to hostile conditions within the host to cause disease . We describe two pathways in the pathogenic fungus Cryptococcus neoformans that are both necessary for adaptation to hypoxia and required for its virulence . One pathway uses a pathway homologous to the mammalian sterol-...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "genetics", "and", "genomics", "cryptococcus", "neoformans", "molecular", "biology" ]	2007	A Link between Virulence and Homeostatic Responses to Hypoxia during Infection by the Human Fungal Pathogen Cryptococcus neoformans
Dmrt1 is a highly conserved transcription factor , which is critically involved in regulation of gonad development of vertebrates . In medaka , a duplicate of dmrt1—acting as master sex-determining gene—has a tightly timely and spatially controlled gonadal expression pattern . In addition to transcriptional regulation ...	The development of the gonads in vertebrates is mainly regulated by dmrt1 , a master sex-determining gene that has a timely and spatially controlled gonadal expression pattern . In addition to transcriptional regulation , a sequence motif located in the 3′ UTR ( D3U-box ) mediates transcript stability of dmrt1 mRNAs . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "fish", "reproductive", "system", "gonads", "messenger", "rna", "vertebrates", "animals", "germ", "cells", "osteichthyes", "developmental", "biology", "sequence", "motif", "analysis", "embryos", "research", "and", "analysis", "...	2019	A novel evolutionary conserved mechanism of RNA stability regulates synexpression of primordial germ cell-specific genes prior to the sex-determination stage in medaka
Fine-tuned Notch and Hedgehog signalling pathways via attenuators and dampers have long been recognized as important mechanisms to ensure the proper size and differentiation of many organs and tissues . This notion is further supported by identification of mutations in these pathways in human cancer cells . However , a...	Growth control mechanisms ensure that organs attain the correct final size , generally averting tumour growth . This control is often linked to spatially confined domains known as organizers ( conserved signalling centres ) , established along the dorsal-ventral and anterior-posterior axes of the organ by the Notch and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Dampening the Signals Transduced through Hedgehog via MicroRNA miR-7 Facilitates Notch-Induced Tumourigenesis
The spatial architecture of signaling pathways and the interaction with cell size and morphology are complex , but little understood . With the advances of single cell imaging and single cell biology , it becomes crucial to understand intracellular processes in time and space . Activation of cell surface receptors ofte...	Frequently , cells detect signals at their surface , which are transmitted to the nucleus . The influence of cell shape and size is often neglected and cells are regarded as well-mixed compartments . However , the advance of modern microscopy has unraveled heterogeneous distribution of signaling molecules in the cell a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "cell", "signaling", "biochemistry", "signal", "transduction", "nuclear", "membrane", "cell", "biology", "post-translational", "modification", "proteins", "signaling", "molecules", "biology", "and", "life", "sciences", "cell", "nucleus", "cellular", "st...	2018	Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction
IgE specific to worm antigen ( SWA ) and pre-treatment eosinophil number , are associated with human immunity to re-infection with schistosomes after chemotherapeutic treatment . Treatment significantly elevates circulating IL-5 24-hr post-treatment of Schistosoma mansoni . Here we investigate if praziquantel treatment...	Partial human immunity to infection with trematode worms of the genus Schistosoma is associated with IgE specific to adult worm-derived antigens and eosinophils . Treatment studies of Schistosoma infection allow us to examine the temporal features of the immune response post-antigen exposure , their inter-dependence an...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "humoral", "immunity", "immune", "cells", "immunity", "immunity", "to", "infections", "immunology", "biology" ]	2013	Rapidly Boosted Plasma IL-5 Induced by Treatment of Human Schistosomiasis haematobium Is Dependent on Antigen Dose, IgE and Eosinophils
Although numerous genetic loci have been associated with coronary artery disease ( CAD ) with genome wide association studies , efforts are needed to identify the causal genes in these loci and link them into fundamental signaling pathways . Recent studies have investigated the disease mechanism of CAD associated gene ...	Coronary artery disease ( CAD ) is the worldwide leading cause of death . The majority of risk for CAD is genetic in nature , i . e . , a feature of the genetic information that is transmitted to each individual from both parents , and primarily affects the disease processes in the blood vessel wall that regulate the d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "gene", "regulation", "coronary", "heart", "disease", "genome", "analysis", "cardiology", "small", "interfering", "rnas", "genomics", "gene", "expression", "smad", "signaling", "genetic", ...	2018	Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk
The heat shock response ( HSR ) is essential to survive acute proteotoxic stress and has been studied extensively in unicellular organisms and tissue culture cells , but to a lesser extent in intact metazoan animals . To identify the regulatory pathways that control the HSR in Caenorhabditis elegans , we performed a ge...	The heat shock response ( HSR ) is an essential stress response that functions to maintain protein folding homeostasis , or proteostasis , and whose critical role in human diseases is recently becoming apparent . Previously , most of our understanding of the HSR has come from cultured cells and unicellular organisms . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "systems", "biology", "genome", "analysis", "tools", "caenorhabditis", "elegans", "animal", "genetics", "model", "organisms", "cellular", "stress", "responses", "genetic", "screens", "gene", "expression", "genetics", "gene", "regulation", "molecular"...	2013	Identification of a Tissue-Selective Heat Shock Response Regulatory Network
H2A . Z is an essential histone variant that has been implicated to have multiple chromosomal functions . To understand how H2A . Z participates in such diverse activities , we sought to identify downstream effector proteins that are recruited to chromatin via H2A . Z . For this purpose , we developed a nucleosome puri...	Within the cell's nucleus , DNA closely associates with histone proteins , forming a structure known as chromatin . Packaging DNA into chromatin allows for efficient storage of the genome , and it also provides an additional means of regulating processes , such as gene expression , that require access to DNA . Two copi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biology", "molecular", "cell", "biology" ]	2012	A Combination of H2A.Z and H4 Acetylation Recruits Brd2 to Chromatin during Transcriptional Activation
Previously , we identified a set of HLA-A020 . 1-restricted trans-sialidase peptides as targets of CD8+ T cell responses in HLA-A0201+ individuals chronically infected by T . cruzi . Herein , we report the identification of peptides encoded by the same trans-sialidase gene family that bind alleles representative of the...	At present , 16–20 million people in Central and South America are infected with Trypanosoma cruzi , the causative agent of Chagas disease in humans . The primary clinical consequence of the infection is a cardiomyopathy , which manifests in approximately 30% of infected individuals , many years after the initial infec...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology", "immunology/immune", "response", "immunology/immunity", "to", "infections" ]	2008	HLA Class I-T Cell Epitopes from trans-Sialidase Proteins Reveal Functionally Distinct Subsets of CD8+ T Cells in Chronic Chagas Disease
Adherent cells use forces at the cell-substrate interface to sense and respond to the physical properties of their environment . These cell forces can be measured with traction force microscopy which inverts the equations of elasticity theory to calculate them from the deformations of soft polymer substrates . We intro...	Adherent cells respond very sensitively not only to biochemical , but also to physical properties of their environment . For example , it has been shown that stem cell differentiation can be guided by substrate rigidity , which is sensed by cells by actively pulling on their environment with actomyosin-generated forces...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Model-based Traction Force Microscopy Reveals Differential Tension in Cellular Actin Bundles
The implementation of soil-transmitted helminth ( STH ) treatment programmes occurs in varied environmental , social and economic contexts . Programme impact will be influenced by factors that affect the reduction in the prevalence and intensity of infections following treatment , as well as the subsequent rate of rein...	Most countries with endemic soil-transmitted helminth ( STH ) infections have started implementing deworming programmes in recent years . However , the achievable impact on the prevalence and intensity of infections will depend on the socioeconomic and environmental context in which the programme is implemented . We us...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Understanding Heterogeneity in the Impact of National Neglected Tropical Disease Control Programmes: Evidence from School-Based Deworming in Kenya
Bacterial genome evolution is characterized by gains , losses , and rearrangements of functional genetic segments . The extent to which large-scale genomic alterations influence genotype-phenotype relationships has not been investigated in a high-throughput manner . In the symbiotic soil bacterium Sinorhizobium melilot...	S . meliloti , which has traditionally facilitated ground-breaking insights into symbiotic communication , is also emerging as an excellent model for studying the evolution of functional relationships between bacterial chromosomes and anciently acquired accessory replicons . Multi-replicon genome architecture is presen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "deletion", "mutation", "chromosome", "structure", "and", "function", "engineering", "and", "technology", "metabolic", "processes", "synthetic", "biology", "microbiology", "mutation", "genome", "analysis", "genetic", "elements", "bacterial", "genetics", "m...	2018	Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti
Immense diversity of prion strains is observed , but its underlying mechanism is less clear . Three [PSI] prion strains—named VH , VK , and VL—were previously isolated in the wild-type yeast genetic background . Here we report the generation and characterization of eight new [PSI] isolates , obtained by propagating the...	A prion is a host-encoded infectious protein that can usually adopt many distinct self-propagating conformations , referred to as prion strains . Upon interspecies transmission , a prion isolate can mutate and give rise to novel strains . It is not well understood how the strain diversity is created . Here we use the [...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology" ]	2011	Inter-Allelic Prion Propagation Reveals Conformational Relationships among a Multitude of [PSI] Strains
Gut microbiota and human relationships are strictly connected to each other . What we eat reflects our body-mind connection and synchronizes with people around us . However , how this impacts on gut microbiota and , conversely , how gut bacteria influence our dietary behaviors has not been explored yet . To quantify th...	Human gut microbiota is able to influence different aspects of physiology , such as human behaviors . Our close social connections , in turn , impact on eating behaviors and diets , which play a key role in driving the gut microbial composition and its metabolic processes . To quantify the dynamic interplay between gut...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "gut", "bacteria", "multiplex", "networks", "metabolic", "networks", "microbiology", "diet", "social", "sciences", "habits", "nutrition", "happiness", "network", "analysis", "microbial", "evolution", "b...	2019	Social dynamics modeling of chrono-nutrition
An increasing number of cis-regulatory RNA elements have been found to regulate gene expression post-transcriptionally in various biological processes in bacterial systems . Effective computational tools for large-scale identification of novel regulatory RNAs are strongly desired to facilitate our exploration of gene r...	RNA is remarkably versatile , acting not only as messengers to transfer genetic information from DNA to protein but also as critical structural components and catalytic enzymes in the cell . More intriguingly , RNA elements in messenger RNAs have been widely found in bacteria to control the expression of their downstre...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/comparative", "sequence", "analysis", "computational", "biology/macromolecular", "sequence", "analysis", "computational", "biology/sequence", "motif", "analysis" ]	2009	Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines
In many species , genomic data have revealed pervasive adaptive evolution indicated by the fixation of beneficial alleles . However , when selection pressures are highly variable along a species' range or through time adaptive alleles may persist at intermediate frequencies for long periods . So called “balanced polymo...	Herein , we investigate the genomic basis of rapid adaptive evolution in response to seasonal fluctuations in the environment . We identify hundreds of polymorphisms ( seasonal SNPs ) that undergo dramatic shifts in allele frequency – on average between 40 and 60% – and oscillate between seasons repeatedly over multipl...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "evolutionary", "ecology", "ecology", "phenotypes", "evolutionary", "processes", "ecological", "economics", "genetics", "biology", "and", "life", "sciences", "dna", "population", "genetics", "evolutionary", "biology", "evolutionary", "genetics", "genetic", ...	2014	Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila
PDZ domain-mediated interactions have greatly expanded during metazoan evolution , becoming important for controlling signal flow via the assembly of multiple signaling components . The evolutionary history of PDZ domain-mediated interactions has never been explored at the molecular level . It is of great interest to u...	Rewiring of interactions is a powerful tool for the evolution of organism complexity . Rewiring among preexisting proteins provides a simple mechanism for the development of new signaling circuits by redirecting information flows without a gain or loss of genes . Particularly , interactions mediated by short linear mot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "genomics", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2012	Rewiring of PDZ Domain-Ligand Interaction Network Contributed to Eukaryotic Evolution
The process of speciation involves populations diverging over time until they are genetically and reproductively isolated . Hybridization between nascent species was long thought to directly oppose speciation . However , the amount of interspecific genetic exchange ( introgression ) mediated by hybridization remains la...	Even though hybridization is thought to be pervasive among animal species , the frequency of introgression , the transfer of genetic material between species , remains largely unknown . In this report we quantify the magnitude and genomic distribution of introgression among three species of Drosophila that encompass th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "markov", "models", "population", "genetics", "invertebrate", "genomics", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "mathematics", "experimental", "organism", "systems", "energy-producing", "organelles", "mitochondria"...	2017	Fine scale mapping of genomic introgressions within the Drosophila yakuba clade
Leishmania species of the subgenus Leishmania and especially L . donovani are responsible for a large proportion of visceral leishmaniasis cases . The debate on the mode of reproduction and population structure of Leishmania parasites remains opened . It has been suggested that Leishmania parasites could alternate diff...	Leishmaniases are a serious public health problem , especially in developing countries , caused by Leishmania parasites and transmitted by sandfly bites . More information is needed on the population biology of these pathogens for diagnostic and epidemiological inquiries and for drug and vaccine elaboration . For studi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "population", "genetics", "microbiology", "parasitology", "parastic", "protozoans", "leishmania", "population", "biology", "zoology", "epidemiology", "biology", "protozoology", "evolutionary", "biology", "genetics", "and", "genomic...	2011	Multifaceted Population Structure and Reproductive Strategy in Leishmania donovani Complex in One Sudanese Village
Schistosoma ( S . ) haematobium is a neglected tropical disease which may affect any part of the genital tract in women . Female genital schistosomiasis ( FGS ) may cause abnormal vaginal discharge , contact bleeding , genital tumours , ectopic pregnancies and increased susceptibility to HIV . Symptoms may mimic those ...	Female genital schistosomiasis commonly remains undiagnosed due to its unacknowledged clinical manifestations . Millions of women in endemic areas are infected , and many suffer from abnormal vaginal discharge , contact bleeding , genital tumours , ectopic pregnancies , and an increased susceptibility to HIV . Sandy pa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "diagnostic", "medicine", "women's", "health", "obstetrics", "and", "gynecology" ]	2014	The Colposcopic Atlas of Schistosomiasis in the Lower Female Genital Tract Based on Studies in Malawi, Zimbabwe, Madagascar and South Africa
Peripheral CD4+ T-cell levels are not fully restored in a significant proportion of HIV+ individuals displaying long-term viral suppression on c-ART . These immunological nonresponders ( INRs ) have a higher risk of developing AIDS and non-AIDS events and a lower life expectancy than the general population , but the un...	Combined antiretroviral therapy ( c-ART ) has dramatically decreased AIDS-related mortality and morbidity . Nevertheless increased morbidity is still present in HIV+ patients namely among those who experience poor immune CD4+ T-cell restoration under c-ART ( i . e . CD4 <500 cells/mm3 ) . The mechanisms associated with...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "immune", "activation", "immunology", "cell", "differentiation", "developmental", "biology", "signs", "and", "symptoms", "cyto...	2016	P2X7 Receptor Inhibition Improves CD34 T-Cell Differentiation in HIV-Infected Immunological Nonresponders on c-ART
One common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes . Here , we use genome wide RNA-seq data from a population sample of Drosophila yakuba to test this ‘gene dosage’ hypothesis . We observe li...	The enclosed work shows that whole gene duplications rarely affect gene expression , in contrast to widely held views that the adaptive value of duplicate genes is related to additive changes in gene expression due to gene copy number . We further explain how tandem duplications that create shuffled gene structures can...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "markov", "models", "gene", "regulation", "invertebrate", "genomics", "mutation", "mathematics", "gene", "types", "hidden", "markov", "models", "gene", "expression", "molecular", "evolution", "chimeric",...	2017	Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba
Activation-induced cytidine deaminase ( AID ) is specifically induced in germinal center B cells to carry out somatic hypermutation and class-switch recombination , two processes responsible for antibody diversification . Because of its mutagenic potential , AID expression and activity are tightly regulated to minimize...	Immune responses to pathogens rely heavily on the ability of B cells to generate a unique set of antibodies that can bind and eliminate the pathogen . Activation-induced cytidine deaminase ( AID ) is the enzyme specifically upregulated in activated B cells to diversify the antibody repertoire by introducing mutations w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Role for Host Activation-Induced Cytidine Deaminase in Innate Immune Defense against KSHV
The mediators of the DNA damage response ( DDR ) are highly phosphorylated by kinases that control cell proliferation , but little is known about the role of this regulation . Here we show that cell cycle phosphorylation of the prototypical DDR mediator Saccharomyces cerevisiae Rad9 depends on cyclin-dependent kinase (...	Human cells activate the DNA damage response ( DDR ) to repair DNA damage and to prevent cells with DNA damage from proliferating . Alterations to the DDR are strongly implicated in the development of cancer . Using the budding yeast model system , we have studied how the regulation of the key DDR component Rad9 is int...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cancer", "genetics", "protein", "interactions", "model", "organisms", "cell", "division", "dna", "chromatin", "protein", "kinase", "signaling", "cascade", "stress", "signaling", "cascade", "chromosome", "biology", "proteins", "biology", "biochemistry", "signal", "trans...	2013	Site-Specific Phosphorylation of the DNA Damage Response Mediator Rad9 by Cyclin-Dependent Kinases Regulates Activation of Checkpoint Kinase 1
Calmodulin kinase II ( CaMKII ) mediates critical signaling pathways responsible for divergent functions in the heart including calcium cycling , hypertrophy and apoptosis . Dysfunction in the CaMKII signaling pathway occurs in heart disease and is associated with increased susceptibility to life-threatening arrhythmia...	Calmodulin kinase II ( CaMKII ) is a multifunctional serine/threonine kinase that regulates diverse functions in heart . Recently , a novel pathway for CaMKII activation was discovered where oxidation of the kinase at specific methionine residues produces persistent activity . This alternative oxidation-dependent pathw...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "cardiovascular", "disorders/arrhythmias,", "electrophysiology,", "and", "pacing", "physiology/cell", "signaling", "physiology/integrative", "physiology", "cardiovascular", "disorders/myocardial", "infarction", "computational", "biology/systems", "biology" ]	2009	Oxidized Calmodulin Kinase II Regulates Conduction Following Myocardial Infarction: A Computational Analysis
Infection and inflammation of the middle ears that characterizes acute and chronic otitis media ( OM ) , is a major reason for doctor visits and antibiotic prescription , particularly among children . Nasopharyngeal pathogens that are commonly associated with OM in humans do not naturally colonize the middle ears of ro...	Bacterial infections of the middle ears ( otitis media ) , particularly among children , is a global problem , causing fever , pain , conductive hearing loss and possible complications due to persistence/recurrence . Current understanding is poor , and advances are slowed by limitations of experimental systems that , f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	A model of chronic, transmissible Otitis Media in mice
Deposition of additional plasma membrane and cargoes during cytokinesis in eukaryotic cells must be coordinated with actomyosin ring contraction , plasma membrane ingression and extracellular matrix remodelling . The process by which the secretory pathway promotes specific incorporation of key factors into the cytokine...	Eukaryotic cells require division of all their cellular components before finally giving rise to two independent cells in a process named cytokinesis . Eukaryotic cells must build a physical barrier of plasma membrane , which is coupled with the remodelling of the extracellular matrix between the dividing cells . Plasm...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chitin", "vesicles", "g1", "phase", "cell", "cycle", "and", "cell", "division", "cell", "processes", "membrane", "proteins", "fungi", "model", "organisms", "materials", "science", "experimental", "organism", "systems", "cytokinesis", "cellular", "structures", "and", ...	2018	Cell polarity protein Spa2 coordinates Chs2 incorporation at the division site in budding yeast
Plants evoke innate immunity against microbial challenges upon recognition of pathogen-associated molecular patterns ( PAMPs ) , such as fungal cell wall chitin . Nevertheless , pathogens may circumvent the host PAMP-triggered immunity . We previously reported that the ascomycete Magnaporthe oryzae , a famine-causing r...	Magnaporthe oryzae , Cochlioborus miyabeanus , and Rhizoctonia solani are the top three fungal pathogens that are responsible for devastating damage to the production of rice , a staple cereal for half of the world's population . These fungal pathogens infect host plants despite the plants' innate immunity , which is a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "agriculture", "biology" ]	2012	Surface α-1,3-Glucan Facilitates Fungal Stealth Infection by Interfering with Innate Immunity in Plants
In virus-infected cells , RIG-I-like receptor ( RLR ) recognizes cytoplasmic viral RNA and triggers innate immune responses including production of type I and III interferon ( IFN ) and the subsequent expression of IFN-inducible genes . Interferon-β promoter stimulator 1 ( IPS-1 , also known as MAVS , VISA and Cardif )...	Virus-infections , such as influenza and chronic hepatitis C , are prominent diseases and outbreaks of newly emerging viruses are serious problems for modern society . Higher animals , including humans , are genetically equipped with mechanisms , collectively known as innate immunity , to counteract viral infections . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/innate", "immunity" ]	2010	Virus-Infection or 5′ppp-RNA Activates Antiviral Signal through Redistribution of IPS-1 Mediated by MFN1
In Drosophila melanogaster , the germband forms directly on the egg surface and solely consists of embryonic tissue . In contrast , most insect embryos undergo a complicated set of tissue rearrangements to generate a condensed , multilayered germband . The ventral side of the germband is embryonic , while the dorsal si...	In many animals , certain groups of cells in the embryo do not directly contribute to the formation of adult structures . Instead , these so-called ‘extraembryonic tissues’ that support and facilitate development are discarded and degenerate prior to birth/hatching . Embryos of most insect species are thought to have t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "condensation", "condensed", "matter", "physics", "animals", "blastulas", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "...	2018	A revised understanding of Tribolium morphogenesis further reconciles short and long germ development
Systems biology offers promising approaches for identifying response-specific signatures to vaccination and assessing their predictive value . Here , we designed a modelling strategy aiming to predict the quality of late T-cell responses after vaccination from early transcriptome analysis of dendritic cells . Using sta...	Vaccines are designed to elicit effective immune responses against antigens . The various vector platforms used in vaccine development are diverse and complex , rendering the selection of promising vaccines vector challenging . We have designed a modeling strategy that predicts the propensity of vaccine vectors to elic...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "spleen", "immunology", "vaccines", "preventive", "medicine", "mathematics", "forecasting", "statistics", "(mathematics)", "genome", "analysis", "bioassays", "and", "ph...	2016	Early Transcriptome Signatures from Immunized Mouse Dendritic Cells Predict Late Vaccine-Induced T-Cell Responses
Endoplasmic reticulum-associated degradation ( ERAD ) is an important function for cellular homeostasis . The mechanism of how picornavirus infection interferes with ERAD remains unclear . In this study , we demonstrated that enterovirus 71 ( EV71 ) infection significantly inhibits cellular ERAD by targeting multiple k...	Understanding of viral-host interactions is important for learning about viral pathogenesis and providing potential anti-viral targets . The protein quality control system , which consists of ERAD and autophagic degradation , is necessary for cellular homeostasis . Our previous studies and others have demonstrated that...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "enzymes", "293t", "cells", "endoplasmic", "reticulum", "cell", "processes", "microbiology", "enzymology", "biological", "cultures", "hepaciviru...	2017	Enterovirus 71 protease 2Apro and 3Cpro differentially inhibit the cellular endoplasmic reticulum-associated degradation (ERAD) pathway via distinct mechanisms, and enterovirus 71 hijacks ERAD component p97 to promote its replication
Mutations in the Plasmodium falciparum ‘chloroquine resistance transporter’ ( PfCRT ) confer resistance to chloroquine ( CQ ) and related antimalarials by enabling the protein to transport these drugs away from their targets within the parasite’s digestive vacuole ( DV ) . However , CQ resistance-conferring isoforms of...	In acquiring resistance to one drug , many pathogens and cancer cells become hypersensitive to other drugs . This phenomenon could be exploited to combat existing drug resistance and to delay the emergence of resistance to new drugs . However , much remains to be understood about the mechanisms that underlie drug hyper...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "alkaloids", "medicine", "and", "health", "sciences", "chemical", "compounds", "drugs", "immunology", "microbiology", "vertebrates", "animals", "parasitic", "protozoans", "antimalarials", "xenopus", "germ", "cells", "animal", "models", "oocytes", "clinical", "medicine", ...	2016	Molecular Mechanisms for Drug Hypersensitivity Induced by the Malaria Parasite’s Chloroquine Resistance Transporter
Virus-Induced Chaperone-Enriched ( VICE ) domains form adjacent to nuclear viral replication compartments ( RC ) during the early stages of HSV-1 infection . Between 2 and 3 hours post infection at a MOI of 10 , host protein quality control machinery such as molecular chaperones ( e . g . Hsc70 ) , the 20S proteasome a...	Protein quality control is a protective cellular mechanism by which damaged proteins are refolded or degraded so that they cannot interfere with essential cellular processes . In the event that protein quality control machinery cannot refold or degrade damaged proteins , sequestration of misfolded protein is an alterna...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/nucleolus", "and", "nuclear", "bodies", "biochemistry/protein", "folding", "virology", "cell", "biology/nuclear", "structure", "and", "function" ]	2009	Virus-Induced Chaperone-Enriched (VICE) Domains Function as Nuclear Protein Quality Control Centers during HSV-1 Infection
Cryptococcus neoformans is an environmental fungal pathogen that requires atmospheric levels of oxygen for optimal growth . For the fungus to be able to establish an infection , it must adapt to the low oxygen concentrations in the host environment compared to its natural habitat . In order to investigate the oxygen se...	Cryptococcus neoformans is an obligate aerobic fungus that requires atmospheric levels of oxygen ( 21% ) for optimal growth . However , the fungus is able to cause life-threatening brain infections in humans , where the oxygen tension is significantly lower than 21% . To understand the pathobiology of Cryptococcus neof...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "biology/microbial", "physiology", "and", "metabolism", "immunology/cellular", "microbiology", "and", "pathogenesis", "genetics", "and", "genomics/gene", "expression", "infectious", "diseases/fungal", "infections", "genetics", "and", "genomics/gene", "function", "micr...	2008	Importance of Mitochondria in Survival of Cryptococcus neoformans Under Low Oxygen Conditions and Tolerance to Cobalt Chloride
A major analytical challenge in computational biology is the detection and description of clusters of specified site types , such as polymorphic or substituted sites within DNA or protein sequences . Progress has been stymied by a lack of suitable methods to detect clusters and to estimate the extent of clustering in d...	The invention and application of high-throughput technologies for DNA sequencing have resulted in an increasing abundance of biological sequence data . DNA or protein sequence data are naturally arranged as discrete linear sequences , and one of the fundamental challenges of analysis of sequence data is the description...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computational", "biology/population", "genetics", "computational", "biology/macromolecular", "structure", "analysis", "computer", "science/applications", "genetics", "and", "genomics/comparative", "genomics", "computational", "biology/sequence", "motif", "analysis", "evolutionary"...	2009	Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences
Mosquitoes are vectors of many serious pathogens in tropical and sub-tropical countries . Current control strategies almost entirely rely upon insecticides , which increasingly face the problems of high cost , increasing mosquito resistance and negative effects on non-target organisms . Alternative strategies include t...	Mosquitoes transmit diseases when they are actively searching for a source of blood . This so called probing behavior comprises the “searching” time , the beginning of the feeding process until the first sign of blood can be seen within the insect body . The manipulation of this behavior can have important consequences...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology/behavioral", "ecology" ]	2009	Human Probing Behavior of Aedes aegypti when Infected with a Life-Shortening Strain of Wolbachia
Quantification of cell-free DNA ( cfDNA ) in circulating blood derived from a transplanted organ is a powerful approach to monitoring post-transplant injury . Genome transplant dynamics ( GTD ) quantifies donor-derived cfDNA ( dd-cfDNA ) by taking advantage of single-nucleotide polymorphisms ( SNPs ) distributed across...	More than 180 , 000 people live with organ transplants in the US . Monitoring the health of the allograft is a critically important component of post-transplant therapy . Recently , we have demonstrated that cell-free DNA ( cfDNA ) enables diagnosis of post-transplant rejection . In this approach , genotyping of the re...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "organ", "transplantation", "cardiac", "transplantation", "biopsy", "cardiovascular", "anatomy", "variant", "genotypes", "genetic", "mapping", "surgical", "and", "invasive", "medical", "procedures", "molecular", "biology", "techniq...	2017	Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype
The debilitating skin disease Buruli ulcer ( BU ) is caused by infection with Mycobacterium ulcerans . While various hypotheses on potential reservoirs and vectors of M . ulcerans exist , the mode of transmission has remained unclear . Epidemiological studies have indicated that children below the age of four are less ...	Buruli ulcer is a debilitating skin disease caused by Mycobacterium ulcerans . Although the understanding of this enigmatic pathogen has improved after decades of research , the mode of transmission is yet to be fully elucidated . Recent epidemiological studies have shown an underrepresentation of Buruli ulcer cases in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	A Sero-epidemiological Approach to Explore Transmission of Mycobacterium ulcerans
Zika virus ( ZIKV ) infection in pregnancy can cause microcephaly and a wide spectrum of severe adverse outcomes , collectively called “Congenital Zika Syndrome” ( CZS ) . Parenting a child with disabilities can have adverse mental health impacts , but these associations have not been fully explored in the context of C...	The 2015 Zika epidemic in Brazil gained international attention with the birth of thousands of babies with severe adverse outcomes , collectively called “Congenital Zika Syndrome” ( CZS ) . Parenting a child with disabilities can be extremely stressful , and in other settings is linked to depression , anxiety and other...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "disabilities", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "social", "sciences", "viruses", "age", "groups", "rna", "viruses", "anxiety", "mood", "disorders", "families", "public", "a...	2019	The association of depression, anxiety, and stress with caring for a child with Congenital Zika Syndrome in Brazil; Results of a cross-sectional study
In the brain , the postsynaptic response of a neuron to time-varying inputs is determined by the interaction of presynaptic spike times with the short-term dynamics of each synapse . For a neuron driven by stochastic synapses , synaptic depression results in a quite different postsynaptic response to a large population...	The synapses that connect neurons in the brain are far from being simple relay points that pass a signal from one neuron to another . There is now much evidence that long term changes in the strength of such connections , which determines the amplitude of the received signal , underpin learning and memory in the brain ...	[ "Abstract", "Introduction", "Models", "and", "methods", "Results", "Discussion" ]	[ "resonance", "frequency", "action", "potentials", "medicine", "and", "health", "sciences", "vesicles", "nervous", "system", "membrane", "potential", "electrophysiology", "neuroscience", "cellular", "structures", "and", "organelles", "mood", "disorders", "crystallographic", ...	2017	Phase changes in neuronal postsynaptic spiking due to short term plasticity
How do high-level visual regions process the temporal aspects of our visual experience ? While the temporal sensitivity of early visual cortex has been studied with fMRI in humans , temporal processing in high-level visual cortex is largely unknown . By modeling neural responses with millisecond precision in separate s...	How does the brain encode the timing of our visual experience ? Using functional magnetic resonance imaging ( fMRI ) and a generative temporal model with millisecond resolution , we discovered that visual regions in the lateral and ventral processing streams fundamentally differ in their temporal processing of the visu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "auditory", "cortex", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "experimental", "design", "brain", "social", "sciences", "neuroscience", "learning", "and", "memory", "magnetic", "resonance", "im...	2019	Differential sustained and transient temporal processing across visual streams
Quorum sensing is the regulation of gene expression in response to changes in cell density . To measure their cell density , bacterial populations produce and detect diffusible molecules called autoinducers . Individual bacteria internally represent the external concentration of autoinducers via the level of monitor pr...	Bacteria regulate gene expression in response to changes in cell density in a process called quorum sensing . To synchronize their gene-expression programs , these bacteria need to glean as much information as possible about their cell density . Our study is the first to physically model the flow of information in a qu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Optimal Census by Quorum Sensing
The flavivirus NS5 harbors a methyltransferase ( MTase ) in its N-terminal ≈265 residues and an RNA-dependent RNA polymerase ( RdRP ) within the C-terminal part . One of the major interests and challenges in NS5 is to understand the interplay between RdRP and MTase as a unique natural fusion protein in viral genome rep...	Due to limited coding capacity , RNA viruses often generate proteins that contain more than one enzyme module to fulfill their rather complicated life cycle . Among those , the flavivirus nonstructural protein NS5 comprises an N-terminal methyltransferase ( MTase ) and a C-terminal RNA-dependent RNA polymerase ( RdRP )...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "proteins", "virology", "protein", "structure", "viral", "enzymes", "biology", "microbiology", "viral", "replication" ]	2013	Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5 Reveals a Conserved Methyltransferase-Polymerase Interface
Schistosomiasis is a chronic and debilitating disease caused by blood flukes ( digenetic trematodes ) of the genus Schistosoma . Schistosomes are sexually dimorphic and exhibit dramatic morphological changes during a complex lifecycle which requires subtle gene regulatory mechanisms to fulfil these complex biological p...	Schistosomiasis is a persistent but neglected parasitic disease , afflicting more than 200 million people worldwide . Complex gene regulatory mechanisms are equipped by its causative reagents , parasites of the genus Schistosoma . Dissecting these mechanisms thus will be beneficial for better control of the disease . D...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "schistosoma", "invertebrates", "helminths", "gene", "regulation", "messenger", "rna", "dna-binding", "proteins", "animals", "micrornas", "bioassays", "and", "physiological", "analysis", "research", "and", "analysis", "methods", "schistosoma", "japonicum", "proteins", "ge...	2016	Comprehensive Transcriptome Analysis of Sex-Biased Expressed Genes Reveals Discrete Biological and Physiological Features of Male and Female Schistosoma japonicum
DNA methylation is essential for plant and animal development . In plants , methylation occurs at CG , CHG , and CHH ( H = A , C or T ) sites via distinct pathways . Cotton is an allotetraploid consisting of two progenitor genomes . Each cotton fiber is a rapidly-elongating cell derived from the ovule epidermis , but t...	Cotton is the world’s largest source of renewable textile fiber and is an allotetraploid crop consisting of two progenitor genomes . In plants , de novo CHH ( H = A , T , or C ) methylation depends on RNA-directed DNA methylation ( RdDM ) and CHROMOMETHYLASE2 ( CMT2 ) -mediated pathways . The biological significance of...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton
Ectodermal organs such as teeth , hair follicles , and mammary glands begin their development as placodes . These are local epithelial thickenings that invaginate into mesenchymal space . There is currently little mechanistic understanding of the cellular processes driving the early morphogenesis of these organs and of...	Teeth , hair follicles , and skin ducts ( including mammary and sweat glands ) are initially formed in the embryo as slight thickenings of a flat epithelium that are called placodes . These then invaginate to form dimples or pits that make the characteristic structures found in the adult . While some invagination mecha...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "skin", "medicine", "and", "health", "sciences", "keratinocytes", "reproductive", "system", "integumentary", "system", "classical", "mechanics", "geometry", "aspect", "ratio", "epithelial", "cells", "mathematics", "damage", "mechanics", "basal", "cells", "digestive", "s...	2016	Invagination of Ectodermal Placodes Is Driven by Cell Intercalation-Mediated Contraction of the Suprabasal Tissue Canopy
Flaviviruses comprise major emerging pathogens such as dengue virus ( DENV ) or Zika virus ( ZIKV ) . The flavivirus RNA genome is replicated by the RNA-dependent-RNA polymerase ( RdRp ) domain of non-structural protein 5 ( NS5 ) . This essential enzymatic activity renders the RdRp attractive for antiviral therapy . NS...	Dengue virus ( DENV ) is the world’s most prevalent mosquito-borne viral disease and nearly 40% of the world’s population is at risk of infection . Currently , no specific drugs are available to treat dengue or other flaviviral diseases . DENV NS5 is a large protein of 900 amino acids composed of two domains with key e...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "luciferase", "nucleic", "acid", "synthesis", "medicine", "and", "health", "sciences", "crystal", "structure", "enzymes", "condensed", "matter", "physics", "dna-binding", "proteins", "enzymology", "microbiology", "limbs", "(anatomy)", "thumbs", "ribozymes", "polymerases",...	2016	Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling
RsaE is the only known trans-acting small regulatory RNA ( sRNA ) besides the ubiquitous 6S RNA that is conserved between the human pathogen Staphylococcus aureus and the soil-dwelling Firmicute Bacillus subtilis . Although a number of RsaE targets are known in S . aureus , neither the environmental signals that lead t...	Bacteria have evolved various strategies to continually monitor the redox state of the internal and external environments to prevent cell damage and/or to protect them from host defense mechanisms . These signals modify the expression of genes , allowing bacteria to adapt to altered redox environments and to maintain h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Nitric Oxide Regulated Small RNA Controls Expression of Genes Involved in Redox Homeostasis in Bacillus subtilis
Genetic variants in genome-wide association studies ( GWAS ) are tested for disease association mostly using simple regression , one variant at a time . Standard approaches to improve power in detecting disease-associated SNPs use multiple regression with Bayesian variable selection in which a sparsity-enforcing prior ...	In recent years , genome wide association studies ( GWAS ) have become the primary approach for identifying genetic variants associated with the origination of complex diseases . In case-control GWAS , the genotypes of roughly equal number of diseased ( “cases” ) and healthy ( “controls” ) people are compared to determ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "statistics", "metaanalysis", "coronary", "heart", "disease", "mathematics", "probability", "distribution", "genome", "analysis", "molecular", "genetics", "research", "and", "analysis", "met...	2018	Bayesian multiple logistic regression for case-control GWAS
Host-targeting type IV secretion systems ( T4SS ) evolved from conjugative T4SS machineries that mediate interbacterial plasmid transfer . However , the origins of effectors secreted by these virulence devices have remained largely elusive . Previous work showed that some effectors exhibit homology to toxins of bacteri...	Many bacterial pathogens use secretion systems to translocate effector proteins into host cells where they manipulate cell functions in favor of the pathogen . It is well-known that these secretion systems evolved from ancestors with functions in genuine bacterial contexts , but the origins of their secreted effectors ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "horizontal", "gene", "transfer", "organismal", "evolution", "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "pathogens", "plasmids", "microbiology", "gene", "transfer", "toxicolog...	2017	A bacterial toxin-antitoxin module is the origin of inter-bacterial and inter-kingdom effectors of Bartonella
Most studies in the life sciences and other disciplines involve generating and analyzing numerical data of some type as the foundation for scientific findings . Working with numerical data involves multiple challenges . These include reproducible data acquisition , appropriate data storage , computationally correct dat...	Data expressed as numbers are ubiquitous in research in the life sciences and other fields . The typical scientific workflow using such numerical data consists of analyzing the raw data to obtain numerical results , followed by interpreting the results and presenting derived findings . In this article , we present some...	[ "Abstract", "Introduction", "Keep", "your", "data", "correct", "Correctly", "interpret", "your", "data", "Present", "your", "data", "in", "a", "useful", "way" ]	[ "data", "acquisition", "education", "statistics", "enzymology", "mathematics", "information", "technology", "enzyme", "kinetics", "data", "processing", "research", "and", "analysis", "methods", "computer", "and", "information", "sciences", "mathematical", "and", "statisti...	2018	Ten quick tips for getting the most scientific value out of numerical data

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