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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
Experimental autoimmune orchitis ( EAO ) , the principal model of non-infectious testicular inflammatory disease , can be induced in susceptible mouse strains by immunization with autologous testicular homogenate and appropriate adjuvants . As previously established , the genome of DBA/2J mice encodes genes that are ca...	Although the etiology of autoimmunity is not well known , a variety of studies have demonstrated that genetic predisposition is a major contributor to disease susceptibility and resistance . The major histocompatibility complex ( MHC ) is the primary genetic determinant of autoimmune disease susceptibility with multipl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "immunology", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Identification of Orch3, a Locus Controlling Dominant Resistance to Autoimmune Orchitis, as Kinesin Family Member 1C
Malaria parasites must undergo sexual and sporogonic development in mosquitoes before they can infect their vertebrate hosts . We report the discovery and characterization of MISFIT , the first protein with paternal effect on the development of the rodent malaria parasite Plasmodium berghei in Anopheles mosquitoes . MI...	The unicellular protozoan parasites that cause malaria must undergo sexual development and subsequent proliferation in mosquitoes before they can infect humans and cause malaria . We characterized the first protein with paternal effect on the development of malaria parasites in the mosquito . This protein , which we na...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "replication", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/gene", "expression", "cell", "biology/cell", "growth", "and", "division", "cell", "biology/developm...	2009	Paternal Effect of the Nuclear Formin-like Protein MISFIT on Plasmodium Development in the Mosquito Vector
Highly active antiretroviral therapy ( HAART ) can suppress HIV-1 replication and normalize the chronic immune activation associated with infection , but restoration of naïve CD4+ T cell populations is slow and usually incomplete for reasons that have yet to be determined . We tested the hypothesis that damage to the l...	The hallmark of HIV-1 infection is depletion of CD4 T cells , whose loss leads to the opportunistic infections and cancers characteristic of AIDS . Highly active antiretroviral therapy ( HAART ) can control HIV-1 replication , but reconstitution particularly of naïve T cells is often incomplete and slow . We show here ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "microbiology" ]	2012	Lymphoid Tissue Damage in HIV-1 Infection Depletes Naïve T Cells and Limits T Cell Reconstitution after Antiretroviral Therapy
Herpes simplex virus ( HSV ) enters cells by means of four essential glycoproteins - gD , gH/gL , gB , activated in a cascade fashion by gD binding to one of its receptors , nectin1 and HVEM . We report that the engineering in gH of a heterologous ligand – a single-chain antibody ( scFv ) to the cancer-specific HER2 re...	To enter cells , all herpesviruses use the core fusion glycoproteins gH/gL and gB , in addition to species-specific glycoproteins responsible for specific tropism , etc . In HSV , the additional glycoprotein is the essential gD . We engineered in gH a heterologous ligand to the HER2 cancer receptor . The recombinant vi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Engineering of a Novel Ligand in gH Confers to HSV an Expanded Tropism Independent of gD Activation by Its Receptors
Lafora disease is the most common teenage-onset neurodegenerative disease , the main teenage-onset form of progressive myoclonus epilepsy ( PME ) , and one of the severest epilepsies . Pathologically , a starch-like compound , polyglucosan , accumulates in neuronal cell bodies and overtakes neuronal small processes , m...	Lafora disease ( LD ) is a fatal epilepsy that afflicts previously normal teenagers . It is caused by mutations in the EPM2A or EPM2B genes encoding the laforin carbohydrate-binding phosphatase and the malin E3 ubiquitin ligase . LD is the most common neurodegenerative epilepsy of adolescents . Affected children suffer...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "neurodegenerative", "diseases", "neuroscience", "pediatrics", "animal", "models", "histology", "model", "organisms", "developmental", "and", "pediatric", "neurology", "glycogen", "storage", "diseases", "epilepsy", "pediatrics", "and", "child", "health", "biol...	2011	PTG Depletion Removes Lafora Bodies and Rescues the Fatal Epilepsy of Lafora Disease
Plant male gametogenesis involves complex and dynamic changes in gene expression . At present , little is known about the transcription factors involved in this process and how their activities are regulated . Here , we show that a pollen-specific transcription factor , WRKY34 , and its close homolog , WRKY2 , are requ...	Pollen development , or male gametogenesis , is a process by which a haploid uninucleate microspore undergoes cell division and specification to form a mature pollen grain containing two sperm cells . The highly defined cell linage makes pollen development an ideal model to understand the regulation of plant cellular d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "signal", "transduction", "developmental", "biology", "plant", "science", "model", "organisms", "plant", "and", "algal", "models", "cell", "biology", "arabidopsis", "thaliana", "plant", "growth", "and", "development", "biology", "and", "life", "sciences", "brassica", ...	2014	Phosphorylation of a WRKY Transcription Factor by MAPKs Is Required for Pollen Development and Function in Arabidopsis
Understanding how neurons cooperate to integrate sensory inputs and guide behavior is a fundamental problem in neuroscience . A large body of methods have been developed to study neuronal firing at the single cell and population levels , generally seeking interpretability as well as predictivity . However , these metho...	The thalamus is a brain structure that relays sensory information to the cortex and mediates cortico-cortical interaction . Unraveling the dialogue between the thalamus and the cortex is thus a central question in neuroscience , with direct implications on our understanding of how the brain operates at the macro scale ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "machine", "learning", "algorithms", "medicine", "and", "health", "sciences", "action", "potentials", "neural", "networks", "engineering", "and", "technology", "sleep", "applied", "mathematics", "membrane", "potential", "electrophysiology", "neuroscience", "decision", "tr...	2018	Brain-state invariant thalamo-cortical coordination revealed by non-linear encoders
Antibody-dependent enhancement of viral infection is a well-described phenomenon that is based on the cellular uptake of infectious virus-antibody complexes following their interaction with Fcγ receptors expressed on myeloid cells . Here we describe a novel mechanism of antibody-mediated enhancement of infection by a f...	Antibodies are an important component of antiviral host responses and their binding to the surface of virus particles usually leads to neutralization of viral infectivity . In some instances , however , antibodies at sub-neutralizing concentrations can enhance infection of certain cells , because they facilitate the up...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "cell", "physiology", "dengue", "virus", "dimers", "(chemical", "physics)", "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "physiology", "vesicles", "pathology", "and", "laboratory", "medicine", "hela", "cells", "...	2017	A novel mechanism of antibody-mediated enhancement of flavivirus infection
This study aims to analyze the clinical characteristics and treatment outcomes of 590 patients with brucellosis in Xinjiang , China . The clinical characteristics , laboratory findings , complications and prognosis of 590 patients infected with brucellosis were retrospectively analyzed . These patients had a mean age o...	Brucellosis is a highly contagious zoonosis caused by bacteria of the genus Brucella and affecting mammals . Human Brucellosis is caused by ingestion of unpasteurized or undercooked food product from infected animals , or close contact with them . The infection with same bacteria even with same type can lead to manifes...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "brucellosis", "surgical", "and", "invasive", "medical", "procedures", "bacterial", "diseases", "signs", "and", "symptoms", "pharmaceutics", ...	2017	The clinical features of 590 patients with brucellosis in Xinjiang, China with the emphasis on the treatment of complications
Type 3 secretion systems ( T3SSs ) are essential components of two complex bacterial machineries: the flagellum , which drives cell motility , and the non-flagellar T3SS ( NF-T3SS ) , which delivers effectors into eukaryotic cells . Yet the origin , specialization , and diversification of these machineries remained unc...	Most motile bacteria use a flagellum to move . The extracellular components of flagella are secreted by their own Type 3 Secretion System ( T3SS ) . The non-flagellar T3SS ( NF-T3SS ) , also named injectisome , includes many proteins that are homologous to flagellar components . NF-T3SSs are employed by many plant and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "ecology", "microbiology", "host-pathogen", "interaction", "coevolution", "emerging", "infectious", "diseases", "molecular", "genetics", "bacterial", "pathogens", "emergence", "forms", "of", "evolution", "comparative", "genomics", "biology", "adaptation", "g...	2012	The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems
We have examined the remains of a Pilgrim burial from St Mary Magdalen , Winchester . The individual was a young adult male , aged around 18–25 years at the time of death . Radiocarbon dating showed the remains dated to the late 11th–early 12th centuries , a time when pilgrimages were at their height in Europe . Severa...	This multidisciplinary research article , involving biomolecular analysis , osteology , strontium and oxygen isotopic analyses and archaeology , examines the remains of a Pilgrim burial excavated from the medieval leprosy hospital of St Mary Magdalen , Winchester , UK . Radiocarbon dating showed the remains dated to th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "chemical", "characterization", "tropical", "diseases", "geographical", "locations", "social", "sciences", "bacterial", "diseases", "archaeology", "strontium", "osteology", "neglected", "tropical", "diseases", "molecular", "biology",...	2017	Investigation of a Medieval Pilgrim Burial Excavated from the Leprosarium of St Mary Magdalen Winchester, UK
The ability of clonal bacterial populations to generate genomic and phenotypic heterogeneity is thought to be of great importance for many commensal and pathogenic bacteria . One common mechanism contributing to diversity formation relies on the inversion of small genomic DNA segments in a process commonly referred to ...	Bacteria in many ecological niches experience a common challenge in the form of unpredictable environmental fluctuations . Rapid adaptation to challenging conditions is important for bacterial survival and successful proliferation . Altering gene expression through DNA inversion is a common mechanism adopted by many ba...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "gut", "bacteria", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "light", "microscopy", "pili", "and", "fimbriae", "organisms", "microscopy", "genome", "analysis", "bacterial", "geneti...	2018	Genome-wide detection of conservative site-specific recombination in bacteria
Spermatogenesis is a dynamic process that is regulated by adhesive interactions between germ and Sertoli cells . Germ cells express the Junctional Adhesion Molecule-C ( JAM-C , encoded by Jam3 ) , which localizes to germ/Sertoli cell contacts . JAM-C is involved in germ cell polarity and acrosome formation . Using a pr...	Spermatogenesis defects are a common cause of male sterility . Spermatogenesis occurs in the seminiferous tubules of the testes and involves adhesive interactions between developing germ cells and Sertoli cells . Knock-out mouse models identified several adhesion molecules that are critically involved in spermatogenesi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "meiosis", "medicine", "and", "health", "sciences", "reproductive", "system", "spermatocytes", "nuclear", "staining", "cell", "cycle", "and", "cell", "division", "cell", "processes", "reproductive", "physiology", "germ", "cells", "cellular", "structures", "and", "orga...	2017	Genetic, structural, and chemical insights into the dual function of GRASP55 in germ cell Golgi remodeling and JAM-C polarized localization during spermatogenesis
Sexual reproduction is critical for successful evolution of eukaryotic organisms in adaptation to changing environments . In the opportunistic human fungal pathogens , the Cryptococcus pathogenic species complex , C . neoformans primarily undergoes bisexual reproduction , while C . deneoformans undergoes both unisexual...	Sexuality is ubiquitous in eukaryotic systems , but it is present in diverse forms , ranging from distinct sexual individuals to parthenogenic organisms in both animals and plants . Consequently , different organisms have evolved different reproduction strategies in which cell-cell fusion and nuclear fusion ( karyogamy...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "membrane", "proteins", "fungi", "membrane", "fusion", "model", "organisms", "experiment...	2017	PRM1 and KAR5 function in cell-cell fusion and karyogamy to drive distinct bisexual and unisexual cycles in the Cryptococcus pathogenic species complex
Central corneal thickness ( CCT ) , one of the most highly heritable human traits ( h2 typically>0 . 9 ) , is important for the diagnosis of glaucoma and a potential risk factor for glaucoma susceptibility . We conducted genome-wide association studies in five cohorts from Australia and the United Kingdom ( total N = 5...	Central corneal thickness ( CCT ) is an important eye measurement . It has been considered as a prognosticator for the development of glaucoma , with a thin cornea potentially increasing the risk of developing a subtype known as open-angle glaucoma . CCT is highly heritable , yet its genetic determinants are poorly cha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ophthalmology", "genetics", "and", "genomics" ]	2010	Common Genetic Variants near the Brittle Cornea Syndrome Locus ZNF469 Influence the Blinding Disease Risk Factor Central Corneal Thickness
This study employed various monitoring methods to assess the impact of repeated rounds of mass drug administration ( MDA ) on bancroftian filariasis in Papua New Guinea , which has the largest filariasis problem in the Pacific region . Residents of rural villages near Madang were studied prior to and one year after eac...	Lymphatic filariasis ( LF ) is a deforming and disabling disease that is caused by parasitic worms that are transmitted by mosquitoes . While a number of countries have initiated LF elimination programs based on mass drug administration ( MDA ) , relatively little good information is available on the impact of MDA on f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "infectious", "diseases/neglected", "tropical", "diseases" ]	2008	The Impact of Repeated Rounds of Mass Drug Administration with Diethylcarbamazine Plus Albendazole on Bancroftian Filariasis in Papua New Guinea
There is continuing interest in understanding factors that facilitate the evolution and stability of cooperation within and between species . Such interactions will often involve plasticity in investment behavior , in response to the interacting partner's investments . Our aim here is to investigate the evolution and s...	Mutualistic interactions between species are often best understood as gradually adjustable reciprocal investments made continuously or iteratively between participants . Prime examples are the mycorrhizal and rhizobial mutualisms so strongly affecting the productivity of plants . When such interactions are described by...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "science", "computer", "modeling", "theoretical", "biology", "ecology", "biology", "computational", "biology", "evolutionary", "biology", "numerical", "analysis" ]	2012	Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles
The differential modulation of agonist and antagonist binding to opioid receptors ( ORs ) by sodium ( Na+ ) has been known for decades . To shed light on the molecular determinants , thermodynamics , and kinetics of Na+ translocation through the μ-OR ( MOR ) , we used a multi-ensemble Markov model framework combining e...	Notwithstanding years of research supporting the notion that μ-opioid receptor ( MOR ) function can be modulated by sodium ions ( Na+ ) , a complete understanding of Na+ translocation through the receptor and its effect on ligand binding at MOR requires additional information . Here , we use computer simulations to elu...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods" ]	[ "crystal", "structure", "molecular", "dynamics", "markov", "models", "condensed", "matter", "physics", "sodium", "simulation", "and", "modeling", "mathematics", "crystallography", "thermodynamics", "g", "protein", "coupled", "receptors", "research", "and", "analysis", "...	2019	Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis
Correlations in local neocortical spiking activity can provide insight into the underlying organization of cortical microcircuitry . However , identifying structure in patterned multi-neuronal spiking remains a daunting task due to the high dimensionality of the activity . Using two-photon imaging , we monitored sponta...	Information in the brain is represented and processed by populations of interconnected neurons . However , there is a lack of a clear understanding of the structure and organization of circuit wiring , particularly at the mesoscale which spans multiple columns and layers . In this study , we sought to evaluate whether ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "and", "information", "sciences", "computational", "techniques", "network", "analysis", "biology", "and", "life", "sciences", "graph", "theory", "neuroscience", "research", "and", "analysis", "methods" ]	2014	Analysis of Graph Invariants in Functional Neocortical Circuitry Reveals Generalized Features Common to Three Areas of Sensory Cortex
Although livestock vaccination is effective in preventing Rift Valley fever ( RVF ) epidemics , there are concerns about safety and effectiveness of the only commercially available RVF Smithburn vaccine . We conducted a randomized controlled field trial to evaluate the immunogenicity and safety of the new RVF Clone 13 ...	Although livestock vaccination is effective in preventing Rift Valley fever ( RVF ) outbreaks , there are concerns about safety and effectiveness of the only commercially available vaccine for the disease . Here , we conducted a field trial in Kenya to evaluate the safety and ability to induce protection for a new RVF ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Randomized Controlled Field Trial to Assess the Immunogenicity and Safety of Rift Valley Fever Clone 13 Vaccine in Livestock
Osteoarthritis ( OA ) is a degenerative condition caused by dysregulation of multiple molecular signalling pathways . Such dysregulation results in damage to cartilage , a smooth and protective tissue that enables low friction articulation of synovial joints . Matrix metalloproteinases ( MMPs ) , especially MMP-13 , ar...	Osteoarthritis ( OA ) is a debilitating disease that is a consequence of cartilage degeneration , often for a variety of reasons . Age is typically the driving force behind OA , and one reason is that biological pathways change as we get older and can become damaging . Transforming growth factor beta ( TGFβ ) is one su...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "rheumatology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chondrocytes", "immunology", "simulation", "and", "modeling", "signs", "and", "symptoms", "connective", "tissue", "cells", "cartilage", "research", "and", "analysis",...	2019	Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli
Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation . The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain ( NBD ) modulate substrate recognition at the Substrate Bin...	Allostery , or the capability of proteins to respond to ligand binding events with a variation in structure or dynamics at a distant site , is a common feature for biomolecular function and regulation in a large number of proteins . Intra-protein connections and inter-residue coordinations underlie allosteric mechanism...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "biochemistry", "chemistry", "biology", "computational", "biology", "chemical", "biology", "biophysics" ]	2012	Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations
Persistent hepatitis B virus ( HBV ) infection relies on the establishment and maintenance of covalently closed circular ( ccc ) DNA , a 3 . 2 kb episome that serves as a viral transcription template , in the nucleus of an infected hepatocyte . Although evidence suggests that cccDNA is the repair product of nucleocapsi...	CCC DNA is the most refractory HBV replication intermediate under long-term antiviral therapies and is responsible for the viral rebound after treatment cessation . Therefore , understanding the biosynthesis and maintenance of cccDNA minichromosome is crucial for the development of novel antiviral therapeutics to cure ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "molecular", "probe", "techniques", "gene", "regulation", "dna-binding", "proteins", "polymerases", "dna", "replication", "hirt", "extraction", "dna", "molecular", "biology", "techniques", "gel", "electrophoresis", "extraction", "techniques", "research", "and", "analysis"...	2019	DNA Polymerase alpha is essential for intracellular amplification of hepatitis B virus covalently closed circular DNA
Eimeria spp . are a highly successful group of intracellular protozoan parasites that develop within intestinal epithelial cells of poultry , causing coccidiosis . As a result of resistance against anticoccidial drugs and the expense of manufacturing live vaccines , it is necessary to understand the relationship betwee...	Eimeria spp . are highly successful protozoan parasites of the intestine of birds and one of the most important diseases in modern poultry farming . The economic impact is significant causing billion dollar losses to the industry and as a result there is pressing need for new therapeutic approaches . Anticoccidial drug...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "protein", "interactions", "immunology", "microbiology", "host-pathogen", "interaction", "chemical", "biology", "parasitology", "parastic", "protozoans", "protein", "structure", "veterinary", "science", "veterinary", "medicine", "veterinary", "diseases", "veterinary", "parasi...	2011	The Role of Sialyl Glycan Recognition in Host Tissue Tropism of the Avian Parasite Eimeria tenella
During cell division , the mitotic spindle segregates replicated chromosomes to opposite poles of the cell , while the position of the spindle determines the plane of cleavage . Spindle positioning and chromosome segregation depend on pulling forces on microtubules extending from the centrosomes to the cell cortex . Cr...	Protein kinases control biological processes by phosphorylating specific amino acids of substrate proteins . It remains a major challenge to identify which phosphorylation events are critical in vivo and how phosphorylation affects protein function . Recent developments in CRISPR/Cas9-based genetic engineering make it ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "invertebrates", "rna", "interference", "chemical", "compounds", "caenorhabditis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animals", "organic", "compounds", "biochemical", "analysis", "animal", "models", "developmental", "biolo...	2016	Multisite Phosphorylation of NuMA-Related LIN-5 Controls Mitotic Spindle Positioning in C. elegans
Telomeres are nucleoprotein structures located at the linear ends of eukaryotic chromosomes . Telomere integrity is required for cell proliferation and survival . Although the vast majority of eukaryotic species use telomerase as a primary means for telomere maintenance , a few species can use recombination or retrotra...	Telomeres are the specialized structures at the ends of eukaryotic linear chromosomes . The simple guanine-rich DNA repeats at telomeres and their associated proteins are important for chromosome stability . Most eukaryotic species have evolved an enzyme named telomerase to replicate their telomeric DNA . Telomerase us...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/recombination", "molecular", "biology/chromosome", "structure" ]	2009	Telomere Recombination Accelerates Cellular Aging in Saccharomyces cerevisiae
Ebola virus disease afflicts both human and animal populations and is caused by four ebolaviruses . These different ebolaviruses may have distinct reservoir hosts and ecological contexts that determine how , where , and when different ebolavirus spillover events occur . Understanding these virus-specific relationships ...	Multiple Ebola virus disease outbreaks have occurred over the past 40 years , yet we still do not know the geographical distributions , definitive host species , and suitable habitats for animal-to-human transmission of different ebolaviruses . Each Ebola virus disease outbreak has started with at least one transmissio...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "animal", "types", "ecology", "and", "environmental", "sciences", "ecological", "niches", "microbiology", "vertebrates", "animals", "mammals", "primates", "habitats", "theoretical", "ecology", "zoology", "fruit", "bats", "microbial", "ecology", "wildlife", "ecology", "g...	2016	Ecological Contexts of Index Cases and Spillover Events of Different Ebolaviruses
In internal membrane-containing viruses , a lipid vesicle enclosed by the icosahedral capsid protects the genome . It has been postulated that this internal membrane is the genome delivery device of the virus . Viruses built with this architectural principle infect hosts in all three domains of cellular life . Here , u...	Viral survival and propagation depend on the ability of the viruses to transfer their genetic material to a host cell . Viral genome delivery has been described for viruses that directly enclose their genome in a capsid or nucleocapsid , but not for internal membrane-containing viruses in which the genome is protected ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Mechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery
Vaccination with Mycobacterium bovis bacille Calmette-Guérin ( BCG ) is widely used to reduce the risk of childhood tuberculosis and has been reported to have efficacy against two other mycobacterial diseases , leprosy and Buruli ulcer caused by M . ulcerans ( Mu ) . Studies in experimental models have also shown some ...	Vaccination with Mycobacterium bovis bacille Calmette-Guérin ( BCG ) is used to reduce the risk of childhood tuberculosis and is reported to have efficacy against two other diseases also caused by mycobacteria , leprosy and Buruli ulcer caused by M . ulcerans . We hypothesized that there may be differences in the effec...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "microbiology/immunity", "to", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/skin", "infections", "infectious", "diseases/bacterial", "infections", "immunology/immunity", "to", "infections", "public", "health", "and", "epidemi...	2011	BCG-Mediated Protection against Mycobacterium ulcerans Infection in the Mouse
Aspergillus fumigatus is a mold that causes severe pulmonary infections . Our knowledge of how A . fumigatus growth is controlled in the respiratory tract is developing , but still limited . Alveolar macrophages , lung resident macrophages , and airway epithelial cells constitute the first lines of defense against inha...	Aspergillus spp . are ubiquitous in the environment , and even though individuals are regularly exposed to fungal spores clinical invasive disease is a rare manifestation . In contrast , individuals with weakened immune systems develop severe disease , such as invasive pulmonary aspergillosis ( IPA ) . IPA is associate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	IL-1α Signaling Is Critical for Leukocyte Recruitment after Pulmonary Aspergillus fumigatus Challenge
Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes , but not their functional organization into biological pathways and processes . Conversely , genetic interaction ( GI ) screens can provide insights into the biological role ( s ) of ...	Genome-wide genetic interaction ( GI ) screens have been performed in yeast , but no analogous large-scale studies have yet been reported for bacteria . Here , we have used E . coli synthetic genetic array ( eSGA ) technology developed by our group to quantitatively map GIs to reveal epistatic dependencies and function...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "functional", "genomics", "protein", "interactions", "macromolecular", "assemblies", "microbiology", "gene", "function", "escherichia", "coli", "prokaryotic", "models", "model", "organisms", "medical", "microbiology", "comparative", "genomics", "biology", "p...	2014	Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli
The mammalian immune system has the ability to discriminate between pathogens and innocuous microbes by detecting conserved molecular patterns . In addition to conserved microbial patterns , the mammalian immune system may recognize distinct pathogen-induced processes through a mechanism which is poorly understood . Pr...	The type III secretion system ( T3SS ) is a macromolecular protein export pathway found in gram-negative bacteria . It delivers bacterial toxins into eukaryotic cells to promote pathogenic infection . T3SSs and the bacterial toxins delivered are critical arsenals for many bacterial pathogens of clinical significance , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "infectious", "disease", "immunology", "white", "blood", "cells", "immune", "cells", "cell", "biology", "animal", "cells", "clinical", "immunology", "medical", "microbiology", "yersinia", "microbial", "pathogens", "biology", "and", "life", "sciences"...	2014	The GAP Activity of Type III Effector YopE Triggers Killing of Yersinia in Macrophages
Standard human landing catches ( sHLCs ) have historically been a key component of Onchocerca volvulus transmission monitoring , but expose health-workers to potentially hazardous vector bites . Novel human-bait-free trapping methods have been developed , but do not always work where they are needed and may not generat...	Standard human landing catches ( sHLCs ) have historically been used to obtain key Onchocerca volvulus transmission data that has helped with the design and monitoring of the WHO´s onchocerciasis control programmes . To avoid the health risks associated with sHLCs , alternative human-bait-free blackfly trapping methods...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "onchocerca", "volvulus", "chemical", "compounds", "helminths", "tropical", "diseases", "black", "flies", "vector-borne", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "onchocerca", "...	2019	Blackflies in the ointment: O. volvulus vector biting can be significantly reduced by the skin-application of mineral oil during human landing catches
Elucidating the mechanism of action of trypanocidal compounds is an important step in the development of more efficient drugs against Trypanosoma brucei . In a screening approach using an RNAi library in T . brucei bloodstream forms , we identified a member of the mitochondrial carrier family , TbMCP14 , as a prime can...	Human and animal trypanosomiases caused by Trypanosoma brucei parasites represent major burdens to human welfare and agricultural development in rural sub-Saharan Africa . Although the numbers of infected humans have decreased continuously during the last decades , emerging resistance and adverse side effects against c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	An Atypical Mitochondrial Carrier That Mediates Drug Action in Trypanosoma brucei
It is a long-held belief in evolutionary biology that the rate of molecular evolution for a given DNA sequence is inversely related to the level of functional constraint . This belief holds true for the protein-coding homeotic ( Hox ) genes originally discovered in Drosophila melanogaster . Expression of the Hox genes ...	The fertilized animal embryo is a mass of uniform cells that becomes a complex , segmented , and highly organized structure of differentiated cells through the process of development . This vital process is controlled by networks of developmental genes interacting with each other on the molecular level . Because these ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "molecular", "biology/molecular", "evolution", "developmental", "biology/developmental", "evolution", "evolutionary", "biology/pattern", "formation", "...	2009	Functional Evolution of cis-Regulatory Modules at a Homeotic Gene in Drosophila
Acinetobacter baumannii is a common pathogen whose recent resistance to drugs has emerged as a major health problem . Ethanol has been found to increase the virulence of A . baumannii in Dictyostelium discoideum and Caenorhabditis elegans models of infection . To better understand the causes of this effect , we examine...	Acinetobacter baumannii has recently emerged as a frequent opportunistic pathogen . In the presence of ethanol A . baumannii increases its pathogenicity towards Dictyostelium discoideum and Caenorhabditis elegans , and community-acquired infections of A . baumannii are associated with alcoholism . Ethanol negatively af...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis", "genetics", "and", "genomics" ]	2010	Molecular Mechanisms of Ethanol-Induced Pathogenesis Revealed by RNA-Sequencing
Bacteria prudently regulate their metabolic phenotypes by sensing the availability of specific nutrients , expressing the required genes for their metabolism , and repressing them after specific metabolites are depleted . It is unclear , however , how genetic networks maintain and transmit phenotypic states between gen...	Bacterial adaptation to new environments typically involves reorganization of gene expression that temporarily decreases growth rates . By exposing cells to fluctuating conditions using an innovative microfluidic device , we discover that E . coli cells can remember past environments , which accelerates their physiolog...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "systems", "biology", "bacterial", "physiology", "microbial", "metabolism", "microbial", "physiology", "gene", "regulatory", "networks", "biology", "and", "life", "sciences", "microbiology", "computational", "biology" ]	2014	Memory and Fitness Optimization of Bacteria under Fluctuating Environments
The complex life cycle of the genus Schistosoma drives the parasites to employ subtle developmentally dependent gene regulatory machineries . Small non-coding RNAs ( sncRNAs ) are essential gene regulatory factors that , through their impact on mRNA and genome stability , control stage-specific gene expression . Abunda...	Schistosomiasis , a chronic disease caused by agents of the genus Schistosoma , still afflicts more than 230 million people worldwide . The genomes of the three major pathogenic blood flukes , Schistosoma japonicum , Schistosoma mansoni , and Schistosoma haematobium , have been decoded as valuable entities for a system...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "medicine", "infectious", "diseases", "schistosomiasis", "neglected", "tropical", "diseases", "parasitic", "diseases" ]	2012	Identification and Characterization of Argonaute Protein, Ago2 and Its Associated Small RNAs in Schistosoma japonicum
In response to iron deficiency , the budding yeast Saccharomyces cerevisiae undergoes a metabolic remodeling in order to optimize iron utilization . The tandem zinc finger ( TZF ) -containing protein Cth2 plays a critical role in this adaptation by binding and promoting the degradation of multiple mRNAs that contain AU...	Iron is essential for eukaryotes because it is required for many fundamental processes such as DNA replication , protein translation or respiration , but it is very insoluble and can , therefore , easily go scarce . For this reason , eukaryotic cells have developed adaptive responses to iron deficiency . Under iron lim...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "messenger", "rna", "rna", "extraction", "polyribosomes", "plasmid", "construction", "fungi", "nutrition", "dna", "construction", "molecular", "biology", "techniques", "cellular", "structures", "and", "organelles", "extraction", ...	2018	Yeast Cth2 protein represses the translation of ARE-containing mRNAs in response to iron deficiency
Annotating and interpreting the results of genome-wide association studies ( GWAS ) remains challenging . Assigning function to genetic variants as expression quantitative trait loci is an expanding and useful approach , but focuses exclusively on mRNA rather than protein levels . Many variants remain without annotatio...	The central dogma of biology explains that DNA is transcribed to mRNA that is further translated into protein . Many genome-wide studies have implicated genetic variation that influences gene expression and that ultimately affect downstream complex traits including response to drugs . However , because of technical lim...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "genome-wide", "association", "studies", "genome", "expression", "analysis", "genome", "complexity", "genomics", "genome", "analysis", "transcriptome", "analysis", "genetics", "biology", "and", "life", "sciences", "genomic", "medicine", "computational", "...	2014	Protein Quantitative Trait Loci Identify Novel Candidates Modulating Cellular Response to Chemotherapy
Gene expression as an intermediate molecular phenotype has been a focus of research interest . In particular , studies of expression quantitative trait loci ( eQTL ) have offered promise for understanding gene regulation through the discovery of genetic variants that explain variation in gene expression levels . Existi...	The uniqueness of individuals is due to differences in the combination of genetic , epigenetic and environmental determinants . Understanding the genetic basis of phenotypic variation is a key objective in genetics . Gene expression has been considered as an intermediate phenotype , and the association between gene exp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Aberrant Gene Expression in Humans
Hypertension ( HTN ) is a devastating disease with a higher incidence in African Americans than European Americans , inspiring searches for genetic variants that contribute to this difference . We report the results of a large-scale admixture scan for genes contributing HTN risk , in which we screened 1 , 670 African A...	High blood pressure is more frequent and severe among African Americans than European Americans . To explore whether there are genetic underpinnings to this pattern , we screened the genomes of 1 , 670 African Americans , searching for loci at which people with hypertension ( HTN ) have more than the average proportion...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "homo", "(human)", "genetics", "and", "genomics" ]	2007	A High-Density Admixture Scan in 1,670 African Americans with Hypertension
clinicaltrials . gov NTC02092116 Antiretroviral therapy ( ART ) effectively suppresses viral replication and partially restores immune functions in human immunodeficiency virus type-1 ( HIV-1 ) infected individuals [1] . However , HIV-1 integrates into the host DNA , thus establishing the basis for latent infection . A...	One proposed way of curing HIV is to activate virus transcription and kill latently infected cells while the presence of antiretroviral therapy prevents spreading the infection . Induction of global T cell activation by mitogenic or other potent activators effectively reverses HIV-1 from latency ex vivo , but such comp...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Depsipeptide Romidepsin Reverses HIV-1 Latency In Vivo
It is acknowledged that some obesity trajectories are set early in life , and that rapid weight gain in infancy is a risk factor for later development of obesity . Identifying modifiable factors associated with early rapid weight gain is a prerequisite for curtailing the growing worldwide obesity epidemic . Recently , ...	Some obesity trajectories are set early in life , with rapid weight gain being a risk factor for later development of obesity . Recently , much attention has been given to findings indicating that gut microbiota may play a role in obesity development . The existence of time-dependent exposure windows , which rely on st...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "medicine", "growth", "retardation", "mathematics", "diagnostic", "medicine", "pathology", "statistics", "clinical", "pathology", "biostatistics", "clinical", "microbiology", "pediatrics" ]	2013	Novel Developmental Analyses Identify Longitudinal Patterns of Early Gut Microbiota that Affect Infant Growth
In the phytopathogenic basidiomycete Ustilago maydis , sexual and pathogenic development are tightly connected and controlled by the heterodimeric bE/bW transcription factor complex encoded by the b-mating type locus . The formation of the active bE/bW heterodimer leads to the formation of filaments , induces a G2 cell...	The basidiomycetous fungus Ustilago maydis is the causal agent of the smut disease on corn . The fungus exhibits two different life-styles , a saprophytic and a pathogenic stage , where it grows yeast-like by budding , or as filamentous , dikaryotic hyphae , respectively . The switch between these two stages is control...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "microbiology/plant-biotic", "interactions", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "cell", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/microbial", "growth", "and", "development", "microb...	2010	The Transcription Factor Rbf1 Is the Master Regulator for b-Mating Type Controlled Pathogenic Development in Ustilago maydis
Understanding the factors that affect the host-feeding preferences of triatomine bugs is crucial for estimating transmission risks and predicting the effects of control tactics targeting domestic animals . We tested whether Triatoma infestans bugs prefer to feed on dogs vs . chickens and on dogs vs . cats and whether v...	Chagas disease is a complex zoonosis with more than 150 mammalian host species , nearly a dozen blood-sucking triatomine species as main vectors , and 9–11 million people infected with Trypanosoma cruzi ( its causal agent ) in the Americas . Triatoma infestans , a highly domesticated species and one of the main vectors...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/protozoal", "infections", "ecology/population", "ecology", "infectious", "diseases/epidemiology", "and", "control", "of", "infec...	2009	Strong Host-Feeding Preferences of the Vector Triatoma infestans Modified by Vector Density: Implications for the Epidemiology of Chagas Disease
Mycobacterium ulcerans infection , commonly known as Buruli ulcer ( BU ) , is a debilitating neglected tropical disease . Its management remains complex and has three main components: antibiotic treatment combining rifampicin and streptomycin for 56 days , wound dressings and skin grafts for large ulcerations , and phy...	The management of Buruli ulcer ( BU ) is complex , resulting in high costs to families and health systems . Early detection and treatment heals lesions without functional limitations . Decentralization of the management of this disease into the peripheral health system remains a challenge for national control programs ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "medical", "personnel", "drugs", "sociology", "tropical", "diseases", "microbiology", "geographical", "locations", "social", "sciences", "anthropology", "surgical", "a...	2018	Implementation of a decentralized community-based treatment program to improve the management of Buruli ulcer in the Ouinhi district of Benin, West Africa
Visceral Leishmaniasis ( VL; also known as Kala-azar ) is an ultimately fatal disease endemic in Bihar . A 2007 observational cohort study in Bihar of 251 patients with VL treated with 20 mg/Kg intravenous liposomal amphotericin B ( Ambisome ) demonstrated a 98% cure rate at 6-months . Between July 2007 and August 2012...	Visceral leishmaniasis ( VL ) , also known as Kala-azar , is a protozoan parasitic disease transmitted by phlebotomine sandflies . After malaria , VL accounts for the second-highest burden of parasitic diseases worldwide . India has half of all the VL patients worldwide , of which up to 90% are in Bihar state . Between...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "leishmaniasis", "neglected", "tropical", "diseases", "parasitic", "diseases" ]	2014	Five-Year Field Results and Long-Term Effectiveness of 20 mg/kg Liposomal Amphotericin B (Ambisome) for Visceral Leishmaniasis in Bihar, India
Simian Foamy Virus ( SFV ) can be transmitted from non-human primates ( NHP ) to humans . However , there are no documented cases of human to human transmission , and significant differences exist between infection in NHP and human hosts . The mechanism for these between-host differences is not completely understood . ...	Simian Foamy Virus ( SFV ) is a very common retrovirus in monkeys . When an infected monkey bites a human it can transmit the virus to the human; however , there are no documented cases of human to human transmission . There also appear to be significant differences between infection in monkey and human hosts . The rea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics", "immunity", "virology", "innate", "immunity", "statistics", "immunology", "biology", "microbiology" ]	2014	A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses
Rabies remains a major public health threat in many parts of the world and is responsible for an estimated 55 , 000 human deaths annually . The burden of rabies is estimated to be around US$20 million in Africa , with the highest financial expenditure being the cost of post-exposure prophylaxis ( PEP ) . However , thes...	Rabies remains a major public health problem , although the means to control and prevent this disease are available through mass dog vaccination and provision of post-exposure prophylaxis ( PEP ) to people exposed to bites by rabid or suspect rabid animals . Despite its necessity as a life-saving measure to prevent the...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	The Burden of Rabies in Tanzania and Its Impact on Local Communities
Viral infections of central nervous system ( CNS ) often trigger inflammatory responses that give rise to a wide range of pathological outcomes . The CNS is equipped with an elaborate network of innate immune sentinels ( e . g . microglia , macrophages , dendritic cells ) that routinely serve as first responders to the...	The central nervous system is equipped with innate immune cells that serve as first responders to sterile injuries and infections . The mechanisms that program the movement and morphological transformations of these cells following infection remain undefined . Here , we utilized a combination of genomic and in vivo ima...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "immunology", "biology" ]	2013	Type I Interferon Programs Innate Myeloid Dynamics and Gene Expression in the Virally Infected Nervous System
Pentavalent antimonials have been the first line treatment for dermal leishmaniasis in Colombia for over 30 years . Miltefosine is administered as second line treatment since 2005 . The susceptibility of circulating populations of Leishmania to these drugs is unknown despite clinical evidence supporting the emergence o...	Treatment of dermal leishmaniasis is unsuccessful in an important proportion of cases and evidence of loss of susceptibility to antimonial drugs and miltefosine has been demonstrated in some cases of treatment failure with these medications . Despite the variability in the clinical outcome of treatment , little is know...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences" ]	2014	Miltefosine and Antimonial Drug Susceptibility of Leishmania Viannia Species and Populations in Regions of High Transmission in Colombia
Cell shape changes and proliferation are two fundamental strategies for morphogenesis in animal development . During embryogenesis of the simple chordate Ciona intestinalis , elongation of individual notochord cells constitutes a crucial stage of notochord growth , which contributes to the establishment of the larval b...	The actomyosin cytoskeleton is the primary force that drives cell shape changes . These fibers are organized in elaborate structures that form sarcomeres in the muscle and the contractile ring during cytokinesis . In cytokinesis , the establishment of an equatorial actomyosin ring is preceded and regulated by many cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "cellular", "structures", "model", "organisms", "molecular", "cell", "biology", "ciona", "intestinalis", "biology", "evolutionary", "biology", "morphogenesis", "cytoskeleton", "evolutionary", "developmental", "biology" ]	2014	An Equatorial Contractile Mechanism Drives Cell Elongation but not Cell Division
MicroRNAs ( miRNAs ) are a class of short non-coding RNA that play important roles in disease processes in animals and are present in a highly stable cell-free form in body fluids . Here , we examine the capacity of host and parasite miRNAs to serve as tissue or serum biomarkers of Schistosoma mansoni infection . We us...	Schistosomiasis is a chronic disease caused by blood flukes that affects over 200 million people worldwide , of which 90% live in Sub-Saharan Africa . In the field setting schistosomiasis caused by S . mansoni is diagnosed by detection of parasite eggs in stool samples using microscopic techniques . Here we investigate...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "diagnostic", "medicine", "pathology", "general", "pathology", "biomarkers", "parasitic", "diseases" ]	2014	Parasite-Derived MicroRNAs in Host Serum As Novel Biomarkers of Helminth Infection
The fission yeast Schizosaccharomyces pombe Rec12 protein , the homolog of Spo11 in other organisms , initiates meiotic recombination by creating DNA double-strand breaks ( DSBs ) and becoming covalently linked to the DNA ends of the break . This protein–DNA linkage has previously been detected only in mutants such as ...	During meiosis , which creates haploid gametes from diploid cells , recombination between two homologous chromosomes increases genetic diversity and , in most organisms , is crucial for proper segregation of chromosomes into haploid nuclei . To better understand where recombination occurs and why it occurs there , we i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/chromosome", "biology" ]	2008	Indistinguishable Landscapes of Meiotic DNA Breaks in rad50+ and rad50S Strains of Fission Yeast Revealed by a Novel rad50+ Recombination Intermediate
Death adders ( Acanthophis spp ) are found in Australia , Papua New Guinea and parts of eastern Indonesia . This study aimed to investigate the clinical syndrome of death adder envenoming and response to antivenom treatment . Definite death adder bites were recruited from the Australian Snakebite Project ( ASP ) as def...	Death adders are a genus of venomous snakes found in Australia , Papua New Guinea and Indonesia . Death adder envenoming is a rare but important health problem in Australasia . Definite death adder bites were recruited as part of the Australian Snakebite Project ( ASP ) . Clinical effects , laboratory results and respo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "immunotoxicology", "immunology", "toxicology" ]	2012	Death Adder Envenoming Causes Neurotoxicity Not Reversed by Antivenom - Australian Snakebite Project (ASP-16)
Human leishmaniases are parasitic diseases causing severe morbidity and mortality . No vaccine is available and numerous factors limit the use of current therapies . There is thus an urgent need for innovative initiatives to identify new chemotypes displaying selective activity against intracellular Leishmania amastigo...	Leishmaniases are neglected diseases caused by protozoan parasites that belong to the genus Leishmania . No vaccine exists against any form of leishmaniasis and most of the existing anti-leishmanial drugs have serious side effects . Current strategies for discovering new leishmanicidal molecules are largely using inapp...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "biotechnology", "parastic", "protozoans", "leishmania", "small", "molecules", "protozoology", "host-pathogen", "interaction", "microbiology", "biology", "drug", "discovery" ]	2013	High Content Analysis of Primary Macrophages Hosting Proliferating Leishmania Amastigotes: Application to Anti-leishmanial Drug Discovery
Type 2 diabetes ( T2D ) is a complex metabolic disease associated with obesity , insulin resistance and hypoinsulinemia due to pancreatic β-cell dysfunction . Reduced mitochondrial function is thought to be central to β-cell dysfunction . Mitochondrial dysfunction and reduced insulin secretion are also observed in β-ce...	Mitochondrial dysfunction and reduced insulin secretion are key features of β-cell dysfunction in Type 2 diabetes ( T2D ) . Down syndrome ( DS ) is a genetic disorder caused by trisomy of chromosome 21 that also displays β-cell mitochondrial dysfunction and reduced insulin secretion in humans . Given these similarities...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "diabetic", "endocrinology", "carbohydrates", "organic", "compounds", "glucose", "hormones", "endocrine", "physiology", "animal", "models", "model", "organisms", "mitochondria", "epigenetics", "bioenergetics"...	2016	A Syntenic Cross Species Aneuploidy Genetic Screen Links RCAN1 Expression to β-Cell Mitochondrial Dysfunction in Type 2 Diabetes
Kaposi sarcoma-associated herpesvirus ( KSHV ) establishes a lifelong latent infection and causes several malignancies in humans . Murine herpesvirus 68 ( MHV-68 ) is a related γ2-herpesvirus frequently used as a model to study the biology of γ-herpesviruses in vivo . The KSHV latency-associated nuclear antigen ( kLANA...	Kaposi sarcoma-associated herpesvirus ( KSHV ) causes Kaposi Sarcoma , Primary Effusion lymphoma and the plasma cell variant of Multicentric Castleman's Disease . Its oncogenic effect is linked to its ability to persist in a latent form for the life time of infected individuals . During latency viral genomes are replic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Structural Basis for BRD2/4-Mediated Host Chromatin Interaction and Oligomer Assembly of Kaposi Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus LANA Proteins
The tad operons encode the machinery required for adhesive Flp ( fimbrial low-molecular-weight protein ) pili biogenesis . Vibrio vulnificus , an opportunistic pathogen , harbors three distinct tad loci . Among them , only tad1 locus was highly upregulated in in vivo growing bacteria compared to in vitro culture condit...	Vibrio vulnificus is so called “flesh eating bacterium” causing fatal sepsis accompanying destruction ( necrosis ) of soft tissue . The fatal infection occurs after eating contaminated seafood such as oysters or exposure of pre-existing wounds to seawater . Here we show an important bacterial factor that should be used...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "complement", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "hela", "cells", "pathogens", "vibrio", "immunology", "biological", "c...	2019	A stealth adhesion factor contributes to Vibrio vulnificus pathogenicity: Flp pili play roles in host invasion, survival in the blood stream and resistance to complement activation
Non-coding RNAs are much more common than previously thought . However , for the vast majority of non-coding RNAs , the cellular function remains enigmatic . The two long non-coding RNA ( lncRNA ) genes DLEU1 and DLEU2 map to a critical region at chromosomal band 13q14 . 3 that is recurrently deleted in solid tumors an...	Recent results suggest that genome regions not coding for proteins are read and transcribed into RNA . While the function for the majority of the resulting non-coding RNA molecules remains unclear , some of them are termed according to their length ( typically 200–2 , 000 nucleotides ) as long non-coding RNA ( lncRNA )...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "leukemias", "cancer", "genetics", "gene", "regulation", "cancers", "and", "neoplasms", "basic", "cancer", "research", "dna", "transcription", "gene", "function", "histone", "modification", "hematologic", "cancers", "and", "related", "disorders", "oncology",...	2013	Epigenetic Upregulation of lncRNAs at 13q14.3 in Leukemia Is Linked to the In Cis Downregulation of a Gene Cluster That Targets NF-kB
Computational efforts to identify functional elements within genomes leverage comparative sequence information by looking for regions that exhibit evidence of selective constraint . One way of detecting constrained elements is to follow a bottom-up approach by computing constraint scores for individual positions of a m...	There are millions of sequences in the human genome that perform essential functions , such as protein-coding exons , noncoding RNAs , and regulatory sequences that control the transcription of genes . However , these functional sequences are embedded in a background of DNA that serves no discernible function . Thus , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "computational", "biology/comparative", "sequence", "analysis", "evolutionary", "biology/genomics", "evolutionary", "biology/bioinformatics", "computational", "biology/genomics", "evolutionary", "biology", "c...	2010	Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++
Mycobacterium ulcerans is the causative agent of Buruli ulcer ( BU ) . In West Africa there is an association between BU and residence in low-lying rural villages where aquatic sources are plentiful . Infection occurs through unknown environmental exposure; human-to-human infection is rare . Molecular evidence for M . ...	Buruli ulcer , a severe , cutaneous disease in West and Central Africa is caused by Mycobacterium ulcerans . Person-to-person spread of M . ulcerans is rare . There is a strong epidemiological association with residence near slow moving water , but lack of accurate case data in Africa has greatly complicated transmissi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology" ]	2012	Detection of Mycobacterium ulcerans in the Environment Predicts Prevalence of Buruli Ulcer in Benin
Schistosomiasis is a neglected tropical disease caused by Schistosoma parasites . Intervention relies on identifying high-risk regions , yet rapid Schistosoma diagnostics ( Kato-Katz stool assays ( KK ) and circulating cathodic antigen urine assays ( CCA ) ) yield different prevalence estimates . We mapped S . mansoni ...	Schistosomiasis control efforts rely on rapid diagnostic tests to generate maps of disease prevalence . This is so that high-risk areas can be identified and provided with treatments . A range of tests are available , yet it is unclear how their differing results can inform disease mitigation . This study compared the ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "schoolchildren", "medicine", "and", "health", "sciences", "education", "helminths", "sociology", "geographical", "locations", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "animals", "neglec...	2019	Mapping Schistosoma mansoni endemicity in Rwanda: a critical assessment of geographical disparities arising from circulating cathodic antigen versus Kato-Katz diagnostics
Prions induce lethal neurodegeneration and consist of PrPSc , an aggregated conformer of the cellular prion protein PrPC . Antibody-derived ligands to the globular domain of PrPC ( collectively termed GDL ) are also neurotoxic . Here we show that GDL and prion infections activate the same pathways . Firstly , both GDL ...	Prion diseases are a group of infectious , invariably fatal neurodegenerative diseases . Progress in developing therapeutics is slow , partly because animal models of prion diseases require stringent biosafety and are very slow . We recently found that treatment of cerebellar slices with antibodies targeting the globul...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Prion Infections and Anti-PrP Antibodies Trigger Converging Neurotoxic Pathways
Ivermectin-based mass drug administration ( MDA ) programs have achieved remarkable success towards the elimination of onchocerciasis and lymphatic filariasis . However , their full implementation has been hindered in Central Africa by the occurrence of ivermectin-related severe adverse events ( SAEs ) in a subset of i...	Loiasis affects over 10 million people in sub-Saharan Africa , and there are no commercial assays to detect Loa loa infection . New diagnostics for L . loa are urgently needed for two different purposes . First , although L . loa is generally a relatively asymptomatic infection , it has been associated with serious ren...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "onchocerca", "volvulus", "immune", "physiology", "engineering", "and", "technology", "helminths", "immunology", "tropical", "diseases", "parasitic", "diseases", "animals", "onchocerc...	2017	A novel rapid test for detecting antibody responses to Loa loa infections
CD8+ T lymphocytes play an important role in controlling infections by intracellular pathogens . Chemokines and their receptors are crucial for the migration of CD8+ T-lymphocytes , which are the main IFNγ producers and cytotoxic effectors cells . Although the participation of chemokine ligands and receptors has been l...	Chemokine receptors and cell adhesion molecules are essential for T lymphocytes migration into infected tissues . Previously , our group demonstrated that CXCR3 receptor was highly expressed on specific CD8+ T-cells surface after immunization and infection by T . cruzi . Also , recirculation of specific CD8+ T-cells wa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "cell", "motility", "medicine", "and", "health", "sciences", "immune", "cells", "cd", "coreceptors", "cardiovascular", "anatomy", "immunology", "parasitic", "diseases", "parasitic", "protozoans", "protozoans", "heart", "cytotoxic", "t", "cells", "cor...	2019	CXCR3 chemokine receptor guides Trypanosoma cruzi-specific T-cells triggered by DNA/adenovirus ASP2 vaccine to heart tissue after challenge
In many biological systems , the interactions that describe the coupling between different units in a genetic network are nonlinear and stochastic . We study the interplay between stochasticity and nonlinearity using the responses of Chinese hamster ovary ( CHO ) mammalian cells to different temperature shocks . The ex...	The structure of an unknown biological system is uncovered by experimentally perturbing the system with a series of input signals . The response to these perturbations is measured as output signals . Then , the mathematical relation between the input and the output signals constitutes a model for the system . As a resu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mus", "(mouse)", "computational", "biology" ]	2007	Heat Shock Response in CHO Mammalian Cells Is Controlled by a Nonlinear Stochastic Process
Retinoblastoma ( Rb ) , the most common pediatric intraocular neoplasm , results from inactivation of both alleles of the RB1 tumor suppressor gene . The second allele is most commonly lost , as demonstrated by loss of heterozygosity studies . RB1 germline carriers usually develop bilateral tumors , but some Rb familie...	Complex genotype-phenotype correlations lead to clinically and emotionally difficult situations . Improved understanding of these correlations is of utmost importance in medical genetics . Low penetrance retinoblastoma families segregating the c . 1981C>T / p . Arg661Trp mutation are a good model as germline carriers d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "blastomas", "cancers", "and", "neoplasms", "ocular", "anatomy", "rna", "extraction", "nucleotides", "organic", "compounds", "oncology", "ophthalmologic", "tumors", "mutation", "forms", "of", "dna", "py...	2016	A Parent-of-Origin Effect Impacts the Phenotype in Low Penetrance Retinoblastoma Families Segregating the c.1981C>T/p.Arg661Trp Mutation of RB1
A fundamental goal of microbial ecology is to understand what determines the diversity , stability , and structure of microbial ecosystems . The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and p...	The diversity , stability and functional structure of microbial communities have dramatic effects on the health of humans and of ecosystems . The complexity of these communities has so far precluded the development of a general predictive model that would capture the dependence of these features on environmental condit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "community", "ecology", "biochemistry", "ecological", "metrics", "ecology", "and", "environmental", "sciences", "community", "assembly", "ecology", "ecosystems", "community", "structure", "biology", "and", "life", "sciences", "bioenergetics", "microbiology", "biodiversity",...	2019	Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities
In northern Ethiopia the prevalence of visceral leishmaniasis is steadily rising posing an increasing public health concern . In order to develop effective control strategies on the transmission of the disease it is important to generate knowledge on the epidemiological determinants of the infection . We conducted a cr...	Visceral leishmaniasis is a vector borne disease that can be fatal if left untreated . Its prevalence is steadily rising in northern Ethiopia posing a public health challenge in the region . We conducted a study on the factors associated to asymptomatic infection in Libo Kemkem and Fogera , Amhara regional state , wher...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "behavioral", "and", "social", "aspects", "of", "health", "epidemiology", "infectious", "disease", "epidemiology", "leishmaniasis", "neglected", "tropical", "diseases", "infectious", "disease...	2012	Factors Associated with Leishmania Asymptomatic Infection: Results from a Cross-Sectional Survey in Highland Northern Ethiopia
CD36 is a platelet membrane glycoprotein whose engagement with oxidized low-density lipoprotein ( oxLDL ) results in platelet activation . The CD36 gene has been associated with platelet count , platelet volume , as well as lipid levels and CVD risk by genome-wide association studies . Platelet CD36 expression levels h...	Platelets are anucleate cells that are best known as regulators of vascular hemostasis and thrombosis but also play important roles in cancer , angiogenesis , and inflammation . CD36 is a platelet surface marker that can activate platelet in response to oxidized low density lipoprotein ( oxLDL ) . CD36 has been associa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "sequencing", "techniques", "luciferase", "assay", "medicine", "and", "health", "sciences", "luciferase", "body", "fluids", "enzymes", "enzymology", "plasmid", "construction", "biochemical", "analysis", "enzyme", "assays", "genome", "analysis", "platel...	2019	Functionalization of CD36 cardiovascular disease and expression associated variants by interdisciplinary high throughput analysis
Systemic lupus erythematosus ( SLE ) is a genetically complex disease with heterogeneous clinical manifestations . Recent studies have greatly expanded the number of established SLE risk alleles , but the distribution of multiple risk alleles in cases versus controls and their relationship to subphenotypes have not bee...	Systemic lupus erythematosus is a chronic disabling autoimmune disease , most commonly striking women in their thirties or forties . It can cause a wide variety of clinical manifestations , including kidney disease , arthritis , and skin disorders . Prognosis varies greatly depending on these clinical features , with k...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "genetics", "and", "genomics/complex", "traits", "rheumatology/systemic", "lupus", "erythematosos", "rheumatology/autoimmunity,", "autoimmune,", "and", "inflammatory", "diseases", "genetics", "and", "g...	2011	Risk Alleles for Systemic Lupus Erythematosus in a Large Case-Control Collection and Associations with Clinical Subphenotypes
The phytopathogenic bacterium Xanthomonas campestris pv . vesicatoria ( Xcv ) requires type III effector proteins ( T3Es ) for virulence . After translocation into the host cell , T3Es are thought to interact with components of host immunity to suppress defence responses . XopJ is a T3E protein from Xcv that interferes...	Many bacteria that are pathogens for mammals , insects or plants use a specialized apparatus called the type III secretion system to inject a diverse set of effector proteins into the cytoplasm of their eukaryotic host cells in order to alter cellular processes in favour of the pathogen's lifestyle . However , direct c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gram", "negative", "plant", "science", "plant", "pathogens", "plant", "pathology", "host-pathogen", "interaction", "biology", "microbiology", "bacterial", "pathogens" ]	2013	The Xanthomonas campestris Type III Effector XopJ Targets the Host Cell Proteasome to Suppress Salicylic-Acid Mediated Plant Defence
Protein kinases play critical roles in learning and memory and in long term potentiation ( LTP ) , a form of synaptic plasticity . The induction of late-phase LTP ( L-LTP ) in the CA1 region of the hippocampus requires several kinases , including CaMKII and PKA , which are activated by calcium-dependent signaling proce...	The hippocampus is a part of the cerebral cortex intimately involved in learning and memory behavior . A common cellular model of learning is a long lasting form of long term potentiation ( L-LTP ) in the hippocampus , because it shares several characteristics with learning . For example , both learning and long term p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/computational", "neuroscience" ]	2010	Temporal Sensitivity of Protein Kinase A Activation in Late-Phase Long Term Potentiation
Neuronal computations strongly depend on inhibitory interactions . One such example occurs at the first retinal synapse , where horizontal cells inhibit photoreceptors . This interaction generates the center/surround organization of bipolar cell receptive fields and is crucial for contrast enhancement . Despite its ess...	At the first retinal synapse , specific cells—horizontal cells ( HCs ) —inhibit photoreceptors and help to organize the receptive fields of another retinal cell type , bipolar cells . This synaptic interaction is crucial for visual contrast enhancement . Here we show that horizontal cells feed back to photoreceptors vi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "visual", "system", "specimen", "preparation", "and", "treatment", "mechanical", "treatment", "of", "specimens", "specimen", "disruption", "biology", "and", "life", "sciences", "sensory", "systems", "electroporation", "neuroscience", "research", "and", "analysis", "meth...	2014	Extracellular ATP Hydrolysis Inhibits Synaptic Transmission by Increasing pH Buffering in the Synaptic Cleft
It is crucial to determine whether rapid eye movement ( REM ) sleep and slow-wave sleep ( SWS ) ( or non-REM sleep ) , identified in most mammals and birds , also exist in lizards , as they share a common ancestor with these groups . Recently , a study in the bearded dragon ( P . vitticeps ) reported states analogous t...	Until recently , the general understanding about sleep was that only mammals and birds show two sleep states: slow-wave sleep and rapid eye movement ( REM ) sleep . Consequently , it was thought that these two states appeared independently in these warm-blooded animals . However , a recent paper reported the presence o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "eye", "muscles", "medicine", "and", "health", "sciences", "sleep", "ocular", "anatomy", "vertebrates", "neuroscience", "animals", "mammals", "lizards", "physiological", "processes", "reptiles", "bioassays", "and", "physiological", "analysis", "muscle", "electrophysiology...	2018	Partial homologies between sleep states in lizards, mammals, and birds suggest a complex evolution of sleep states in amniotes
The influence of genetic ancestry on Trypanosoma cruzi infection and Chagas disease outcomes is unknown . We used 370 , 539 Single Nucleotide Polymorphisms ( SNPs ) to examine the association between individual proportions of African , European and Native American genomic ancestry with T . cruzi infection and related o...	Chagas disease ( ChD ) , which is caused by the protozoan Trypanosoma cruzi , affects approximately 8 million people worldwide . ChD is known as a neglected tropical disease . The disease is endemic in South and Central American countries , and is an emerging issue in North America and Europe . This study examined , fo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cardiomyopathies", "medicine", "and", "health", "sciences", "parasitic", "protozoans", "health", "care", "ethnicities", "research", "design", "electrocardiography", "protozoans", "cohort", "studies", "bioassays", "and", "physiological", "analysis", "families", "research", ...	2016	Genomic African and Native American Ancestry and Chagas Disease: The Bambui (Brazil) Epigen Cohort Study of Aging
A recently characterized calmodulin-like protein is an endogenous RNA silencing suppressor that suppresses sense-RNA induced post-transcriptional gene silencing ( S-PTGS ) and enhances virus infection , but the mechanism underlying calmodulin-like protein-mediated S-PTGS suppression is obscure . Here , we show that a c...	Post-transcriptional gene silencing ( PTGS ) is an elaborately regulated process for defense against virus infection in plants . To achieve effective infection , a betasatellite molecule associated with geminivirus induced high levels of an endogenous RNA silencing suppressor , calmodulin-like protein ( CaM ) , to coun...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "cell", "death", "plant", "anatomy", "autophagic", "cell", "death", "rna", "interference", "gene", "regulation", "cell", "processes", "plant", "science", "genetically", "modified", "plants", "epigenetics", "plants", "flowering", "plants", "genetic", "...	2017	A calmodulin-like protein suppresses RNA silencing and promotes geminivirus infection by degrading SGS3 via the autophagy pathway in Nicotiana benthamiana
Advances in large-scale analysis of human genomic variability provide unprecedented opportunities to study the genetic basis of susceptibility to infectious agents . We report here the use of an in vitro system for the identification of a locus on HSA8q24 . 3 associated with cellular susceptibility to HIV-1 . This locu...	Individuals differ in their susceptibility to the HIV-1 virus , and the determinants of susceptibility are encoded in the human genome . Genetic variants influencing this trait have been identified by investigating candidate genes thought likely to be involved in HIV-1 pathogenesis or by whole-genome association studie...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "genetics", "and", "genomics" ]	2008	In Vitro Whole-Genome Analysis Identifies a Susceptibility Locus for HIV-1
With only ∼3 , 000 wild individuals surviving restricted to just 7% of their historical range , tigers are now a globally threatened species . Therefore , conservation efforts must prioritize regions that harbor more tigers , as well try to capture most of the remaining genetic variation and habitat diversity . Only su...	Tiger range and numbers have collapsed globally despite substantial conservation efforts . Genetic data quantifying variation from 73 wild tigers in 28 reserves in the Indian subcontinent suggests historically high numbers for tigers , and simulations reveal a signature of a 200-year-old , possibly human-induced declin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "ecology/population", "ecology", "ecology/conservation", "and", "restoration", "ecology", "genetics", "and", "genomics/population", "genetics" ]	2009	Why the Indian Subcontinent Holds the Key to Global Tiger Recovery
A central challenge in sensory neuroscience involves understanding how neural circuits shape computations across cascaded cell layers . Here we attempt to reconstruct the response properties of experimentally unobserved neurons in the interior of a multilayered neural circuit , using cascaded linear-nonlinear ( LN-LN )...	Computation in neural circuits arises from the cascaded processing of inputs through multiple cell layers . Each of these cell layers performs operations such as filtering and thresholding in order to shape a circuit’s output . It remains a challenge to describe both the computations and the mechanisms that mediate the...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "nervous", "system", "signal", "processing", "applied", "mathematics", "ocular", "anatomy", "neuroscience", "simulation", "and", "modeling", "algorithms", "optimization", "mathematics", "ganglion...	2018	Inferring hidden structure in multilayered neural circuits
Certain environmental microorganisms can cause severe human infections , even in the absence of an obvious requirement for transition through an animal host for replication ( “accidental virulence” ) . To understand this process , we compared eleven isolate genomes of Burkholderia pseudomallei ( Bp ) , a tropical soil ...	With recent advances in genomics now permitting the systematic comparison of dozens , if not hundreds , of closely related bacterial strains , the opportunity arises for developing novel approaches to identify the complete repertoire of molecular factors governing interactions between hosts and pathogens . We explored ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases", "computational", "biology/genomics" ]	2010	A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence
High content image-based screening was developed as an approach to test a protease inhibitor small molecule library for antiviral activity against Rift Valley fever virus ( RVFV ) and to determine their mechanism of action . RVFV is the causative agent of severe disease of humans and animals throughout Africa and the A...	Rift Valley fever ( RVF ) is an arthropod-borne viral zoonosis that occurs in large parts of sub-Saharan and North Africa and in 2000 emerged outside the African continent for the first time , raising concerns that it could further expand its geographical range . The disease in humans can result in encephalitis or hemo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences" ]	2014	High Content Image-Based Screening of a Protease Inhibitor Library Reveals Compounds Broadly Active against Rift Valley Fever Virus and Other Highly Pathogenic RNA Viruses
Antigenic variation plays a vital role in the pathogenesis of many infectious bacteria and protozoa including Borrelia burgdorferi , the causative agent of Lyme disease . VlsE , a 35 kDa surface-exposed lipoprotein , undergoes antigenic variation during B . burgdorferi infection of mammalian hosts , and is believed to ...	Lyme disease is the most prevalent tick-borne infection in North America and Eurasia . It is caused by the bacterium Borrelia burgdorferi and is transmitted to humans via the bite of infected ticks . These spirochetes can cause both acute and chronic infection and inflammation of the skin , joints , heart , and central...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "physiology/immunity", "to", "infections", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/gene", "function", "infectious", "diseases/bacterial", "infections", "immunology/immunity", ...	2009	Central Role of the Holliday Junction Helicase RuvAB in vlsE Recombination and Infectivity of Borrelia burgdorferi
The bacterial stringent response , triggered by nutritional deprivation , causes an accumulation of the signaling nucleotides pppGpp and ppGpp . We characterize the replication arrest that occurs during the stringent response in Escherichia coli . Wild type cells undergo a RelA-dependent arrest after treatment with ser...	Management of cell growth and division in response to environmental conditions is important for all cells . In bacteria , nutritional downturns are signaled by accumulation of the nucleotide ppGpp . Amino acid starvation causes a programmed change in transcription , known as the “stringent response”; ppGpp also causes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/microbial", "growth", "and", "development", "genetics", "and", "genomics/chromosome", "biology", "microbiology/microbial", "physiology", "and", "metabolism" ]	2008	The Stringent Response and Cell Cycle Arrest in Escherichia coli
Sound waveforms convey information largely via amplitude modulations ( AM ) . A large body of experimental evidence has provided support for a modulation ( bandpass ) filterbank . Details of this model have varied over time partly reflecting different experimental conditions and diverse datasets from distinct task stra...	Amplitude modulations are considered the key carriers of intelligible information in auditory signals , and consequently it is of significant interest to discover how they are neurally analyzed and perceptually encoded . A dominant model has emerged from extensive experimental and theoretical studies of this phenomenon...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "engineering", "and", "technology", "signal", "processing", "applied", "mathematics", "social", "sciences", "neuroscience", "signal", "filtering", "autocorrelation", "algorithms", "simulation", "and", "modeling", "systems", "science", "mathematics", "statistics", "(mathemat...	2016	Dynamic Reweighting of Auditory Modulation Filters
Intra-protein information is transmitted over distances via allosteric processes . This ubiquitous protein process allows for protein function changes due to ligand binding events . Understanding protein allostery is essential to understanding protein functions . In this study , allostery in the second PDZ domain ( PDZ...	Allostery is a fundamental dynamics property of many proteins , and plays a critical role in protein functions . Despite extensive experimental and theoretical studies of protein allosteric mechanisms , the current understanding and predicting power of protein allostery are still limited . One of the main challenges in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "allosteric", "regulation", "perturbation", "(geology)", "enzymology", "random", "variables", "covariance", "simulation", "and", "modeling", "multivariate", "analysis", "mathematics", "statistics", "(mathematics)", "geology", "protein", "structure", "thermodynamics", "enzyme"...	2016	Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery
The oscillations of the somitogenesis clock are linked to the fundamental process of vertebrate embryo segmentation , yet little is known about their generation . In zebrafish , it has been proposed that Her proteins repress the transcription of their own mRNA . However , in its simplest form , this model is incompatib...	Vertebrate embryos acquire a segmented structure along the anteroposterior axis . Segmentation is critical for patterning of other structures ( such as nerves , vertebrae , muscles , and blood vessels ) and occurs by the rhythmic separation of balls of cells , called somites , from the anterior end of their precursor t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "danio", "(zebrafish)", "developmental", "biology", "computational", "biology" ]	2007	Repressor Dimerization in the Zebrafish Somitogenesis Clock
The three-dimensional ( 3D ) structure of the genome is important for orchestration of gene expression and cell differentiation . While mapping genomes in 3D has for a long time been elusive , recent adaptations of high-throughput sequencing to chromosome conformation capture ( 3C ) techniques , allows for genome-wide ...	Understanding how the genome is folded in three-dimensional ( 3D ) space is crucial for unravelling the complex regulatory mechanisms underlying the differentiation and proliferation of cells . With recent high-throughput adaptations of chromosome conformation capture in techniques such as single-cell Hi-C , it is now ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Manifold Based Optimization for Single-Cell 3D Genome Reconstruction
Vaccinia virus ( VACV ) , the prototype poxvirus , encodes numerous proteins that modulate the host response to infection . Two such proteins , B14 and A52 , act inside infected cells to inhibit activation of NF-κB , thereby blocking the production of pro-inflammatory cytokines . We have solved the crystal structures o...	Cells possess formidable defences against virus infection , but viruses have evolved sophisticated counter-measures to evade such defences . Vaccinia virus , the vaccine used to eradicate smallpox , has about 200 genes , and many of these encode proteins that help the virus evade the host's immune defences . This paper...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "virology/immune", "evasion", "virology/virus", "evolution", "and", "symbiosis", "immunology/immune", "response", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2008	Vaccinia Virus Proteins A52 and B14 Share a Bcl-2–Like Fold but Have Evolved to Inhibit NF-κB rather than Apoptosis
Tsetse flies ( Glossina spp . ) vector pathogenic African trypanosomes , which cause sleeping sickness in humans and nagana in domesticated animals . Additionally , tsetse harbors 3 maternally transmitted endosymbiotic bacteria that modulate their host's physiology . Tsetse is highly resistant to infection with trypano...	Tsetse flies serve as a host to many micro-organisms . Specifically , this fly houses beneficial endosymbiotic bacteria , and can also serve as a vector of pathogenic trypanosomes across much of sub-Saharan Africa . Although flies feed on parasite-infected reservoir hosts , only a small proportion ( 1–5% ) of individua...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunity", "vector", "biology", "immune", "activation", "innate", "immunity", "immunity", "to", "infections", "immunology", "biology", "microbiology", "tsetse", "fly", "host-pathogen", "interaction", "parasitology", "immune", "response" ]	2013	Trypanosome Infection Establishment in the Tsetse Fly Gut Is Influenced by Microbiome-Regulated Host Immune Barriers
Dengue fever is the most rapidly spreading mosquito-borne viral disease over the past 50 years , with a 30-fold increase in global incidence . Dengue vector control is a key component for the dengue control strategy , since no absolutely effective vaccine or drug is available yet . However , the rapid rise and spread o...	Dengue fever is one of neglected vector-borne tropical diseases with a 30-fold increase in global incidence recently . In 2012 , World Health Organization set a goal to reduce dengue mortality by at least 50% by 2020 . Being faced with more challenges in the dengue control programs , such as the increase of dengue outb...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "animals", "viruses", "rna", "viruses", "neglected", "tropical", "diseases",...	2018	Antivirus effectiveness of ivermectin on dengue virus type 2 in Aedes albopictus
Giardia duodenalis , originally regarded as a commensal organism , is the etiologic agent of giardiasis , a gastrointestinal disease of humans and animals . Giardiasis causes major public and veterinary health concerns worldwide . Transmission is either direct , through the faecal-oral route , or indirect , through ing...	Giardia duodenalis is a parasite causing a gastrointestinal disease in humans , pets , livestock , and wildlife . The role of animals in human disease is unclear , because Giardia from humans and animals is morphologically indistinguishable . An international consortium of both veterinary and public health institutions...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "gastroenterology", "and", "hepatology/gastrointestinal", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections", "computer", "science/information", "technology", "genetics", "and...	2009	Identification of Zoonotic Genotypes of Giardia duodenalis
Parasitic roundworm infections plague more than 2 billion people ( 1/3 of humanity ) and cause drastic losses in crops and livestock . New anthelmintic drugs are urgently needed as new drug resistance and environmental concerns arise . A “chokepoint reaction” is defined as a reaction that either consumes a unique subst...	The World Health Organization estimates that 2 . 9 million people are infected with parasitic roundworms , causing high-morbidity and mortality rates , developmental delays in children , and low productivity of affected individuals . The agricultural industry experiences drastic losses in crop and livestock due to para...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "pesticides", "medicine", "infectious", "diseases", "veterinary", "diseases", "veterinary", "parasitology", "pest", "control", "parasitic", "diseases", "veterinary", "science", "agriculture" ]	2013	Discovery of Anthelmintic Drug Targets and Drugs Using Chokepoints in Nematode Metabolic Pathways
Genes underlying important phenotypic differences between Plasmodium species , the causative agents of malaria , are frequently found in only a subset of species and cluster at dynamically evolving subtelomeric regions of chromosomes . We hypothesized that chromosome-internal regions of Plasmodium genomes harbour addit...	With more than 250 million infections and over a million deaths each year , malaria remains one of the most devastating infectious diseases worldwide . With the availability of complete genome sequences of both human and non-human Plasmodium parasites , the causative agents of malaria , it is now possible to use compar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parasite", "groups", "genomics", "parasite", "evolution", "biology", "computational", "biology", "evolutionary", "biology", "microbiology", "genetics", "and", "genomics", "parasitology" ]	2011	Genome Comparison of Human and Non-Human Malaria Parasites Reveals Species Subset-Specific Genes Potentially Linked to Human Disease
Regulated cell polarity is central to many cellular processes . We investigated the mechanisms that govern the rapid switching of cell polarity ( reversals ) during motility of the bacterium Myxococcus xanthus . Cellular reversals are mediated by pole-to-pole oscillations of motility proteins and the frequency of the o...	Motile cells have evolved complex regulatory networks to respond to environmental cues and change their direction of movement appropriately . In this process , an arsenal of receptor-coupled small G-proteins acts as a cellular compass to dynamically polarize the leading edge and regulate the motility response . However...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "cell", "biology", "cell", "biology/microbial", "growth", "and", "development", "microbiology", "microbiology/microbial", "growth", "and", "development" ]	2010	A Bacterial Ras-Like Small GTP-Binding Protein and Its Cognate GAP Establish a Dynamic Spatial Polarity Axis to Control Directed Motility
Metronidazole is the most commonly used drug for the treatment of giardiasis in humans . In spite of its therapeutic efficacy for giardiasis , low patient compliance , especially in children , side effects , and the emergence of metronidazole-resistant strains may restrict its use . Albendazole has been used to treat G...	Giardiasis is one of the most common intestinal protozoal infections worldwide . Although metronidazole is the most common drug used to treat giardiasis in humans , its use is associated with a variety of side effects . Poor compliance and the emergence of metronidazole-resistant strains may restrict use of the drug . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "microbiology/parasitology" ]	2010	A Meta-analysis of the Effectiveness of Albendazole Compared with Metronidazole as Treatments for Infections with Giardia duodenalis
Leprosy reactions are a significant cause of morbidity in leprosy population . Erythema nodosum leprosum ( ENL ) is an immunological complication affecting approximately 50% of patients with lepromatous leprosy ( LL ) and 10% of borderline lepromatous ( BL ) leprosy . ENL is associated with clinical features such as sk...	Leprosy reactions ( Type 1 and 2 ) are important causes of nerve damage and illness . Erythema Nodosum Leprosum ( ENL ) also called type 2 reactions is a severe multisystem immune-mediated complication of borderline and lepromatous leprosy . ENL causes high morbidity and mortality and usually requires urgent medical at...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "inflammatory", "diseases", "rheumatology", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "biopsy", "immunology", "tropical", "diseases", "geographical", "locations", "surgical", "and", "invas...	2017	Clinico-pathological features of erythema nodosum leprosum: A case-control study at ALERT hospital, Ethiopia
Analyses of circulating metabolites in large prospective epidemiological studies could lead to improved prediction and better biological understanding of coronary heart disease ( CHD ) . We performed a mass spectrometry-based non-targeted metabolomics study for association with incident CHD events in 1 , 028 individual...	Non-targeted metabolomic profiling of large population-based studies has become feasible only in the past 1–2 years and this hypothesis-free exploration of the metabolome holds a great potential to fuel the discovery of novel biomarkers for coronary heart disease ( CHD ) . Such biomarkers are not only important for ris...	[ "Abstract", "Introduction", "Discussion", "Materials", "and", "Methods" ]	[ "metabolism", "biochemistry", "biology", "and", "life", "sciences", "metabolomics" ]	2014	Large-scale Metabolomic Profiling Identifies Novel Biomarkers for Incident Coronary Heart Disease

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