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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
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Mycobacterium tuberculosis ( Mtb ) primarily resides in the lung but can also persist in extrapulmonary sites . Macrophages are considered the prime cellular habitat in all tissues . Here we demonstrate that Mtb resides inside adipocytes of fat tissue where it expresses stress-related genes . Moreover , perigonadal fat... | In 2015 , tuberculosis ( TB ) affected 10 . 4 million individuals causing 1 . 8 million deaths per year . Yet , a much larger group– 2 billion people–harbors latent TB infection ( LTBI ) without clinical symptoms , but at lifelong risk of reactivation . The physiological niches of Mycobacterium tuberculosis ( Mtb ) per... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immunology",
"adipocytes",
"connective",
"tissue",
"cells",
"cytotoxic",
"t",
"cells",
"bacteria",
"lipids",
"white",
"blood",
"cells",
"animal",
"cells",
"fats",
"gene",
"expression",
... | 2017 | Mycobacterium tuberculosis infection modulates adipose tissue biology |
Relatively little is known about the filarial proteins that interact with the human host . Although the filarial genome has recently been completed , protein profiles have been limited to only a few recombinants or purified proteins of interest . Here , we describe a large-scale proteomic analysis using microcapillary ... | Human lymphatic filariasis caused by the nematode parasites Brugia malayi and Wuchereria bancrofti are a major cause of concern in tropical countries . Studies over several decades have identified various proteins of these parasites that have highlighted their role in host–parasite interactions and possible chemotherap... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/helminth",
"infections",
"biotechnology/protein",
"chemistry",
"and",
"proteomics"
] | 2009 | Brugia malayi Excreted/Secreted Proteins at the Host/Parasite Interface: Stage- and Gender-Specific Proteomic Profiling |
RNA-protein interactions are critical in many biological processes , yet how such interactions affect the evolution of both partners is still unknown . RNA and protein structures are impacted very differently by mechanisms of genomic change . While most protein families are identifiable at the nucleotide level across l... | RNA-protein interactions are important for many biological processes , and aberrant interactions have been implicated in many human diseases . However , how the specificity of such interactions may change over time and impact the evolution of both partners is still largely unexplored . In this work we examine four homo... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Co-evolution of Bacterial Ribosomal Protein S15 with Diverse mRNA Regulatory Structures |
The two-component signalling system ( TCS ) comprising a histidine kinase ( HK ) and a response regulator ( RR ) is the predominant bacterial sense-and-response machinery . Because bacterial cells usually encode a number of TCSs to adapt to various ecological niches , the specificity of a TCS is in the centre of regula... | c-di-GMP is a multifunctional bacterial second messenger that controls various physiological processes . The nucleotide derivative binds to riboswitches or proteins as effectors during regulation . Here , we found that c-di-GMP physically binds to a histidine kinase , RavS , of a plant pathogenic bacterium . The bindin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"cell",
"motility",
"swimming",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"xanthomonas",
"campestris",
"pathogens",
"biological",
"locomotion",
"mutation",
"plant",
"science",
"plant",
"pathology",
"cellular"... | 2019 | Cyclic-di-GMP binds to histidine kinase RavS to control RavS-RavR phosphotransfer and regulates the bacterial lifestyle transition between virulence and swimming |
Gastric cancer development is strongly correlated with infection by Helicobacter pylori possessing the effector protein CagA . Using a transgenic Drosophila melanogaster model , we show that CagA expression in the simple model epithelium of the larval wing imaginal disc causes dramatic tissue perturbations and apoptosi... | The gastric pathogen Helicobacter pylori infects an estimated 50% of the world's population and is a major risk factor for the development of gastric cancer . Strains of H . pylori that can inject the CagA effector protein into host cells are known to be more virulent , but the potential contributions of host genetics ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"death",
"cellular",
"stress",
"responses",
"cancer",
"genetics",
"microbiology",
"host-pathogen",
"interaction",
"signaling",
"in",
"selected",
"disciplines",
"epithelial",
"cells",
"animal",
"models",
"c-jun",
"n-terminal",
"kinase",
"signaling",
"cascade",
"d... | 2012 | Transgenic Expression of the Helicobacter pylori Virulence Factor CagA Promotes Apoptosis or Tumorigenesis through JNK Activation in Drosophila |
Vibrio cholerae infections cluster in households . This study's objective was to quantify the relative contribution of direct , within-household exposure ( for example , via contamination of household food , water , or surfaces ) to endemic cholera transmission . Quantifying the relative contribution of direct exposure... | Since John Snow's ground-breaking investigations of the devastating outbreaks in 19th-century London , cholera has been considered the quintessential waterborne human infection , transmitting via fecal contamination of environmental water sources . Recently , renewed interest has been paid to the potential importance o... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"tropical",
"diseases",
"microbiology",
"health",
"care",
"multivariate",
"analysis",
"bacterial",
"diseases",
"mathematics",
"statistics",
"(mathematics)",
"global",
"health",
"neglected",
"tropical",
"diseases",
"population",
"bi... | 2014 | Household Transmission of Vibrio cholerae in Bangladesh |
Mutations in the BREVIPEDICELLUS ( BP ) gene of Arabidopsis thaliana condition a pleiotropic phenotype featuring defects in internode elongation , the homeotic conversion of internode to node tissue , and downward pointing flowers and pedicels . We have characterized five mutant alleles of BP , generated by EMS , fast ... | Chromosome evolution involves both small-scale ( e . g . single nucleotide ) changes , as well as large-scale rearrangements such as inversions , translocations , and fusion events . We investigated mutations of the BREVIPEDICELLUS gene of Arabidopsis , which is a master regulator of inflorescence architecture . These ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"developmental",
"biology",
"plant",
"science",
"plant",
"growth",
"and",
"development",
"molecular",
"development",
"plant",
"genomics",
"plant",
"biology",
"biology"
] | 2012 | Chromosome Fragile Sites in Arabidopsis Harbor Matrix Attachment Regions That May Be Associated with Ancestral Chromosome Rearrangement Events |
Type 1 Epstein-Barr virus ( EBV ) strains immortalize B lymphocytes in vitro much more efficiently than type 2 EBV , a difference previously mapped to the EBNA-2 locus . Here we demonstrate that the greater transforming activity of type 1 EBV correlates with a stronger and more rapid induction of the viral oncogene LMP... | Epstein-Barr virus ( EBV ) is a common human virus that is involved in several types of cancer and directly causes human B lymphocytes to proliferate when they become infected . EBV occurs naturally as two different viral types ( type 1 and type 2 ) . The genomes of these viruses are mostly very similar but they differ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology"
] | 2011 | C-Terminal Region of EBNA-2 Determines the Superior Transforming Ability of Type 1 Epstein-Barr Virus by Enhanced Gene Regulation of LMP-1 and CXCR7 |
We hypothesized that variants in genes expressed as a consequence of interactions between ovarian cancer cells and the host micro-environment could contribute to cancer susceptibility . We therefore used a two-stage approach to evaluate common single nucleotide polymorphisms ( SNPs ) in 173 genes involved in stromal ep... | In this article , we report the findings from a large-scale analysis of common variation in genes that are expressed as a consequence of interactions between ovarian cancer cells and their host micro-environment that could influence serous ovarian cancer risk . We evaluated 1 , 302 common variants within or near 173 ge... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"public",
"health",
"and",
"epidemiology/epidemiology",
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"genetics",
"and",
"genomics/complex",
"traits",
"genetics",
"and",
"genomics/cancer",
"genetics"
] | 2010 | Evaluation of Candidate Stromal Epithelial Cross-Talk Genes Identifies Association between Risk of Serous Ovarian Cancer and TERT, a Cancer Susceptibility “Hot-Spot” |
Aedes aegypti poses a serious risk to human health due to its wide global distribution , high vector competence for several arboviruses , frequent human biting , and ability to thrive in urban environments . Pyrethroid insecticides remain the primary means of controlling adult A . aegypti populations during disease out... | Cytochrome P450 monooxygenases ( CYPs ) are one of the most important mechanism of insecticide resistance in mosquitoes . These CYP enzymes break down insecticides into non-toxic forms that can be readily excreted . An increase of CYP-mediated detoxification is commonly found in pyrethroid resistant Aedes aegypti , how... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"animals",
"molecular",
"biology",
"techniques",
"molecular",
"genetics",
"insect",
"vectors",
"research",
"and",
"analysis",
"methods",
"agrochemicals",
"infectious",
"diseases",
"artificial",
"gene",
"amplificati... | 2018 | CYP-mediated permethrin resistance in Aedes aegypti and evidence for trans-regulation |
The vigorous cytokine response of immune cells to Gram-negative bacteria is primarily mediated by a recognition molecule , Toll-like receptor 4 ( TLR4 ) , which recognizes lipopolysaccharide ( LPS ) and initiates a series of intracellular NF-κB–associated signaling events . Recently , bladder epithelial cells ( BECs ) ... | In spite of frequent cross contamination by bacteria from the gut , urinary tract infections are relatively infrequent . Although much of the credit goes to cells lining the urinary tract , such as bladder cells , how this is achieved remains unclear . Human bladder cells display , on their surfaces , special molecules... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"immunology",
"homo",
"(human)"
] | 2007 | A Novel TLR4-Mediated Signaling Pathway Leading to IL-6 Responses in Human Bladder Epithelial Cells |
Mining gene expression profiles has proven valuable for identifying signatures serving as surrogates of cancer phenotypes . However , the similarities of such signatures across different cancer types have not been strong enough to conclude that they represent a universal biological mechanism shared among multiple cance... | Cancer is known to be characterized by several unifying biological capabilities or “hallmarks . ” However , attempts to computationally identify patterns , such as gene expression signatures , shared across many different cancer types have been largely unsuccessful . A typical approach has been to classify samples into... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"biology",
"computational",
"biology",
"genetics",
"and",
"genomics"
] | 2013 | Biomolecular Events in Cancer Revealed by Attractor Metagenes |
Lymphatic filariasis , commonly known as elephantiasis , is a painful and profoundly disfiguring disease . Wuchreria bancrofti ( Wb ) is responsible for >90% of infections and the remainder are caused by Brugia spp . Mosquitoes of the genera Culex ( in urban and semi-urban areas ) , Anopheles ( in rural areas of Africa... | Lymphatic filariasis ( LF ) is caused by infection with nematodes of the family Filarioidea . 90% of infections are caused by Wuchereria bancrofti and the remainder by Brugia spp . In endemic countries , LF has a major social and economic impact with an estimated annual loss of $1 billion . Filarial infection can cause... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"body",
"fluids",
"enzymes",
"enzymology",
"parasitic",
"diseases",
"animals",
"nematode",
"infections",
"endocrine",
"physiology",
"serine",
"proteases",
"infectious",
"disease",
"control... | 2018 | Insulin receptor knockdown blocks filarial parasite development and alters egg production in the southern house mosquito, Culex quinquefasciatus |
All class I phosphoinositide 3-kinases ( PI3Ks ) associate tightly with regulatory subunits through interactions that have been thought to be constitutive . PI3Kγ is key to the regulation of immune cell responses activated by G protein-coupled receptors ( GPCRs ) . Remarkably we find that PKCβ phosphorylates Ser582 in ... | Phosphoinositide 3-kinases ( PI3Ks ) are involved in most essential cellular processes . Class I PI3Ks are heterodimers: class IA PI3Ks are made up of one of a group of regulatory p85-like subunits and one p110α , p110β , or p110δ catalytic p110 subunit , and are activated via binding of their p85 subunit to phosphoryl... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"enzyme",
"structure",
"signal",
"transduction",
"phosphoinositide",
"signal",
"transduction",
"inflammation",
"immunity",
"enzymes",
"allergy",
"and",
"hypersensitivity",
"immunology",
"signaling",
"pathways",
"biology",
"molecular",
"cell",
"biology"
] | 2013 | PKCβ Phosphorylates PI3Kγ to Activate It and Release It from GPCR Control |
Natural proteins often partake in several highly specific protein-protein interactions . They are thus subject to multiple opposing forces during evolutionary selection . To be functional , such multispecific proteins need to be stable in complex with each interaction partner , and , at the same time , to maintain affi... | In nature , some proteins are more social than others , interacting with a large number of partners . These “promiscuous” proteins play key roles in cellular signaling pathways whose disruption may lead to diseases such as cancer . The amino acid sequences of such proteins must have evolved to be optimal for combined i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/macromolecular",
"structure",
"analysis",
"molecular",
"biology/molecular",
"evolution",
"biochemistry/protein",
"folding",
"biophysics/theory",
"and",
"simulation",
"molecular",
"biology/bioinformatics",
"computational",
"biology/macromolecular",
"sequence"... | 2009 | Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins |
Recent imaging studies of mitochondrial dynamics have implicated a cycle of fusion , fission , and autophagy in the quality control of mitochondrial function by selectively increasing the membrane potential of some mitochondria at the expense of the turnover of others . This complex , dynamical system creates spatially... | Mitochondria are the powerhouses of eukaryotic cells , oxidizing glucose to produce ATP . Most cells harbor tens to hundreds of mitochondria in a constant state of flux , in which they fuse with one another , undergo fission , import proteins to grow larger , and eventually are recycled by autophagy . These dynamic pro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"biophysic",
"al",
"simulations",
"biology",
"computational",
"biology"
] | 2013 | Optimal Dynamics for Quality Control in Spatially Distributed Mitochondrial Networks |
The SWR1 chromatin remodeling complex , which deposits the histone variant H2A . Z into nucleosomes , has been well characterized in yeast and animals , but its composition in plants has remained uncertain . We used the conserved SWR1 subunit ACTIN RELATED PROTEIN 6 ( ARP6 ) as bait in tandem affinity purification expe... | The histone H2A variant , H2A . Z , is found in all known eukaryotes and plays important roles in transcriptional regulation . H2A . Z is selectively incorporated into nucleosomes within many genes by the activity of a conserved ATP-dependent chromatin remodeling complex in yeast , insects , and mammals . Whether this ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"biotechnology",
"engineering",
"and",
"technology",
"brassica",
"dna-binding",
"proteins",
"fungi",
"plant",
"science",
"model",
"organisms",
"genetically",
"modified",
"plants",
"experimental",
"organism",
"systems",
"epigenetics",
"molecular",
"biology",
"techniques",
... | 2019 | Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome |
Bacterial microcompartments ( MCPs ) are protein-bound organelles that carry out diverse metabolic pathways in a wide range of bacteria . These supramolecular assemblies consist of a thin outer protein shell , reminiscent of a viral capsid , which encapsulates sequentially acting enzymes . The most complex MCP elucidat... | Many bacteria produce giant proteinaceous structures within their cells , which they use to carry out special metabolic reactions in their interior . Much has been learned recently about the individual components—shell proteins and encapsulated enzymes—that assemble together , thousands of subunits in all , to make the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment |
Analysis by liquid chromatography and tandem mass spectrometry ( LC-MS/MS ) can identify and quantify thousands of proteins in microgram-level samples , such as those comprised of thousands of cells . This process , however , remains challenging for smaller samples , such as the proteomes of single mammalian cells , be... | Identifying and quantifying proteins in single cells gives researchers the ability to tackle complex biological problems that involve single cell heterogeneity , such as the treatment of solid tumors . Mass spectrometry analysis of peptides can identify their sequence from their masses and the masses of their fragment ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immunology",
"experimental",
"design",
"database",
"searching",
"research",
"design",
"probability",
"distribution",
"mathematics",
"research",
"and",
"analysis",
"methods",
"information",
"r... | 2019 | DART-ID increases single-cell proteome coverage |
Ten years on from the finishing of the human reference genome sequence , it remains unclear what fraction of the human genome confers function , where this sequence resides , and how much is shared with other mammalian species . When addressing these questions , functional sequence has often been equated with pan-mamma... | Nearly 99% of the human genome does not encode proteins , and while there recently has been extensive biochemical annotation of the remaining noncoding fraction , it remains unclear whether or not the bulk of these DNA sequences have important functional roles . By comparing the genome sequences of different species we... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genomics",
"functional",
"genomics",
"genome",
"evolution",
"genetics",
"biology",
"and",
"life",
"sciences",
"comparative",
"genomics",
"computational",
"biology"
] | 2014 | 8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage |
The oral microbiome–organisms residing in the oral cavity and their collective genome–are critical components of health and disease . The fungal component of the oral microbiota has not been characterized . In this study , we used a novel multitag pyrosequencing approach to characterize fungi present in the oral cavity... | We characterized the fungal microbiome ( mycobiome ) of the oral cavity in healthy individuals . Our results demonstrate that the fungal component of the oral microbiome is diverse as revealed by the presence of 74 culturable and 11 non-culturable fungal genera in the oral cavity . A total of 101 species were identifie... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"molecular",
"biology/bioinformatics",
"microbiology/microbial",
"physiology",
"and",
"metabolism",
"microbiology"
] | 2010 | Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals |
Escherichia coli bacteria respond to DNA damage by a highly orchestrated series of events known as the SOS response , regulated by transcription factors , protein–protein binding , and active protein degradation . We present a dynamical model of the UV-induced SOS response , incorporating mutagenesis by the error-prone... | Ultraviolet light damages the DNA of cells , which prevents duplication and thereby cell division . Bacteria respond to such damage by producing a number of proteins that help to detect , bypass , and repair the damage . This SOS response system displays intricate dynamical behavior—in particular the tightly regulated ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"eubacteria",
"computational",
"biology"
] | 2007 | UV-Induced Mutagenesis in Escherichia coli SOS Response: A Quantitative Model |
House dust mites are common pests with an unusual evolutionary history , being descendants of a parasitic ancestor . Transition to parasitism is frequently accompanied by genome rearrangements , possibly to accommodate the genetic change needed to access new ecology . Transposable element ( TE ) activity is a source of... | Investigation of small RNA populations in dust mites revealed absence of the piwi-associated RNA ( piRNA ) pathway . Apart from several nematode and platyhelminths lineages , piRNAs are an essential component of animal genome surveillance , actively targeting and silencing transposable elements . In dust mites , expans... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"sequencing",
"techniques",
"invertebrates",
"rna",
"interference",
"gene",
"regulation",
"invertebrate",
"genomics",
"animals",
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"experimental",
"organism",
"systems",
"sequence",
"motif",
"analysis",
... | 2018 | Rewired RNAi-mediated genome surveillance in house dust mites |
Metabolic fluxes are a cornerstone of cellular physiology that emerge from a complex interplay of enzymes , carriers , and nutrients . The experimental assessment of in vivo intracellular fluxes using stable isotopic tracers is essential if we are to understand metabolic function and regulation . Flux estimation based ... | Living cells adapt to ever-changing environments by regulating metabolic fluxes , the rates of nutrient flow through the metabolic network , to produce metabolites that are currently in demand . 13C-labeling techniques coupled with metabolic flux analyses are widely used to estimate metabolic fluxes and provide insight... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"carbohydrate",
"metabolism",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"pathogens",
"metabolic",
"networks",
"experimental",
"design",
"bacillus",
"microbiology",
"carbohydrates",
... | 2016 | SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis |
Cellular sophistication is not exclusive to multicellular organisms , and unicellular eukaryotes can resemble differentiated animal cells in their complex network of membrane-bound structures . These comparisons can be illuminated by genome-wide surveys of key gene families . We report a systematic analysis of Rabs in ... | Single-celled organisms appear simple compared to multicellular organisms , but this may not be true at the level of the individual cell . In fact , microscopic observations suggest that protists can possess networks of organelles just as elaborate as those in animal cells . Consistent with this idea , recent analysis ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"evolutionary",
"biology/genomics",
"cell",
"biology/membranes",
"and",
"sorting",
"evolutionary",
"biology/developmental",
"molecular",
"mechanisms",
"evolutionary",
"biology/morphogenesis",
"and",
"cell",
"b... | 2010 | Comprehensive Analysis Reveals Dynamic and Evolutionary Plasticity of Rab GTPases and Membrane Traffic in Tetrahymena thermophila |
CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs ( sgRNAs ) . This approach has been widely adopted for diverse applications , from disease modelling of individual loci , to parallelized loss-of-function screens of thousands of regulatory elements . However , no s... | CRISPR-Cas9 is a revolutionary biological technique for precisely editing cells’ genomes . Amongst its many capabilities is the deletion of defined regions of DNA , creating a wide range of applications from modelling rare human diseases , to performing very large knock-out screens of candidate regulatory DNA . CRISPR-... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"genome",
"engineering",
"engineering",
"and",
"technology",
"synthetic",
"biology",
"genomic",
"library",
"screening",
"invertebrate",
"genomics",
"synthetic",
"bioengineering",
"crispr",
"genomic",
"databases",
"genome",
"analysis",
"mammalian",
"genomics... | 2017 | Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion |
Mycetoma , one of the badly neglected tropical diseases , it is a localised chronic granulomatous inflammatory disease characterised by painless subcutaneous mass and formation of multiple sinuses that produce purulent discharge and grains . If untreated early and appropriately , it usually spread to affect the deep st... | Mycetoma enjoys all the neglected tropical diseases ( NTDs ) characteristics . It frequently affects the poorest of the poor in poor communities in remote regions . The affected population are of low socio-economic status , of low visibility and low political and social voice and hence they are neglected . The disease ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"mycetoma",
"tropical",
"diseases",
"patient",
"advocacy",
"geographical",
"locations",
"sudan",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"health",
"care",
"signs",
"... | 2018 | A holistic approach to the mycetoma management |
Helicobacter pylori’s ability to respond to environmental cues in the stomach is integral to its survival . By directly visualizing H . pylori swimming behavior when encountering a microscopic gradient consisting of the repellent acid and attractant urea , we found that H . pylori is able to simultaneously detect both ... | Helicobacter pylori is a bacterium that chronically infects the stomachs of 50% of humans , and infection can lead to serious diseases like peptic ulcers and stomach cancer . To survive , H . pylori rapidly senses acid and swims away to the protective mucus layer covering the stomach surface . The bacteria also burrow ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"urea",
"swimming",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"ureases",
"enzymes",
"pathogens",
"microbiology",
"enzymology",
"organic",
"compounds",
"biomechanics",
"biological",
"locomotion",
"helico... | 2017 | Multiple Acid Sensors Control Helicobacter pylori Colonization of the Stomach |
Microbes may maximize the number of daughter cells per time or per amount of nutrients consumed . These two strategies correspond , respectively , to the use of enzyme-efficient or substrate-efficient metabolic pathways . In reality , fast growth is often associated with wasteful , yield-inefficient metabolism , and a ... | When cells compete for nutrients , those that grow faster and produce more offspring per time are favored by natural selection . In contrast , when cells need to maximize the cell number at a limited nutrient supply , fast growth does not matter and an efficient use of nutrients ( i . e . high biomass yield ) is essent... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"physiology",
"carbohydrate",
"metabolism",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"enzymes",
"oxygen",
"enzymology",
"carbohydrates",
"glucose",
"metabolism",
"organic",
"compounds",
"glucose",
"cell",
"metabolism",
"physiological",
"pr... | 2018 | Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield |
Whole-genome regression methods are being increasingly used for the analysis and prediction of complex traits and diseases . In human genetics , these methods are commonly used for inferences about genetic parameters , such as the amount of genetic variance among individuals or the proportion of phenotypic variance tha... | Whole-genome regression ( WGR ) methods are being increasingly used for inferring the proportion of variance that can be explained by a linear regression on a massive number of markers , called ‘genomic heritability . ’ However , the statistical assumptions involved in WGRs are somewhat at odds with important quantitat... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Discussion"
] | [] | 2015 | Genomic Heritability: What Is It? |
In the Old World , sandfly species of the genus Phlebotomus are known vectors of Leishmania , Bartonella and several viruses . Recent sandfly catches and autochthonous cases of leishmaniasis hint on spreading tendencies of the vectors towards Central Europe . However , studies addressing potential future distribution o... | Growing evidence exists on the emergence of sandfly-borne diseases in the light of climate change . Determining the principle responses of phlebotomine sandflies to climatic changes supports our understanding of future regions that will be threatened by new-establishments of this important group of disease vectors . Th... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"geography",
"public",
"health",
"and",
"epidemiology",
"mathematics",
"environmental",
"sciences",
"ecology",
"earth",
"sciences",
"statistics",
"biology",
"public",
"health",
"physical",
"geography",
"veterinary",
"science",
"veteri... | 2011 | Combining Climatic Projections and Dispersal Ability: A Method for Estimating the Responses of Sandfly Vector Species to Climate Change |
Hundreds of genes show aberrant DNA hypermethylation in cancer , yet little is known about the causes of this hypermethylation . We identified RIL as a frequent methylation target in cancer . In search for factors that influence RIL hypermethylation , we found a 12-bp polymorphic sequence around its transcription start... | The factors that guide DNA hypermethylation in cancer are poorly understood . We identified the candidate tumor-suppressor gene , RIL , as a frequent methylation target in cancer . Here , we report on a 12-bp polymorphic sequence around its transcription start site that creates a long allele . Methylation analysis show... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"gastroenterology",
"and",
"hepatology/gastrointestinal",
"cancers",
"genetics",
"and",
"genomics/gene",
"expression",
"hematology/acute",
"myeloid",
"leukemia",
"molecular",
"biology/dna",
"methylation",
"oncology/gastrointestinal",
"cancers",
"genetics",
"and",
"genomics/epigen... | 2008 | An Sp1/Sp3 Binding Polymorphism Confers Methylation Protection |
Human Papillomaviruses ( HPV ) cause widespread infections in humans , resulting in latent infections or diseases ranging from benign hyperplasia to cancers . HPV-induced pathologies result from complex interplays between viral proteins and the host proteome . Given the major public health concern due to HPV-associated... | Over 100 types of human papillomaviruses are responsible for widespread infections in humans . They cause a wide range of pathologies , ranging from inapparent infections to benign lesions , hyperplasia or cancers . Such heterogeneity results from variable interplay among viral and host cell proteins . Aiming to identi... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"virology",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"genetics",
"and",
"genomics"
] | 2012 | Large Scale Genotype Comparison of Human Papillomavirus E2-Host Interaction Networks Provides New Insights for E2 Molecular Functions |
CD8+ T cell exhaustion represents a major hallmark of chronic HIV infection . Two key transcription factors governing CD8+ T cell differentiation , T-bet and Eomesodermin ( Eomes ) , have previously been shown in mice to differentially regulate T cell exhaustion in part through direct modulation of PD-1 . Here , we exa... | CD8+ T cells display numerous traits of severe dysfunction in both treated and untreated HIV infection . Previous studies have demonstrated that HIV-specific CD8+ T cells in most individuals possess poor polyfunctionality , and an immature/skewed maturation phenotype . However , it remains unclear which transcriptional... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immunology",
"microbiology",
"immunodeficiency",
"viruses",
"infectious",
"diseases",
"white",
"blood",
"cells",
"animal",
"cells",
"medical",
"microbiology",
"hiv",
"t",
"cells",
"microbia... | 2014 | T-bet and Eomes Are Differentially Linked to the Exhausted Phenotype of CD8+ T Cells in HIV Infection |
Disordered protein-protein interactions ( PPIs ) , those involving a folded protein and an intrinsically disordered protein ( IDP ) , are prevalent in the cell , including important signaling and regulatory pathways . IDPs do not adopt a single dominant structure in isolation but often become ordered upon binding . To ... | A substantial fraction of the proteins encoded in genomes are intrinsically disordered proteins ( IDPs ) , which lack a single stable structure in the native state . IDPs serve many functions including mediating protein-protein interactions ( PPIs ) . Such disordered PPIs are prevalent in important regulatory pathways ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"molecular",
"dynamics",
"protein",
"structure",
"prediction",
"protein",
"structure",
"intrinsically",
"disordered",
"proteins",
"research",
"and",
"analysis",
"methods",
"protein",
"structure",
"determination",
"proteins",
"biological",
"databases",
"structural",
"protein... | 2017 | Modeling disordered protein interactions from biophysical principles |
Inferior olivary activity causes both short-term and long-term changes in cerebellar output underlying motor performance and motor learning . Many of its neurons engage in coherent subthreshold oscillations and are extensively coupled via gap junctions . Studies in reduced preparations suggest that these properties pro... | Activity of the inferior olive , transmitted via climbing fibers to the cerebellum , regulates initiation and amplitude of movements , signals unexpected sensory feedback , and directs cerebellar learning . It is characterized by widespread subthreshold oscillations and synchronization promoted by strong electrotonic c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"olives",
"cell",
"physiology",
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"potentials",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"nervous",
"system",
"membrane",
"potential",
"junctional",
"complexes",
"electrophysiology",
"neuroscience",
"gap",
"junctions",
"network",
"analysis",
... | 2019 | Quasiperiodic rhythms of the inferior olive |
Visually evoked signals in the retina pass through the dorsal geniculate nucleus ( dLGN ) on the way to the visual cortex . This is however not a simple feedforward flow of information: there is a significant feedback from cortical cells back to both relay cells and interneurons in the dLGN . Despite four decades of ex... | On route from the retina to primary visual cortex , visually evoked signals have to pass through the dorsal lateral geniculate nucleus ( dLGN ) . However , this is not an exclusive feedforward flow of information as feedback exists from neurons in the cortex back to both relay cells and interneurons in the dLGN . The f... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Discussion"
] | [
"fourier",
"analysis",
"engineering",
"and",
"technology",
"signal",
"processing",
"social",
"sciences",
"vertebrates",
"neuroscience",
"animals",
"mammals",
"kernel",
"functions",
"mathematics",
"ganglion",
"cells",
"amniotes",
"interneurons",
"vision",
"research",
"and"... | 2018 | Firing-rate based network modeling of the dLGN circuit: Effects of cortical feedback on spatiotemporal response properties of relay cells |
Experimental recordings in hippocampal slices indicate that astrocytic dysfunction may cause neuronal hyper-excitation or seizures . Considering that astrocytes play important roles in mediating local uptake and spatial buffering of K+ in the extracellular space of the cortical circuit , we constructed a novel model of... | Astrocytes are critical regulators of normal physiological activity in the central nervous system , and one of their key functions is removing extracellular K+ . In recent years , numerous biological studies have shown that astrocytic Kir4 . 1 channels and gap junctions between astrocytes act as major K+ clearance mech... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"medicine",
"and",
"health",
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"networks",
"nervous",
"system",
"astrocytes",
"membrane",
"potential",
"junctional",
"complexes",
"electrophysiology",
"neuroscience",
"macroglial",
"cells",
"epileptic",
"seizures",
"gap",
"junctio... | 2018 | Astrocytic Kir4.1 channels and gap junctions account for spontaneous epileptic seizure |
Comorbidity patterns have become a major source of information to explore shared mechanisms of pathogenesis between disorders . In hypothesis-free exploration of comorbid conditions , disease-disease networks are usually identified by pairwise methods . However , interpretation of the results is hindered by several con... | Depression is one of the most common of psychiatric disorders and its causation is correspondingly multifactorial , complex and heterogeneous . It occurs in combination with a number of physical illnesses far more commonly than expected by chance . Such comorbidities may be important clues pointing to shared environmen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"body",
"weight",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"migraine",
"headaches",
"physiological",
"parameters",
"signs",
"and",
"symptoms",
"obesity",
"mood",
"disorders",
"genetic",
"epidemiology",
"epidemiology",
"hyper... | 2017 | Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression |
Motility and phagocytosis are key processes that are involved in invasive amoebiasis disease caused by intestinal parasite Entamoeba histolytica . Previous studies have reported unconventional myosins to play significant role in membrane based motility as well as endocytic processes . EhMyosin IB is the only unconventi... | Entamoeba histolyica is a highly motile human pathogen which eats the blood cells and immune cells by phagocytosis during progression of Amoebiasis disease . E . histolytica infections are a major concern in the developing countries . Myosins are motor proteins that move over actin cytoskeleton to drive the cellular pr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"motility",
"actin",
"filaments",
"cell",
"processes",
"parasitic",
"protozoans",
"guanine",
"nucleotide",
"exchange",
"factors",
"molecular",
"motors",
"actin",
"motors",
"protozoans",
"motor",
"proteins",
"contractile",
"proteins",
"actins",
"proteins",
"entam... | 2019 | EhFP10: A FYVE family GEF interacts with myosin IB to regulate cytoskeletal dynamics during endocytosis in Entamoeba histolytica |
Emerging pathogens are a major threat to public health , however understanding how pathogens adapt to new niches remains a challenge . New methods are urgently required to provide functional insights into pathogens from the massive genomic data sets now being generated from routine pathogen surveillance for epidemiolog... | Researchers are now collecting a wealth of genomic data from bacterial pathogens , and this will continue to grow with the introduction of routine sequencing for disease surveillance . However , our ability to use this data to predict how changes in genome sequence lead to differences in disease is limited . Here , we ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"markov",
"models",
"engineering",
"and",
"technology",
"pathogens",
"microbiology",
"decision",
"analysis",
"bacterial",
"diseases",
"mathematics",
"management",
"engineering",
"entero... | 2018 | Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica |
The Fell and Dales are rare native UK pony breeds at risk due to falling numbers , in-breeding , and inherited disease . Specifically , the lethal Mendelian recessive disease Foal Immunodeficiency Syndrome ( FIS ) , which manifests as B-lymphocyte immunodeficiency and progressive anemia , is a substantial threat . A si... | Foal Immunodeficiency Syndrome ( FIS ) is a genetic disease that affects two related British pony breeds , namely the Fell and the Dales . Foals with FIS appear to be normal at birth but within a few weeks develop evidence of infection such as diarrhoea , pneumonia , etc . The infections are resistant to treatment , an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"types",
"animal",
"genetics",
"immunology",
"lymphoid",
"organs",
"veterinary",
"diagnostics",
"veterinary",
"science",
"veterinary",
"medicine",
"biology",
"immune",
"system",
"veterinary",
"immunology",
"genetics",
"of",
"the",
"immune",
"system",
"large",
... | 2011 | Identification of a Mutation Associated with Fatal Foal Immunodeficiency Syndrome in the Fell and Dales Pony |
Reversible infantile liver failure ( RILF ) is a unique heritable liver disease characterized by acute liver failure followed by spontaneous recovery at an early stage of life . Genetic mutations in MTU1 have been identified in RILF patients . MTU1 is a mitochondrial enzyme that catalyzes the 2-thiolation of 5-taurinom... | Mitochondrial transfer tRNA ( mt-tRNA ) contains a variety of chemical modifications that are introduced post-transcriptionally . Three mt-tRNAs for Lys , Gln and Glu contain 5-taurinomethyl-2-thiouridine ( τm5s2U ) in their anticodons . It is known that the loss of 2-thiolation of τm5s2U is strongly associated with th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"transfer",
"rna",
"medicine",
"and",
"health",
"sciences",
"liver",
"oxidative",
"stress",
"animal",
"models",
"developmental",
"biology",
"model",
"organisms",
"mitochondria",
"bioenergetics",
"embryos",
"cellular",
"structures",
"and",
"organelles",
"research",
"and"... | 2016 | Mtu1-Mediated Thiouridine Formation of Mitochondrial tRNAs Is Required for Mitochondrial Translation and Is Involved in Reversible Infantile Liver Injury |
The mechanism underlying immune system recognition of different types of pathogens has been extensively studied over the past few decades; however , the mechanism by which healthy self-tissue evades an attack by its own immune system is less well-understood . Here , we established an autoimmune model of melanotic mass ... | Autoimmune diseases may be caused by failures in the immune system or by altered selfness in target tissues; however , which of these is more critical is controversial . To better understand such diseases , it is necessary to first define the molecular mechanisms that provide self-tolerance to healthy tissues . As a mo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics",
"biology",
"and",
"life",
"sciences",
"immunology",
"developmental",
"biology"
] | 2014 | Basement Membrane and Cell Integrity of Self-Tissues in Maintaining Drosophila Immunological Tolerance |
The genus Enterovirus of the family Picornaviridae contains many important human pathogens ( e . g . , poliovirus , coxsackievirus , rhinovirus , and enterovirus 71 ) for which no antiviral drugs are available . The viral RNA-dependent RNA polymerase is an attractive target for antiviral therapy . Nucleoside-based inhi... | Virus replication relies on multiplication of viral genomes by viral polymerases . For enteroviruses , a large group of clinically important human pathogens for which no antiviral therapy is available , this function is performed by 3Dpol , the RNA-dependent RNA polymerase . 3Dpol is therefore an attractive target for ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The RNA Template Channel of the RNA-Dependent RNA Polymerase as a Target for Development of Antiviral Therapy of Multiple Genera within a Virus Family |
Important cellular processes such as migration , differentiation , and development often rely on precise timing . Yet , the molecular machinery that regulates timing is inherently noisy . How do cells achieve precise timing with noisy components ? We investigate this question using a first-passage-time approach , for a... | Cells control important processes with precise timing , even though their underlying molecular machinery is inherently imprecise . In the case of Caenorhabditis elegans development , migrating neuroblast cells produce a molecule until a certain abundance is reached , at which time the cells stop moving . Precise timing... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"cell",
"motility",
"engineering",
"and",
"technology",
"caenorhabditis",
"cell",
"cycle",
"and",
"cell",
"division",
"signal",
"processing",
"cell",
"processes",
"animals",
"noise",
"reduction",
"animal",
"models",
"developmental",
"biology",
"regulato... | 2018 | Temporal precision of regulated gene expression |
Nutrient availability is an important environmental variable during development that has significant effects on the metabolism , health , and viability of an organism . To understand these interactions for the nutrient copper , we used a chemical genetic screen for zebrafish mutants sensitive to developmental copper de... | Copper is an essential nutrient required for multiple biologic functions . Proper uptake , transport , and excretion of copper are critical for use of this metal while reducing its inherent toxicity . While several key proteins involved in this process have been identified , there are still gaps in our understanding of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/animal",
"genetics",
"genetics",
"and",
"genomics/gene",
"discovery",
"nutrition",
"genetics",
"and",
"genomics/disease",
"models",
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"genetics",
"and",
"genomics/gene",
"function",
"neuro... | 2008 | Zebrafish Mutants calamity and catastrophe Define Critical Pathways of Gene–Nutrient Interactions in Developmental Copper Metabolism |
Intestinal homeostasis requires precise control of intestinal stem cell ( ISC ) proliferation . In Drosophila , this control declines with age largely due to chronic activation of stress signaling and associated chronic inflammatory conditions . An important contributor to this condition is the age-associated increase ... | The long-term maintenance of tissue homeostasis in barrier epithelia requires precise coordination of cellular stress and inflammatory responses with regenerative processes . This coordination is lost with age , resulting in degenerative and proliferative diseases . The Unfolded Protein Response of the Endoplasmic Reti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | PERK Limits Drosophila Lifespan by Promoting Intestinal Stem Cell Proliferation in Response to ER Stress |
Insects determine their body segments in two different ways . Short-germband insects , such as the flour beetle Tribolium castaneum , use a molecular clock to establish segments sequentially . In contrast , long-germband insects , such as the vinegar fly Drosophila melanogaster , determine all segments simultaneously t... | Different insect species exhibit one of two distinct modes of determining their body segments ( known as segmentation ) during development: they either use a molecular oscillator to position segments sequentially , or they generate segments simultaneously through a hierarchical gene-regulatory cascade . The sequential ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"morphogenic",
"segmentation",
"gene",
"regulation",
"animals",
"blastulas",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organisms",
"systems",
"science",
"mathematics",
"experimental",
"organism",
"systems",
"emb... | 2018 | A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila |
The mortality of salmon smolts during their migration out of freshwater and into the ocean has been difficult to measure . In the Columbia River , which has an extensive network of hydroelectric dams , the decline in abundance of adult salmon returning from the ocean since the late 1970s has been ascribed in large meas... | Miniature electronic technologies now allow researchers to track a salmon's migration from its birthplace in a river's headwaters in the Rocky Mountains to the North Pacific , opening a window on the mysteries of migration and survival . Surprisingly , outward migrating salmon ( smolts ) have similar survival during mi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"ecology"
] | 2008 | Survival of Migrating Salmon Smolts in Large Rivers With and Without Dams |
Grid cells have attracted broad attention because of their highly symmetric hexagonal firing patterns . Recently , research has shifted its focus from the global symmetry of grid cell activity to local distortions both in space and time , such as drifts in orientation , local defects of the hexagonal symmetry , and the... | Grid cells are neurons in mammals whose activity depends on the location of the animal in a striking way: grid cells fire spikes at multiple locations that form a symmetric lattice of repeating hexagons . Recent experiments have shown that the symmetry of these patterns is not as stable as initially thought . For examp... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"ecology",
"and",
"environmental",
"sciences",
"cell",
"cycle",
"and",
"cell",
"division",
"applied",
"mathematics",
"cell",
"processes",
"condensed",
"matter",
"physics",
"social",
"sciences",
"light",
"neuroscience",
"electromagnetic",
"radiation",
"simulation",
"and"... | 2019 | A local measure of symmetry and orientation for individual spikes of grid cells |
Mycobacterium tuberculosis ( Mtb ) virulence is decreased by genetic deletion of the lipoprotein LprG , but the function of LprG remains unclear . We report that LprG expressed in Mtb binds to lipoglycans , such as lipoarabinomannan ( LAM ) , that mediate Mtb immune evasion . Lipoglycan binding to LprG was dependent on... | The causative agent of tuberculosis , Mycobacterium tuberculosis ( Mtb ) , persists in phagosomes inside infected macrophages . Mtb expresses lipoarabinomannan ( LAM ) , which inhibits fusion of phagosomes with lysosomes as a means for Mtb to evade host defense . LAM is present in the cell envelope , which surrounds Mt... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"microbiology",
"bacterial",
"diseases",
"immunomodulation",
"infectious",
"diseases",
"proteins",
"medical",
"microbiology",
"tuber... | 2014 | Mycobacterium tuberculosis Lipoprotein LprG Binds Lipoarabinomannan and Determines Its Cell Envelope Localization to Control Phagolysosomal Fusion |
In many bacteria the ParA-ParB protein system is responsible for actively segregating DNA during replication . ParB proteins move by interacting with DNA bound ParA-ATP , stimulating their unbinding by catalyzing hydrolysis , that leads to rectified motion due to the creation of a wake of depleted ParA . Recent in vitr... | Segregating genetic material is essential for cell survival over multiple generations . The process underlying the required spatio-temporal organization of DNA is mediated by the ParA-ParB-parS system . Recently , experiments have shown that directed motion can be reconstituted in vitro . In these experiments , a magne... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Operational Principles for the Dynamics of the In Vitro ParA-ParB System |
Schistosomiasis is a chronic parasitic trematode disease that affects over 240 million people worldwide . The Schistosoma lifecycle is complex , involving transmission via specific intermediate-host freshwater snails . Predictive mathematical models of Schistosoma transmission have often chosen to simplify or ignore th... | Infection with blood fluke Schistosoma parasites is a major cause of disease burden around the world . Control of schistosomiasis , which is transmitted through intermediate host freshwater snails , is a priority for national and global health programs working in at-risk regions of Africa , the Mideast , Asia , the Phi... | [
"Abstract",
"Introduction",
"Methods",
"and",
"models",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"helminths",
"tropical",
"diseases",
"parasitic",
"diseases",
"animals",
"systems",
"science",
"gastropods",
"mathematics",
"neglected",
"tropical",
"diseases",
"population",
"biology",
"infectious",
... | 2018 | The human-snail transmission environment shapes long term schistosomiasis control outcomes: Implications for improving the accuracy of predictive modeling |
In phenotypically heterogeneous microbial populations , the decision to adopt one or another phenotype is often stochastically regulated . However , how this stochasticity affects interactions between competing microbes in mixed communities is difficult to assess . One example of such an interaction system is the compe... | Competition is the dominant interaction type between species of bacteria . Bacterial toxin-mediated competition is often accompanied by a division of labor between toxin-producing cells and reproducers within a species . In populations with large cell numbers , the stochastic dynamics that determine if an individual ce... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"toxins",
"pathology",
"and",
"laboratory",
"medicine",
"toxicology",
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"and",
"modeling",
"luminescent",
"proteins",
"phase",
"diagrams",
"yellow",
"fluorescent",
"protein",
"bioassays",
"and",
"... | 2017 | Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli |
Obesity is a growing epidemic characterized by excess fat storage in adipocytes . Although lipoprotein receptors play important roles in lipid uptake , their role in controlling food intake and obesity is not known . Here we show that the lipoprotein receptor LRP1 regulates leptin signaling and energy homeostasis . Con... | The World Health Organization estimates that at least 1 in 10 adults worldwide are obese , and in some western countries , a far greater percentage ( 25% or more ) is affected . Obesity is a serious concern because it increases the risk of cardiovascular disease , type 2 diabetes , and some cancers , among other health... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"diabetes",
"and",
"endocrinology/obesity",
"neuroscience/neuronal",
"signaling",
"mechanisms",
"neurological",
"disorders/neuroendocrinology",
"and",
"pituitary"
] | 2011 | Lipoprotein Receptor LRP1 Regulates Leptin Signaling and Energy Homeostasis in the Adult Central Nervous System |
Antitumor cyclopalladated complexes with low toxicity to laboratory animals have shown leishmanicidal effect . These findings stimulated us to test the leishmanicidal property of one palladacycle compound called DPPE 1 . 2 on Leishmania ( Leishmania ) amazonensis , an agent of simple and diffuse forms of cutaneous leis... | Leishmaniasis is an important public health problem with an estimated annual incidence of 1 . 5 million of new human cases of cutaneous leishmaniasis and 500 , 000 of visceral leishmaniasis . Treatment of the diseases is limited by toxicity and parasite resistance to the drugs currently in use , validating the need to ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"microbiology",
"parasitology"
] | 2012 | In Vitro and In Vivo Activity of a Palladacycle Complex on Leishmania (Leishmania) amazonensis |
T . pallidum subsp . endemicum ( TEN ) is the causative agent of bejel ( also known as endemic syphilis ) . Clinical symptoms of syphilis and bejel are overlapping and the epidemiological context is important for correct diagnosis of both diseases . In contrast to syphilis , caused by T . pallidum subsp . pallidum ( TP... | Uncultivable treponemes represent bacterial species and subspecies that are obligate pathogens of humans and animals causing diseases with distinct clinical manifestations . Treponema pallidum subsp . pallidum causes sexually transmitted syphilis , a multistage disease characterized in humans by localized , disseminate... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"genetics",
"biology",
"and",
"life",
"sciences",
"microbiology",
"molecular",
"biology"
] | 2014 | Whole Genome Sequence of the Treponema pallidum subsp. endemicum Strain Bosnia A: The Genome Is Related to Yaws Treponemes but Contains Few Loci Similar to Syphilis Treponemes |
Although mosquitoes serve as vectors of many pathogens of public health importance , their response to viral infection is poorly understood . It also remains to be investigated whether viruses deploy some mechanism to be able to overcome this immune response . Here , we have used an RNA-Seq approach to identify differe... | Mosquitoes are responsible for transmitting a large number of human and livestock viruses , like West Nile , dengue and Japanese encephalitis viruses . Infection of female mosquitoes with these viruses during blood feeding elicits an immune response . It is not known how the viruses manage to replicate in spite of this... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Cullin4 Is Pro-Viral during West Nile Virus Infection of Culex Mosquitoes |
We used the bioorthogonal protein precursor , homopropargylglycine ( HPG ) and chemical ligation to fluorescent capture agents , to define spatiotemporal regulation of global translation during herpes simplex virus ( HSV ) cell-to-cell spread at single cell resolution . Translational activity was spatially stratified d... | All viruses reprogram protein synthesis within infected cells for the production of their own proteins and for suppression of host antiviral responses . On the other hand , cells also modulate translation to suppress virus replication . Thus , global protein synthesis in infected cells represents the temporally regulat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"herpes",
"simplex",
"virus",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"pathogens",
"messenger",
"rna",
"microbiology",
"organic",
"compounds",
"geoinformatics",
"biochemical",
"analysis",
"viruses",
... | 2018 | A bimodal switch in global protein translation coupled to eIF4H relocalisation during advancing cell-cell transmission of herpes simplex virus |
Retroviruses affect a large number of species , from fish and birds to mammals and humans , with global socioeconomic negative impacts . Here the authors report and experimentally validate a novel approach for the analysis of the molecular networks that are involved in the recognition of substrates by retroviral protea... | Retroviruses are associated with a broad range of diseases that include tumor formation , neurological disorders , and immunodeficiency syndromes , including those of HIV . The extraordinary mutational plasticity of HIV-1 causes the rapid appearance of highly diverse quasi-species in a very short time , leading to seve... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"biochemistry",
"infectious",
"diseases",
"hiv",
"drug",
"resistance",
"multivariate",
"modelling",
"proteases",
"computational",
"biology",
"retroviruses"
] | 2007 | A Look Inside HIV Resistance through Retroviral Protease Interaction Maps |
Recent in-vitro studies have suggested that mast cells are involved in Dengue virus infection . To clarify the role of mast cells in the development of clinical Dengue fever , we compared the plasma levels of several mast cell-derived mediators ( vascular endothelial cell growth factor [VEGF] , soluble VEGF receptors [... | To clarify the involvement of mast cells in the development of severe Dengue diseases , plasma levels of mast cell-derived mediators , namely vascular endothelial cell growth factor ( VEGF ) , tryptase , and chymase , were estimated in Dengue patients and control subjects in Vietnam . The levels of the mediators were s... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"neglected",
"tropical",
"diseases"
] | 2012 | Association of Mast Cell-Derived VEGF and Proteases in Dengue Shock Syndrome |
Mycobacterium africanum , made up of lineages 5 and 6 within the Mycobacterium tuberculosis complex ( MTC ) , causes up to half of all tuberculosis cases in West Africa , but is rarely found outside of this region . The reasons for this geographical restriction remain unknown . Possible reasons include a geographically... | Mycobacterium africanum consists of two lineages , lineages 5 and 6 , within the Mycobacterium tuberculosis complex ( MTC ) that cause human tuberculosis in West Africa , but are found rarely outside of this region . Our analysis of the whole genome sequences of 26 lineage 5 and 6 isolates , and 66 isolates from other ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2016 | Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction |
Q fever is a widespread zoonosis that is caused by Coxiella burnetii ( C . burnetii ) , and ruminants are identified as the main sources of human infections . Some human cases have been described , but very limited information was available about Q fever in ruminants on Reunion Island , a tropical island in the Indian ... | Q fever is a disease that could be transmitted from animals ( cattle , sheep and goats ) to humans and caused by a bacterium called Coxiella burnetii ( C . burnetii ) . Some human cases exhibiting characteristic clinical signs of that disease have been detected on Reunion Island , a tropical island in the Indian Ocean ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"bacterial",
"diseases",
"infectious",
"diseases",
"veterinary",
"diseases",
"zoonoses",
"veterinary",
"epidemiology",
"medicine",
"and",
"health",
"sciences",
"veterinary",
"microbiology",
"biology",
"and",
"life",
"sciences",
"q",
"fever",
"veterinary",
"science"
] | 2014 | Emergence of Coxiella burnetii in Ruminants on Reunion Island? Prevalence and Risk Factors |
Rates of spontaneous mutation determine the ability of viruses to evolve , infect new hosts , evade immunity and undergo drug resistance . Contrarily to RNA viruses , few mutation rate estimates have been obtained for DNA viruses , because their high replication fidelity implies that new mutations typically fall below ... | Next-generation sequencing has provided a powerful tool for studying microbial genetic diversity but suffers from relatively low per-base accuracy , limiting our ability to detect low-frequency polymorphisms and spontaneous mutations . However , this limitation has been solved recently by the development of high-fideli... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing",
"techniques",
"microbial",
"mutation",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"insertion",
"mutation",
"pathogens",
"microbiology",
"viruses",
"mutation",
"substitution",
"mutation",
"dna",
"viruses",
"sequence... | 2016 | Genome-Wide Estimation of the Spontaneous Mutation Rate of Human Adenovirus 5 by High-Fidelity Deep Sequencing |
To survive , organisms must extract information from the past that is relevant for their future . How this process is expressed at the neural level remains unclear . We address this problem by developing a novel approach from first principles . We show here how to generate low-complexity representations of the past tha... | A crucial aspect of all life is the ability to use past events in order to guide future behavior . To do that , creatures need the ability to predict future events . Indeed , predictability has been shown to affect neuronal responses in many animals and under many conditions . Clearly , the quality of predictions shoul... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing",
"techniques",
"auditory",
"cortex",
"medicine",
"and",
"health",
"sciences",
"computational",
"biology",
"brain",
"random",
"variables",
"neuroscience",
"learning",
"and",
"memory",
"probability",
"distribution",
"mathematics",
"forecasting",
"statistics",
"... | 2016 | The Representation of Prediction Error in Auditory Cortex |
The factors influencing variation in the clinical forms of Chagas disease have not been elucidated; however , it is likely that the genetics of both the host and the parasite are involved . Several studies have attempted to correlate the T . cruzi strains involved in infection with the clinical forms of the disease by ... | Serological tests are preferentially used for the diagnosis of Chagas disease during the chronic phase because of the low parasitemia and high anti-T . cruzi antibody titers . However , contradictory or inconclusive results , mainly related to the characteristics of the antigens used , are often observed . Additionally... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Identification of Strain-Specific B-cell Epitopes in Trypanosoma cruzi Using Genome-Scale Epitope Prediction and High-Throughput Immunoscreening with Peptide Arrays |
The gastrointestinal microbiota influences immune function throughout the body . The gut-lung axis refers to the concept that alterations of gut commensal microorganisms can have a distant effect on immune function in the lung . Overgrowth of intestinal Candida albicans has been previously observed to exacerbate allerg... | The microbiome is the ecosystem of bacteria , fungi , viruses , and other microorganisms that live in and on us . The intestines are where most of these organisms reside , and the composition of the intestinal microbiota has a profound effect on immune system function throughout the body . In this manuscript , we obser... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"antimicrobials",
"medicine",
"and",
"health",
"sciences",
"microbiome",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"drugs",
"microbiology",
"animal",
"models",
"fungi",
"model",
"organisms",
"antibiotics",
"experimental",
"organism",
"systems",
"pharmacol... | 2018 | Expansion of commensal fungus Wallemia mellicola in the gastrointestinal mycobiota enhances the severity of allergic airway disease in mice |
Currently , there is no effective vaccine to halt HIV transmission . However , pre-exposure prophylaxis ( PrEP ) with the drug combination Truvada can substantially decrease HIV transmission in individuals at risk . Despite its benefits , Truvada-based PrEP is expensive and needs to be taken once-daily , which often le... | Pre-exposure prophylaxis ( PrEP ) is a novel , promising strategy to halt HIV transmission . PrEP with Truvada can substantially decrease the risk of infection . However , individuals often inadequately adhere to the once-daily regimen and the drug is expensive . These shortcomings may be overcome by next-generation Pr... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"antimicrobials",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"drugs",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"preventive",
"medicine",
"pre-exposure",
"prophyla... | 2019 | Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis |
The cell wall is a dynamic structure that is important for the pathogenicity of Candida albicans . Mannan , which is located in the outermost layer of the cell wall , has been shown to contribute to the pathogenesis of C . albicans , however , the molecular mechanism by which this occurs remains unclear . Here we ident... | Mannan plays a crucial role in cell wall structure and virulence of the opportunistic pathogen Candida albicans . Both the invasive ability of the pathogen and the host defense against the pathogen contribute to the outcome of invasive infection . In the present study , we identified a novel α-1 , 6-mannosyltransferase... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"cell",
"walls",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"cytokines",
"pathogens",
"immunology",
"microbiology",
"mutation",
"fung... | 2016 | Mnn10 Maintains Pathogenicity in Candida albicans by Extending α-1,6-Mannose Backbone to Evade Host Dectin-1 Mediated Antifungal Immunity |
The corn smut Ustilago maydis establishes a biotrophic interaction with its host plant maize . This interaction requires efficient suppression of plant immune responses , which is attributed to secreted effector proteins . Previously we identified Pep1 ( Protein essential during penetration-1 ) as a secreted effector w... | The maize pathogen U . maydis establishes a biotrophic interaction with its host plant and causes the formation of plant tumors . The U . maydis infection is initiated by a direct penetration of the plant epidermis and relies on living plant tissue . Therefore , suppression of the host immune system is essential for su... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"science",
"plant",
"biology",
"plant",
"pathogens",
"microbial",
"pathogens",
"plant",
"pathology",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"pathogenesis"
] | 2012 | The Ustilago maydis Effector Pep1 Suppresses Plant Immunity by Inhibition of Host Peroxidase Activity |
Meiotic chromosomes assemble characteristic “axial element” structures that are essential for fertility and provide the chromosomal context for meiotic recombination , synapsis and checkpoint signaling . Whether these meiotic processes are equally dependent on axial element integrity has remained unclear . Here , we in... | Meiosis is a specialized cellular division that reduces chromosome copy by half to produce four gametes . To ensure proper chromosome segregation , a meiotic cell must induce DNA double strand breaks , repair them with the homologous chromosome , and fully align the homologs . These aspects of meiosis are dependent on ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"phosphorylation",
"meiosis",
"medicine",
"and",
"health",
"sciences",
"homologous",
"chromosomes",
"chromosome",
"structure",
"and",
"function",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"meiotic",
"prophase",
"surgical",
"and",
"invasive",
"me... | 2017 | Reduced dosage of the chromosome axis factor Red1 selectively disrupts the meiotic recombination checkpoint in Saccharomyces cerevisiae |
One of the characteristics of prions is their ability to infect some species but not others and prion resistant species have been of special interest because of their potential in deciphering the determinants for susceptibility . Previously , we developed different in vitro and in vivo models to assess the susceptibili... | Detection of individuals or whole species resistant to any infectious disease is vital to understand the determinants of susceptibility and to develop appropriate therapeutic and preventative strategies . Canids have long been considered resistant to prion infection given the absence of clinical disease despite exposur... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"biotechnology",
"animal",
"types",
"animal",
"diseases",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"ruminants",
"immunology",
"vertebrates",
"pets",
"and",
"companion",
"animals",
"dogs",
"animals",
"mammals",
"animal",
"models",
"animal",
"pri... | 2017 | Unraveling the key to the resistance of canids to prion diseases |
The HCV NS5A protein plays multiple roles during viral replication , including viral genome replication and virus particle assembly . The crystal structures of the NS5A N-terminal domain indicated the potential existence of the NS5A dimers formed via at least two or more distinct dimeric interfaces . However , it is un... | HCV NS5A is a multifunctional protein involved in both viral RNA replication and infectious virus production , and is a target of one of the most potent antivirals available to date . However , the mode of action of NS5A inhibitors is still unclear due to the lack of mechanistic detail regarding NS5A functions during H... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"dimers",
"(chemical",
"physics)",
"microbial",
"mutation",
"medicine",
"and",
"health",
"sciences",
"crystal",
"structure",
"pathology",
"and",
"laboratory",
"medicine",
"intracellular",
"pathogens",
"pathogens",
"biological",
"cultures",
"condensed",
"matter",
"physics"... | 2018 | HCV NS5A dimer interface residues regulate HCV replication by controlling its self-interaction, hyperphosphorylation, subcellular localization and interaction with cyclophilin A |
Altered cell metabolism is inherently connected with pathological conditions including cancer and viral infections . Kaposi's sarcoma-associated herpesvirus ( KSHV ) is the etiological agent of Kaposi's sarcoma ( KS ) . KS tumour cells display features of lymphatic endothelial differentiation and in their vast majority... | Kaposi's sarcoma ( KS ) is the most common cancer in HIV-infected untreated individuals . Kaposi's sarcoma-associated herpesvirus ( KSHV ) is the infectious cause of this neoplasm . The discovery of KSHV and its oncogenic enigmas has enlightened many fields of tumor biology and viral oncogenesis . The metabolic propert... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"rna",
"micrornas",
"virology",
"biology",
"and",
"life",
"sciences",
"microbiology",
"metabolism",
"energy",
"metabolism"
] | 2014 | Kaposi's Sarcoma Herpesvirus MicroRNAs Induce Metabolic Transformation of Infected Cells |
Bone involvement in human cystic echinococcosis ( CE ) is rare , but affects the spine in approximately 50% of cases . Despite significant advances in diagnostic imaging techniques as well as surgical and medical treatment of spinal CE , our basic understanding of the parasite's predilection for the spine remains incom... | Spinal cystic echinococcosis ( CE ) is a rare but malignant form of a truly neglected tropical disease . Despite significant advances in diagnostic imaging techniques as well as surgical and medical treatment of spinal CE , our basic understanding of the parasite's predilection for the spine remains poor at best . Info... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Spinal Cystic Echinococcosis – A Systematic Analysis and Review of the Literature: Part 1. Epidemiology and Anatomy |
We have empirically assessed the distribution of published effect sizes and estimated power by analyzing 26 , 841 statistical records from 3 , 801 cognitive neuroscience and psychology papers published recently . The reported median effect size was D = 0 . 93 ( interquartile range: 0 . 64–1 . 46 ) for nominally statist... | Biomedical science , psychology , and many other fields may be suffering from a serious replication crisis . In order to gain insight into some factors behind this crisis , we have analyzed statistical information extracted from thousands of cognitive neuroscience and psychology research papers . We established that th... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"applied",
"mathematics",
"social",
"sciences",
"neuroscience",
"simulation",
"and",
"modeling",
"algorithms",
"cognitive",
"neuroscience",
"mathematics",
"statistics",
"(mathematics)",
"neuroimaging",
"research",
"and",
"analysis",
"methods",
"statistical",
"distributions",
... | 2017 | Empirical assessment of published effect sizes and power in the recent cognitive neuroscience and psychology literature |
A national survey in 1997 demonstrated that trachoma was endemic in Mali . Interventions to control trachoma including mass drug administration ( MDA ) with azithromycin were launched in the regions of Kayes and Koulikoro in 2003 . MDA was discontinued after three annual rounds in 2006 , and an impact survey conducted ... | Trachoma , a blinding bacterial disease , is targeted for elimination by 2020 . To achieve the elimination target , the World Health Organization ( WHO ) recommends member states implement the SAFE strategy; surgery , mass administration of antibiotics , promotion of hygiene and facial cleanliness and water and sanitat... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology/global",
"health",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases"
] | 2010 | Where Do We Go from Here? Prevalence of Trachoma Three Years after Stopping Mass Distribution of Antibiotics in the Regions of Kayes and Koulikoro, Mali |
Self-association is a common phenomenon in biology and one that can have positive and negative impacts , from the construction of the architectural cytoskeleton of cells to the formation of fibrils in amyloid diseases . Understanding the nature and mechanisms of self-association is important for modulating these system... | The self-association of peptides and proteins plays an important role in many serious diseases , such as Alzheimer's disease . A complete understanding of how peptides and proteins self-associate is important in creating therapeutics for such diseases . Additionally , self-associating peptides can be used as templates ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"computer",
"applications",
"medicine",
"and",
"health",
"sciences",
"engineering",
"and",
"technology",
"computer-aided",
"design",
"social",
"sciences",
"optimization",
"systems",
"science",
"mathematics",
"alzheimer",
"disease",
"bioengineering",
"comput... | 2014 | De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides |
Disease manifestations in neurocysticercosis ( NCC ) are frequently due to inflammation of degenerating Taenia solium brain cysts . Exacerbated inflammation post anthelmintic treatment is associated with leakage of the blood brain barrier ( BBB ) using Evans blue ( EB ) staining . How well EB extravasation into the bra... | Neurocysticercosis ( NCC ) is a frequent parasitic infection of the human brain in developing countries . The symptomatology of human NCC after antiparasitic treatment is generally related to inflammation . The presence and degree of enhancement after intravascular injection of the contrast agent gadolinium in magnetic... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"livestock",
"medicine",
"and",
"health",
"sciences",
"diagnostic",
"radiology",
"pathology",
"and",
"laboratory",
"medicine",
"pig",
"models",
"immunology",
"brain",
"vertebrates",
"cerebral",
"hemispheres",
"animals",
"mammals",
"left",
"hemisphere",
"magnetic",
"reso... | 2016 | Perilesional Inflammation in Neurocysticercosis - Relationship Between Contrast-Enhanced Magnetic Resonance Imaging, Evans Blue Staining and Histopathology in the Pig Model |
The robustness of complex biological processes in the face of environmental and genetic perturbations is a key biological trait . However , while robustness has been extensively studied , little is known regarding the fragility of biological processes . Here , we have examined the susceptibility of DNA replication and ... | Many biological processes are mediated by complex protein-protein interaction networks . The most highly connected proteins in such networks , termed hub proteins , precisely regulate biological processes by the regulated and sequential binding and releasing of partner proteins . In the case of DNA replication and repa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"biochemistry/molecular",
"evolution",
"molecular",
"biology/dna",
"replication",
"molecular",
"biology/dna",
"repair"
] | 2010 | Subtle Alterations in PCNA-Partner Interactions Severely Impair DNA Replication and Repair |
Few animals are known to lay eggs in the absence of ovulation or copulation , as it is presumably energetically wasteful and subjected to negative selection . Characterization of Smed-boule , a member of the DAZ family of germline RNA-binding proteins , revealed that egg capsule ( or capsule ) production and deposition... | Our work shows that production and deposition of egg capsules by planarian flatworms does not require fertilization , mating , ovulation , or even the existence of gametes . We also uncovered evidence for the existence of gender-specific germline stem cells in Schmidtea mediterranea , a hermaphroditic species of flatwo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"rna",
"interference",
"animals",
"germ",
"cells",
"oocytes",
"stem",
"cells",
"epigenetics",
"planarians",
"sperm",
"genetic",
"interference",
"animal",
"cells",
"flatworms",
"gene",
... | 2016 | Germline Defects Caused by Smed-boule RNA-Interference Reveal That Egg Capsule Deposition Occurs Independently of Fertilization, Ovulation, Mating, or the Presence of Gametes in Planarian Flatworms |
Vectors derived from human adenovirus type 5 , which typically lack the E1A and E1B genes , induce robust innate immune responses that limit their therapeutic efficacy . We reported previously that the E1B 55 kDa protein inhibits expression of a set of cellular genes that is highly enriched for those associated with an... | The most frequently used therapeutic vectors for gene transfer or cancer treatment are derived from human adenovirus type 5 ( Ad5 ) . We have observed previously that the E1B 55 kDa protein encoded by a gene routinely deleted from these vectors represses expression of numerous cellular genes regulated by interferon ( I... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"viral",
"immune",
"evasion",
"immunity",
"virology",
"innate",
"immunity",
"immunology",
"biology",
"microbiology",
"immune",
"response"
] | 2012 | The Human Adenovirus Type 5 E1B 55 kDa Protein Obstructs Inhibition of Viral Replication by Type I Interferon in Normal Human Cells |
Human metapneumovirus ( HMPV ) , a member of the Paramyxoviridae family , is a leading cause of lower respiratory illness . Although receptor binding is thought to initiate fusion at the plasma membrane for paramyxoviruses , the entry mechanism for HMPV is largely uncharacterized . Here we sought to determine whether H... | Human metapneumovirus ( HMPV ) is a paramyxovirus that causes severe lower respiratory tract infections . HMPV infection is initiated by the viral surface fusion ( F ) glycoprotein . HMPV F attaches to cellular receptors , including RGD-binding integrins , and catalyzes virus membrane fusion with cellular membranes dur... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Human Metapneumovirus Is Capable of Entering Cells by Fusion with Endosomal Membranes |
Heme crystallization as hemozoin represents the dominant mechanism of heme disposal in blood feeding triatomine insect vectors of the Chagas disease . The absence of drugs or vaccine for the Chagas disease causative agent , the parasite Trypanosoma cruzi , makes the control of vector population the best available strat... | Chagas disease is a fatal illness caused by Trypanosoma cruzi parasites , which are transmitted by blood sucking triatomine insect vectors . Although blood is a natural food source for these insects , its digestion releases toxic products , which poses a dietary challenge for both triatomine insects and trypanosomes . ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"heme",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"condensed",
"matter",
"physics",
"parasitic",
"protozoans",
"animals",
"protozoans",
"crystallography",
"insect",
"vectors",
"zoology",
"crystallization",
"oxidation-reduction",
"reactions"... | 2018 | Heme crystallization in a Chagas disease vector acts as a redox-protective mechanism to allow insect reproduction and parasite infection |
In an endeavor to find an orally active and affordable antileishmanial drug , we tested the efficacy of a cationic amphiphilic drug , imipramine , commonly used for the treatment of depression in humans . The only available orally active antileishmanial drug is miltefosine with long half life and teratogenic potential ... | The disease Kala-azar or visceral leishmaniasis is still a big problem in the Indian subcontinent . The antimonials were used for the chemotherapy of Kala-azar but with time its efficacy has reduced dramatically . The newer version of orally active drug miltefosine has been introduced , but its efficacy has decreased c... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases"
] | 2012 | Imipramine Is an Orally Active Drug against Both Antimony Sensitive and Resistant Leishmania donovani Clinical Isolates in Experimental Infection |
The guidance cue UNC-6/Netrin regulates both attractive and repulsive axon guidance . Our previous work showed that in C . elegans , the attractive UNC-6/Netrin receptor UNC-40/DCC stimulates growth cone protrusion , and that the repulsive receptor , an UNC-5:UNC-40 heterodimer , inhibits growth cone protrusion . We ha... | Mechanisms that guide axons to their targets in the developing nervous system have been elucidated , but how these pathways affect behavior of the growth cone of the axon during outgrowth remains poorly understood . We previously showed that the guidance cue UNC-6/Netrin and its receptors UNC-40/DCC and UNC-5 inhibit l... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"caenorhabditis",
"nervous",
"system",
"enzymes",
"enzymology",
"neuroscience",
"animals",
"motor",
"neurons",
"animal",
"models",
"caenorhabditis",
"elegans",
"model",
"organisms",
"experimental",
"organism",
"sys... | 2017 | Flavin monooxygenases regulate Caenorhabditis elegans axon guidance and growth cone protrusion with UNC-6/Netrin signaling and Rac GTPases |
This work introduces a coordinate-independent method to analyse movement variability of tasks performed with hand-held tools , such as a pen or a surgical scalpel . We extend the classical uncontrolled manifold ( UCM ) approach by exploiting the geometry of rigid body motions , used to describe tool configurations . In... | Daily motor tasks typically involve more degrees-of-freedom than strictly required . For instance , pressing a button in the elevator only requires positioning the fingertip at a three-dimensional location in space . However , to move the arm we need to control many more degrees-of-freedom ( at least seven , only consi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"motor",
"systems",
"biology",
"neuroscience"
] | 2013 | Analysis of Accuracy in Pointing with Redundant Hand-held Tools: A Geometric Approach to the Uncontrolled Manifold Method |
A key challenge in genetics is identifying the functional roles of genes in pathways . Numerous functional genomics techniques ( e . g . machine learning ) that predict protein function have been developed to address this question . These methods generally build from existing annotations of genes to pathways and thus a... | Due to technical and ethical challenges many human diseases or biological processes are studied in model organisms . Discoveries in these organisms are then transferred back to human or other model organisms . Traditional methods for transferring novel gene function annotations have relied on finding genes with high se... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genomics",
"functional",
"genomics",
"biology",
"computational",
"biology",
"genetics",
"and",
"genomics"
] | 2013 | Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes |
In order to extract retinal disparity from a visual scene , the brain must match corresponding points in the left and right retinae . This computationally demanding task is known as the stereo correspondence problem . The initial stage of the solution to the correspondence problem is generally thought to consist of a c... | Relating neural activity to perception is one of the most challenging tasks in neuroscience . Stereopsis—the ability of many animals to see in stereoscopic 3D—is a particularly tractable problem because the computational and geometric challenges faced by the brain are very well understood . In essence , the brain has t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"social",
"sciences",
"neuroscience",
"simulation",
"and",
"modeling",
"human",
"performance",
"vision",
"eyes",
"neuronal",
"tuning",
"research",
"and",
"analysis",
"methods",
"animal",
"cells",
"behavior",
"head",
"cellular",... | 2016 | A Single Mechanism Can Account for Human Perception of Depth in Mixed Correlation Random Dot Stereograms |
Despite years of intensive research , much remains to be discovered to understand the regulatory networks coordinating bacterial cell growth and division . The mechanisms by which Streptococcus pneumoniae achieves its characteristic ellipsoid-cell shape remain largely unknown . In this study , we analyzed the interplay... | Over the last decade , bacterial genomics have revealed the presence of eukaryotic-type serine/threonine protein kinases ( STKPs ) in many bacteria . However , their role and mode of action is still elusive . Recent studies have suggested that STKPs could play an important role in regulating cell division of some bacte... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"bacterial",
"physiology",
"medical",
"microbiology",
"streptococcus",
"microbial",
"pathogens",
"biology",
"and",
"life",
"sciences",
"microbiology",
"bacterial",
"pathogens"
] | 2014 | Interplay of the Serine/Threonine-Kinase StkP and the Paralogs DivIVA and GpsB in Pneumococcal Cell Elongation and Division |
Dengue often presents with non-specific clinical signs , and given the current paucity of accurate , rapid diagnostic laboratory tests , identifying easily obtainable bedside markers of dengue remains a priority . Previous studies in febrile Asian children have suggested that the combination of a positive tourniquet te... | In the Americas , the incidence and severity of dengue cases has increased dramatically in the past 30 years . Early diagnosis and initiation of appropriate therapy can substantially reduce dengue morbidity and mortality . However the absence of a point-of-care diagnostic test and the non-specific clinical signs and sy... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"test",
"evaluation",
"public",
"health",
"and",
"epidemiology",
"diagnostic",
"medicine",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"global",
"health",
"neglected",
"tropical",
"diseases",
"dengue",
"fever",
"viral",
... | 2011 | Utility of the Tourniquet Test and the White Blood Cell Count to Differentiate Dengue among Acute Febrile Illnesses in the Emergency Room |
Chlamydia is an obligate intracellular pathogen that causes a wide range of diseases in humans . Attachment and entry are key processes in infectivity and subsequent pathogenesis of Chlamydia , yet the mechanisms governing these interactions are unknown . It was recently shown that a cell line , CHO6 , that is resistan... | Chlamydia is a large burden on global health . It is the most common cause of infectious blindness , and the CDC ( Centers for Disease Control and Prevention ) estimates that in the United States alone there are more than 2 million people with sexually transmitted Chlamydia infections . Chlamydia is an obligate intrace... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"microbiology/microbial",
"growth",
"and",
"development"
] | 2009 | Attachment and Entry of Chlamydia Have Distinct Requirements for Host Protein Disulfide Isomerase |
Enteric infections are common where public health infrastructure is lacking . This study assesses risk factors for a range of enteric infections among children living in low-income , unplanned communities of urban Maputo , Mozambique . We conducted a cross-sectional survey in 17 neighborhoods of Maputo to assess the pr... | Enteric pathogens such as bacteria , protozoa , and viruses can cause diarrhea and other longer-term health problems . Poor sanitary conditions , including inadequate sanitation facilities , can lead to contamination of the living environment and higher risk of exposure to and transmission of enteric pathogens . Young ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Disclaimer"
] | [
"children",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"pathogens",
"microbiology",
"parasitic",
"diseases",
"health",
"care",
"diarrhea",
"age",
"groups",
"signs",
"and",
"sympto... | 2018 | Risk factors for childhood enteric infection in urban Maputo, Mozambique: A cross-sectional study |
Jacob , the protein encoded by the Nsmf gene , is involved in synapto-nuclear signaling and docks an N-Methyl-D-Aspartate receptor ( NMDAR ) -derived signalosome to nuclear target sites like the transcription factor cAMP-response-element-binding protein ( CREB ) . Several reports indicate that mutations in NSMF are rel... | Kallmann syndrome ( KS ) is a neurodevelopmental disorder that is characterized by a migration deficit of GnRH neurons that fail to migrate into the hypothalamus during embryonic development . The affected patients suffer from idiopathic hypogonadotropic hypogonadism associated with anosmia or hyposmia . Mutations in N... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"nuclear",
"import",
"medicine",
"and",
"health",
"sciences",
"nervous",
"system",
"cell",
"processes",
"brain",
"vertebrates",
"electrophysiology",
"mice",
"neuroscience",
"animals",
"mammals",
"animal",
"behavior",
"zoology",
"neuronal",
"dendrites",
"animal",
"cells"... | 2016 | A Jacob/Nsmf Gene Knockout Results in Hippocampal Dysplasia and Impaired BDNF Signaling in Dendritogenesis |
The developing crossveins of the wing of Drosophila melanogaster are specified by long-range BMP signaling and are especially sensitive to loss of extracellular modulators of BMP signaling such as the Chordin homolog Short gastrulation ( Sog ) . However , the role of the extracellular matrix in BMP signaling and Sog ac... | Signaling between cells regulates many processes , including the choices cells make between different fates during development and regeneration , and misregulation of such signaling underlies many human pathologies . To understand how such signals control developmental decisions , it is necessary to elucidate both how ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | The Gyc76C Receptor Guanylyl Cyclase and the Foraging cGMP-Dependent Kinase Regulate Extracellular Matrix Organization and BMP Signaling in the Developing Wing of Drosophila melanogaster |
Marker frequency analysis of the Escherichia coli recB mutant chromosome has revealed a deficit of DNA in a specific zone of the terminus , centred on the dif/TerC region . Using fluorescence microscopy of a marked chromosomal site , we show that the dif region is lost after replication completion , at the time of cell... | RecBCD protein complex is an important player of DSB repair in bacteria and bacteria that cannot repair DNA double-stranded breaks ( DSB ) have a low viability . Whole genome sequencing analyses showed a deficit in specific sequences of the chromosome terminus region in recB mutant cells , suggesting terminus DNA degra... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"chemical",
"compounds",
"cell",
"division",
"analysis",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"carbohydrates",
"organic",
"compounds",
"glucose",
"dna",
"replication",
"bioassays",
"and",
"physiological",
"analysis",
"dna",
"sequence",
"mot... | 2017 | Division-induced DNA double strand breaks in the chromosome terminus region of Escherichia coli lacking RecBCD DNA repair enzyme |
The interaction between fungal pathogens with the host frequently results in morphological changes , such as hyphae formation . The encapsulated pathogenic fungus Cryptococcus neoformans is not considered a dimorphic fungus , and is predominantly found in host tissues as round yeast cells . However , there is a specifi... | In this article we describe the formation of giant cells by the human fungal pathogen Cryptococcus neoformans during infection , involving an approximately 900-fold increase in volume compared to that of yeast cells grown in vitro . This switch to gigantism is a dramatic transition that is posited to have important con... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/fungal",
"infections"
] | 2010 | Fungal Cell Gigantism during Mammalian Infection |
Adverse drug effects ( ADEs ) are one of the leading causes of death in developed countries and are the main reason for drug recalls from the market , whereas the ADEs that are associated with action on the cardiovascular system are the most dangerous and widespread . The treatment of human diseases often requires the ... | Assessment of adverse drug effects as well as the influence of drug-drug interactions on their manifestation is a nontrivial task that requires numerous experimental and clinical studies . We developed a computational approach for the prediction of adverse effects that are induced by drug-drug interactions , which are ... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"heart",
"rate",
"myocardial",
"infarction",
"stroke",
"medicine",
"and",
"health",
"sciences",
"cerebrovascular",
"diseases",
"drug-drug",
"interactions",
"drug",
"research",
"and",
"development",
"vascular",
"medicine",
"ischemic",
"stroke",
"neurology",
"tachycardia",
... | 2019 | Assessment of the cardiovascular adverse effects of drug-drug interactions through a combined analysis of spontaneous reports and predicted drug-target interactions |
Vibrio cholerae and a subset of other Gram-negative bacteria , including Acinetobacter baumannii , express proteins with a C-terminal tripartite domain called GlyGly-CTERM , which consists of a motif rich in glycines and serines , followed by a hydrophobic region and positively charged residues . Here we show that VesB... | The type II secretion system ( T2SS ) critically contributes to pathogenesis of many Gram-negative bacteria by transporting toxins and a variety of enzymes including proteases , lipases , nucleases and carbohydrases to the extracellular environment . Cholera toxin , the principal virulence factor of Vibrio cholerae , i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"bacteriology",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"aliphatic",
"amino",
"acids",
"molecular",
"probe",
"techniques",
"enzymes",
"pathogens",
"vibrio",
"microbiology",
"enzymology",
"immunoblotti... | 2018 | C-terminal processing of GlyGly-CTERM containing proteins by rhombosortase in Vibrio cholerae |
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