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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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Streptococcus agalactiae is a common human commensal and a major life-threatening pathogen in neonates . Adherence to host epithelial cells is the first critical step of the infectious process . Pili have been observed on the surface of several gram-positive bacteria including S . agalactiae . We previously characteriz... | Streptococcus agalactiae ( Group B Streptococcus ) is a leading cause of sepsis ( blood infection ) and meningitis ( brain infection ) in newborns . Most bacterial pathogens have long filamentous structures known as pili or fimbriae , which are often involved in the initial adhesion of bacteria to host tissues but also... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis"
] | 2009 | Dual Role for Pilus in Adherence to Epithelial Cells and Biofilm Formation in Streptococcus agalactiae |
In eukaryotes , the highly conserved U3 small nucleolar RNA ( snoRNA ) base-pairs to multiple sites in the pre-ribosomal RNA ( pre-rRNA ) to promote early cleavage and folding events . Binding of the U3 box A region to the pre-rRNA is mutually exclusive with folding of the central pseudoknot ( CPK ) , a universally con... | Ribosomes are intricate assemblies of RNA and protein that are responsible for decoding a cell’s genetic information . Their assembly is a very rapid and dynamic process , requiring many ancillary factors in eukaryotic cells . One critical factor is the U3 snoRNA , which binds to the immature ribosomal RNA to direct ea... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The DEAH-box Helicase Dhr1 Dissociates U3 from the Pre-rRNA to Promote Formation of the Central Pseudoknot |
Venom recurrence or persistence in the circulation after antivenom treatment has been documented many times in viper envenoming . However , it has not been associated with clinical recurrence for many snakes , including Russell's viper ( Daboia spp . ) . We compare the recovery of coagulopathy to the recurrence or pers... | Snakebite is a major public health problem and understanding the effectiveness of antivenom is essential to improving health outcomes . The measurement of venom in blood has been used to assess the effectiveness of antivenom . The absence of venom post-antivenom indicating that sufficient antivenom has been given , and... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"clinical",
"medicine",
"blood",
"coagulation",
"clinical",
"immunology",
"pharmacodynamics",
"biology",
"and",
"life",
"sciences",
"immunology",
"pharmacology",
"critical",
"care",
"and",
"emergency",
"medicine",
"hematology",
"... | 2014 | Detection of Venom after Antivenom Is Not Associated with Persistent Coagulopathy in a Prospective Cohort of Russell's Viper (Daboia russelii) Envenomings |
Foot-and-mouth disease ( FMD ) virus causes an acute vesicular disease of domesticated and wild ruminants and pigs . Identifying sources of FMD outbreaks is often confounded by incomplete epidemiological evidence and the numerous routes by which virus can spread ( movements of infected animals or their products , conta... | Foot-and-mouth disease ( FMD ) outbreaks in the United Kingdom during August and September 2007 have caused severe disruption to the farming sector and cost hundreds of millions of pounds . Investigating and determining the source of these outbreaks is imperative for their effective management and future prevention . F... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"virology"
] | 2008 | Transmission Pathways of Foot-and-Mouth Disease Virus in the United Kingdom in 2007 |
Shading is known to produce vivid perceptions of depth . However , the influence of specular highlights on perceived shape is unclear: some studies have shown that highlights improve quantitative shape perception while others have shown no effect . Here we ask how specular highlights combine with Lambertian shading cue... | A primary goal of the human visual system is to reconstruct the three-dimensional structure of the environment from two-dimensional retinal images . This process is under-determined: an infinite number of combinations of shape , material properties and illumination conditions could give rise to any single image . Rathe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods",
"and",
"Model"
] | [
"psychology",
"cognitive",
"psychology",
"psychophysics",
"biology",
"and",
"life",
"sciences",
"sensory",
"perception",
"social",
"sciences",
"cognitive",
"science",
"neuroscience"
] | 2014 | Effects of Specular Highlights on Perceived Surface Convexity |
In 2004 Niger established a large scale schistosomiasis and soil-transmitted helminths control programme targeting children aged 5–14 years and adults . In two years 4 . 3 million treatments were delivered in 40 districts using school based and community distribution . Four districts were surveyed in 2006 to estimate t... | Schistosomiasis and soil-transmitted helminth control programmes are important , relatively low cost means to improve the health of those affected , in particular rural school age children . It can also reduce schistosomiasis related morbidity in their later lives . The paper presents information on the implementation ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"schistosomiasis",
"global",
"health",
"neglected",
"tropical",
"diseases",
"infectious",
"disease",
"control"
] | 2011 | Schistosomiais and Soil-Transmitted Helminth Control in Niger: Cost Effectiveness of School Based and Community Distributed Mass Drug Administration |
Cyclic GMP-AMP ( cGAMP ) synthase ( cGAS ) stimulator of interferon genes ( STING ) senses pathogen-derived or abnormal self-DNA in the cytosol and triggers an innate immune defense against microbial infection and cancer . STING agonists induce both innate and adaptive immune responses and are a new class of cancer imm... | Pathogens often find ways to turn down cell-intrinsic antipathogen immune responses by the host . Similarly , cancer cells use various mechanisms to evade attack by immune cells . One of the common mechanisms is suppression of the stimulator of interferon genes ( STING ) -dependent innate immune response . Using potent... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"poxviruses",
"pathology",
"and",
"laboratory",
"medicine",
"gene",
"regulation",
"pathogens",
"cancer",
"treatment",
"immunology",
"microbiology",
"dna-binding",
"proteins",
"viruses",
"oncol... | 2018 | KDM5 histone demethylases repress immune response via suppression of STING |
Flaviviruses bud into the endoplasmic reticulum and are transported through the secretory pathway , where the mildly acidic environment triggers particle rearrangement and allows furin processing of the prM protein to pr and M . The peripheral pr peptide remains bound to virus at low pH and inhibits virus-membrane inte... | Enveloped viruses infect cells by fusing their membrane with that of the host cell . Dengue virus ( DENV ) is an important human pathogen whose membrane fusion is triggered by low pH during virus entry into the cell . However , newly synthesized DENV must also transit through a low pH environment during virus exit . DE... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/virion",
"structure,",
"assembly,",
"and",
"egress",
"virology/host",
"invasion",
"and",
"cell",
"entry",
"virology/new",
"therapies,",
"including",
"antivirals",
"and",
"immunotherapy",
"virology/emerging",
"viral",
"diseases"
] | 2010 | In Vitro and In Vivo Studies Identify Important Features of Dengue Virus pr-E Protein Interactions |
Adult neurogenesis in the dentate gyrus plays a critical role in hippocampus-dependent spatial learning . It remains unknown , however , how new neurons become functionally integrated into spatial circuits and contribute to hippocampus-mediated forms of learning and memory . To investigate these issues , we used a mous... | Previous studies have implicated adult-born hippocampal neurons in the formation of spatial and contextual memories by using mouse models where newly generated neurons are either eliminated or increased in number . Nonetheless , how new neurons are integrated in the existing circuits and contribute to memory formation ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience"
] | 2008 | The Timing of Differentiation of Adult Hippocampal Neurons Is Crucial for Spatial Memory |
The Caenorhabditis elegans DAF-16 transcription factor is critical for diverse biological processes , particularly longevity and stress resistance . Disruption of the DAF-2 signaling cascade promotes DAF-16 activation , and confers resistance to killing by pathogenic bacteria , such as Pseudomonas aeruginosa , Staphylo... | In the natural environment , animals encounter different pathogens . Thus , different tissues within an organism must develop specific immune systems for survival . The epidermis acts as a physical barrier and represents a first line of defense against infection and physical injury in a variety of animals . Natural nem... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | The DAF-16/FOXO Transcription Factor Functions as a Regulator of Epidermal Innate Immunity |
Plague in Brazil is poorly known and now rarely seen , so studies of its ecology are difficult . We used ecological niche models of historical ( 1966-present ) records of human plague cases across northeastern Brazil to assess hypotheses regarding environmental correlates of plague occurrences across the region . Resul... | We analyzed the spatial and environmental distributions of human plague cases across northeastern Brazil from 1966-present , where the disease is now only rarely transmitted to humans , but persists as a zoonosis of native rodent populations . We elucidated environmental correlates of plague occurrences by way of ecolo... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"infectious",
"diseases/epidemiology",
"and",
"control",
"of",
"infectious",
"diseases",
"ecology/physiological",
"ecology"
] | 2011 | Ecology and Geography of Plague Transmission Areas in Northeastern Brazil |
Microbial pathogens impose selective pressures on their hosts , and combatting these pathogens is fundamental to the propagation of a species . Innate immunity is an ancient system that provides the foundation for pathogen resistance , with epithelial cells in humans increasingly appreciated to play key roles in innate... | Infectious diseases caused by microbes create some of the strongest forces in evolution , by killing their hosts , and impairing their ability to produce progeny . Microsporidia are very common microbes that cause disease in all animals , including roundworms , insects , fish and people . We investigated microsporidia ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite |
TAF4b is a gonadal-enriched subunit of the general transcription factor TFIID that is implicated in promoting healthy ovarian aging and female fertility in mice and humans . To further explore the potential mechanism of TAF4b in promoting ovarian follicle development , we analyzed global gene expression at multiple tim... | Proper regulation of early oogenesis is essential for long-term ovarian health and fertility , as female mammals ( and women ) possess a finite pool of oocytes at birth . Meiotic progression during these early stages of oogenesis ensures genomic integrity and proper chromosome segregation in the reproductive years and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"meiosis",
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"reproductive",
"physiology",
"germ",
"cells",
"oocytes",
"regulator",
"genes",
"immunoprecipitation",
"gene",
"types",
"rese... | 2016 | TAF4b Regulates Oocyte-Specific Genes Essential for Meiosis |
We evaluated the effect of Trypanosoma cruzi infection on fertility , gestation outcome , and maternal-fetal transmission in guinea pigs ( Cavia porcellus ) . Animals were infected with T . cruzi H4 strain ( TcI lineage ) before gestation ( IBG ) or during gestation ( IDG ) . Tissue and sera samples of dams and fetuses... | Chagas disease is endemic in Latin America where the vector , hematophagous triatomine , is widely distributed . The exposure of women to T . cruzi may result in birth defects . However , congenital transmission of Trypanosoma cruzi from infected mothers to fetuses is scantily studied . Herein , we have developed a gui... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"pathology",
"and",
"laboratory",
"medicine",
"parasite",
"replication",
"cardiovascular",
"anatomy",
"immunology",
"vertebrates",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"animals",
"mammals",
... | 2018 | Quantitative and histological assessment of maternal-fetal transmission of Trypanosoma cruzi in guinea pigs: An experimental model of congenital Chagas disease |
Oomycete pathogens cause diverse plant diseases . To successfully colonize their hosts , they deliver a suite of effector proteins that can attenuate plant defenses . In the oomycete downy mildews , effectors carry a signal peptide and an RxLR motif . Hyaloperonospora arabidopsidis ( Hpa ) causes downy mildew on the mo... | Hyaloperonospora arabidopsidis ( Hpa ) is an obligate biotroph whose population coevolves with its host , Arabidopsis thaliana . The Hpa isolate Emoy2 genome has been sequenced , allowing the discovery of dozens of secreted candidate effectors . We set out to assign functions to these candidate effectors , investigatin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"science",
"model",
"organisms",
"plant",
"biology",
"plant",
"pathogens",
"plant",
"pathology",
"immunology",
"biology",
"immune",
"response"
] | 2011 | Multiple Candidate Effectors from the Oomycete Pathogen Hyaloperonospora arabidopsidis Suppress Host Plant Immunity |
This study aimed to assess analytical parameters of a prototype LAMP kit that was designed for detection of Trypanosoma cruzi DNA in human blood . The prototype is based on the amplification of the highly repetitive satellite sequence of T . cruzi in microtubes containing dried reagents on the inside of the caps . The ... | Trypanosoma cruzi , a parasite transmitted to humans from hematophagous insects , causes Chagas Disease , a Neglected Tropical Disease with public health impact , affecting 7 million people in Latin America . Although mainly related to low income populations inhabiting rural environments , migrations have conveyed Chag... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"engineering",
"and",
"technology",
"purification",
"techniques",
"tropical",
"diseases",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoans",
"forms",
"of",
"dna",
"neglected",
"tropical",
"disease... | 2017 | Analytical sensitivity and specificity of a loop-mediated isothermal amplification (LAMP) kit prototype for detection of Trypanosoma cruzi DNA in human blood samples |
Intracellular calcium cycling is a vital component of cardiac excitation-contraction coupling . The key structures responsible for controlling calcium dynamics are the cell membrane ( comprising the surface sarcolemma and transverse-tubules ) , the intracellular calcium store ( the sarcoplasmic reticulum ) , and the co... | The organisation of the membrane and sub-cellular structures of cells in the heart closely controls the coupling between its electrical and mechanical function . Computational models of the cellular calcium handling system , which is responsible for this electro-mechanical coupling , have been developed in recent years... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"muscle",
"tissue",
"endoplasmic",
"reticulum",
"cell",
"processes",
"mathematical",
"models",
"simulation",
"and",
"modeling",
"waves",
"cellular",
"structures",
"and",
"organelles",
"research",
"and",
"analysis",
"methods",
"... | 2017 | A computational model of spatio-temporal cardiac intracellular calcium handling with realistic structure and spatial flux distribution from sarcoplasmic reticulum and t-tubule reconstructions |
During meiotic prophase , telomeres cluster , forming the bouquet chromosome arrangement , and facilitate homologous chromosome pairing . In fission yeast , bouquet formation requires switching of telomere and centromere positions . Centromeres are located at the spindle pole body ( SPB ) during mitotic interphase , an... | Meiosis is a type of cell division , that generates haploid gametes and is essential for sexual reproduction . During meiosis , telomeres cluster on a small region of the nuclear periphery , forming a conserved chromosome arrangement referred to as the “bouquet” . Because the bouquet arrangement facilitates homologous ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"meiosis",
"homologous",
"chromosomes",
"microtubules",
"chromosome",
"structure",
"and",
"function",
"centromeres",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"chromatids",
"germ",
"cells",
"zygotes",
"telomeres",
"molecular",
"biology",
"techniqu... | 2016 | A Taz1- and Microtubule-Dependent Regulatory Relationship between Telomere and Centromere Positions in Bouquet Formation Secures Proper Meiotic Divisions |
Oscillations are ubiquitous phenomena in the animal and human brain . Among them , the alpha rhythm in human EEG is one of the most prominent examples . However , its precise mechanisms of generation are still poorly understood . It was mainly this lack of knowledge that motivated a number of simultaneous electroenceph... | In this article , we show how a large-scale neuronal model involving a thalamo-cortical circuit can reproduce findings from human and animal brain oscillatory activity and how this can help understanding the mechanisms , which generate this activity . Amongst the brain rhythms , the alpha rhythm ( 8-12Hz ) is the most ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Relating Alpha Power and Phase to Population Firing and Hemodynamic Activity Using a Thalamo-cortical Neural Mass Model |
Gene fusion and fission events are key mechanisms in the evolution of gene architecture , whose effects are visible in protein architecture when they occur in coding sequences . Until now , the detection of fusion and fission events has been performed at the level of protein sequences with a post facto removal of super... | One consequence of genome remodelling in evolution is the modification of genes , either by fusion with other genes , or by fission into several parts . By tracking the mathematical relations between groups of similar genes , rather than between individual genes , we can paint a global picture of remodelling across man... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"and",
"genomics/comparative",
"genomics",
"computational",
"biology/genomics",
"evolutionary",
"biology/genomics"
] | 2008 | Fusion and Fission of Genes Define a Metric between Fungal Genomes |
The ability to store nutrients in lipid droplets ( LDs ) is an ancient function that provides the primary source of metabolic energy during periods of nutrient insufficiency and between meals . The Fat storage-Inducing Transmembrane ( FIT ) proteins are conserved ER–resident proteins that facilitate fat storage by part... | The ability to form lipid droplets is a conserved property of eukaryotic cells that allows the storage of excess metabolic energy in a form that can be readily accessed . In adipose tissue , the storage of excess calories in lipid droplets normally protects other tissues from lipotoxicity and insulin resistance , but t... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"biology"
] | 2012 | SCS3 and YFT2 Link Transcription of Phospholipid Biosynthetic Genes to ER Stress and the UPR |
Under nitrogen deprivation , the one-dimensional cyanobacterial organism Anabaena sp . PCC 7120 develops patterns of single , nitrogen-fixing cells separated by nearly regular intervals of photosynthetic vegetative cells . We study a minimal , stochastic model of developmental patterns in Anabaena that includes a nondi... | Multicellular organisms , from simple to complex , often undergo a developmental process in which cells differentiate into various types , improving survivability under adverse conditions . We study experimentally and theoretically the developmental mechanism of pattern formation in Anabaena sp . PCC 7120 , a multicell... | [
"Abstract",
"Introduction",
"The",
"stochastic",
"model",
"The",
"deterministic",
"limit",
"Stochastic",
"Turing",
"patterns",
"Growing",
"domain",
"Discussion",
"Methods"
] | [
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"cell",
"differentiation",
"developmental",
"biology",
"regulator",
"genes",
"signal",
"inhibition",
"molecular",
"development",
"gene",
"types",
"morphogenesis",
"bacteria",
"pattern",
"formation",
"prote... | 2018 | Robust stochastic Turing patterns in the development of a one-dimensional cyanobacterial organism |
To better understand telomere biology in budding yeast , we have performed systematic suppressor/enhancer analyses on yeast strains containing a point mutation in the essential telomere capping gene CDC13 ( cdc13-1 ) or containing a null mutation in the DNA damage response and telomere capping gene YKU70 ( yku70Δ ) . W... | Telomeres , specialized structures at the end of linear chromosomes , ensure that chromosome ends are not mistakenly treated as DNA double-strand breaks . Defects in the telomere cap contribute to ageing and cancer . In yeast , defects in telomere capping proteins can cause telomeres to behave like double-strand breaks... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"biology/systems",
"biology",
"genetics",
"and",
"genomics/chromosome",
"biology",
"genetics",
"and",
"genomics/functional",
"genomics"
] | 2011 | Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects |
In order to understand the evolution of enzyme reactions and to gain an overview of biological catalysis we have combined sequence and structural data to generate phylogenetic trees in an analysis of 276 structurally defined enzyme superfamilies , and used these to study how enzyme functions have evolved . We describe ... | Enzymes , as biological catalysts , are crucial to life . Understanding how enzymes have evolved to perform the wide variety of reactions found across all kingdoms of life is fundamental to a broad range of biological studies , especially those leading to new therapeutics . To unravel the evolution of novel enzyme func... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"evolutionary",
"biology",
"proteins",
"biology",
"computational",
"biology",
"macromolecular",
"structure",
"analysis"
] | 2012 | Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies |
Genome-wide association studies typically target inherited autosomal variants , but less studied genetic mechanisms can play a role in complex disease . Sex-linked variants aside , three genetic phenomena can induce differential risk in maternal versus paternal lineages of affected individuals: 1 . maternal effects , r... | Genetic studies often collect family histories from diagnosed individuals . Some diseases exhibit inter-lineage asymmetry: mothers and their progenitors have higher ( or lower ) risk than fathers and their progenitors , and descendants of female cases have higher ( or lower ) risk than descendants of male cases . We de... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"oncology",
"medicine",
"genetic",
"causes",
"of",
"cancer",
"epidemiology",
"genetics",
"cancer",
"risk",
"factors",
"population",
"biology",
"biology",
"genetic",
"epidemiology"
] | 2014 | Asymmetry in Family History Implicates Nonstandard Genetic Mechanisms: Application to the Genetics of Breast Cancer |
Alpha-hemolysin ( α-HL ) is a self-assembling , channel-forming toxin produced by most Staphylococcus aureus strains as a 33 . 2-kDa soluble monomer . Upon binding to a susceptible cell membrane , the monomer self-assembles to form a 232 . 4-kDa heptamer that ultimately causes host cell lysis and death . Consequently ,... | The mechanism controlling protein-ligand interactions is one of the most important processes in rational drug design . X-ray crystallography is a traditional tool used to investigate the interaction of ligands and proteins in a complex . However , protein crystallography is inefficient , and the development of crystal ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"medicine",
"biochemistry",
"infectious",
"diseases",
"bacterial",
"diseases",
"biology",
"computational",
"biology",
"infectious",
"disease",
"control"
] | 2013 | Oroxylin A Inhibits Hemolysis via Hindering the Self-Assembly of α-Hemolysin Heptameric Transmembrane Pore |
Bax/Bak-mediated mitochondrial outer membrane permeabilization ( MOMP ) is essential for “intrinsic” apoptotic cell death . Published studies used synthetic liposomes to reveal an intrinsic pore-forming activity of Bax , but it is unclear how other mitochondrial outer membrane ( MOM ) proteins might facilitate this fun... | Mitochondria are the key energy-producing structures inside cells , but are also crucial players in a common form of programmed cell death , apoptosis . A critical event in mitochondrion-driven apoptosis involves the formation of large pores in the mitochondrial outer membrane ( MOM ) . These pores cause long-term dama... | [
"Abstract",
"Introduction",
"Results",
"and",
"Conclusions",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"biochemistry",
"cellular",
"structures",
"subcellular",
"organelles",
"cell",
"death",
"model",
"organisms",
"molecular",
"cell",
"biology",
"cell",
"biology",
"xenopus",
"laevis",
"macromolecular",
"assemblies",
"biology",
"biophysics",
"rat"
] | 2012 | Bax Activation Initiates the Assembly of a Multimeric Catalyst that Facilitates Bax Pore Formation in Mitochondrial Outer Membranes |
Human gamma herpesviruses , including Kaposi’s sarcoma-associated herpesvirus ( KSHV ) and Epstein-Barr virus ( EBV ) , are capable of inducing tumors , particularly in in immune-compromised individuals . Due to the stringent host tropism , rodents are resistant to infection by human gamma herpesviruses , creating a si... | Human gamma herpesviruses , including Epstein-Barr virus ( EBV ) and Kaposi’s sarcoma-associated herpesvirus ( KSHV ) , are causatively linked to a spectrum of human oncogenic malignancies . Due to the stringent host restriction , rodents are generally not amenable to infection by EBV and KSHV . Murine gamma herpesviru... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Recombinant Murine Gamma Herpesvirus 68 Carrying KSHV G Protein-Coupled Receptor Induces Angiogenic Lesions in Mice |
The early events that shape the innate immune response to restrain pathogens during skin infections remain elusive . Methicillin-resistant Staphylococcus aureus ( MRSA ) infection engages phagocyte chemotaxis , abscess formation , and microbial clearance . Upon infection , neutrophils and monocytes find a gradient of c... | Staphylococcus aureus skin infection is orchestrated by resident and recruited immune cells . The signals that required for the control of S . aureus infection have been studied . However , most studies have focused on the actions of inflammatory mediators produced after hours post infection and the early events ( seco... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"dermatology",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"biopsy",
"pathogens",
"drugs",
"immunology",
"microbiology",
"staphylococcus",
"aureus",
"surgical",
"and",
"invasive",
"medical",... | 2018 | Macrophage-derived LTB4 promotes abscess formation and clearance of Staphylococcus aureus skin infection in mice |
Vibrio cholerae O1 is a natural inhabitant of aquatic environments and causes the diarrheal disease , cholera . Two of its primary virulence regulators , TcpP and ToxR , are localized in the inner membrane . TcpP is encoded on the Vibrio Pathogenicity Island ( VPI ) , a horizontally acquired mobile genetic element , an... | Non-obligate bacterial pathogens must alter their gene expression profiles when transitioning between environments . Vibrio cholerae is a natural inhabitant of aquatic ecosystems and the etiological agent of the severe diarrheal disease , cholera . Its virulence gene regulation is controlled by a complex transcriptiona... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Proteolysis of Virulence Regulator ToxR Is Associated with Entry of Vibrio cholerae into a Dormant State |
Advances in high-throughput DNA sequencing technologies have determined an explosion in the number of sequenced bacterial genomes . Comparative sequence analysis frequently reveals evidences of homologous recombination occurring with different mechanisms and rates in different species , but the large-scale use of compu... | The extent to which recombination occurs in natural populations is either unknown or controversial but it is widely accepted that recombination plays a crucial role in the evolution of many bacterial species . Numerous methods have been developed for the investigation of recombination events , but most of them require ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"sequence",
"analysis",
"genome",
"analysis",
"tools",
"genomics",
"genome",
"evolution",
"population",
"genetics",
"biology",
"computational",
"biology",
"comparative",
"genomics",
"gene",
"flow",
"genetics",
"and",
"genomics"
] | 2012 | A Novel Computational Method Identifies Intra- and Inter-Species Recombination Events in Staphylococcus aureus and Streptococcus pneumoniae |
It is well known that inbreeding increases the risk of recessive monogenic diseases , but it is less certain whether it contributes to the etiology of complex diseases such as schizophrenia . One way to estimate the effects of inbreeding is to examine the association between disease diagnosis and genome-wide autozygosi... | It is well known that mating between relatives increases the risk that a child will have a rare recessive genetic disease , but there has also been increasing interest and inconsistent findings on whether inbreeding is a risk factor for common , complex psychiatric disorders such as schizophrenia . The best powered stu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Conclusion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"replication",
"studies",
"sociology",
"social",
"sciences",
"research",
"design",
"mathematics",
"statistics",
"(mathematics)",
"mood",
"disorders",
"research",
"and",
"analysis",
"methods",
"genome",
"complexity",
"depression",
... | 2016 | No Reliable Association between Runs of Homozygosity and Schizophrenia in a Well-Powered Replication Study |
Searching for stimulators of the innate antiviral response is an appealing approach to develop novel therapeutics against viral infections . Here , we established a cell-based reporter assay to identify compounds stimulating expression of interferon-inducible antiviral genes . DD264 was selected out of 41 , 353 compoun... | Our therapeutic arsenal to treat viral diseases is extremely limited , and there is a critical need for molecules that could be used against multiple viruses . Among possible strategies , there is a growing interest for molecules stimulating cellular defense mechanisms . We recently developed a functional assay to iden... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Inhibition of Pyrimidine Biosynthesis Pathway Suppresses Viral Growth through Innate Immunity |
Tissue-resident memory CD8 T ( TRM ) cells defend against microbial reinfections at mucosal barriers; determinants driving durable TRM cell responses in non-mucosal tissues , which often harbor opportunistic persistent pathogens , are unknown . JC polyomavirus ( JCPyV ) is a ubiquitous constituent of the human virome .... | Tissue resident memory cells ( TRM ) persist in nonlymphoid organs serving as frontline defense against microbial reinfection . The requirements for generating pathogen-specific TRM to acutely resolved infections is well documented; however , little is known about the development of TRM to persistent infections . In th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"t",
"helper",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"nervous",
"system",
"spleen",
"immunology",
"microbiology",
"cloning",
"cell",
"differentiation",
"developmental",
"biology",
"cytotoxic",
"t... | 2018 | CD4 T cells control development and maintenance of brain-resident CD8 T cells during polyomavirus infection |
Deworming is recommended by the WHO in girls and pregnant and lactating women to reduce anaemia in areas where hookworm and anaemia are common . There is conflicting evidence on the harm and the benefits of intestinal geohelminth infections on the incidence and severity of malaria , and consequently on the risks and be... | Intestinal worms , particularly hookworm and whipworm , can cause anaemia , which is harmful for pregnant women . The WHO recommends deworming in pregnancy in areas where hookworm infections are frequent . Some studies indicate that coinfection with worms and malaria adversely affects pregnancy whereas other studies ha... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"evidence-based",
"healthcare/clinical",
"decision-making",
"pediatrics",
"and",
"child",
"health/neonatology",
"public",
"health",
"and",
"epidemiology/health",
"policy",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"obstetrics/pregnancy",
"infectious",
"diseases/... | 2010 | Complex Interactions between Soil-Transmitted Helminths and Malaria in Pregnant Women on the Thai-Burmese Border |
Insulin resistance ( IR ) and impaired insulin secretion contribute to type 2 diabetes and cardiovascular disease . Both are associated with changes in the circulating metabolome , but causal directions have been difficult to disentangle . We combined untargeted plasma metabolomics by liquid chromatography/mass spectro... | Impaired glucose homeostasis leads to diabetes and cardiovascular disease and has two main components: failure to secrete enough insulin from pancreatic β-cells and reduced insulin-stimulated cellular uptake of glucose and other nutrients in target tissues ( insulin resistance , IR ) . We used metabolomics analysis in ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"carbohydrate",
"metabolism",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"chemical",
"compounds",
"glucose",
"metabolism",
"organic",
"compounds",
"endocrine",
"physiology",
"metabolomics",
"tyrosine",
"metabolites",
"amino",
"acids",
"pharmacology",
"drug... | 2016 | Effect of Insulin Resistance on Monounsaturated Fatty Acid Levels: A Multi-cohort Non-targeted Metabolomics and Mendelian Randomization Study |
In patients with cerebral malaria ( CM ) , higher levels of cell-specific microparticles ( MP ) correlate with the presence of neurological symptoms . MP are submicron plasma membrane-derived vesicles that express antigens of their cell of origin and phosphatidylserine ( PS ) on their surface , facilitating their role ... | Cerebral malaria ( CM ) is a potentially fatal neurological syndrome characterised by unrousable coma . Since the detection of high levels of plasma microparticles ( MP ) in patients with CM , it has been demonstrated that inhibition of MP production confers protection from murine CM . However , the precise mechanisms ... | [
"Abstract",
"Introduction",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases"
] | 2014 | Production, Fate and Pathogenicity of Plasma Microparticles in Murine Cerebral Malaria |
Repetitive DNA sequences within eukaryotic heterochromatin are poorly transcribed and replicate late in S-phase . In Saccharomyces cerevisiae , the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA arrays ( rDNA ) . Despite the widespread associ... | Eukaryotic genomes typically contain large regions of repetitive DNA , referred to as heterochromatin , that are both transcriptionally silent and late replicating . We provide a possible explanation for the association between transcriptional silencing and late replication . Budding yeast contains a histone deacetylas... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"enzymes",
"enzymology",
"dna",
"transcription",
"fungi",
"model",
"organisms",
"dna",
"replication",
"experimental",
"organism",
"systems",
"epigenetics",
"dna",
"molecular",
"biology",
"techniques",
"chromatin",
"genetic",
"footprinting",
"heterochromatin",
"research",
... | 2019 | Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats |
Many tissues are sustained by adult stem cells , which replace lost cells by differentiation and maintain their own population through self-renewal . The mechanisms through which adult stem cells maintain their identity are thus important for tissue homeostasis and repair throughout life . Here , we show that a histone... | Many tissues in the body are maintained by adult stem cells , which are dedicated but undifferentiated precursors that both maintain their population throughout life and produce daughter cells that differentiate to replace cells lost to turnover or damage . Here we show that the histone variant His2Av is required cell ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | The Histone Variant His2Av is Required for Adult Stem Cell Maintenance in the Drosophila Testis |
Complex tissues , such as the brain , are composed of multiple different cell types , each of which have distinct and important roles , for example in neural function . Moreover , it has recently been appreciated that the cells that make up these sub-cell types themselves harbour significant cell-to-cell heterogeneity ... | Tissues within complex multi-cellular organisms have historically been defined in terms of their anatomy and function . More recently , experimental approaches have shown that different tissues express distinct batteries of genes , thus providing an additional metric for characterising them . These experiments have bee... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience",
"biology",
"and",
"life",
"sciences",
"developmental",
"biology",
"computational",
"biology"
] | 2014 | Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets |
Most transcriptional activity of exponentially growing cells is carried out by the RNA Polymerase I ( Pol I ) , which produces a ribosomal RNA ( rRNA ) precursor . In budding yeast , Pol I is a multimeric enzyme with 14 subunits . Among them , Rpa49 forms with Rpa34 a Pol I-specific heterodimer ( homologous to PAF53/CA... | The nuclear genome of eukaryotic cells is transcribed by three RNA polymerases . RNA polymerase I ( Pol I ) is a multimeric enzyme specialized in the synthesis of ribosomal RNA . Deregulation of the Pol I function is linked to the etiology of a broad range of human diseases . Understanding the Pol I activity and regula... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"dna-binding",
"proteins",
"mutation",
"fungi",
"polymerases",
"gene",
"types",
"cellular",
"structures",
"and",
"organelles",
"gel",
"electrophoresis",
"research",
"and",
"analysis",
"methods",
"electrophoretic",
"techniques",
"proteins",
"rna",
"polymerase",
"ribosomes"... | 2019 | Genetic analyses led to the discovery of a super-active mutant of the RNA polymerase I |
Tumour cells show a varying susceptibility to radiation damage as a function of the current cell cycle phase . While this sensitivity is averaged out in an unperturbed tumour due to unsynchronised cell cycle progression , external stimuli such as radiation or drug doses can induce a resynchronisation of the cell cycle ... | The sensitivity of a cell to a dose of radiation is largely affected by its current position within the cell cycle . While under normal circumstances progression through the cell cycle will be asynchronous in a tumour mass , external influences such as chemo- or radiotherapy can induce a synchronisation . Such a common... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | In Silico Analysis of Cell Cycle Synchronisation Effects in Radiotherapy of Tumour Spheroids |
Can lateral connectivity in the primary visual cortex account for the time dependence and intrinsic task difficulty of human contour detection ? To answer this question , we created a synthetic image set that prevents sole reliance on either low-level visual features or high-level context for the detection of target ob... | Current computer vision algorithms reproducing the feed-forward features of the primate visual pathway still fall far behind the capabilities of human subjects in detecting objects in cluttered backgrounds . Here we investigate the possibility that recurrent lateral interactions , long hypothesized to form cortical ass... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"neuroscience",
"biology",
"neuroscience"
] | 2011 | Model Cortical Association Fields Account for the Time Course and Dependence on Target Complexity of Human Contour Perception |
Research has shown that RNA virus populations are highly variable , most likely due to low fidelity replication of RNA genomes . It is generally assumed that populations of DNA viruses will be less complex and show reduced variability when compared to RNA viruses . Here , we describe the use of high throughput sequenci... | Human Cytomegalovirus ( HCMV ) is a dsDNA virus that is the leading source of birth defects associated with an infectious agent . There is currently no effective HCMV vaccine and few treatment strategies for congenital infections exist . Thus , a better understanding of HCMV infections is warranted . Limited data has s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/genomics",
"virology/virus",
"evolution",
"and",
"symbiosis",
"virology"
] | 2011 | Extensive Genome-Wide Variability of Human Cytomegalovirus in Congenitally Infected Infants |
Many bacteria and eukaryotic cells express adhesive proteins at the end of tethers that elongate reversibly at constant or near constant force , which we refer to as yielding elasticity . Here we address the function of yielding elastic adhesive tethers with Escherichia coli bacteria as a model for cell adhesion , usin... | Cells adhere to surfaces and each other in the presence of forces that would easily overpower the individual noncovalent receptor-ligand bonds that mediate this adhesion , raising the question as to how these bonds cooperate to withstand such high forces . Here we show that cooperation and robust adhesion depends on th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"pili",
"and",
"fimbriae",
"cell",
"biology",
"cell",
"adhesion",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"cell",
"mechanics",
"cellular",
"structures",
"and",
"organelles",
"biophysics",
"biomechanics",
"biophysical",
"simulations"
] | 2014 | Yielding Elastic Tethers Stabilize Robust Cell Adhesion |
Cancer cells frequently undergo chromosome missegregation events during mitosis , whereby the copies of a given chromosome are not distributed evenly among the two daughter cells , thus creating cells with heterogeneous karyotypes . A stochastic model tracing cellular karyotypes derived from clonal populations over hun... | Chromosomal instability ( CIN ) is a hallmark of cancer and it results from persistent chromosome segregation errors during cell division . CIN has been shown to play a key role in drug resistance and tumor metastasis . While our understanding of CIN on the cellular level has grown over the past decade , our ability to... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"markov",
"models",
"chromosome",
"structure",
"and",
"function",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"eigenvalues",
"mathematics",
"algebra",
"karyotypes",
"chromosomal",
"duplications",
"chromosome",
"biology",
"chromosomal",
"aberrations",
... | 2018 | A Markov chain for numerical chromosomal instability in clonally expanding populations |
Widespread success of the intracellular bacterium Wolbachia across insects and nematodes is due to efficient vertical transmission and reproductive manipulations . Many strains , including wMel from Drosophila melanogaster , exhibit a specific concentration to the germplasm at the posterior pole of the mature oocyte , ... | The intracellular bacterial symbiont Wolbachia uses host motor proteins for microtubule-based transport to the posterior pole of the developing host oocyte , coincident with the future germline , and yet it does not interfere in this process . We present evidence here that Wolbachia competes poorly with key host cargos... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"kinesins",
"nuclear",
"staining",
"propidium",
"iodide",
"staining",
"animals",
"wolbachia",
"germ",
"cells",
"animal",
"models",
"developmental",
"biology",
"oocytes",
"drosophila",
"melanogaster",
"model",
"organisms",
"molecular",
"motors",
"experimen... | 2018 | Wolbachia and host germline components compete for kinesin-mediated transport to the posterior pole of the Drosophila oocyte |
Small globular proteins and peptides commonly exhibit two-state folding kinetics in which the rate limiting step of folding is the surmounting of a single free energy barrier at the transition state ( TS ) separating the folded and the unfolded states . An intriguing question is whether the polypeptide chain reaches , ... | The folding dynamics of many small protein/peptides investigated recently are in terms of simple two-state model in which only two populations exist ( folded and unfolded ) , separated by a single free energy barrier with only one kinetically important transition state ( TS ) . However , dynamical characterization of t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"protein",
"chemistry",
"biophysic",
"al",
"simulations",
"protein",
"folding",
"biology",
"computational",
"biology",
"biophysics"
] | 2011 | Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations |
Regulation of gene expression via specific cis-regulatory promoter elements has evolved in cellular organisms as a major adaptive mechanism to respond to environmental change . Assuming a simple model of transcriptional regulation , genes that are differentially expressed in response to a large number of different exte... | The induction or repression of specific genes has evolved in living organisms as a mechanism to respond to environmental changes . At the molecular level , this process is mediated via molecular switches , so-called regulatory elements , generally located in the genomic region adjacent to the gene they control , the ge... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mathematics",
"arabidopsis",
"(thale",
"cress)",
"plant",
"biology",
"computational",
"biology",
"evolutionary",
"biology",
"molecular",
"biology"
] | 2007 | The Regulatory Code for Transcriptional Response Diversity and Its Relation to Genome Structural Properties in A. thaliana |
Neurodegenerative lysosomal storage disorders ( LSDs ) are severe and untreatable , and mechanisms underlying cellular dysfunction are poorly understood . We found that toxic lipids relevant to three different LSDs disrupt multiple lysosomal and other cellular functions . Unbiased drug discovery revealed several struct... | Neurodegenerative lysosomal storage disorders ( LSDs ) are severe and untreatable recessive genetic disorders that cause devastating damage to the nervous system . These diseases exhibit severe disruption of lysosomes ( a cellular organelle that breaks down lipids and proteins ) and other aspects of cell function . How... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infographics",
"lysosomes",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"cell",
"disruption",
"toxic",
"agents",
"toxicology",
"animal",
"models",
"toxicity",
... | 2016 | Lysosomal Re-acidification Prevents Lysosphingolipid-Induced Lysosomal Impairment and Cellular Toxicity |
Computational tools are widely used for interpreting variants detected in sequencing projects . The choice of these tools is critical for reliable variant impact interpretation for precision medicine and should be based on systematic performance assessment . The performance of the methods varies widely in different per... | In precision/personalized medicine of many conditions it is essential to investigate individual’s genome . Interpretation of the observed variation ( mutation ) sets is feasible only with computational approaches . We assessed the performance of variant pathogenicity/tolerance prediction programs on benign variants . V... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"statistics",
"computational",
"biology",
"geographical",
"locations",
"alleles",
"organic",
"compounds",
"mutation",
"mathematics",
"drug",
"design",
"forecasting",
"amino",
"acid",
"substitution",
"genome... | 2019 | How good are pathogenicity predictors in detecting benign variants? |
The Iowa Gambling Task ( IGT ) is one of the most common paradigms used to assess decision-making and executive functioning in neurological and psychiatric disorders . Several reinforcement-learning ( RL ) models were recently proposed to refine the qualitative and quantitative inferences that can be made about these p... | The ability to perform decisions and learn from their outcomes is a fundamental function of the central nervous system . In order to maintain their homeostasis and maximize their biological fitness , organisms must maximize rewards and minimize punishments . Yet , pure exploitation often leads to suboptimal solutions .... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"recreation",
"learning",
"medicine",
"and",
"health",
"sciences",
"decision",
"making",
"social",
"sciences",
"neuroscience",
"learning",
"and",
"memory",
"simulation",
"and",
"modeling",
"physiological",
"processes",
"developmental",
"biology",
"cognitive",
"psychology"... | 2019 | Sequential exploration in the Iowa gambling task: Validation of a new computational model in a large dataset of young and old healthy participants |
FNR is a well-studied global regulator of anaerobiosis , which is widely conserved across bacteria . Despite the importance of FNR and anaerobiosis in microbial lifestyles , the factors that influence its function on a genome-wide scale are poorly understood . Here , we report a functional genomic analysis of FNR actio... | Regulation of gene expression by transcription factors ( TFs ) is key to adaptation to environmental changes . Our comprehensive , genome-scale analysis of a prototypical global TF , the anaerobic regulator FNR from Escherichia coli , leads to several novel and unanticipated insights into the influences on FNR binding ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"escherichia",
"coli",
"microarrays",
"genome",
"expression",
"analysis",
"prokaryotic",
"models",
"functional",
"genomics",
"model",
"organisms",
"microbial",
"physiology",
"regulatory",
"networks",
"biology",
"genomics",
"microbiology",
"computational",
"biology"
] | 2013 | Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding |
The layout of sensory brain areas is thought to subtend perception . The principles shaping these architectures and their role in information processing are still poorly understood . We investigate mathematically and computationally the representation of orientation and spatial frequency in cat primary visual cortex . ... | Brain areas receiving sensory input often show specific functional organizations whose layout may subtend perception . We aim at understanding possible principles shaping these architectures and their role in information processing . Cat primary visual cortex provides our choice model . Pinwheel singularities of the ce... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Parsimony, Exhaustivity and Balanced Detection in Neocortex |
Snakebite is a major problem affecting the rural poor in many of the poorest countries in the tropics . However , the scale of the socio-economic burden has rarely been studied . We undertook a comprehensive assessment of the burden in Sri Lanka . Data from a representative nation-wide community based household survey ... | Snakebite predominantly affects poor people in the rural tropics . The effect that snakebite has on these populations , both economically and in terms of death and disability , is poorly understood . We used data from a national household survey of snakebite in Sri Lanka to estimate the burden of death and disability a... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"poisoning",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"health",
"care",
"signs",
"and",
"symptoms",
"global",
"health",
"neglected",
"tropical",
"d... | 2017 | The socio-economic burden of snakebite in Sri Lanka |
This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele ( MA ) host-pathogen interactions , focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum ( chiltepin ) . Chiltepin grows in a variety of wild habita... | Viruses cause plant diseases , whose severity is considered to increase under plant cultivation . Hence , it is highly relevant to understand the genetics of plant virus resistance , and its variation in wild and cultivated plants . Analyses of plant pathogen resistance have focused on R proteins , which recognize path... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"sequencing",
"techniques",
"biogeography",
"ecology",
"and",
"environmental",
"sciences",
"medicine",
"and",
"health",
"sciences",
"population",
"genetics",
"parasitic",
"diseases",
"viruses",
"rna",
"viruses",
"molecular",
"biology",
"techniques",
"population",
"biology... | 2016 | Human Management of a Wild Plant Modulates the Evolutionary Dynamics of a Gene Determining Recessive Resistance to Virus Infection |
Cardiomyopathy is the main clinical form of Chagas disease ( CD ) ; however , cerebral manifestations , such as meningoencephalitis , ischemic stroke and cognitive impairment , can also occur . The aim of the present study was to investigate functional microvascular alterations and oxidative stress in the brain of mice... | Chagas disease ( CD ) is a neglected tropical illness caused by the parasite Trypanosoma cruzi ( T . cruzi ) . It is endemic in Latin America and affects 10 million people worldwide . Meningoencephalitis occurs in children with acute CD and in immunosuppressed patients suffering acute CD reactivation . During the chron... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"neurobiology",
"of",
"disease",
"and",
"regeneration",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"microbiology",
"neuroscience",
"parasitic",
"protozoans",
"parasitology",
"protozoans",
"inflammation",
"pathogenesi... | 2014 | Acute Chagas Disease Induces Cerebral Microvasculopathy in Mice |
Cell-to-cell movement of plant viruses occurs via plasmodesmata ( PD ) , organelles that evolved to facilitate intercellular communications . Viral movement proteins ( MP ) modify PD to allow passage of the virus particles or nucleoproteins . This passage occurs via several distinct mechanisms one of which is MP-depend... | To establish infection , plant viruses spread cell-to-cell via narrow channels in the cell wall , the plasmodesmata ( PD ) . Movement proteins ( MP ) are virus-encoded proteins essential for virus intercellular transport through PD . Plasmodesmata located plant proteins ( PDLPs ) , are specifically recognised by the MP... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"science",
"virology",
"plant",
"pathogens",
"plant",
"biology",
"plant",
"pathology",
"biology",
"microbiology"
] | 2011 | Tubule-Guided Cell-to-Cell Movement of a Plant Virus Requires Class XI Myosin Motors |
A recent study has shown that treatment of visceral leishmaniasis ( VL ) with the standard dose of 15 mg/kg/day of paromomycin sulphate ( PM ) for 21 days was not efficacious in patients in Sudan . We therefore decided to test the efficacy of paramomycin for a longer treatment duration ( 15 mg/kg/day for 28 days ) and ... | Visceral leishmaniasis ( VL ) is a parasitic disease transmitted through the bite of sandflies . The WHO estimates 500 , 000 new cases of VL each year , with more than 90% of cases occurring in Southeast Asia , East Africa , and South America . If left untreated , VL can be fatal . We had previously conducted a large m... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"infectious",
"diseases",
"infectious",
"diseases/epidemiology",
"and",
"control",
"of",
"infectious",
"diseases"
] | 2010 | Paromomycin for the Treatment of Visceral Leishmaniasis in Sudan: A Randomized, Open-Label, Dose-Finding Study |
Protein Phosphatase type 2A ( PP2A ) represents a family of holoenzyme complexes with diverse biological activities . Specific holoenzyme complexes are thought to be deregulated during oncogenic transformation and oncogene-induced signaling . Since most studies on the role of this phosphatase family have relied on the ... | Protein Phosphatase type 2A ( PP2A ) represent a family of holoenzyme complexes involved in wide range of activities such as growth , differentiation , and cell death . The PP2A holoenzyme complex is made up of a catalytic , a structural , and one of various “B” subunits . These “B” subunits are thought to provide the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"in",
"vitro",
"genetics",
"and",
"genomics",
"mammals",
"homo",
"(human)"
] | 2007 | A RNA Interference Screen Identifies the Protein Phosphatase 2A Subunit PR55γ as a Stress-Sensitive Inhibitor of c-SRC |
Left-censored missing values commonly exist in targeted metabolomics datasets and can be considered as missing not at random ( MNAR ) . Improper data processing procedures for missing values will cause adverse impacts on subsequent statistical analyses . However , few imputation methods have been developed and applied ... | Missing values caused by the limit of detection/quantification ( LOD/LOQ ) were widely observed in mass spectrometry ( MS ) -based targeted metabolomics studies and could be recognized as missing not at random ( MNAR ) . MNAR leads to biased parameter estimations and jeopardizes following statistical analyses in differ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"simulation",
"and",
"modeling",
"multivariate",
"analysis",
"metabolomics",
"probability",
"distribution",
"mathematics",
"forecasting",
"statistics",
"(mathematics)",
"information",
"technology",
"data",
"processing",
"research",
"and",
"analysis",
"methods",
"computer",
... | 2018 | GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies |
Mechanisms by which hepatitis C virus ( HCV ) evades cellular immunity to establish persistence in chronically infected individuals are not clear . Mutations in human leukocyte antigen ( HLA ) class I-restricted epitopes targeted by CD8+ T cells are associated with persistence , but the extent to which these mutations ... | Hepatitis C virus ( HCV ) -associated liver disease is a leading indication for liver transplantation in the United States . With more than 170 million people infected with HCV worldwide and more than 70% of those infected unable to clear the virus , it is of paramount importance to elucidate the factors leading to vir... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"virology/immune",
"evasion",
"immunology/immunity",
"to",
"infections",
"immunology/immune",
"response",
"virology/host",
"antiviral",
"responses"
] | 2008 | Stable Cytotoxic T Cell Escape Mutation in Hepatitis C Virus Is Linked to Maintenance of Viral Fitness |
Wolbachia are ubiquitous inherited endosymbionts of invertebrates that invade host populations by modifying host reproductive systems . However , some strains lack the ability to impose reproductive modification and yet are still capable of successfully invading host populations . To explain this paradox , theory predi... | Wolbachia are bacteria that infect millions of insect species worldwide . Wolbachia aren't infectious , but are maternally inherited symbionts passed from mother to offspring . To infect a host population , Wolbachia behave as reproductive parasites and alter the host reproductive system in a manner that increases infe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"ecology/environmental",
"microbiology",
"ecology/evolutionary",
"ecology",
"microbiology/parasitology",
"evolutionary",
"biology/evolutionary",
"ecology"
] | 2009 | Evidence for Metabolic Provisioning by a Common Invertebrate Endosymbiont, Wolbachia pipientis, during Periods of Nutritional Stress |
We carried out genome-wide association ( GWA ) studies in inbred mouse strains characterized for their lung tumor susceptibility phenotypes ( spontaneous or urethane-induced ) with panels of 12 , 959 ( 13K ) or 138 , 793 ( 140K ) single-nucleotide polymorphisms ( SNPs ) . Above the statistical thresholds , we detected ... | Genome-wide mapping is now popular in both humans and experimental animals , but results of these studies are not validated by independent approaches . We conducted a genome-wide mapping analysis of lung cancer phenotypes in mouse strains and compared our results with those in three previous studies . We found that mos... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/animal",
"genetics",
"genetics",
"and",
"genomics/complex",
"traits",
"genetics",
"and",
"genomics/disease",
"models",
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"genetics",
"and",
"genomics/cancer",
"genetics",
"genetics",
"and"... | 2009 | Mouse Genome-Wide Association Mapping Needs Linkage Analysis to Avoid False-Positive Loci |
The release of signaling molecules from neurons must be regulated , to accommodate their highly polarized structure . In the developing Drosophila visual system , photoreceptor neurons secrete the epidermal growth factor receptor ligand Spitz ( Spi ) from their cell bodies , as well as from their axonal termini . Here ... | Cells secrete signaling molecules that trigger a variety of responses in neighboring cells by activating their respective cell-surface receptors . Because many cells in an organism are polarized , regulating the precise location of ligand secretion is important for controlling the position and nature of the response . ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/morphogenesis",
"and",
"cell",
"biology",
"cell",
"biology/cell",
"signaling",
"cell",
"biology/neuronal",
"signaling",
"mechanisms",
"cell",
"biology/membranes",
"and",
"sorting",
"developmental",
"biology/cell",
"differentiation",
"developmental",
... | 2010 | Polarized Secretion of Drosophila EGFR Ligand from Photoreceptor Neurons Is Controlled by ER Localization of the Ligand-Processing Machinery |
Keratins are cytoskeletal intermediate filament proteins that are increasingly being recognised for their diverse cellular functions . Here we report the consequences of germ line inactivation of Keratin 76 ( Krt76 ) in mice . Homozygous disruption of this epidermally expressed gene causes neonatal skin flaking , hyper... | The generation of knockout mice is a central approach to studying gene function . We have examined the consequences of the germ line inactivation of Keratin 76 in mice and in doing so we reveal a previously undescribed mechanism by which keratin intermediate filaments regulate cellular interactions and tissue homeostas... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"genetics",
"epithelial",
"cells",
"animal",
"models",
"developmental",
"biology",
"mutation",
"model",
"organisms",
"organism",
"development",
"molecular",
"development",
"research",
"and",
"analysis",
"methods",
"embryology",
"adhesion",
"molecules",
"biologic... | 2014 | Keratin 76 Is Required for Tight Junction Function and Maintenance of the Skin Barrier |
The only oral drug available for the treatment of leishmaniasis is miltefosine , described and approved for visceral leishmaniasis in India . Miltefosine is under evaluation for the treatment of cutaneous leishmaniasis in the Americas although its efficacy for the treatment of human visceral leishmaniasis caused by Lei... | Studies to determine drug efficacy in experimental models of leishmaniasis involve several difficulties . Parasite quantification in tissues is generally done by techniques that are laborious and time consuming , such as limiting dilution and microscopic counting of amastigotes in imprinting of infected organs . To ove... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Generation of Luciferase-Expressing Leishmania infantum chagasi and Assessment of Miltefosine Efficacy in Infected Hamsters through Bioimaging |
Dengue hemorrhagic fever ( DHF ) is a severe form of dengue , characterized by bleeding and plasma leakage . A number of DHF risk factors had been suggested . However , these risk factors may not be generalized to all populations and epidemics for screening and clinical management of patients at risk of developing DHF ... | Dengue is a major vector borne disease in the tropical and subtropical regions . An estimated 50 million infections occur per annum in over 100 countries . A severe form of dengue , characterized by bleeding and plasma leakage , known as dengue hemorrhagic fever ( DHF ) is estimated to occur in 1–5% of hospitalized cas... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"viral",
"hemorrhagic",
"fevers",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"clinical",
"epidemiology",
"tropical",
"diseases",
"(non-neglected)",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"dengue",
"fever",
"neglected",... | 2012 | Diabetes with Hypertension as Risk Factors for Adult Dengue Hemorrhagic Fever in a Predominantly Dengue Serotype 2 Epidemic: A Case Control Study |
The idea that synaptic properties are defined by specific pre- and postsynaptic activity histories is one of the oldest and most influential tenets of contemporary neuroscience . Recent studies also indicate , however , that synaptic properties often change spontaneously , even in the absence of specific activity patte... | The modification of synaptic connections by specific activity histories ( a phenomenon known as synaptic plasticity ) is widely believed to represent a major substrate of processes collectively referred to as learning and memory . Recent studies indicate , however , that synapses also change spontaneously , even in the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"fluorescence",
"imaging",
"medicine",
"and",
"health",
"sciences",
"fluorescence",
"neural",
"networks",
"nervous",
"system",
"random",
"variables",
"electrophysiology",
"neuroscience",
"covariance",
"electromagnetic",
"radiation",
"mathematics",
"nerve",
"fibers",
"neuron... | 2016 | Relative Contributions of Specific Activity Histories and Spontaneous Processes to Size Remodeling of Glutamatergic Synapses |
Conservation priority-setting schemes have not yet combined geographic priorities with a framework that can guide the allocation of funds among alternate conservation actions that address specific threats . We develop such a framework , and apply it to 17 of the world's 39 Mediterranean ecoregions . This framework offe... | Given limited funds for biodiversity conservation , we need to carefully prioritise where funds are spent . Various schemes have been developed to set priorities for conservation spending among different countries and regions . However , there is no framework for guiding the allocation of funds among alternative conser... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"ecology",
"vertebrates",
"plants"
] | 2007 | Conserving Biodiversity Efficiently: What to Do, Where, and When |
Household contacts constitute the highest risk group for leprosy development , and despite significant progress in the disease control , early diagnosis remains the primary goals for leprosy management programs . We have recruited 175 seropositive and 35 seronegative household contacts from 2014 to 2016 , who were subj... | Despite the apparent progress observed in recent years in leprosy control , early identification of cases remains one of the primary objectives of control programs . In addition , the failure of the current therapeutic scheme on the incidence of leprosy demonstrates that the disease elimination as a public health progr... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"dermatology",
"mycobacterium",
"leprae",
"medicine",
"and",
"health",
"sciences",
"enzyme-linked",
"immunoassays",
"body",
"fluids",
"biopsy",
"tropical",
"diseases",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"biochemical",
"analysis",
"bacterial",
"disease... | 2018 | Molecular, immunological and neurophysiological evaluations for early diagnosis of neural impairment in seropositive leprosy household contacts |
Quantitation of the nonlinear heterogeneities in Leishmania parasites , sand fly vectors , and mammalian host relationships provides insights to better understand leishmanial transmission epidemiology towards improving its control . The parasite manipulates the sand fly via production of promastigote secretory gel ( PS... | We review recent research that sheds light on the quantitative biology of leishmanial transmission between sand flies and mammalian hosts and use these insights to better understand transmission , the observed epidemiology of the disease , and their implications in choice of control strategy . Using animal models , we ... | [
"Abstract",
"Introduction",
"Leishmaniasis",
"clusters",
"in",
"time",
"and",
"space",
"Mammalian",
"infection",
"reservoirs",
"Asymptomatic",
"infection",
"Influence",
"of",
"sand",
"fly",
"infecting",
"dose",
"on",
"the",
"efficiency",
"of",
"subsequent",
"transmiss... | [
"kala-azar",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"tropical",
"diseases",
"vector-borne",
"diseases",
"sand",
"flies",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"review",
"protozoans",
"leishmania",
"neglected",
"tropical",
"diseases",
"i... | 2017 | Combining epidemiology with basic biology of sand flies, parasites, and hosts to inform leishmaniasis transmission dynamics and control |
Living creatures must accurately infer the nature of their environments . They do this despite being confronted by stochastic and context sensitive contingencies—and so must constantly update their beliefs regarding their uncertainty about what might come next . In this work , we examine how we deal with uncertainty th... | Humans are constantly confronted with surprising events . To navigate such a world , we must understand the chances of an unexpected event occurring at any given point in time . We do this by creating a model of the world around us , in which we allow for these unexpected events to occur by holding beliefs about how vo... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"statistics",
"pervasive",
"developmental",
"disorders",
"brain",
"electrophysiology",
"social",
"sciences",
"autism",
"mathematical",
"models",
"developmental",
"psychology",
"neuroscience",
"electrophysiology",
"simulation",
"and",
... | 2019 | With an eye on uncertainty: Modelling pupillary responses to environmental volatility |
Cutaneous leishmaniasis ( CL ) is a major public health problem in Libya . In this paper , we describe the eco-epidemiological parameters of CL during the armed conflict period from January 2011 till December 2012 . Current spatiotemporal distributions of CL cases were explored and projected to the future using a corre... | Cutaneous leishmaniasis ( CL ) is a skin infection caused by a single-celled parasite that is transmitted by the bite of a phlebotomine sandfly . CL is the most common form of leishmaniasis characterized by localized lesions in the skin and mucous membranes . The disease is prevalent in all countries around the Mediter... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"geographical",
"regions",
"geographical",
"locations",
"tropical",
"diseases",
"sand",
"flies",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoans",
"signs",
"and",
"sym... | 2017 | Spatiotemporal and molecular epidemiology of cutaneous leishmaniasis in Libya |
Salmonella enterica serovar typhimurium extensively remodels the host late endocytic compartments to establish its vacuolar niche within the host cells conducive for its replication , also known as the Salmonella-containing vacuole ( SCV ) . By maintaining a prolonged interaction with late endosomes and lysosomes of th... | Intracellular pathogens have devised various strategies to subvert the host membrane trafficking pathways for their growth and survival inside the host cells . Salmonella is one such successful intracellular pathogen that redirects membrane and nutrients from the host endocytic compartments to its replicative niche kno... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"lysosomes",
"vesicles",
"pathology",
"and",
"laboratory",
"medicine",
"hela",
"cells",
"gene",
"regulation",
"pathogens",
"biological",
"cultures",
"microbiology",
"salmonellosis",
"bacterial",
"diseases",
"membrane",
"fusion",
... | 2017 | Salmonella exploits the host endolysosomal tethering factor HOPS complex to promote its intravacuolar replication |
Neural populations encode information about their stimulus in a collective fashion , by joint activity patterns of spiking and silence . A full account of this mapping from stimulus to neural activity is given by the conditional probability distribution over neural codewords given the sensory input . For large populati... | In the sensory periphery , stimuli are represented by patterns of spikes and silences across a population of sensory neurons . Because the neurons form an interconnected network , the code cannot be understood by looking at single cells alone . Recent recordings in the retina have enabled us to study populations of a h... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"physics",
"visual",
"system",
"statistical",
"mechanics",
"computational",
"neuroscience",
"biophysics",
"theory",
"biology",
"sensory",
"systems",
"biophysics",
"neuroscience",
"coding",
"mechanisms"
] | 2013 | Stimulus-dependent Maximum Entropy Models of Neural Population Codes |
Parasitic helminths such as schistosomes , as well as filarial and soil-transmitted nematodes , are estimated to infect at least a billion people worldwide , with devastating impacts on human health and economic development . Diagnosis and monitoring of infection dynamics and efficacy of treatment depend almost entirel... | Schistosomes infect hundreds of millions of people worldwide , with devastating effects on human health and economic development . One of the major challenges in treatment and control of these diseases is the accurate diagnosis of infection and monitoring of transmission dynamics . Current parasitological and serologic... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Molecular Detection of Schistosome Infections with a Disposable Microfluidic Cassette |
The introduction ten years ago of RNA interference ( RNAi ) as a tool for molecular exploration in Trypanosoma brucei has led to a surge in our understanding of the pathogenesis and biology of this human parasite . In particular , a genome-wide RNAi screen has recently been combined with next-generation Illumina sequen... | RNA interference ( RNAi ) , a naturally-occurring pathway whereby the presence of double-stranded RNA in a cell triggers the degradation of homologous mRNA , has been harnessed in many organisms as an invaluable molecular biology tool to interrogate gene function . Although this technology is widely used in the protozo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"parasite",
"groups",
"genetic",
"mutation",
"rna",
"interference",
"parasite",
"evolution",
"microbiology",
"parasitology",
"gene",
"function",
"parastic",
"protozoans",
"molecular",
"genetics",
"proteins",
"biology",
"recombinant",
"proteins",
"molecular",
"biology",
"m... | 2012 | Comparative Genomics Reveals Two Novel RNAi Factors in Trypanosoma brucei and Provides Insight into the Core Machinery |
The human genome encodes thousands of long noncoding RNA ( lncRNA ) genes; the function of majority of them is poorly understood . Aberrant expression of a significant number of lncRNAs is observed in various diseases , including cancer . To gain insights into the role of lncRNAs in breast cancer progression , we perfo... | Breast cancer is the most common cancer in women worldwide . The molecular mechanisms underlying the disease have been extensively studied , leading to dramatic improvements in diagnostic and prognostic approaches . Despite the overall improvements in survival rate , numerous cases of death by breast cancer are still r... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"methods"
] | [
"rna-binding",
"proteins",
"medicine",
"and",
"health",
"sciences",
"breast",
"tumors",
"gene",
"regulation",
"messenger",
"rna",
"rna",
"extraction",
"cancers",
"and",
"neoplasms",
"long",
"non-coding",
"rnas",
"rna",
"stability",
"oncology",
"extraction",
"technique... | 2018 | A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability |
Brucellosis is regarded as a major zoonotic infection worldwide . Awareness and knowledge of brucellosis among occupational workers is considered an important aspect of brucellosis control in both humans and animals . The aim of this study was to explore the distributions of the pooled awareness level and the knowledge... | Brucellosis is considered a neglected zoonotic disease that creates a very large obstacle to the development of animal production and is a great threat to human health . High brucellosis awareness and knowledge is critical for the implementation of correct practices and habits and consequently the control and preventio... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"livestock",
"medicine",
"and",
"health",
"sciences",
"health",
"education",
"and",
"awareness",
"ruminants",
"china",
"tropical",
"diseases",
"geographical",
"locations",
"vertebrates",
"animals",
"mammals",
"brucellosis",
"health",
"care",
"bacterial",
"diseases",
"ne... | 2019 | Brucellosis awareness and knowledge in communities worldwide: A systematic review and meta-analysis of 79 observational studies |
Despite more than 25 years of research , the molecular targets of quinoline-3-carboxamides have been elusive although these compounds are currently in Phase II and III development for treatment of autoimmune/inflammatory diseases in humans . Using photoaffinity cross-linking of a radioactively labelled quinoline-3-carb... | What molecules and mechanisms underlie the development of autoimmune diseases such as multiple sclerosis , rheumatoid arthritis , and systemic lupus erythematosus are largely unknown . To gain some insight into the process , we use a class of chemical compounds , quinoline-3-carboxamides ( Q compounds ) , which modify ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"neurological",
"disorders",
"chemistry",
"immunology"
] | 2009 | Identification of Human S100A9 as a Novel Target for Treatment of Autoimmune Disease via Binding to Quinoline-3-Carboxamides |
A subset of patients with stable asthma has prominent neutrophilic and reduced eosinophilic inflammation , which is associated with attenuated airways hyper-responsiveness ( AHR ) . Haemophilus influenzae has been isolated from the airways of neutrophilic asthmatics; however , the nature of the association between infe... | Approximately 50% of asthmatics have non-eosinophilic inflammation , and 20% of these patients have severe neutrophilic inflammation and increased IL-8 levels . These so-called neutrophilic asthmatics have persistent airway colonization with bacteria , and Haemophilus influenzae is one of the bacteria most commonly iso... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"immunology",
"biology",
"microbiology"
] | 2011 | Haemophilus influenzae Infection Drives IL-17-Mediated Neutrophilic Allergic Airways Disease |
Snakebite poisoning is a significant medical problem in agricultural societies in Sub Saharan Africa . Antivenom ( AV ) is the standard treatment , and we assessed the cost-effectiveness of making it available in 16 countries in West Africa . We determined the cost-effectiveness of AV based on a decision-tree model fro... | Antivenom is the main intervention against snakebite poisoning but is relatively scarce , unaffordable and the situation has been compounded further by the recent cessation of production of effective antivenoms and marketing of inappropriate products . Given this crisis , we assessed the cost effectiveness of providing... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"cost-effectiveness",
"analysis",
"economic",
"analysis",
"ears",
"blood",
"counts",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"vertebrates",
"animals",
"reptiles",
"neglected",
... | 2016 | Cost-Effectiveness of Antivenoms for Snakebite Envenoming in 16 Countries in West Africa |
Paired sense and antisense ( S/AS ) genes located in cis represent a structural feature common to the genomes of both prokaryotes and eukaryotes , and produce partially complementary transcripts . We used published genome and transcriptome sequence data and found that over 20% of genes ( 645 pairs ) in the budding yeas... | In the compact genome of the budding yeast Saccharomyces cerevisiae , genes are frequently organized into convergent pairs that are transcribed from opposing DNA strands in opposite directions and have overlapping 3′-UTRs . Here we explore the negative correlation in expression levels between convergent genes using a s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"expression",
"analysis",
"model",
"organisms",
"rna",
"interference",
"genome",
"evolution",
"gene",
"expression",
"genetics",
"yeast",
"and",
"fungal",
"models",
"biology",
"genomics",
"evolutionary",
"biology",
"genomic",
"evolution",
"saccharomyces",
"cere... | 2014 | 3′ Untranslated Regions Mediate Transcriptional Interference between Convergent Genes Both Locally and Ectopically in Saccharomyces cerevisiae |
Health is a multidimensional landscape . If we just consider the host , there are many outputs that interest us: evolutionary fitness determining parameters like fecundity , survival and pathogen clearance as well as medically important health parameters like sleep , energy stores and appetite . Hosts use a variety of ... | The importance of individual immune responses is incredibly infection dependent , and this paper harnesses the variability in two mutant lines to explain the relative importance of two aspects of fly immunity: melanization and phagocytosis . Increased phagocytic activity is beneficial during S . pneumoniae infection du... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"immunopathology",
"pathogenesis",
"drosophila",
"melanogaster",
"model",
"organisms",
"immunity",
"innate",
"immunity",
"immunology",
"biology",
"microbiology",
"bacterial",
"pathogens",
"gram",
"positive"
] | 2012 | How the Fly Balances Its Ability to Combat Different Pathogens |
Cells rely on a network of conserved pathways to govern DNA replication fidelity . Loss of polymerase proofreading or mismatch repair elevates spontaneous mutation and facilitates cellular adaptation . However , double mutants are inviable , suggesting that extreme mutation rates exceed an error threshold . Here we com... | Organisms strike a balance between genetic continuity and change . Most cells are well adapted to their niches and therefore invest heavily in mechanisms that maintain accurate DNA replication . When cell populations are confronted with changing environmental conditions , “mutator” clones with high mutation rates emerg... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mutagenesis",
"biochemistry",
"cancer",
"genetics",
"genetic",
"mutation",
"mutation",
"types",
"genetics",
"biology",
"genetics",
"and",
"genomics",
"mutational",
"hypotheses",
"gene",
"function"
] | 2011 | Mutator Suppression and Escape from Replication Error–Induced Extinction in Yeast |
There is no currently licensed vaccine for respiratory syncytial virus ( RSV ) despite being the leading cause of lower respiratory tract infections in children . Children previously immunized with a formalin-inactivated RSV ( FI-RSV ) vaccine exhibited enhanced respiratory disease following natural RSV infection . Sub... | RSV is a significant healthcare burden and is the leading cause of bronchiolitis and pneumonia during childhood . The failure of the 1960's FI-RSV vaccine trial to not only elicit protection against RSV infection , but also provoke enhanced morbidity and mortality in vaccinees has significantly hampered development of ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | RSV Vaccine-Enhanced Disease Is Orchestrated by the Combined Actions of Distinct CD4 T Cell Subsets |
Palmitoylation is a key post-translational modification mediated by a family of DHHC-containing palmitoyl acyl-transferases ( PATs ) . Unlike other lipid modifications , palmitoylation is reversible and thus often regulates dynamic protein interactions . We find that the mouse hair loss mutant , depilated , ( dep ) is ... | During embryonic development , growth and patterning are regulated at many levels . Signals that mediate transcriptional activity , where and when genes are expressed , are a primary level of regulation . However , developmental signals can be further fine-tuned by modulating protein stability , localization , and acti... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"dermatology",
"developmental",
"biology/stem",
"cells",
"genetics",
"and",
"genomics/functional",
"genomics",
"genetics",
"and",
"genomics/gene",
"function",
"developmental",
"biology/molecular",
"development",
"developmental",
"biology/organogenesis"
] | 2009 | Palmitoylation Regulates Epidermal Homeostasis and Hair Follicle Differentiation |
In addition to its surface glycoprotein ( GP1 , 2 ) , Ebola virus ( EBOV ) directs the production of large quantities of a truncated glycoprotein isoform ( sGP ) that is secreted into the extracellular space . The generation of secreted antigens has been studied in several viruses and suggested as a mechanism of host i... | The function of the Ebola virus ( EBOV ) secreted glycoprotein ( sGP ) has been long debated , and the fact that sGP production is conserved among all known EBOV species strongly indicates an important role in the viral life cycle . Furthermore , the recent finding that EBOV mutates to a predominantly non-sGP-forming p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"immunity",
"to",
"infections",
"immunology",
"microbiology",
"ebola",
"hemorrhagic",
"fever",
"infectious",
"disease",
"control",
"immunomodulation",
"infectious",
"diseases",
"viral",
"immune",
"evasion",
"biology",
"immune",
"response",
"immunity",
"virolog... | 2012 | Antigenic Subversion: A Novel Mechanism of Host Immune Evasion by Ebola Virus |
The calpains are physiologically important Ca2+-activated regulatory proteases , which are divided into typical or atypical sub-families based on constituent domains . Both sub-families are present in mammals , but our understanding of calpain function is based primarily on typical sub-family members . Here , we take a... | Calpains are calcium activated non-lysosomal proteases that cleave proteins with exquisite selectivity . Proteins can be activated by calpain cleavage , because they are released from inhibitory constraints , or they can be targeted for further degradation to facilitate their normal physiological turnover or to promote... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"developmental",
"biology",
"genomics",
"model",
"organisms",
"molecular",
"cell",
"biology",
"genetics",
"biology",
"computational",
"biology",
"evolutionary",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | The Atypical Calpains: Evolutionary Analyses and Roles in Caenorhabditis elegans Cellular Degeneration |
Within the first three weeks of human immunodeficiency virus ( HIV ) infection , virus replication peaks in peripheral blood . Despite the critical , causal role of virus replication in determining transmissibility and kinetics of progression to acquired immune deficiency syndrome ( AIDS ) , there is limited understand... | We infected macaques with simian immunodeficiency virus ( SIV ) to identify phenomena that may compromise immunological containment of HIV replication following transmission . Within the first days of infection , we detected a significant increase in plasma levels of microbial products . This ‘microbial translocation’ ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"hiv",
"infections",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"vertebrates",
"animals",
"mammals",
"retroviruses",
"primates",
"immunodeficiency",
"viruses",
"viruse... | 2016 | Microbial Translocation and Inflammation Occur in Hyperacute Immunodeficiency Virus Infection and Compromise Host Control of Virus Replication |
In computational biology , modeling is a fundamental tool for formulating , analyzing and predicting complex phenomena . Most neuron models , however , are designed to reproduce certain small sets of empirical data . Hence their outcome is usually not compatible or comparable with other models or datasets , making it u... | Computational models help our understanding of complex biological systems , by identifying their key elements and revealing their operational principles . Close comparisons between model predictions and empirical observations ensure our confidence in a model as a building block for further applications . Most current n... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"simulation",
"and",
"modeling",
"ion",
"channels",
"computational",
"neuroscience",
"neuronal",
"tuning",
"coding",
"mechanisms",
"research",
"a... | 2017 | Physiological models of the lateral superior olive |
Measles virus ( MV ) is a highly contagious member of the Morbillivirus genus that remains a major cause of childhood mortality worldwide . Although infection induces a strong MV-specific immune response that clears viral load and confers lifelong immunity , transient immunosuppression can also occur , leaving the host... | Measles is a highly contagious virus from the Morbillivirus genus that induces a strong adaptive immune response , despite also causing transient immunosuppression . How viral clearance is achieved amidst these seemingly contradictory dynamics ( the so-called ‘measles paradox’ ) is poorly understood . To identify key f... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"pathogens",
"immunology",
"cell-mediated",
"immunity",
"microbiology",
"vert... | 2018 | Modeling the measles paradox reveals the importance of cellular immunity in regulating viral clearance |
The apicomplexan , Cryptosporidium parvum , possesses a bacterial-type lactate dehydrogenase ( CpLDH ) . This is considered to be an essential enzyme , as this parasite lacks the Krebs cycle and cytochrome-based respiration , and mainly–if not solely , relies on glycolysis to produce ATP . Here , we provide evidence th... | Cryptosporidians are unique among the apicomplexans in regards to their parasitic life style ( e . g . , they are intracellular , but undergo extracytoplasmic development within a host membrane-derived structure termed parasitophorous vacuole membrane , PVM ) and their metabolism ( e . g . , they are incapable of de no... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Cryptosporidium Lactate Dehydrogenase Is Associated with the Parasitophorous Vacuole Membrane and Is a Potential Target for Developing Therapeutics |
Genetic and developmental architecture may bias the mutationally available phenotypic spectrum . Although such asymmetries in the introduction of variation may influence possible evolutionary trajectories , we lack quantitative characterization of biases in mutationally inducible phenotypic variation , their genotype-d... | Random mutation does not generate random phenotypic variation because genetic and developmental architecture may constrain and bias the mutationally inducible phenotypic spectrum . Understanding such biases in the introduction of phenotypic variation is thus essential to reveal which phenotypes can ultimately be explor... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics",
"developmental",
"biology/developmental",
"evolution",
"developmental",
"biology/pattern",
"formation",
"evolutionary",
"biology/pattern",
"formation",
"evolutionary",
"biology/developmental",
"evolution"
] | 2010 | Bias and Evolution of the Mutationally Accessible Phenotypic Space in a Developmental System |
Many pathogens associated with chronic infections evolve so rapidly that strains found late in an infection have little in common with the initial strain . This raises questions at different levels of analysis because rapid within-host evolution affects the course of an infection , but it can also affect the possibilit... | Rapidly mutating viruses , such as hepatitis C virus , can escape host immunity by generating new strains that avoid the immune system . Existing data support the idea that such within-host evolution affects the outcome of the infection . Few theoretical models address this question and most follow viral diversity or q... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Model"
] | [
"virology/virus",
"evolution",
"and",
"symbiosis",
"evolutionary",
"biology/evolutionary",
"ecology",
"computational",
"biology/evolutionary",
"modeling",
"infectious",
"diseases/viral",
"infections",
"virology/immune",
"evasion",
"infectious",
"diseases/epidemiology",
"and",
"co... | 2009 | The Evolutionary Dynamics of a Rapidly Mutating Virus within and between Hosts: The Case of Hepatitis C Virus |
Integrator is an RNA polymerase II ( RNAPII ) -associated complex that was recently identified to have a broad role in both RNA processing and transcription regulation . Importantly , its role in human development and disease is so far largely unexplored . Here , we provide evidence that biallelic Integrator Complex Su... | Neurodevelopmental disorders often have a genetic cause , however the genes and the underlying mechanisms that are involved are increasingly diverse , pointing to the complexity of brain development . For normal cell function and in general for normal development , mechanisms that regulate gene transcription into mRNA ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"deletion",
"mutation",
"medicine",
"and",
"health",
"sciences",
"biological",
"cultures",
"neuronal",
"differentiation",
"rna",
"extraction",
"fibroblasts",
"cell",
"differentiation",
"developmental",
"biology",
"mutation",
"connective",
"tissue",
"cells",
"mutation",
"d... | 2017 | Human mutations in integrator complex subunits link transcriptome integrity to brain development |
Dengue is the most important vector-borne viral disease worldwide and a major cause of childhood fever burden in Sri Lanka , which has experienced a number of large epidemics in the past decade . Despite this , data on the burden and transmission of dengue virus in the Indian Subcontinent are lacking . As part of a lon... | Dengue is an increasing problem in the Asian subcontinent , but little research exists on dengue burden and transmission in this region . Dengue ranges from mild fever to pronounced circulatory shock and potentially death . However , clinical disease gives an incomplete picture of how much dengue is circulating , becau... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"disease",
"ecology",
"infectious",
"disease",
"epidemiology",
"global",
"health",
"epidemiology",
"neglected",
"tropical",
"diseases",
"infectious",
"disease",
"modeling",
"epidemiological",
"methods",
"viral",
"diseases",
"child",
"... | 2013 | Estimates of Dengue Force of Infection in Children in Colombo, Sri Lanka |
Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions . This transmission of information is subjected to molecular noise what can decrease its fidelity . Here , we show instead how such intrinsic noise enhances information transfer in the presence of... | There is increasing evidence that the presence of molecular noise greatly influences function in biological systems . This could imply , for instance , that genetic circuits adopt particular architectures in order to reduce noise . On the other hand , noise can be beneficial . Here , we show that this could be the case... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"engineering",
"and",
"technology",
"gene",
"regulation",
"signal",
"processing",
"population",
"genetics",
"vertebrates",
"animals",
"noise",
"reduction",
"xenopus",
"animal",
"models",
"model",
"organisms",
"amphibians",
"genetic",
"load",
"population",
"biology",
"re... | 2016 | Genetic Redundancies Enhance Information Transfer in Noisy Regulatory Circuits |
The multifunctional Mre11-Rad50-Nbs1 ( MRN ) protein complex recruits ATM/Tel1 checkpoint kinase and CtIP/Ctp1 homologous recombination ( HR ) repair factor to double-strand breaks ( DSBs ) . HR repair commences with the 5′-to-3′ resection of DNA ends , generating 3′ single-strand DNA ( ssDNA ) overhangs that bind Repl... | A double-strand break ( DSB ) is a devastating form of DNA damage . Fortunately , cells are equipped with two DSB repair pathways: homologous recombination ( HR ) and nonhomologous end-joining ( NHEJ ) . The Mre11-Rad50-Nbs1 ( MRN ) protein complex recognizes DSBs and initiates HR repair . The Mre11 subunit harbors a n... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology"
] | 2011 | Release of Ku and MRN from DNA Ends by Mre11 Nuclease Activity and Ctp1 Is Required for Homologous Recombination Repair of Double-Strand Breaks |
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