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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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Geminiviruses constitute a group of plant viruses , with a ssDNA genome , whose replication in the nucleus of an infected cell requires the function of geminivirus-encoded replication initiator protein ( Rep ) . Our results suggest that monoubiquitinated histone 2B ( H2B-ub ) promotes tri-methylation of histone 3 at ly... | Histone post translation modification plays vital role in regulation of gene expression in eukaryotes . In plants , Ubiquitin-Conjugating Enzyme 2 and Histone Monoubiquitination1 monoubiquitinates histone 2B that promotes trimethylation of histone H3 at lysine 4 and both modifications eventually activates host transcri... | [
"Abstract",
"Introduction",
"Results",
"Methods"
] | [
"plant",
"anatomy",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"immunology",
"dna-binding",
"proteins",
"microbiology",
"fluorophotometry",
"plant",
"science",
"immunoprecipitation",
"viral",
"genome",
"antibodies",
"microbial",
"genomics",
"research",... | 2017 | The replication initiator protein of a geminivirus interacts with host monoubiquitination machinery and stimulates transcription of the viral genome |
In budding yeast , intragenic histone modification is linked with transcriptional elongation through the conserved regulator Paf1C . To investigate Paf1C-related function in higher eukaryotes , we analyzed the effects of loss of Paf1C on histone H3 density and patterns of H3 methylated at K4 , K27 , and K36 in Arabidop... | In eukaryotes , DNA is packaged with histones and other proteins into a dynamic fabric called chromatin . Specific modifications of histones—including methylation of key lysine residues—provide genetic information that acts synergistically with the DNA code . In yeast , the conserved transcriptional regulator Paf1C is ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/plant",
"growth",
"and",
"development",
"developmental",
"biology/cell",
"differentiation",
"biochemistry/transcription",
"and",
"translation",
"developmental",
"biology/molecular",
"development",
"plant",
"biology/plant",
"genetics",
"and",
"gene",
"e... | 2008 | Genic and Global Functions for Paf1C in Chromatin Modification and Gene Expression in Arabidopsis |
Wolbachia is a maternally transmitted endosymbiotic bacterium that is estimated to infect up to 65% of insect species . The ability of Wolbachia to both induce pathogen interference and spread into mosquito vector populations makes it possible to develop Wolbachia as a biological control agent for vector-borne disease ... | Aedes polynesiensis is a vector for both dengue and filariasis in the South Pacific . Efforts are ongoing to utilize Wolbachia as a biological control agent targeting this vector through either population suppression via releases of incompatible males or population replacement for spreading disease resistance into a po... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"applied",
"microbiology",
"medicine",
"infectious",
"diseases",
"pest",
"control",
"genetics",
"neglected",
"tropical",
"diseases",
"biology",
"microbiology",
"infectious",
"disease",
"control",
"viral",
"diseases",
"parasitic",
"diseases",
"vectors",
"a... | 2013 | Replacing a Native Wolbachia with a Novel Strain Results in an Increase in Endosymbiont Load and Resistance to Dengue Virus in a Mosquito Vector |
Cross-species transmissions of viruses from animals to humans are at the origin of major human pathogenic viruses . While the role of ecological and epidemiological factors in the emergence of new pathogens is well documented , the importance of host factors is often unknown . Chimpanzees are the closest relatives of h... | Many human pathogens are of zoonotic origin , meaning they originated in animals . This includes HIV-1 , the cause of the human AIDS pandemic , which is the result of cross-species transmissions of lentiviruses from chimpanzees and gorillas . However , little is known about the host factors that provide natural protect... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | The Role of the Antiviral APOBEC3 Gene Family in Protecting Chimpanzees against Lentiviruses from Monkeys |
MHC Ib-restricted CD8+ T cells have been implicated in host defense against Mycobacterium tuberculosis ( Mtb ) infection . However , the relative contribution of various MHC Ib-restricted T cell populations to anti-mycobacterial immunity remains elusive . In this study , we used mice that lack MHC Ia ( Kb-/-Db-/- ) , M... | Tuberculosis , the disease caused by Mycobacterium tuberculosis ( Mtb ) , remains a major global health burden . As T cells are crucial to the control of Mtb infection , it is imperative to decipher the role of different T cell subsets in anti-Mtb immunity for the development of more effective vaccines . While the cont... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"cytokines",
"spleen",
"immunology",
"cell-mediated",
"immunity",
"developmental",
"biology",
"clinical",
"medicine",
"molecular",
"develo... | 2016 | Nonclassical MHC Ib-restricted CD8+ T Cells Recognize Mycobacterium tuberculosis-Derived Protein Antigens and Contribute to Protection Against Infection |
One of the most puzzling features of the prehistoric record of hominid stone tools is its apparent punctuation: it consists of abrupt bursts of dramatic change that separate long periods of largely unchanging technology . Within each such period , small punctuated cultural modifications take place . Punctuation on mult... | The ability to accumulate culture is unique to hominids . Yet , understanding of the processes that drive cultural evolution is limited . We develop a computational model that incorporates characteristics of human innovation and offers an explanation for one of the puzzling observations in the archaeological record of ... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"cognitive",
"science",
"geologic",
"time",
"ecology",
"and",
"environmental",
"sciences",
"paleolithic",
"period",
"population",
"dynamics",
"sociology",
"social",
"sciences",
"anthropology",
"neuroscience",
"cultural",
"evolution",
"archaeology",
"cognition",
"geology",
... | 2016 | Game-Changing Innovations: How Culture Can Change the Parameters of Its Own Evolution and Induce Abrupt Cultural Shifts |
In bacteria , laterally acquired genes are often concentrated within chromosomal regions known as genomic islands . Using a recently developed zebrafish infection model , we set out to identify unique factors encoded within genomic islands that contribute to the fitness and virulence of a reference urosepsis isolate—ex... | Bacterial pathogens , even those belonging to the same species , can be incredibly diverse with regard to the genes they carry . However , the design of vaccines and antibiotics typically relies upon identification of general molecular features shared by the targeted organisms . Thus , we have traditionally focused on ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"bacteriology",
"medicine",
"microbiology",
"host-pathogen",
"interaction",
"escherichia",
"coli",
"bacterial",
"diseases",
"microbial",
"evolution",
"molecular",
"genetics",
"bacterial",
"pathogens",
"infectious",
"diseases",
"microbial",
"pathogens",
"biology",
"pathogenesi... | 2013 | A Phyletically Rare Gene Promotes the Niche-specific Fitness of an E. coli Pathogen during Bacteremia |
Loss of PTPN11/SHP2 in mice or in human metachondromatosis ( MC ) patients causes benign cartilage tumors on the bone surface ( exostoses ) and within bones ( enchondromas ) . To elucidate the mechanisms underlying cartilage tumor formation , we investigated the role of SHP2 in the specification , maturation and organi... | Patients with the inherited disorder , metachondromatosis ( MC ) , develop multiple benign cartilage tumors during childhood . MC patients carry heterozygous loss-of-function mutations in the PTPN11 gene , and their cartilage tumors likely arise when the second PTPN11 allele is lost due to a somatic mutation . PTPN11 e... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"developmental",
"biology",
"model",
"organisms",
"genetics",
"biology",
"and",
"life",
"sciences",
"genomics",
"research",
"and",
"analysis",
"methods"
] | 2014 | SHP2 Regulates Chondrocyte Terminal Differentiation, Growth Plate Architecture and Skeletal Cell Fates |
Non-coding RNAs have important roles in regulating physiology , including immunity . Here , we performed transcriptome profiling of immune-responsive genes in Drosophila melanogaster during a Gram-positive bacterial infection , concentrating on long non-coding RNA ( lncRNA ) genes . The gene most highly induced by a Mi... | Drosophila melanogaster is a powerful genetic model for studying the innate immune mechanisms conserved from flies to humans . With recent methodology , such as whole transcriptome analyses , novel non-protein coding genes in addition to protein coding genes are being increasingly identified . These long and short non-... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"invertebrates",
"carbohydrate",
"metabolism",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immunology",
"glucose",
"metabolism",
"animals",
"long",
"non-coding",
"rnas",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"me... | 2019 | Immune-inducible non-coding RNA molecule lincRNA-IBIN connects immunity and metabolism in Drosophila melanogaster |
Considering that many natural stimuli are sparse , can a sensory system evolve to take advantage of this sparsity ? We explore this question and show that significant downstream reductions in the numbers of neurons transmitting stimuli observed in early sensory pathways might be a consequence of this sparsity . First ,... | In forming a mental percept of the surrounding world , sensory information is processed and transmitted through a wide array of neuronal networks of various sizes and functionalities . Despite , and perhaps because of , this , sensory systems are able to render highly accurate representations of stimuli . In the retina... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computer",
"and",
"information",
"sciences",
"mathematical",
"computing",
"mathematics",
"neural",
"networks",
"computational",
"neuroscience",
"applied",
"mathematics",
"biology",
"and",
"life",
"sciences",
"sensory",
"systems",
"computing",
"methods",
"computational",
... | 2014 | Sparsity and Compressed Coding in Sensory Systems |
The live attenuated yellow fever vaccine ( YF-17D ) has been successfully used for more than 70 years . It is generally considered a safe vaccine , however , recent reports of serious adverse events following vaccination have raised concerns and led to suggestions that even safer YF vaccines should be developed . Repli... | Live attenuated yellow fever vaccine ( YF-17D ) is an efficient and generally safe vaccine . Nevertheless , in recent years the reporting of serious adverse effects together with the given limitations in the use of this live vaccine in certain risk groups has spurred an interest in developing a more generally applicabl... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"viral",
"transmission",
"and",
"infection",
"immunology",
"microbiology",
"viral",
"vectors",
"animal",
"models",
"preventive",
"medicine",
"vaccines",
"model",
"org... | 2016 | Vaccination with Replication Deficient Adenovectors Encoding YF-17D Antigens Induces Long-Lasting Protection from Severe Yellow Fever Virus Infection in Mice |
A widespread mechanism of bacterial signaling occurs through two-component systems , comprised of a sensor histidine kinase ( SHK ) and a transcriptional response regulator ( RR ) . The SHK activates RR by phosphorylation . The most common two-component system structure involves expression from a single operon , the tr... | Bacteria have evolved various mechanisms for surviving unpredictable changes and stresses in the environment , such as nutrient limitation . One common survival mechanism is the two-component system , where a sensor protein responds to a particular type of stress by activating a regulator in the cell . These regulators... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"molecular",
"biology/post-translational",
"regulation",
"of",
"gene",
"expression",
"computational",
"biology/transcriptional",
"regulation",
"microbiology/microbial",
"physiology",
"and",
"metabolism",
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis",
"computational... | 2010 | Adaptable Functionality of Transcriptional Feedback in Bacterial Two-Component Systems |
Two goals have been set for Gambian human African trypanosomiasis ( HAT ) , the first is to achieve elimination as a public health problem in 90% of foci by 2020 , and the second is to achieve zero transmission globally by 2030 . It remains unclear if certain HAT hotspots could achieve elimination as a public health pr... | Gambian sleeping sickness is a tsetse-transmitted disease which , without treatment , usually results in death . Unfortunately no medical prophylaxis exists to prevent infection in humans but curative medicines and vector control options are available . Recently there has been a push to reduce disease burden and a targ... | [
"Abstract",
"Introduction",
"Methods",
"Results"
] | [
"medicine",
"and",
"health",
"sciences",
"african",
"trypanosomiasis",
"tropical",
"diseases",
"vector-borne",
"diseases",
"mathematical",
"models",
"parasitic",
"diseases",
"simulation",
"and",
"modeling",
"global",
"health",
"neglected",
"tropical",
"diseases",
"infecti... | 2017 | Predicting the Impact of Intervention Strategies for Sleeping Sickness in Two High-Endemicity Health Zones of the Democratic Republic of Congo |
An efficient approach to characterizing the disease burden of rare genetic variants is to impute them into large well-phenotyped cohorts with existing genome-wide genotype data using large sequenced referenced panels . The success of this approach hinges on the accuracy of rare variant imputation , which remains contro... | An efficient approach to characterizing the disease burden of rare genetic variants is to impute them into existing well-phenotyped cohorts with genome-wide data by using large sequenced reference panels; however , the efficacy of this approach remains controversial . A recent study suggested that it is not possible to... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [] | 2015 | Imputation of the Rare HOXB13 G84E Mutation and Cancer Risk in a Large Population-Based Cohort |
The type I interferon pathway plays a critical role in both host defense and tolerance against viral infection and thus requires refined regulatory mechanisms . RIPK3-mediated necroptosis has been shown to be involved in anti-viral immunity . However , the exact role of RIPK3 in immunity to Influenza A Virus ( IAV ) is... | Influenza A virus ( IAV ) is a pulmonary pathogen that presents a significant threat to human health through seasonal epidemics and occasional , highly lethal pandemics . Type I IFN is an essential component of anti-viral immunity to influenza infection and pulmonary macrophages are the major source of type I IFN . Rec... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"&",
"methods"
] | [
"blood",
"cells",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"pathogens",
"immunology",
"messenger",
"rna",
"microbiology",
"cell",
"processes"... | 2017 | RIPK3 interacts with MAVS to regulate type I IFN-mediated immunity to Influenza A virus infection |
Mechanistic differences in the development and function of adaptive , high-affinity antibody-producing B-2 cells and innate-like , “natural” antibody-producing B-1a cells remain poorly understood . Here we show that the multi-functional dynein light chain ( DYNLL1/LC8 ) plays important roles in the establishment of B-1... | Antibody-producing B cells can be segregated into two major populations: The better known conventional B-2 cells typically produce high-affinity and mono-specific antibodies , but only after they encounter a particular pathogen or in response to vaccines . In contrast , the B-1a cells constitutively produce lower-affin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"lymphopenia",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"gene",
"regulation",
"spleen",
"regulatory",
"proteins",
"immunology",
"cell",
"process... | 2017 | Dynein light chain regulates adaptive and innate B cell development by distinctive genetic mechanisms |
Most commonly used malaria diagnostic tests , including microscopy and antigen-detecting rapid tests , cannot reliably detect low-density infections which are frequent in low transmission settings . Molecular methods such as polymerase chain reaction ( PCR ) are highly sensitive but remain too laborious for field deplo... | The ability to detect and treat asymptomatic infections will be fundamental to eliminate malaria . This requires highly sensitive screening tests close enough to cases to enable rapid treatment . Very low parasitemias can be detected by molecular methods such as PCR; however , these techniques require considerable trai... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"disease",
"surveillance",
"infectious",
"diseases",
"plant",
"science",
"medicine",
"and",
"health",
"sciences",
"disease",
"surveillance",
"plant",
"pathology",
"biology",
"and",
"life",
"sciences",
"vector-borne",
"diseases",
"infectious",
"disease",
"c... | 2015 | Evaluation of the Loop Mediated Isothermal DNA Amplification (LAMP) Kit for Malaria Diagnosis in P. vivax Endemic Settings of Colombia |
The World Health Organization now recommends the provision of praziquantel treatment to preschool-aged children infected with schistosomiasis . For intestinal schistosomiasis the current operational field diagnostic standard is examination of a thick Kato-Katz smear by microscopy prepared from a single stool specimen ,... | The World Health Organization ( WHO ) now recommends that all children ( 2–16 year olds ) living in schistosomiasis endemic areas should have regular access to praziquantel treatment . While there is extensive information in current literature on the geographical distribution of this disease in school-aged children ( 6... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"schistosomiasis",
"neglected",
"tropical",
"diseases"
] | 2013 | The Urine Circulating Cathodic Antigen (CCA) Dipstick: A Valid Substitute for Microscopy for Mapping and Point-Of-Care Diagnosis of Intestinal Schistosomiasis |
Innovative tools are needed to alleviate the burden of mosquito-borne diseases , and strategies that target the pathogen are being considered . A possible tactic is the use of Wolbachia , a maternally inherited , endosymbiotic bacterium that can ( but does not always ) suppress diverse pathogens when introduced to naiv... | An integrated vector management program utilizes several practices , including pesticide application and source reduction , to reduce mosquito populations . However , mosquitoes are developing resistance to some of these methods and new control approaches are needed . A novel technique involves the bacterium Wolbachia ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"rift",
"valley",
"fever",
"virus",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"vertebrates",
"saliva",
"animals",
"wolbachia",
"mammals",
"viruses",
"rna",
"vi... | 2017 | Wolbachia effects on Rift Valley fever virus infection in Culex tarsalis mosquitoes |
Changes in the physical interaction between cis-regulatory DNA sequences and proteins drive the evolution of gene expression . However , it has proven difficult to accurately quantify evolutionary rates of such binding change or to estimate the relative effects of selection and drift in shaping the binding evolution . ... | A large proportion of the diversity of living organisms results from differential regulation of gene transcription . Transcriptional regulation is thought to differ between species because of evolutionary changes in the physical interactions between regulatory DNA elements and DNA-binding proteins; these can generate v... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genomics",
"functional",
"genomics",
"population",
"genetics",
"biology",
"evolutionary",
"biology",
"comparative",
"genomics",
"genetics",
"and",
"genomics"
] | 2012 | Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome |
The expansion of polyglutamine tracts in a variety of proteins causes devastating , dominantly inherited neurodegenerative diseases , including six forms of spinal cerebellar ataxia ( SCA ) . Although a polyglutamine expansion encoded in a single allele of each of the responsible genes is sufficient for the onset of ea... | Six forms of spinal cerebellar ataxia ( SCA1 , −2 , −3 , −6 , −7 , and −17 ) are caused by dominant mutations in the respective genes . Patients suffering from these different forms of SCA have similar symptoms of progressive adult-onset neurodegeneration , and the same causative mutation , a CAG repeat expansion encod... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"neurological",
"disorders",
"neuroscience",
"genetics",
"and",
"genomics"
] | 2008 | Polyglutamine Genes Interact to Modulate the Severity and Progression of Neurodegeneration in Drosophila |
Micro ( mi ) RNAs are small non-coding RNAs that regulate the expression of their targets' messenger RNAs through both translational inhibition and regulation of target RNA stability . Recently , a number of viruses , particularly of the herpesvirus family , have been shown to express their own miRNAs to control both v... | The recent discovery of miRNAs of viral origin has dramatically changed our view on virus-host interaction . Viral miRNAs have been shown to regulate genes of both cellular and viral origin , contributing to a favorable environment for the virus . However , the real importance of virus-encoded miRNAs during infection o... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/post-translational",
"regulation",
"of",
"gene",
"expression",
"virology/persistence",
"and",
"latency",
"virology/viral",
"replication",
"and",
"gene",
"regulation",
"molecular",
"biology/bioinformatics",
"infectious",
"diseases/viral",
"infections"
] | 2010 | Cytomegalovirus microRNAs Facilitate Persistent Virus Infection in Salivary Glands |
It is believed that life passed through an RNA World stage in which replication was sustained by catalytic RNAs ( ribozymes ) . The two most obvious types of ribozymes are a polymerase , which uses a neighbouring strand as a template to make a complementary sequence to the template , and a nucleotide synthetase , which... | Trans-acting polymerases are cooperative , because they copy neighbouring strands , and do not copy themselves directly . Inaccurate replication creates parasitic strands that act as templates but not ribozymes . It is known that in spatially distributed models with slow strand diffusion , clusters of cooperating polym... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"deletion",
"mutation",
"nucleic",
"acid",
"synthesis",
"parasite",
"evolution",
"enzymes",
"dna-binding",
"proteins",
"enzymology",
"nucleotides",
"ribozymes",
"parasitology",
"mutation",
"monomers",
"(chemistry)",
"polymerases",
"rna",
"synthesis",
"chemical",
"synthesis"... | 2016 | Co-operation between Polymerases and Nucleotide Synthetases in the RNA World |
In October 2010 , Haiti was struck by a large-scale cholera epidemic . The Haitian government , UNICEF and other international partners launched an unprecedented nationwide alert-response strategy in July 2013 . Coordinated NGOs recruited local rapid response mobile teams to conduct case-area targeted interventions ( C... | Cholera is a potentially deadly diarrheal disease caused by toxin-secreting strains of Vibrio cholerae . The bacterium can trigger severe epidemics in countries with limited access to potable water and sanitation . Hygiene promotion , proper sanitation and improved access to safe drinking water are essential to control... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2019 | The case-area targeted rapid response strategy to control cholera in Haiti: a four-year implementation study |
There is an urgent need to substitute the highly toxic compounds still in use for treatment of the encephalitic stage of human African trypanosomiasis ( HAT ) . We here assessed the treatment with the doublet cordycepin and the deaminase inhibitor deoxycoformycin for this stage of infection with Trypanosoma brucei ( T ... | There is an urgent need to substitute the highly toxic arsenic compounds still in use for treatment of the encephalitic stage of African trypanosomiasis , a disease caused by infection with Trypanosoma brucei . We exploited the inability of trypanosomes to engage in de novo purine synthesis as a therapeutic target . Co... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/infectious",
"diseases",
"of",
"the",
"nervous",
"system",
"infectious",
"diseases",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"microbiology/parasitology",
"infectious",
"diseases/protozoal",
"infections",
"infectious",
"diseases/antimicr... | 2009 | Preclinical Assessment of the Treatment of Second-Stage African Trypanosomiasis with Cordycepin and Deoxycoformycin |
Extensive departures from balanced gene dose in aneuploids are highly deleterious . However , we know very little about the relationship between gene copy number and expression in aneuploid cells . We determined copy number and transcript abundance ( expression ) genome-wide in Drosophila S2 cells by DNA-Seq and RNA-Se... | While it is widely recognized that mutations in protein coding genes can have harmful consequences , one can also have too much or too little of a good thing . Except for the sex chromosomes , genes come in sets of two in diploid organisms . Extra or missing copies of genes or chromosomes result in an imbalance that ca... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/epigenetics",
"genetics",
"and",
"genomics/cancer",
"genetics",
"genetics",
"and",
"genomics/chromosome",
"biology",
"genetics",
"and",
"genomics/functional",
"genomics"
] | 2010 | Expression in Aneuploid Drosophila S2 Cells |
Genome-scale metabolic modeling has emerged as a promising way to study the metabolic alterations underlying cancer by identifying novel drug targets and biomarkers . To date , several computational methods have been developed to integrate high-throughput data with existing human metabolic reconstructions to generate c... | Several attempts have been made to develop computational approaches to integrate high-throughput omics data with generic models of human metabolism . However , no comprehensive and quantitative platform is available to examine the performance of these methods both functionally and structurally . Here , we collected num... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"discussion"
] | [
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"cancer",
"genetics",
"applied",
"mathematics",
"metabolic",
"networks",
"cell",
"metabolism",
"oncogenes",
"simulation",
"and",
"modeling",
"algorithms",
"mathematics",
"network",
"analysis",
"genome",
"ana... | 2019 | A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism |
The collection of immunoglobulin genes in an individual’s germline , which gives rise to B cell receptors via recombination , is known to vary significantly across individuals . In humans , for example , each individual has only a fraction of the several hundred known V alleles . Furthermore , the currently-accepted se... | Antibodies are an important component of the adaptive immune system , which itself determines our response to both pathogens and vaccines . They are produced by B cells through somatic recombination of germline DNA , which results in a vast diversity of antigen binding affinities across the B cell repertoire . We typic... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"taxonomy",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"immunology",
"mutation",
"phylogenetics",
"data",
"management",
"phylogenetic",
"analysis",
"sequence",
"motif",
"analysis",
"antibodies",
"research",
"and",
"analysis",
"methods",
"sequence",
... | 2019 | Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data |
Many gram-negative pathogens employ a type III secretion injectisome to translocate effector proteins into eukaryotic host cells . While the structure of the distal “needle complex” is well documented , the composition and role of the functionally important cytosolic complex remain less well understood . Using function... | The type III secretion system , also known as the injectisome , is a key virulence factor in many gram-negative bacteria , and is responsible for the transmission of bacterial proteins directly into host cells . While some elements of the system are well characterized , the cytosolic components involved in substrate re... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Composition, Formation, and Regulation of the Cytosolic C-ring, a Dynamic Component of the Type III Secretion Injectisome |
Infection with Salmonella enterica serovar Typhi ( S . Typhi ) with reduced susceptibility to fluoroquinolones has been associated with fluoroquinolone treatment failure . We studied the relationship between ofloxacin treatment response and the ofloxacin minimum inhibitory concentration ( MIC ) of the infecting isolate... | Typhoid fever is an infection of the bloodstream caused by the organism Salmonella Typhi ( S . Typhi ) . Treatment with antimicrobials is critical for preventing severe infection and even death , yet antimicrobial resistant organisms have become a problem in many places where typhoid is common . Fluoroquinolones are a ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"bacterial",
"diseases",
"infectious",
"diseases",
"medical",
"microbiology",
"microbial",
"pathogens",
"biology",
"microbiology",
"salmonella",
"bacterial",
"pathogens"
] | 2011 | The Influence of Reduced Susceptibility to Fluoroquinolones in Salmonella enterica Serovar Typhi on the Clinical Response to Ofloxacin Therapy |
Cyclic adenosine monophosphate ( cAMP ) has been implicated in the execution of diverse rhythmic behaviors , but how cAMP functions in neurons to generate behavioral outputs remains unclear . During the defecation motor program in C . elegans , a peptide released from the pacemaker ( the intestine ) rhythmically excite... | Breathing , walking and sleeping , are examples of rhythmic behaviors that occur at regular time intervals . The time intervals are determined by pacemakers , which generate the rhythms , and the behaviors are carried out by different tissues such as neurons and muscles . How do timing signals from pacemakers get deliv... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | PKA Controls Calcium Influx into Motor Neurons during a Rhythmic Behavior |
p53-response elements ( p53-REs ) are organized as two repeats of a palindromic DNA segment spaced by 0 to 20 base pairs ( bp ) . Several experiments indicate that in the vast majority of the human p53-REs there are no spacers between the two repeats; those with spacers , particularly with sizes beyond two nucleotides ... | p53-response elements ( p53-REs ) are 20 base pair DNA segments embedded in the genome that are able to bind anti-tumor protein p53 and trigger biological functions such as DNA repair or self-destruction of the cell . These functions are modulated through selective binding of p53 to degenerate p53-REs . Understanding h... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biochemistry",
"biochemistry/bioinformatics",
"computational",
"biology/genomics",
"biophysics",
"computational",
"biology/molecular",
"dynamics"
] | 2009 | Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View |
Plague , a Yersinia pestis infection , is a fatal disease with tremendous transmission capacity . However , the mechanism of how the pathogen stays in a reservoir , circulates and then re-emerges is an enigma . We studied a plague outbreak caused by the construction of a large reservoir in southwest China followed 16-y... | Plague in China is shown to be in 12 kinds of natural foci with a large scale geographic and complex structure . Each plague focus has a unique ecological environment , specific geographic regions , landscape characteristics and specific hosts and vectors for the maintenance and transmission of Y . pestis . Once the en... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"plagues",
"pathology",
"and",
"laboratory",
"medicine",
"china",
"pathogens",
"geographical",
"locations",
"microbiology",
"vertebrates",
"animals",
"mammals",
"animal",
"models",
"bacterial",
"diseases",
"model",... | 2017 | Mechanism study on a plague outbreak driven by the construction of a large reservoir in southwest china (surveillance from 2000-2015) |
The maintenance of key germline derived DNA methylation patterns during preimplantation development depends on stores of DNA cytosine methyltransferase-1o ( DNMT1o ) provided by the oocyte . Dnmt1omat−/− mouse embryos born to Dnmt1Δ1o/Δ1o female mice lack DNMT1o protein and have disrupted genomic imprinting and associa... | During oocyte growth and maturation , vital proteins and enzymes are produced to ensure that , when fertilized , a healthy embryo will arise . When this natural process is interrupted , one or more of these essential elements can fail to be produced thus compromising the health of the future embryo . We are using a mou... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Loss of DNMT1o Disrupts Imprinted X Chromosome Inactivation and Accentuates Placental Defects in Females |
Symbiotic bacteria are important drivers of phenotypic diversity in insects . One of the widespread symbionts to have emerged belongs to the genus Arsenophonus , however , its biological functions in most host insects remain entirely unknown . Here we report two distinct Arsenophonus strains in the brown planthopper ( ... | Symbiotic bacteria are key evolutionary drivers , providing innovations that allow their eukaryotic hosts to evolve new phenotypes . Beneficial traits provided by the acquisition of a specific symbiont have been reported in many kinds of insect host , however the potential of the symbiont infection to confer an ecologi... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"invertebrate",
"genomics",
"animals",
"insect",
"pests",
"metabolomics",
"genome",
"analysis",
"pests",
"agrochemicals",
"metabolic",
"pathways",
"animal",
"genomics",
"insects",
"agriculture",
"arthropoda",
"insecticides",
"biochemistry",
"eukaryota",
"ge... | 2018 | A distinct strain of Arsenophonus symbiont decreases insecticide resistance in its insect host |
Humans respond differently than other primates to a large number of infections . Differences in susceptibility to infectious agents between humans and other primates are probably due to inter-species differences in immune response to infection . Consistent with that notion , genes involved in immunity-related processes... | We know of a large number of diseases or medical conditions that affect humans more severely than non-human primates , such as AIDS , malaria , hepatitis B , and cancer . These differences likely arise from different immune responses to infection among species . However , due to the lack of comparative functional data ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computer",
"science/applications",
"genetics",
"and",
"genomics/functional",
"genomics",
"genetics",
"and",
"genomics/gene",
"expression",
"genetics",
"and",
"genomics/genetics",
"of",
"the",
"immune",
"system",
"immunology/immune",
"response",
"computational",
"biology/sign... | 2010 | Functional Comparison of Innate Immune Signaling Pathways in Primates |
Hypoxia-inducible factors ( HIFs ) are a family of evolutionary conserved alpha-beta heterodimeric transcription factors that induce a wide range of genes in response to low oxygen tension . Molecular mechanisms that mediate oxygen-dependent HIF regulation operate at the level of the alpha subunit , controlling protein... | Adaptation of cells to low oxygen ( hypoxia ) is a physiological response related to important diseases , including heart attacks , stroke , cancer , and diabetes . The mechanisms that mediate adaptation to hypoxia in humans are almost identical to those operating in diverse animal species , including mice , worms , an... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/genomics",
"cell",
"biology/cellular",
"death",
"and",
"stress",
"responses",
"cell",
"biology/cell",
"signaling",
"genetics",
"and",
"genomics/gene",
"function",
"cell",
"biology/gene",
"expression"
] | 2010 | Drosophila Genome-Wide RNAi Screen Identifies Multiple Regulators of HIF–Dependent Transcription in Hypoxia |
It has been proposed that synchronized neural assemblies in the antennal lobe of insects encode the identity of olfactory stimuli . In response to an odor , some projection neurons exhibit synchronous firing , phase-locked to the oscillations of the field potential , whereas others do not . Experimental data indicate t... | A fundamental question in computational neuroscience is to understand how interactions between neurons underlie sensory coding and information storage . In the first relay of the insect olfactory system , odorant stimuli trigger synchronized activities in neuron populations . Synchronized assemblies may arise as a cons... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/theoretical",
"neuroscience",
"biophysics/theory",
"and",
"simulation",
"computational",
"biology/systems",
"biology"
] | 2008 | A Model of Stimulus-Specific Neural Assemblies in the Insect Antennal Lobe |
MPT64 rapid speciation tests are increasingly being used in diagnosis of tuberculosis ( TB ) . Mycobacterium africanum West Africa 2 ( Maf 2 ) remains an important cause of TB in West Africa and causes one third of disease in The Gambia . Since the introduction of MPT64 antigen tests , a higher than expected rate of su... | Diagnostics for rapid confirmation of positive liquid cultures presumptive of Mycobacterium tuberculosis bacteria , based on the detection of the MPT64 antigen , are being used in many TB diagnostic laboratories worldwide . Of note , diagnostic performance of these tests in West Africa , where TB is uniquely caused by ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"messenger",
"rna",
"tropical",
"diseases",
"geographical",
"locations",
"bacterial",
"diseases",
"bacteria",
"africa",
"infectious",
"diseases",
"sputum",
"mucus",
"tuberculosis",
"actinobacteria",
"hematology",
... | 2016 | Impact of the Mycobaterium africanum West Africa 2 Lineage on TB Diagnostics in West Africa: Decreased Sensitivity of Rapid Identification Tests in The Gambia |
Egress from the host cell is a crucial and highly regulated step in the biology of the obligate intracellular parasite , Toxoplasma gondii . Active egress depends on calcium fluxes and appears to be a crucial step in escaping the attack from the immune system and , potentially , in enabling the parasites to shuttle int... | Toxoplasma gondii , an important human pathogen , is an obligate intracellular parasite , thus getting in and out of cells is key for its survival . The process by which Toxoplasma exits cells , known as egress , is controlled by calcium fluxes and can be triggered by ionophores . In vivo , rapid egress from the host c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"protein",
"kinase",
"signaling",
"cascade",
"signal",
"transduction",
"molecular",
"cell",
"biology",
"signaling",
"cascades",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"parasitology",
"parasite",
"physiology"
] | 2012 | A Forward Genetic Screen Reveals that Calcium-dependent Protein Kinase 3 Regulates Egress in Toxoplasma |
Legionella pneumophila is an opportunistic pathogen that can cause a severe pneumonia called Legionnaires' disease . In the environment , L . pneumophila is found in fresh water reservoirs in a large spectrum of environmental conditions , where the bacteria are able to replicate within a variety of protozoan hosts . To... | The survival of intracellular pathogens often involves the modification of the host vacuole in which the pathogen resides . This can be achieved through the function of effector proteins that are delivered into the host cell cytoplasm using specialized transport machinery . In the case of Legionella pneumophila , the b... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/membranes",
"and",
"sorting",
"microbiology/parasitology",
"infectious",
"diseases/bacterial",
"infections"
] | 2009 | A Legionella pneumophila Effector Protein Encoded in a Region of Genomic Plasticity Binds to Dot/Icm-Modified Vacuoles |
Understanding how sets of genes are coordinately regulated in space and time to generate the diversity of cell types that characterise complex metazoans is a major challenge in modern biology . The use of high-throughput approaches , such as large-scale in situ hybridisation and genome-wide expression profiling via DNA... | The task of deciphering the complex transcriptional regulatory networks controlling development is one of the major current challenges for molecular biology . The problem is difficult , if not impossible , to solve without a detailed knowledge of the spatiotemporal dynamics of gene expression . Thus , to understand dev... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"developmental",
"biology",
"mathematics",
"computational",
"biology",
"drosophila",
"genetics",
"and",
"genomics"
] | 2007 | Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster |
The region of the ancient Sahul continent ( present day Australia and New Guinea , and surrounding islands ) is home to extreme linguistic diversity . Even apart from the huge Austronesian language family , which spread into the area after the breakup of the Sahul continent in the Holocene , there are hundreds of langu... | About one-fifth of all the world's languages are spoken in present day Australia , New Guinea , and the surrounding islands . This corresponds to the boundaries of the ancient continent of Sahul , which broke up due to rising sea levels about 9000 years before present . The distribution of languages in this region conv... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"evolutionary",
"biology/human",
"evolution",
"evolutionary",
"biology/bioinformatics"
] | 2009 | Explaining the Linguistic Diversity of Sahul Using Population Models |
We have developed a multi-scale biophysical electromechanics model of the rat left ventricle at room temperature . This model has been applied to investigate the relative roles of cellular scale length dependent regulators of tension generation on the transduction of work from the cell to whole organ pump function . Sp... | The heart achieves an efficient coordinated contraction via a complex web of feedback loops that span multiple spatial and temporal scales . Advances in computational hardware and numerical techniques now allow us to begin to analyse this feedback system through the use of computational models . Applying this approach ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biophysics/theory",
"and",
"simulation",
"computational",
"biology/systems",
"biology"
] | 2009 | The Role of the Frank–Starling Law in the Transduction of Cellular Work to Whole Organ Pump Function: A Computational Modeling Analysis |
When coordinating movements , the nervous system often has to decide how to distribute work across a number of redundant effectors . Here , we show that humans solve this problem by trying to minimize both the variability of motor output and the effort involved . In previous studies that investigated the temporal shape... | When performing actions , we often have many options of how to combine muscles or limbs to achieve a desired outcome . Despite this freedom , certain effector combinations are used consistently . Why ? To examine this question , we asked participants to press one button with a finger from the left hand and another butt... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/motor",
"systems"
] | 2009 | Dissociating Variability and Effort as Determinants of Coordination |
Pollinating bees develop foraging circuits ( traplines ) to visit multiple flowers in a manner that minimizes overall travel distance , a task analogous to the travelling salesman problem . We report on an in-depth exploration of an iterative improvement heuristic model of bumblebee traplining previously found to accur... | Pollinating bees , along with bats , hummingbirds , rodents and primates , typically develop circuits ( traplines ) to visit multiple foraging sites in an efficient stable sequence . The question of how animals encode and process spatial information to develop these impressive foraging patterns remains poorly understoo... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"mathematical",
"computing",
"mathematics",
"theoretical",
"biology",
"physiology",
"biology",
"anatomy",
"and",
"physiology",
"neurological",
"system",
"neuroscience",
"animal",
"cognition"
] | 2013 | A Simple Iterative Model Accurately Captures Complex Trapline Formation by Bumblebees Across Spatial Scales and Flower Arrangements |
Bacteria have diverse mechanisms for competition that include biosynthesis of extracellular enzymes and antibiotic metabolites , as well as changes in community physiology , such as biofilm formation or motility . Considered collectively , networks of competitive functions for any organism determine success or failure ... | Antibiotics are one mechanism among many that bacteria use to compete with each other . Bacteria in the environment and in host organisms likely use networks of competitive mechanisms to survive and to shape the composition and function of diverse communities . In this study , we cultured two species of soil bacteria t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Escape from Lethal Bacterial Competition through Coupled Activation of Antibiotic Resistance and a Mobilized Subpopulation |
In response to environmental changes , Pseudomonas aeruginosa is able to switch from a planktonic ( free swimming ) to a sessile ( biofilm ) lifestyle . The two-component system ( TCS ) GacS/GacA activates the production of two small non-coding RNAs , RsmY and RsmZ , but four histidine kinases ( HKs ) , RetS , GacS , L... | P . aeruginosa is able to switch from a planktonic to a sessile lifestyle by regulating the two small RNAs RsmY and RsmZ . The GacS/GacA TCS is the main system involved in their regulation; however , three HKs , RetS , LadS and PA1611 , modulate this TCS . Here we elucidate the relationship between the LadS signaling p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"cloning",
"plasmid",
"construction",
"pseudomonas",
"aeruginosa",
"vector",
"cloning",
"dna",
"construction",
"molecular",
"biology",
"techniques",
"dna",
... | 2016 | The Hybrid Histidine Kinase LadS Forms a Multicomponent Signal Transduction System with the GacS/GacA Two-Component System in Pseudomonas aeruginosa |
Autosomal Dominant Polycystic Kidney Disease ( ADPKD; MIM ID's 173900 , 601313 , 613095 ) leads to end-stage kidney disease , caused by mutations in PKD1 or PKD2 . Inactivation of Pkd1 before or after P13 in mice results in distinct early- or late-onset disease . Using a mouse model of ADPKD carrying floxed Pkd1 allele... | Autosomal Dominant Polycystic Kidney Disease ( ADPKD ) is the most common genetic cause of polycystic kidney disease and is responsible for 4 . 6% of the end-stage renal disease ( ESRD ) cases in the United States . It is most often caused by mutation in the PKD1 gene . To understand this disease , we made a mouse mode... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"genetic",
"networks",
"polycystic",
"kidney",
"disease",
"genome",
"analysis",
"tools",
"biology",
"autosomal",
"dominant",
"clinical",
"genetics",
"microarrays",
"systems",
"biology",
"genetics",
"genomics",
"gene",
"networks",
"computational",
"biology",
... | 2012 | Network Analysis of a Pkd1-Mouse Model of Autosomal Dominant Polycystic Kidney Disease Identifies HNF4α as a Disease Modifier |
In spite of its major impact on life-long health , the process of microbial succession in the gut of infants remains poorly understood . Here , we analyze the patterns of taxonomic and functional change in the gut microbiota during the first year of life for a birth cohort of 13 infants . We detect that individual inst... | Although knowledge of the complex community of microbes that inhabits the human gut is constantly increasing , the successional process through which it develops during infancy remains poorly understood . Particularly , although gut microbiota composition is known to vary through time among infants , the effect of this... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"sequencing",
"techniques",
"ecology",
"and",
"environmental",
"sciences",
"functional",
"genomics",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"community",
"structure",
"biota",
"microbiology",
"biodiversity",
"genome",
"sequen... | 2014 | Microbial Succession in the Gut: Directional Trends of Taxonomic and Functional Change in a Birth Cohort of Spanish Infants |
NETosis is a process by which neutrophils extrude their DNA together with bactericidal proteins that trap and/or kill pathogens . In the present study , we evaluated the ability of Leptospira spp . to induce NETosis using human ex vivo and murine in vivo models . Microscopy and fluorometric studies showed that incubati... | Neutrophils extracellular traps ( NETs ) are a relatively novel pathogen-killing mechanism for extracellular microbes independent of phagocytic uptake and degranulation . Although it was originally proposed that NETs are formed exclusively in tissues at sites of infection , NETs have also been found within blood vessel... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Neutrophil Extracellular Traps are Involved in the Innate Immune Response to Infection with Leptospira |
Despite the high prevalence of helminth infections among preschool-aged children , control programs in sub-Saharan countries primarily focus on school-aged populations . We assessed the prevalence of helminth infections and determined risk factors for infection among preschool-aged children in the urban setting of Dar ... | In many African countries , children under the age of 5 years are at considerable risk of acquiring parasitic worm infections . Yet , most of the neglected tropical disease control programs in Africa do not include preschool-aged children in deworming campaigns . Chronic parasitic worm infections may impair children’s ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"schistosoma",
"mansoni",
"children",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"helminths",
"tropical",
"diseases",
"parasitic",
"diseases",
"animals",
"urine",
"bacterial",
"diseases",
"age",
"groups",
"families",
"infe... | 2017 | Schistosoma, other helminth infections, and associated risk factors in preschool-aged children in urban Tanzania |
Mathematical models are powerful tools for epidemiology and can be used to compare control actions . However , different models and model parameterizations may provide different prediction of outcomes . In other fields of research , ensemble modeling has been used to combine multiple projections . We explore the possib... | Policy decisions in response to emergent disease outbreaks use simulation models to inform the efficiency of different control actions . However , different projections may be made , depending on the choice of models and parameterizations . Ensemble modeling offers the ability to combine multiple projections and has be... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | A Bayesian Ensemble Approach for Epidemiological Projections |
Sequence data from this study have been submitted to the European Nucleotide Archive ( http://www . ebi . ac . uk/embl ) under accession number ERP000379 .
The schistosomes are considered the most important helminth pathogens in terms of human morbidity and mortality . More than 200 million people are infected and a fu... | Schistosomes , or blood flukes , are responsible for the major neglected tropical disease called schistosomiasis , which afflicts over 200 million people in impoverished regions of the developing world . The genome sequence of these parasites has been decoded . Integration sites of retroviral transgenes into the chromo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"biology"
] | 2012 | Germline Transgenesis and Insertional Mutagenesis in Schistosoma mansoni Mediated by Murine Leukemia Virus |
Quantitative Trait Loci ( QTL ) analyses in immortal populations are a powerful method for exploring the genetic mechanisms that control interactions of organisms with their environment . However , QTL analyses frequently do not culminate in the identification of a causal gene due to the large chromosomal regions often... | A major interest in evolutionary biology is to understand the genetic mechanisms that underlie phenotypic variation in nature and how they interact with the environment . A good example of adaptive genetic variation in response to the environment is the shade avoidance response . Although some plant groups try to outgr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/genomics",
"genetics",
"and",
"genomics/complex",
"traits",
"developmental",
"biology/plant",
"growth",
"and",
"development",
"genetics",
"and",
"genomics/plant",
"genetics",
"and",
"gene",
"expression"
] | 2010 | Network Analysis Identifies ELF3 as a QTL for the Shade Avoidance Response in Arabidopsis |
To cooperatively carry large food items to the nest , individual ants conform their efforts and coordinate their motion . Throughout this expedition , collective motion is driven both by internal interactions between the carrying ants and a response to newly arrived informed ants that orient the cargo towards the nest ... | Among animal groups , ants hold what may perhaps be the richest repertoire of collective behavior such as trail formation , nest excavation and food dissemination . Of the most intriguing of these behaviors is cooperative food transport , where many ants carry items that individuals cannot move . Using experiments and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"velocity",
"collective",
"animal",
"behavior",
"invertebrates",
"tribology",
"classical",
"mechanics",
"engineering",
"and",
"technology",
"animals",
"simulation",
"and",
"modeling",
"animal",
"behavior",
"phase",
"diagrams",
"materials",
"science",
"zoology",
"research"... | 2018 | Bi-stability in cooperative transport by ants in the presence of obstacles |
Schistosomes have a well developed nervous system that coordinates virtually every activity of the parasite and therefore is considered to be a promising target for chemotherapeutic intervention . Neurotransmitter receptors , in particular those involved in neuromuscular control , are proven drug targets in other helmi... | Bloodflukes of the genus Schistosoma are the causative agents of human schistosomiasis , a debilitating disease that afflicts over 200 million people worldwide . There is no vaccine for schistosomiasis and treatment relies heavily on a single drug , praziquantel . Recent reports of praziquantel resistance raise concern... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"molecular",
"cell",
"biology",
"zoology",
"neuroscience"
] | 2012 | A Novel G Protein-Coupled Receptor of Schistosoma mansoni (SmGPR-3) Is Activated by Dopamine and Is Widely Expressed in the Nervous System |
Treponema pallidum subsp . pertenue ( TPE ) is the causative agent of yaws , a multi-stage disease , endemic in tropical regions of Africa , Asia , Oceania , and South America . To date , four TPE strains have been completely sequenced including three TPE strains of human origin ( Samoa D , CDC-2 , and Gauthier ) and o... | The causative agent of yaws , Treponema pallidum subsp . pertenue ( TPE ) , belongs to a group of uncultivable treponemes causing several human and animal infections . Yaws is a multi-stage disease which is endemic in tropical regions of Africa , Asia , Oceania , and South America . In this study , whole genome sequenc... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"sequencing",
"techniques",
"urology",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"tropical",
"diseases",
"microbiology",
"vertebrates",
"rabbits",
"animals",
"mammals",
"animal",
"models",
"treponematoses",
"bacter... | 2017 | Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Ghana, Africa: Identical genome sequences in samples isolated more than 7 years apart |
Phylogenomic analysis of the occurrence and abundance of protein domains in proteomes has recently showed that the α/β architecture is probably the oldest fold design . This holds important implications for the origins of biochemistry . Here we explore structure-function relationships addressing the use of chemical mec... | Structural phylogenomics enables one to construct a historical timeline of the structural scaffolds known as protein folds and of the biocatalytic mechanisms that are embedded in them . This timeline defines a natural history of biocatalysis through its most granular components , the mechanistic steps . This history re... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"Discussion"
] | [
"systems",
"biology",
"biochemistry",
"enzyme",
"structure",
"evolutionary",
"biology",
"biocatalysis",
"catalysis",
"enzymes",
"evolutionary",
"modeling",
"biology",
"and",
"life",
"sciences",
"chemistry",
"chemical",
"reactions",
"physical",
"sciences",
"enzymology",
"c... | 2014 | The Natural History of Biocatalytic Mechanisms |
Cutaneous leishmaniasis ( CL ) , caused by Leishmania braziliensis , is the most important presentation of tegumentary leishmaniasis ( TL ) in Latin American . While the role of dogs as reservoirs of Leishmania infantum , and the clinic features of canine visceral leishmanisis are well described , little is known about... | Cutaneous Leishmaniasis ( CL ) is the major clinical forms of tegumentary leishmaniasis . More than 1 million of people develop cutaneous leishmaniasis worldwide and Leishmania braziliensis is the main causal agent of the disease in Latin American . Wild and domestic animals play an important role in the maintenance of... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"biopsy",
"geographical",
"locations",
"tropical",
"diseases",
"vertebrates",
"parasitic",
"diseases",
"dogs",
"animals",
"mammals",
"parasitic",
"protozoans",
"surgical",
"and",
"inv... | 2019 | Clinical and histopathologic features of canine tegumentary leishmaniasis and the molecular characterization of Leishmania braziliensis in dogs |
Crimean-Congo hemorrhagic fever ( CCHF ) is a zoonosis caused by a Nairovirus of the family Bunyaviridae . Infection is transmitted to humans mostly by Hyalomma ticks and also by direct contact with the blood or tissues of infected humans or viremic livestock . Clinical features usually include a rapid progression char... | Crimean-Congo hemorrhagic fever ( CCHF ) is a widely distributed viral hemorrhagic fever as the disease occurs in much of Africa , the Middle East and Asia , Balkans and Russia . CCHF is a zoonotic viral disease mainly transmitted by ticks , although animal-to-human and human-to-human transmission also occurs . CCHF is... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"virology",
"emerging",
"viral",
"diseases",
"biology",
"microbiology",
"viral",
"disease",
"diagnosis"
] | 2012 | First International External Quality Assessment of Molecular Detection of Crimean-Congo Hemorrhagic Fever Virus |
Measles virus ( MV ) is highly infectious , and has long been thought to enter the host by infecting epithelial cells of the respiratory tract . However , epithelial cells do not express signaling lymphocyte activation molecule ( CD150 ) , which is the high-affinity cellular receptor for wild-type MV strains . We have ... | Measles remains an important vaccine-preventable cause of morbidity and mortality in developing countries . The causative agent , measles virus ( MV ) , is one of the most contagious viruses known . Measles has an incubation time of approximately two weeks , and surprisingly little is known about the early events after... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/cellular",
"microbiology",
"and",
"pathogenesis",
"respiratory",
"medicine/respiratory",
"infections",
"pathology/cellular",
"pathology",
"virology/animal",
"models",
"of",
"infection",
"infectious",
"diseases/viral",
"infections",
"infectious",
"diseases/respiratory",
... | 2011 | Early Target Cells of Measles Virus after Aerosol Infection of Non-Human Primates |
Previous studies have successfully identified genetic variants in several genes associated with human iris ( eye ) color; however , they all used simplified categorical trait information . Here , we quantified continuous eye color variation into hue and saturation values using high-resolution digital full-eye photograp... | We measured human eye color to hue and saturation values from high-resolution , digital , full-eye photographs of several thousand Dutch Europeans . This quantitative approach , which is extremely cost-effective , portable , and time efficient , revealed that human eye color varies along more dimensions than the one re... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics",
"and",
"genomics/comparative",
"genomics",
"neurological",
"disorders",
"ophthalmology",
"genetics",
"and",
"genomics/epigenetics",
"dermatology/pigmentary",
"disorders",
"genetics",
"and",
"genomics/bioinformatics"
] | 2010 | Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci |
The genome of Trypanosoma brucei , the causative agent of African trypanosomiasis , was published five years ago , yet identification of all genes and their transcripts remains to be accomplished . Annotation is challenged by the organization of genes transcribed by RNA polymerase II ( Pol II ) into long unidirectional... | Identifying genes essential for survival in the host is fundamental to unraveling the biology of human pathogens and understanding mechanisms of pathogenesis . The protozoan parasite Trypanosoma brucei causes devastating diseases in humans and animals in sub-Saharan Africa , and the publication in 2005 of the genome se... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"molecular",
"biology/bioinformatics",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"genetics",
"and",
"genomics",
"genetics",
"and",
"genomics/gene",
"expression"
] | 2010 | The Transcriptome of the Human Pathogen Trypanosoma brucei at Single-Nucleotide Resolution |
Ecologists have been compiling ecological networks for over a century , detailing the interactions between species in a variety of ecosystems . To this end , they have built networks for mutualistic ( e . g . , pollination , seed dispersal ) as well as antagonistic ( e . g . , herbivory , parasitism ) interactions . Th... | In the late 1960s , Mark Kac asked , "Can one hear the shape of a drum ? " challenging readers to reconstruct the geometry of the drum from a provided list of overtones . Physicists and mathematicians found that , although in general , one cannot hear the shape of a drum , many of its properties , such as its area and ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"and",
"discussion",
"Conclusion"
] | [
"ecology",
"and",
"environmental",
"sciences",
"crime",
"statistics",
"sociology",
"social",
"sciences",
"plant",
"physiology",
"multivariate",
"analysis",
"plant-herbivore",
"interactions",
"plant",
"science",
"mathematics",
"artificial",
"intelligence",
"algebra",
"crimin... | 2019 | Telling ecological networks apart by their structure: A computational challenge |
The only available vaccine that could be potentially beneficial against mycobacterial diseases contains live attenuated bovine tuberculosis bacillus ( Mycobacterium bovis ) also called Bacillus Calmette-Guérin ( BCG ) . Even though the BCG vaccine is still widely used , results on its effectiveness in preventing mycoba... | After tuberculosis and leprosy , Buruli Ulcer Disease ( BUD ) is the third most common human mycobacterial disease . The only available vaccine that could be potentially beneficial against these diseases is BCG . Even though BCG vaccine is widely used , the results on its effectiveness are partially contradictory , pro... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"mycobacteria",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"medical",
"microbiology",
"microbial",
"pathogens",
"pathogens",
"biology",
"and",
"life",
"sciences",
"microbiology",
"bacterial",
"pathogens"
] | 2015 | Effectiveness of Routine BCG Vaccination on Buruli Ulcer Disease: A Case-Control Study in the Democratic Republic of Congo, Ghana and Togo |
Brains were built by evolution to react swiftly to environmental challenges . Thus , sensory stimuli must be processed ad hoc , i . e . , independent—to a large extent—from the momentary brain state incidentally prevailing during stimulus occurrence . Accordingly , computational neuroscience strives to model the robust... | When Hans Berger described the human EEG in the 1920s , a pivotal finding was the demonstration of prominent oscillations in the frequency range between 8 and 12 Hz , which he called alpha wave rhythm . He also described for the first time the so-called “alpha blockade , ” i . e . , the suppression of the ongoing alpha... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"neuroscience/behavioral",
"neuroscience",
"neuroscience/cognitive",
"neuroscience",
"neuroscience/sensory",
"systems",
"neuroscience/motor",
"systems",
"computational",
"biology/computational",
"neuroscience",
"neuroscience/theoretical",
"neuroscience"
] | 2009 | A Generalized Framework for Quantifying the Dynamics of EEG Event-Related Desynchronization |
In a 2016 survey of 704 National Science Foundation ( NSF ) Biological Sciences Directorate principal investigators ( BIO PIs ) , nearly 90% indicated they are currently or will soon be analyzing large data sets . BIO PIs considered a range of computational needs important to their work , including high performance com... | Our computational needs assessment of 704 principal investigators ( PIs ) with grants from the National Science Foundation ( NSF ) Biological Sciences Directorate ( BIO ) confirmed that biology is awash with big data . Nearly 90% of BIO PIs said they are currently or will soon be analyzing large data sets . They consid... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"sequencing",
"techniques",
"cell",
"division",
"analysis",
"biological",
"data",
"management",
"education",
"biologists",
"data",
"management",
"scientists",
"bioassays",
"and",
"physiological",
"analysis",
"molecular",
"biology",
"techniques",
"science",
"and",
"technol... | 2017 | Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators |
Dengue is a public health problem in many countries . Rapid diagnosis of dengue can assist patient triage and management . Detection of the dengue viral protein , NS1 , represents a new approach to dengue diagnosis . The sensitivity and specificity of the Platelia NS1 ELISA assay and an NS1 lateral flow rapid test ( LF... | Dengue is a viral infection of humans that is transmitted by mosquitoes . Dengue is a very important public health problem in many developing countries . Recently , new tests to help diagnose patients with dengue have been developed . Evaluating these tests to see how well they perform in different countries and in dif... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"infectious",
"diseases/tropical",
"and",
"travel-associated",
"diseases",
"infectious",
"diseases/viral",
"infections"
] | 2009 | Diagnostic Accuracy of NS1 ELISA and Lateral Flow Rapid Tests for Dengue Sensitivity, Specificity and Relationship to Viraemia and Antibody Responses |
Modifications of the Plasmodium falciparum–infected red blood cell ( iRBC ) surface have been linked to parasite-associated pathology . Such modifications enable the parasite to establish long-lasting chronic infection by evading antibody mediate immune recognition and splenic clearance . With the exception of the well... | Malaria remains a huge global health burden , infecting hundreds of millions of people each year . Despite a significant immune response by the host , the parasite can establish long-lasting chronic infections . Parasite-induced modifications on the surface of the infected red blood cell ( rbc ) are linked to the abili... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/protozoal",
"infections",
"infectious",
"diseases/tropical",
"and",
"travel-associated",
"diseases"
] | 2009 | The Plasmodium falciparum STEVOR Multigene Family Mediates Antigenic Variation of the Infected Erythrocyte |
The gaseous phytohormone ethylene participates in the regulation of root growth and development in Arabidopsis . It is known that root growth inhibition by ethylene involves auxin , which is partially mediated by the action of the WEAK ETHYLENE INSENSITIVE2/ANTHRANILATE SYNTHASE α1 ( WEI2/ASA1 ) , encoding a rate-limit... | Ethylene is a gaseous phytohormone that plays critical roles in plant development and defense . It is well known that ethylene inhibits primary root elongation through effects on auxin . However , it is not clear how ethylene signal is translated into auxin . In this report , the highly ethylene-responsive transcriptio... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2016 | Arabidopsis ERF1 Mediates Cross-Talk between Ethylene and Auxin Biosynthesis during Primary Root Elongation by Regulating ASA1 Expression |
When the fungus Candida albicans proliferates in the oropharyngeal cavity during experimental oropharyngeal candidiasis ( OPC ) , it undergoes large-scale genome changes at a much higher frequency than when it grows in vitro . Previously , we identified a specific whole chromosome amplification , trisomy of Chr6 ( Chr6... | Opportunistic fungal pathogens commonly acquire extra copies of chromosomes that can provide a fitness benefit under acute stress such as exposure to antifungal agents but how these extra copies affect fungal life-style and interactions with their hosts is poorly understood . Here we show that in C . albicans the acqui... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"trisomics",
"fungal",
"genetics",
"pathogens",
"immunology",
"microbiology",
"departures",
"from",
"diploidy",
"epithelial",
"cells",
"animal",
... | 2019 | Selection of Candida albicans trisomy during oropharyngeal infection results in a commensal-like phenotype |
Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal RNA ( SSU rRNA ) genes can sample a microbial community two or three orders of magnitude more deeply per dollar and per hour than capillary sequencing of full-length SSU rRNA . As with full-length rRNA surveys , each sequence read i... | Microbes play a critical role in both human and environmental health . The more we explore microbial populations , the more complexity and diversity we find . Phylogenetic trees based on 16S ribosomal RNA genes have been used with great success to identify microbial taxonomy from DNA alone . New DNA sequencing technolo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/environmental",
"microbiology",
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"microbiology/applied",
"microbiology",
"biotechnology/applied",
"microbiology",
"computationa... | 2008 | Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing |
Determining how proteins interact to form stable complexes is of crucial importance , for example in the development of novel therapeutics . Computational methods to determine the thermodynamically stable conformation of complexes from the structure of the binding partners , such as RosettaDock , might potentially emer... | Determining how proteins fold and form complexes is of crucial importance , for example in the development of novel therapeutics . Experimental determination of structures is costly and lengthy . Computational methods to determine the thermodynamically stable conformation of complexes from the structure of the binding ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"crystal",
"structure",
"molecular",
"dynamics",
"condensed",
"matter",
"physics",
"simulation",
"and",
"modeling",
"protein",
"structure",
"prediction",
"protein",
"structure",
"crystallography",
"thermodynamics",
"research",
"and",
"analysis",
"methods",
"solid",
"state... | 2018 | Assessment of ab initio models of protein complexes by molecular dynamics |
Streptococcus pneumoniae is the major bacterial cause of community-acquired pneumonia , and the leading agent of childhood pneumonia deaths worldwide . Nasal colonization is an essential step prior to infection . The cytokine IL-17 protects against such colonization and vaccines that enhance IL-17 responses to pneumoco... | Streptococcus pneumoniae ( the pneumococcus ) is an important human pathogen and the commonest cause of community-acquired pneumonia . The bacterial carbohydrate capsule is a key determinant of virulence and host defence . Pneumonia follows colonization of the nasopharynx and can spread systemically . The cytokine IL-1... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"body",
"fluids",
"respiratory",
"infections",
"pneumococcus",
"pathology",
"and",
"laboratory",
"medicine",
"immune",
"physiology",
"pathogens",
"immunology",
"cell",
"processes",
"microbiolo... | 2018 | IL-17 can be protective or deleterious in murine pneumococcal pneumonia |
All positive strand RNA viruses are known to replicate their genomes in close association with intracellular membranes . In case of the hepatitis C virus ( HCV ) , a member of the family Flaviviridae , infected cells contain accumulations of vesicles forming a membranous web ( MW ) that is thought to be the site of vir... | All positive-strand RNA viruses replicate in the cytoplasm in distinct membranous compartments acting as ‘replication factories’ . Membranes building up these factories are recruited from different sources and serve as platforms for the assembly of multi-subunit protein complexes ( the ‘replicase’ ) that catalyze the a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"gastroenterology",
"and",
"hepatology",
"biology",
"microbiology"
] | 2012 | Three-Dimensional Architecture and Biogenesis of Membrane Structures Associated with Hepatitis C Virus Replication |
Globally , a chronic hepatitis B virus ( HBV ) infection remains the leading cause of primary liver cancer . The mechanisms leading to the development of HBV-associated liver cancer remain incompletely understood . In part , this is because studies have been limited by the lack of effective model systems that are both ... | Chronic infection with the hepatitis B virus ( HBV ) is the leading global cause of primary liver cancer; however , therapeutics for the treatment of chronic HBV are limited in both scope and efficacy . Infection with HBV results in an incompletely understood , complex network of host-virus interactions . To attempt to... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"sequencing",
"techniques",
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"liver",
"pathology",
"and",
"laboratory",
"medicine",
"gene",
"regulation",
"pathogens",
"microbiology",
"cell",
"metabolism",
"hepatitis",
"b",
"virus",
"viruses",
"micrornas",
... | 2016 | Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression |
Orientia tsutsugamushi ( Ots ) frequently causes severe scrub typhus infections in the Asia-Pacific region . Korean investigators have demonstrated that Ots encodes five different autotransporter domain ( ATD ) proteins ( ScaA-ScaE ) . ScaA functions as an adhesin and confers protective immunity in a lethal mouse model... | Orientia tsutsugamushi ( Ots ) frequently causes severe scrub typhus infections in the Asia-Pacific region . Korean investigators had previously demonstrated that Ots encodes five different cell surface ( Sca ) proteins which have functional regions that mediate their transport to the cell surface . One of the proteins... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"taxonomy",
"typhus",
"medicine",
"and",
"health",
"sciences",
"membrane",
"proteins",
"bacterial",
"diseases",
"phylogenetics",
"data",
"management",
"outer",
"membrane",
"proteins",
"phylogenetic",
"analysis",
"molecular",
"biology",
"techniques",
"dna",
"cellular",
"... | 2018 | Detection and distribution of Sca autotransporter protein antigens in diverse isolates of Orientia tsutsugamushi |
A hallmark property of the neurotropic alpha-herpesvirinae is the dissemination of infection to sensory and autonomic ganglia of the peripheral nervous system following an initial exposure at mucosal surfaces . The peripheral ganglia serve as the latent virus reservoir and the source of recurrent infections such as col... | Neuroinvasive members of the alpha-herpesvirinae include human ( i . e . herpes simplex virus type I; HSV-1 ) and veterinary ( i . e . pseudorabies virus; PRV ) pathogens that routinely invade the peripheral nervous system of an immunocompetent host in the absence of overt tissue damage . We have identified an essentia... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"cell",
"processes",
"ocular",
"anatomy",
"microbiology",
"viral",
"structure",
"neuroscience",
"eye",
"diseases",
"nerve",
"fibers",
"eyes",
"animal",
"cells",
"axons",
"biological",
"tissue",
"viral",
"packaging",
"head",
"... | 2017 | The pUL37 tegument protein guides alpha-herpesvirus retrograde axonal transport to promote neuroinvasion |
We unravel how functional plasticity and redundancy are essential mechanisms underlying the ability to survive of metabolic networks . We perform an exhaustive computational screening of synthetic lethal reaction pairs in Escherichia coli in a minimal medium and we find that synthetic lethal pairs divide in two differe... | Plasticity and redundancy are essential features of biological systems , from brain to genome , that underlie the ability of organisms to survive . In metabolic networks , these essential mechanisms are unveiled by the analysis and categorization of synthetic lethal pairs of reactions . We find that plasticity acts as ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"biology",
"and",
"life",
"sciences"
] | 2014 | Essential Plasticity and Redundancy of Metabolism Unveiled by Synthetic Lethality Analysis |
Inverted duplications are a common type of copy number variation ( CNV ) in germline and somatic genomes . Large duplications that include many genes can lead to both neurodevelopmental phenotypes in children and gene amplifications in tumors . There are several models for inverted duplication formation , most of which... | Chromosomes with large inverted duplications and terminal deletions cause neurodevelopmental disorders in children . These chromosome rearrangements typically involve hundreds of genes , leading to significant changes in gene dosage . Though inverted duplications adjacent to terminal deletions are a relatively common t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"mental",
"health",
"genetics",
"biology",
"genomics",
"pediatrics",
"clinical",
"genetics"
] | 2014 | Large Inverted Duplications in the Human Genome Form via a Fold-Back Mechanism |
The broadly-neutralizing anti-HIV antibody 4E10 recognizes an epitope in the membrane-proximal external region of the HIV envelope protein gp41 . Previous attempts to elicit 4E10 by vaccination with envelope-derived or reverse-engineered immunogens have failed . It was presumed that the ontogeny of 4E10-equivalent resp... | 4E10 is an example of an anti-HIV , broadly neutralizing antibody that is uncommon in infected patients and has not been successfully elicited by any vaccine approach attempted . 4E10 has been proposed to neutralize HIV through a mechanism that requires broad recognition of other antigens , including membrane phospholi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Autoreactivity and Exceptional CDR Plasticity (but Not Unusual Polyspecificity) Hinder Elicitation of the Anti-HIV Antibody 4E10 |
Dengue virus ( DENV ) is the causative agent of dengue fever and dengue hemorrhagic fever . The virus is endemic in over 120 countries , causing over 350 million infections per year . Dengue vaccine development is challenging because of the need to induce simultaneous protection against four antigenically distinct DENV... | Dengue virus ( DENV ) is transmitted by mosquitoes and is endemic in over 120 countries , causing over 350 million infections yearly . Most infections are clinically unapparent , but under specific conditions , dengue can cause severe and lethal disease . DENV has 4 distinct serotypes and secondary DENV infections are ... | [
"Abstract",
"Introduction",
"Material",
"and",
"Methods",
"Results",
"Discussion"
] | [
"viral",
"vaccines",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"engineering",
"and",
"technology",
"immunology",
"tropical",
"diseases",
"microbiology",
"vaccines",
"preventive",
"medicine",
"drug",
"delivery",
"system",
"preparation",
"antigen",
... | 2016 | Precisely Molded Nanoparticle Displaying DENV-E Proteins Induces Robust Serotype-Specific Neutralizing Antibody Responses |
Hydatidosis or echinococcosisis considered a neglected zoonotic disease despite its high burden in the livestock industry and the high risk of infection by humans in endemic areas . In a cross-sectional study we estimated the copro-Incidence and also genotyped Echinococcus granulosus isolates from domestic dogs using p... | Echinococcosis is a parasitic disease caused by Echinococcus granulosus . The parasite life cycle is shared between a definitive and an intermediate host with humans as accidental hosts . The dog is a main definitive host while sheep is a major intermediate host . The incidence of E . granulosus infection detected in h... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Incidence of Echinococcus granulosus in Domestic Dogs in Palestine as Revealed by Copro-PCR |
Cell communication is essential for eukaryotic development , but our knowledge of molecules and mechanisms required for intercellular communication is fragmentary . In particular , the connection between signal sensing and regulation of cell polarity is poorly understood . In the filamentous ascomycete Neurospora crass... | Intercellular communication and cellular morphogenesis are essential for eukaryotic development . Our knowledge of molecules and mechanisms associated with these processes is , however , fragmentary . In particular , the molecular connection between signal sensing and regulation of cell polarity is poorly understood . ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"fungal",
"biochemistry",
"signal",
"transduction",
"mycology",
"fungi",
"model",
"organisms",
"molecular",
"cell",
"biology",
"neurospora",
"crassa",
"cell",
"biology",
"cell",
"growth",
"yeast",
"and",
"fungal",
"models",
"biology",
"microbiology",
"microbial",
"gro... | 2012 | The NDR Kinase Scaffold HYM1/MO25 Is Essential for MAK2 MAP Kinase Signaling in Neurospora crassa |
The protozoan parasite Trypanosoma cruzi is able to target the thymus and induce alterations of the thymic microenvironmental and lymphoid compartments . Acute infection results in severe atrophy of the organ and early release of immature thymocytes into the periphery . To date , the pathophysiological effects of thymi... | The formation of mature lineage-committed T cells requires the specialized environment of the thymus , a central organ of the immune system supporting the development of self-tolerant T cells . Key events of intrathymic T-cell development include lineage commitment , selection events and thymic emigration . This organ ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"disease",
"immunology",
"biology",
"and",
"life",
"sciences",
"immunology",
"clinical",
"immunology"
] | 2014 | Early Double-Negative Thymocyte Export in Trypanosoma cruzi Infection Is Restricted by Sphingosine Receptors and Associated with Human Chagas Disease |
As the major burden of Buruli ulcer disease ( BUD ) occurs in remote rural areas , development of point-of-care ( POC ) tests is considered a research priority to bring diagnostic services closer to the patients . Loop-mediated isothermal amplification ( LAMP ) , a simple , robust and cost-effective technology , has be... | Buruli ulcer disease ( BUD ) mainly occurs in remote rural areas of Sub-Saharan Africa , affects skin and soft tissue , and may lead to severe disabilities . Therefore , early diagnosis and treatment with antimycobacterial therapy are essential whereby the WHO recommends laboratory confirmation of 70% of the cases . As... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Loop-Mediated Isothermal Amplification for Laboratory Confirmation of Buruli Ulcer Disease—Towards a Point-of-Care Test |
Single-laboratory studies conducted under highly standardized conditions are the gold standard in preclinical animal research . Using simulations based on 440 preclinical studies across 13 different interventions in animal models of stroke , myocardial infarction , and breast cancer , we compared the accuracy of effect... | Preclinical animal research is mostly based on studies conducted in a single laboratory and under highly standardized conditions . This entails the risk that the study results may only be valid under the specific conditions of the test laboratory , which may explain the poor reproducibility of preclinical animal resear... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"animal",
"models",
"of",
"disease",
"analysis",
"of",
"variance",
"mathematics",
"signs",
"and",
"symptoms",
"statistics",
"(mathematics)",
"research",
"facilities",
"research",
"a... | 2018 | Reproducibility of preclinical animal research improves with heterogeneity of study samples |
Push–pull networks , in which two antagonistic enzymes control the activity of a messenger protein , are ubiquitous in signal transduction pathways . A classical example is the chemotaxis system of the bacterium Escherichia coli , in which the kinase CheA and the phosphatase CheZ regulate the phosphorylation level of t... | In both prokaryotes and eukaryotes , extra- and intracellular signals are often processed by biochemical networks in which two enzymes together control the activity of a messenger protein via opposite modification reactions . A well-known example is the chemotaxis network of Escherichia coli that controls the swimming ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biophysics/theory",
"and",
"simulation",
"computer",
"science/numerical",
"analysis",
"and",
"theoretical",
"computing",
"biochemistry/cell",
"signaling",
"and",
"trafficking",
"structures",
"biochemistry/theory",
"and",
"simulation",
"computational",
"biology/signaling",
"net... | 2009 | Differential Affinity and Catalytic Activity of CheZ in E.
coli Chemotaxis |
Brucella species are facultative intracellular bacterial pathogens that cause brucellosis , a global zoonosis of profound importance . Although recent studies have demonstrated that Brucella spp . replicate within an intracellular compartment that contains endoplasmic reticulum ( ER ) resident proteins , the molecular ... | Brucella spp . are facultative intracellular pathogens that cause brucellosis in a broad range of hosts , including humans . Brucella melitensis , B . abortus , and B . suis are highly infectious and can be readily transmitted in aerosolized form , and a human vaccine against brucellosis is unavailable . Therefore , th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology",
"infectious",
"diseases/bacterial",
"infections",
"microbiology/microbial",
"growth",
"and",
"development",
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis",
"microbiology/medical",
"microbiology"
] | 2008 | RNAi Screen of Endoplasmic Reticulum–Associated Host Factors Reveals a Role for IRE1α in Supporting Brucella Replication |
Protein design remains an important problem in computational structural biology . Current computational protein design methods largely use physics-based methods , which make use of information from a single protein structure . This is despite the fact that multiple structures of many protein folds are now readily avail... | To engineer proteins that bind a target protein , computational protein design methods have been employed to reduce the set of candidate protein variants that are then experimentally validated . Current protein design methods use protein backbone information from a single protein structure . In order to use alternative... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biotechnology",
"medicine",
"and",
"health",
"sciences",
"crystal",
"structure",
"molecular",
"dynamics",
"engineering",
"and",
"technology",
"synthetic",
"biology",
"condensed",
"matter",
"physics",
"synthetic",
"bioengineering",
"protein",
"structure",
"macromolecular",
... | 2017 | Data driven flexible backbone protein design |
Conducting clinical trials to assess experimental treatments for potentially pandemic infectious diseases is challenging . Since many outbreaks of infectious diseases last only six to eight weeks , there is a need for trial designs that can be implemented rapidly in the face of uncertainty . Outbreaks are sudden and un... | Since many outbreaks of infectious diseases last only six to eight weeks , there is a need for trial designs that can be implemented rapidly in the face of uncertainty . The Generic Ordinal Sequential Trial ( GOST ) is a flexible statistical design for a randomised clinical trial comparing an experimental treatment for... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"tropical",
"diseases",
"geographical",
"locations",
"ebola",
"hemorrhagic",
"fever",
"randomized",
"controlled",
"trials",
"clinical",
"medicine",
"mathematics",
"emerging",
"infectious",
"diseases",
"statistics",
"(mathematics)",
... | 2017 | GOST: A generic ordinal sequential trial design for a treatment trial in an emerging pandemic |
Giardia lamblia parasitizes the human small intestine to cause diarrhea and malabsorption . It undergoes differentiation from a pathogenic trophozoite form into a resistant walled cyst form . Few cyst proteins have been identified to date , including three cyst wall proteins ( CWPs ) and one High Cysteine Non-variant C... | The biological goal of Giardia lamblia life cycle is differentiation into a cyst form ( encystation ) that can survive in the environment and infect a new host . Since cystic stages are key to transmission of parasites , this differentiation may be a target for interruption of the life cycle . Synthesis and assembly of... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"developmental",
"biology/developmental",
"evolution",
"developmental",
"biology/microbial",
"growth",
"and",
"development",
"biochemistry/cell",
"sign... | 2010 | A Novel Family of Cyst Proteins with Epidermal Growth Factor Repeats in Giardia lamblia |
Difficulties in scaling up theoretical and experimental results have raised controversy over the consequences of biodiversity loss for the functioning of natural ecosystems . Using a global survey of reef fish assemblages , we show that in contrast to previous theoretical and experimental studies , ecosystem functionin... | The increasing intensity of human disturbance worldwide is triggering unprecedented biodiversity losses , which is raising concerns over whether ecosystems will work and continue delivering goods and services to humanity . In contrast to previous experimental studies , which describe saturating relationships between ec... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"ecology"
] | 2011 | Global Human Footprint on the Linkage between Biodiversity and Ecosystem Functioning in Reef Fishes |
Modern time series gene expression and other omics data sets have enabled unprecedented resolution of the dynamics of cellular processes such as cell cycle and response to pharmaceutical compounds . In anticipation of the proliferation of time series data sets in the near future , we use the Hopfield model , a recurren... | Cell cycle—the process in which a parent cell replicates its DNA and divides into two daughter cells—is an upregulated process in many forms of cancer . Identifying gene inhibition targets to regulate cell cycle is important to the development of effective therapies . Although modern high throughput techniques offer un... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"cycle",
"inhibitors",
"hela",
"cells",
"cell",
"cycle",
"and",
"cell",
"division",
"applied",
"mathematics",
"cell",
"processes",
"biological",
"cultures",
"enzymology",
"genetic",
"algorithms",
"simulation",
"and",
"modeling",
"algorithms",
"fungi",
"model",... | 2017 | Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems |
Epstein-Barr Virus ( EBV ) can establish latent infections with distinct gene expression patterns referred to as latency types . These different latency types are epigenetically stable and correspond to different promoter utilization . Here we explore the three-dimensional conformations of the EBV genome in different l... | Epstein-Barr Virus ( EBV ) latent infection is associated with several human malignancies . The viral genes expressed during latent infection can vary depending on host cell or tumor type . The different gene expression programs , referred to as latency types , are determined by alternative viral promoter usage . In th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"biology"
] | 2011 | EBV Latency Types Adopt Alternative Chromatin Conformations |
There is much uncertainty about the future impact of climate change on vector-borne diseases . Such uncertainty reflects the difficulties in modelling the complex interactions between disease , climatic and socioeconomic determinants . We used a comprehensive panel dataset from Mexico covering 23 years of province-spec... | Relationships between weather and mosquito-borne diseases are nonlinear in nature . This means that the number of disease cases does not vary equally with changes in the climate system . Identifying adequately the form of the relationship between disease outcomes and their drivers in an empirical fashion can be tedious... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | The Effects of Weather and Climate Change on Dengue |
Innate immune cells shape the host response to microbial pathogens . Here we elucidate critical differences in the molecular response of macrophages vs . dendritic cells ( DCs ) to Histoplasma capsulatum , an intracellular fungal pathogen of humans . It has long been known that macrophages are permissive for Histoplasm... | Innate immune cells such as macrophages and dendritic cells ( DCs ) are critical elements of the initial response to pathogens . Whereas both of these cell types utilize robust anti-microbial strategies to kill internalized microbes , intracellular pathogens have developed mechanisms to manipulate the host response and... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"yeast",
"infections",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"pathogens",
"immunology",
"microbiology",
"animal",
"models",
"model",
"org... | 2016 | CD103+ Conventional Dendritic Cells Are Critical for TLR7/9-Dependent Host Defense against Histoplasma capsulatum, an Endemic Fungal Pathogen of Humans |
The microaerophilic protozoan parasite Giardia intestinalis , causative of one of the most common human intestinal diseases worldwide , infects the mucosa of the proximal small intestine , where it has to cope with O2 and nitric oxide ( NO ) . Elucidating the antioxidant defense system of this pathogen lacking catalase... | Giardia intestinalis causes one of the most common human intestinal diseases worldwide , called giardiasis . This microorganism infects the small intestine where it has to cope with O2 , nitric oxide ( NO ) and related reactive species that are toxic for Giardia as it lacks most of the conventional antioxidant enzymes ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"cellular",
"stress",
"responses",
"neurochemistry",
"giardiasis",
"enzymes",
"microbiology",
"basic",
"cancer",
"research",
"parastic",
"protozoans",
"oncology",
"neglected",
"tropical",
"diseases",
"enzyme",
"kinetics",
"giardia",
"lamblia",
"infectious",
"d... | 2014 | Functional Characterization of Peroxiredoxins from the Human Protozoan Parasite Giardia intestinalis |
Leishmania parasites are transmitted in the presence of sand fly saliva . Together with the parasite , the sand fly injects salivary components that change the environment at the feeding site . Mice immunized with Phlebotomus papatasi salivary gland ( SG ) homogenate are protected against Leishmania major infection , w... | Sand fly saliva contains potent , biologically active proteins that allow the insect to stop host responses to acquire a blood meal . After repeated exposures , a number of these salivary proteins also induce a response in the host such as antibody production and/or cellular-mediated immunity . In animal models , these... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"leishmaniasis",
"neglected",
"tropical",
"diseases",
"immunology",
"biology",
"parasitic",
"diseases",
"immune",
"response"
] | 2013 | Functional Transcriptomics of Wild-Caught Lutzomyia intermedia Salivary Glands: Identification of a Protective Salivary Protein against Leishmania braziliensis Infection |
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