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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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The long-held principle that functionally important proteins evolve slowly has recently been challenged by studies in mice and yeast showing that the severity of a protein knockout only weakly predicts that protein’s rate of evolution . However , the relevance of these studies to evolutionary changes within proteins is... | Different proteins evolve at dramatically different rates . To understand this variation , it is necessary to determine which characteristics of proteins are visible to natural selection and how the strength of selection depends on those characteristics . One protein characteristic that is evidently visible to natural ... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"vertebrates",
"animals",
"systems",
"science",
"mathematics",
"statistics",
"(mathematics)",
"fungal",
"evolution",
"discrete",
"mathematics",
"combinatorics",
"research",
"and",
"analysis",
"methods",
"mycology",
"evolutionary",
"rate",
"computer",
"and",
"information",
... | 2016 | Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution |
Protozoan parasites belonging to genera Leishmania and Trypanosoma are the etiological agents of severe neglected tropical diseases ( NTDs ) that cause enormous social and economic impact in many countries of tropical and sub-tropical areas of the world . In our screening program for new drug leads from natural sources... | Protozoans belonging to genera Leishmania and Trypanosoma are single-cell organisms that can infect humans and cause disfiguring lesions and debilitating or fatal diseases , with enormous social and economic impact in many tropical and sub-tropical areas of the world . The drugs currently available to treat the differe... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"chemistry/organic",
"chemistry",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"infectious",
"diseases/protozoal",
"infections",
"biochemistry/small",
"molecule",
"chemistry",
"biochemistry/drug",
"discovery"
] | 2008 | Leishmanicidal Metabolites from Cochliobolus sp., an Endophytic Fungus Isolated from Piptadenia adiantoides (Fabaceae) |
Although Leishmania parasites have been shown to modulate their host cell's responses to multiple stimuli , there is limited evidence that parasite molecules are released into infected cells . In this study , we present an implementation of the change mediated antigen technology ( CMAT ) to identify parasite molecules ... | Leishmania are intracellular parasites that reside within parasitophorous vacuoles ( PV ) in phagocytes . From within these compartments parasites control the host cell's responses to multiple stimuli . There is limited knowledge of the molecules that Leishmania parasites elaborate in the host cell to target processes ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"and",
"Discussion"
] | [
"infectious",
"diseases/protozoal",
"infections",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"infectious",
"diseases/skin",
"infections"
] | 2010 | Identification of Leishmania Proteins Preferentially Released in Infected Cells Using Change Mediated Antigen Technology (CMAT) |
A major challenge in computational neurobiology is to understand how populations of noisy , broadly-tuned neurons produce accurate goal-directed actions such as saccades . Saccades are high-velocity eye movements that have stereotyped , nonlinear kinematics; their duration increases with amplitude , while peak eye-velo... | As the fovea is the only spot on the retina with high spatial resolution , primates need to move their eyes to peripheral targets for detailed inspection . Saccades are the fastest movements of the body , and theoretical studies suggest that their trajectories are optimized to bring the fovea as fast and accurately as ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"anatomy",
"and",
"physiology",
"electrophysiology",
"neuroscience",
"motor",
"systems",
"cognitive",
"neuroscience",
"computational",
"neuroscience",
"neurological",
"system",
"coding",
"mechanisms",
"robotics",
"musculoskeletal",
"system",
"biology",
"systems",
"biology",
... | 2012 | Optimal Control of Saccades by Spatial-Temporal Activity Patterns in the Monkey Superior Colliculus |
Cell-surface transferrin receptor ( CD71+ ) erythroid cells are abundant in newborns with immunomodulatory properties . Here , we show that neonatal CD71+ erythroid cells express significant levels of V-domain Immunoglobulin ( Ig ) Suppressor of T Cell Activation ( VISTA ) and , via constitutive production of transform... | The primary role of the red blood cells is to transport oxygen , but we know relatively little about the other functions they perform . Following maturation , red blood cells exit the bone marrow and enter blood circulation . Their immature counterparts are normally absent or in very low frequency in the blood of healt... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"spleen",
"immunology",
"developmental",
"biology",
"antibodies",
"immune",
"system",
"proteins",
"white",
"blood",
"cells",
"animal",
"cells",
"proteins",
"gene",
... | 2018 | CD71+VISTA+ erythroid cells promote the development and function of regulatory T cells through TGF-β |
Diagnosis of leptospirosis by the microscopic agglutination test ( MAT ) or by culture is confined to specialized laboratories . Although ELISA techniques are more common , they still require laboratory facilities . Rapid Diagnostic Tests ( RDTs ) can be used for easy point-of-care diagnosis . This study aims to evalua... | Leptospirosis is one of the world's most spread zoonoses causing acute fever . The illness can rapidly develop into a severe , potentially fatal , form with a high mortality rate . Laboratory tests are needed to confirm the diagnosis . Culturing leptospires from patient material can take months to grow . Therefore , mo... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"bacterial",
"diseases",
"infectious",
"diseases",
"immunoassays",
"neglected",
"tropical",
"diseases",
"immunology",
"biology",
"immunologic",
"techniques",
"leptospirosis"
] | 2013 | Prospective Evaluation of Three Rapid Diagnostic Tests for Diagnosis of Human Leptospirosis |
A Schistosoma mansoni cercarial antigen preparation ( cercarial transformation fluid – SmCTF ) was evaluated for detection of anti-schistosome antibodies in human sera in 4 collaborating laboratories . The performance of SmCTF was compared with that of S . mansoni egg antigens ( SmSEA ) in an indirect enzyme-immunoassa... | Diagnosis of schistosomiasis is problematic since no method is yet available that gives both 100% sensitivity and 100% specificity . The method traditionally used is microscopy , but because of inherent insensitivity this technique often wrongly diagnoses patients as uninfected . Use of serological assays involving det... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"clinical",
"laboratory",
"sciences",
"immunology",
"microbiology",
"parasitic",
"diseases",
"parasitology",
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"evaluation",
"neglected",
"tropical",
"diseases",
"infectious",
"disease",
"control",
"infectious",
"diseases",
"travel-associated",
"diseases",
... | 2012 | Comparison of Schistosoma mansoni Soluble Cercarial Antigens and Soluble Egg Antigens for Serodiagnosing Schistosome Infections |
Molecular xenomonitoring ( MX ) —pathogen detection in the mosquito rather than human—is a promising tool for lymphatic filariasis ( LF ) surveillance . In the Recife Metropolitan Region ( RMR ) , the last LF focus in Brazil , Culex quinquefasciatus mosquitoes have been implicated in transmitting Wuchereria bancrofti p... | Lymphatic filariasis ( LF ) is a parasitic disease transmitted by mosquitoes , and can cause elephantiasis . It is the world’s leading cause of disability due to infectious diseases , affects over 120 million people globally , and is scheduled for global elimination via mass drug administration ( MDA ) and mosquito con... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"geographical",
"locations",
"tropical",
"diseases",
"vector-borne",
"diseases",
"parasitic",
"diseases",
"animals",
"filariasis",
"neglected",
"tropical",
"diseases",
"insect",
"vectors",
"lymphatic",
"filariasis",
... | 2018 | Development of an urban molecular xenomonitoring system for lymphatic filariasis in the Recife Metropolitan Region, Brazil |
Variation in susceptibility to infectious disease often has a substantial genetic component in animal and plant populations . We have used genome-wide association studies ( GWAS ) in Drosophila melanogaster to identify the genetic basis of variation in susceptibility to viral infection . We found that there is substant... | In most animal populations , individuals vary genetically in how susceptible they are to infectious disease . To understand the genetic basis of this variation , we have infected a panel of inbred lines of the fruit fly D . melanogaster with viruses and have looked for genetic variants associated with resistance to inf... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"population",
"genetics",
"immunology",
"parasitology",
"population",
"biology",
"zoology",
"infectious",
"diseases",
"genetic",
"polymorphism",
"biology",
"genetics",
"of",
"the",
"immune",
"system",
"natural",
"select... | 2012 | Genome-Wide Association Studies Reveal a Simple Genetic Basis of Resistance to Naturally Coevolving Viruses in Drosophila melanogaster |
Tsetse flies are important vectors of human and animal trypanosomiasis . Ability to reduce tsetse populations is an effective means of disease control . Lactation is an essential component of tsetse’s viviparous reproductive physiology and requires a dramatic increase in the expression and synthesis of milk proteins by... | Tsetse flies are vectors for trypanosomes that cause both African sleeping sickness in humans and Nagana in animals . The reduction of tsetse populations is the most efficient way to reduce the prevalence of this economically important disease with current control methods including pesticide application , traps , and s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"milk",
"autophagic",
"cell",
"death",
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"fluids",
"maternal",
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"and",
"gynecology",
"gene",
"regulation",
"cell",
"processes",
"diet",
"reproductive",
"physiology",
"endocrine",
... | 2018 | Rapid autophagic regression of the milk gland during involution is critical for maximizing tsetse viviparous reproductive output |
When the primary visual cortex ( V1 ) is damaged , the principal visual pathway is lost , causing a loss of vision in the opposite visual field . While conscious vision is impaired , patients can still respond to certain images; this is known as ‘blindsight’ . Recently , a direct anatomical connection between the later... | When the primary visual cortex ( V1 ) is damaged in one hemisphere , we lose the ability to see one half of the world around us . Clinical tests show that in this blind region of vision , we cannot see even the brightest flashes of light . However , many years of research have shown that individuals who are blind in th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
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] | [
"medicine",
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"brain",
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"cerebral",
"hemispheres",
"left",
"hemisphere",
"magnetic",
... | 2018 | Blindsight relies on a functional connection between hMT+ and the lateral geniculate nucleus, not the pulvinar |
Eumycetoma is a progressive and destructive chronic granulomatous subcutaneous inflammatory disease caused by certain fungi , the most common being Madurella mycetomatis . The host defence mechanisms against fungi usually range from an early non-specific immune response to activation and induction of specific adaptive ... | Madurella mycetomatis is the most common causative agent for eumycetoma , which is a progressive and destructive subcutaneous inflammatory disease . It is a neglected tropical disease affecting the population in poor and remote endemic tropical and subtropical areas . Currently , the susceptibility and resistance to my... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"mycetoma",
"immunology",
"tropical",
"diseases",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"developme... | 2016 | Th-1, Th-2 Cytokines Profile among Madurella mycetomatis Eumycetoma Patients |
Fragile X syndrome ( FXS ) is a form of inherited mental retardation in humans that results from expansion of a CGG repeat in the Fmr1 gene . Recent studies suggest a role of astrocytes in neuronal development . However , the mechanisms involved in the regulation process of astrocytes from FXS remain unclear . In this ... | Fragile X syndrome is a form of inherited mental retardation in humans that results from expansion of a CGG repeat in the Fmr1 gene . Recent studies suggest that astrocytes play a role in neuronal growth . In this study , we find that astrocytes derived from a Fragile X model , the Fmr1 knockout ( KO ) mouse , inhibit ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroglial",
"development",
"neurobiology",
"of",
"disease",
"and",
"regeneration",
"developmental",
"neuroscience",
"cellular",
"neuroscience",
"neuronal",
"morphology",
"biology",
"neuroscience"
] | 2012 | Excessive Astrocyte-Derived Neurotrophin-3 Contributes to the Abnormal Neuronal Dendritic Development in a Mouse Model of Fragile X Syndrome |
Leptospirosis is a worldwide spread zoonotic and neglected infectious disease of human and veterinary concern that is caused by pathogenic Leptospira species . In severe infections , hemostatic impairments such as coagulation/fibrinolysis dysfunction are frequently observed . These complications often occur when the ho... | Leptospirosis is one of the most relevant and spread zoonotic and neglected infectious diseases affecting humans and other mammals , and is caused by pathogenic bacteria of the genus Leptospira . During infectious diseases , when bacterial pathogens control and/or modulate the host response , impaired hemostasis and in... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"inflammatory",
"diseases",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"leptospira",
"pathology",
"and",
"laboratory",
"medicine",
"coagulation",
"factors",
"pathogens",
"tropical",
"diseases",
"microbiology",
"bacterial",
"diseases",
"neglected",
"tropica... | 2016 | Modulation of Hemostatic and Inflammatory Responses by Leptospira Spp. |
As a master regulator of jasmonic acid ( JA ) –signaled plant immune responses , the basic helix-loop-helix ( bHLH ) Leu zipper transcription factor MYC2 differentially regulates different subsets of JA–responsive genes through distinct mechanisms . However , how MYC2 itself is regulated at the protein level remains un... | The plant hormone jasmonic acid ( JA ) regulates a wide range of plant immune responses involving genome-wide transcriptional reprogramming that are regulated by the basic helix-loop-helix ( bHLH ) Leu zipper transcription factor MYC2 . As a master regulator of JA signaling , MYC2 differentially regulates the transcrip... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology"
] | 2013 | Phosphorylation-Coupled Proteolysis of the Transcription Factor MYC2 Is Important for Jasmonate-Signaled Plant Immunity |
Theoretical advances in the science of consciousness have proposed that it is concomitant with balanced cortical integration and differentiation , enabled by efficient networks of information transfer across multiple scales . Here , we apply graph theory to compare key signatures of such networks in high-density electr... | What are the neural signatures of consciousness ? This is an elusive yet fascinating challenge to current cognitive neuroscience , but it takes on an immediate clinical and societal significance in patients diagnosed as vegetative and minimally conscious . In these patients , it leads us to ask whether we can test for ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"brain",
"electrophysiology",
"electrophysiology",
"neuroscience",
"cognitive",
"neuroscience",
"brain",
"mapping",
"computational",
"neuroscience",
"bioassays",
"and",
"physiological",
"analysis",
"electroencephalography",
"research",
... | 2014 | Spectral Signatures of Reorganised Brain Networks in Disorders of Consciousness |
Reinforcement Learning has greatly influenced models of conditioning , providing powerful explanations of acquired behaviour and underlying physiological observations . However , in recent autoshaping experiments in rats , variation in the form of Pavlovian conditioned responses ( CRs ) and associated dopamine activity... | Acquisition of responses towards full predictors of rewards , namely Pavlovian conditioning , has long been explained using the reinforcement learning theory . This theory formalizes learning processes that , by attributing values to situations and actions , makes it possible to direct behaviours towards rewarding obje... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"behavioral",
"neuroscience",
"computational",
"neuroscience",
"biology",
"neuroscience",
"learning",
"and",
"memory"
] | 2014 | Modelling Individual Differences in the Form of Pavlovian Conditioned Approach Responses: A Dual Learning Systems Approach with Factored Representations |
In most organisms , the heat-shock response involves increased heat-shock gene transcription . In Kinetoplastid protists , however , virtually all control of gene expression is post-transcriptional . Correspondingly , Trypanosoma brucei heat-shock protein 70 ( HSP70 ) synthesis after heat shock depends on regulation of... | When organisms are placed at a temperature that is higher than normal , their proteins start to unfold . The organisms protect themselves by increasing the synthesis of “heat-shock” proteins which can re-fold other proteins when the temperature returns to normal . In trypanosomes , the degradation of mRNAs that encode ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"rna",
"cellular",
"stress",
"responses",
"molecular",
"cell",
"biology",
"cell",
"biology",
"nucleic",
"acids",
"biology",
"microbiology",
"rna",
"stability",
"molecular",
"biology",
"parasitology",
"parasite",
"physiology"
] | 2013 | Post-Transcriptional Regulation of the Trypanosome Heat Shock Response by a Zinc Finger Protein |
The genealogical relationship of human , chimpanzee , and gorilla varies along the genome . We develop a hidden Markov model ( HMM ) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes . Our HMM is an analytically tra... | Primate evolution is a central topic in biology and much information can be obtained from DNA sequence data . A key parameter is the time “when we became human , ” i . e . , the time in the past when descendents of the human–chimp ancestor split into human and chimpanzee . Other important parameters are the time in the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"primates",
"genetics",
"and",
"genomics"
] | 2007 | Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model |
Borrelia burgdorferi , the causative agent of Lyme disease in humans , is maintained in a complex biphasic life cycle , which alternates between tick and vertebrate hosts . To successfully survive and complete its enzootic cycle , B . burgdorferi adapts to diverse hosts by regulating genes required for survival in spec... | Borrelia burgdorferi , the causative agent of Lyme disease , must adjust to environmental changes as it moves between its tick and vertebrate hosts . We performed a screen of a B . burgdorferi transposon library using massively parallel sequencing ( Tn-seq ) to identify fitness defects involved in survival in its tick ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"lipoprotein",
"metabolism",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"developmental",
"biology",
"molecular",
"biology",
"techniques",
"bacteria",
"lipoprotein",
"structure",
"ba... | 2019 | Genome-wide screen identifies novel genes required for Borrelia burgdorferi survival in its Ixodes tick vector |
Taenia solium taeniosis/cysticercosis is a parasitic infection occurring in many developing countries . Data on the status of human infections in Zambia is largely lacking . We conducted a community-based study in Eastern Zambia to determine the prevalence of human taeniosis and cysticercosis in a rural community . Sto... | Taenia solium taeniosis/cysticercosis is a zoonotic infection endemic in many developing countries , with humans as the definitive host ( taeniosis ) and pigs and humans as the intermediate hosts ( cysticercosis ) . When humans act as the intermediate host , the result can be neurocysticercosis , which is associated wi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"epidemiology",
"neglected",
"tropical",
"diseases",
"parasitic",
"diseases"
] | 2012 | Taenia solium Infections in a Rural Area of Eastern Zambia-A Community Based Study |
The discovery of expression quantitative trait loci ( “eQTLs” ) can help to unravel genetic contributions to complex traits . We identified genetic determinants of human liver gene expression variation using two independent collections of primary tissue profiled with Agilent ( n = 206 ) and Illumina ( n = 60 ) expressi... | Many disease-associated genetic variants do not alter protein sequences and are difficult to precisely identify . Discovery of expression quantitative trait loci ( eQTL ) , or correlations between genetic variants and gene expression levels , offers one means of addressing this challenge . However , eQTL studies in pri... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"genome",
"expression",
"analysis",
"genomics",
"gene",
"expression",
"genetics",
"biology",
"human",
"genetics",
"genetics",
"and",
"genomics"
] | 2011 | Identification, Replication, and Functional Fine-Mapping of
Expression Quantitative Trait Loci in Primary Human Liver Tissue |
Trypanosoma cruzi is the causative agent of the life-threatening Chagas disease , in which increased platelet aggregation related to myocarditis is observed . Platelet-activating factor ( PAF ) is a potent intercellular lipid mediator and second messenger that exerts its activity through a PAF-specific receptor ( PAFR ... | Chagas disease , caused by the parasite Trypanosoma cruzi , was exclusively confined to Latin America but it has recently spread to other regions of the world . Chagas disease affects 8–10 million people and kills thousands of them every year . Lysophosphatidylcholine ( LPC ) is a major bioactive phospholipid of human ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biochemistry",
"lipids",
"lipid",
"mediators",
"biology",
"and",
"life",
"sciences",
"microbiology",
"parasitology"
] | 2014 | Structural and Functional Analysis of a Platelet-Activating Lysophosphatidylcholine of Trypanosoma cruzi |
Yeast pseudohyphal filamentation is a stress-responsive growth transition relevant to processes required for virulence in pathogenic fungi . Pseudohyphal growth is controlled through a regulatory network encompassing conserved MAPK ( Ste20p , Ste11p , Ste7p , Kss1p , and Fus3p ) , protein kinase A ( Tpk2p ) , Elm1p , a... | Eukaryotic cells affect precise changes in shape and growth in response to environmental and nutritional stress , enabling cell survival and wild-type function . The single-celled budding yeast provides a striking example , undergoing a set of changes under conditions of nitrogen or glucose limitation resulting in the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Large-Scale Analysis of Kinase Signaling in Yeast Pseudohyphal Development Identifies Regulation of Ribonucleoprotein Granules |
Sensitive , specific and rapid diagnostic tests for the detection of Orientia tsutsugamushi ( O . tsutsugamushi ) and Rickettsia typhi ( R . typhi ) , the causative agents of scrub typhus and murine typhus , respectively , are necessary to accurately and promptly diagnose patients and ensure that they receive proper tr... | Historically , rickettsial pathogens are among the leading causes of morbidity and mortality during military operations . Rickettsial diseases , lately , are reemerging in areas of known abundance or emerging in areas of unknown existence , posing a significant medical concern for local residents and travelers . The di... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Development of Recombinase Polymerase Amplification Assays for Detection of Orientia tsutsugamushi or Rickettsia typhi |
Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts . The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization . However , such correlations are of long-standing interest i... | Data from many fields are available primarily in the form of proportions , also referred to as compositions , which impose mathematical constraints on identifying interactions among components in the underlying systems . In particular , correlations cannot be calculated directly from proportions or from count data that... | [
"Abstract",
"Introduction",
"Methods",
"BAnOCC:",
"Bayesian",
"analysis",
"of",
"compositional",
"covariance",
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... | [
"ecology",
"and",
"environmental",
"sciences",
"microbiome",
"microbiology",
"random",
"variables",
"covariance",
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"and",
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"mathematics",
"theoretical",
"ecology",
"microbial",
"genomics",
"research",
"and",
"analysis",
"methods",
"medical",
"micro... | 2017 | A Bayesian method for detecting pairwise associations in compositional data |
Intestinal nematodes suppress immune responses in the context of allergy , gut inflammation , secondary infection and vaccination . Several mechanisms have been proposed for this suppression including alterations in Th2 cell differentiation and increased Treg cell suppressive function . In this study , we show that chr... | Infections with intestinal nematodes may be one explanation to why BCG vaccination is less effective in areas of high worm burden . In support of this , we recently showed that chronic intestinal nematode infection resulted in reduced immune responses and higher mycobacterial burden at distal sites . How a gut-dwelling... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
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] | [
"blood",
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"nematode",
"infections",
"skin",
"infections",
"cytotoxic",
"t",
"cells",
"digestive",
"system",
"infectious",
... | 2018 | Atrophy of skin-draining lymph nodes predisposes for impaired immune responses to secondary infection in mice with chronic intestinal nematode infection |
Genetic variation at immunoglobulin ( Ig ) gene variable regions in B-cells is created through a multi-step process involving deamination of cytosine bases by activation-induced cytidine deaminase ( AID ) and their subsequent mutagenic repair . To protect the genome from dangerous , potentially oncogenic effects of off... | To produce a limitless diversity of antibodies within the constraints of a finite genome , activated B cells introduce random mutations into antibody genes through a process of targeted DNA damage and subsequent mutagenic repair . At the same time , the rest of the genome must be protected from mutagenesis to prevent o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/genetics",
"of",
"the",
"immune",
"system",
"biochemistry/replication",
"and",
"repair",
"biochemistry"
] | 2010 | The BRCT Domain of PARP-1 Is Required for Immunoglobulin Gene Conversion |
The ability to predict the response of a cancer patient to a therapeutic agent is a major goal in modern oncology that should ultimately lead to personalized treatment . Existing approaches to predicting drug sensitivity rely primarily on profiling of cancer cell line panels that have been treated with different drugs ... | In this study , using the Cancer Cell Line Encyclopedia ( CCLE ) and Cancer Genome Project ( CGP ) studies as benchmark datasets , we explored the application of similarity information between cell lines and drugs in drug response prediction . We found that similar cell lines by gene expression profiles exhibit similar... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model |
Genetic exchange by recombination , or reassortment of genomic segments , has been shown to be an important process in RNA virus evolution , resulting often in important phenotypic changes affecting host range and virulence . However , data from numerous systems indicate that reassortant or recombinant genotypes could ... | The exchange of genomic regions between viral strains or species is an important process in virus evolution , resulting often in dramatic changes in virulence and host range and in the emergence of new viral diseases . In spite of its potential importance , little is known about what factors affect the frequency of the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"viruses",
"virology",
"evolutionary",
"biology",
"plants",
"genetics",
"and",
"genomics"
] | 2007 | Constraints to Genetic Exchange Support Gene Coadaptation in a Tripartite RNA Virus |
Sleeping sickness is spread over 36 Sub-Saharan African countries . In West and Central Africa , the disease is caused by Trypanosoma brucei gambiense , which produces a chronic clinical manifestation . The Luba focus ( Bioko Island , Equatorial Guinea ) has not reported autochthonous sleeping sickness cases since 1995... | Sleeping sickness is a neglected disease with an important impact on public health of many countries of Sub-Saharan Africa . It is transmitted by tsetse fly bites ( the vector ) and mainly affects remote and rural populations . The chronic form , caused by Trypanosoma brucei gambiense , includes almost 90% of reported ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"public",
"health",
"and",
"epidemiology/screening",
"infectious",
"diseases/protozoal",
"infections",
"infectious",
"diseases/epidemiology",
"and",
"co... | 2010 | Screening of Trypanosoma brucei gambiense in Domestic Livestock and Tsetse Flies from an Insular Endemic Focus (Luba, Equatorial Guinea) |
Both environmental factors and genetic loci have been associated with coronary artery disease ( CAD ) , however gene-gene and gene-environment interactions that might identify molecular mechanisms of risk are not easily studied by human genetic approaches . We have previously identified the transcription factor TCF21 a... | Coronary heart disease is the leading cause of death in the world . Both genes and the environment are important risk factors for the progression of disease , however , how genes may modulate the harmful response to the disease promoting environment is unknown and difficult to study . Here , we show that a common herit... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"and",
"health",
"sciences",
"gene",
"regulation",
"regulatory",
"proteins",
"dna-binding",
"proteins",
"dna",
"transcription",
"coronary",
"heart",
"disease",
"genome",
"analysis",
"transcription",
"factors",
"cardiolo... | 2017 | TCF21 and the environmental sensor aryl-hydrocarbon receptor cooperate to activate a pro-inflammatory gene expression program in coronary artery smooth muscle cells |
The 2009 H1N1 influenza pandemic ( pH1N1 ) led to record sales of neuraminidase ( NA ) inhibitors , which has contributed significantly to the recent increase in oseltamivir-resistant viruses . Therefore , development and careful evaluation of novel NA inhibitors is of great interest . Recently , a highly potent NA inh... | The influenza neuraminidase ( NA ) enzyme is the most successful drug target against the seasonal and pandemic flu . The 2009 H1N1 flu pandemic led to record sales of the NA inhibitors oseltamivir ( Tamiflu ) and zanamivir ( Relenza ) . Recently , a new drug , laninamivir ( Inavir ) , has been approved for use in Japan... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"proteins",
"protein",
"structure",
"biology",
"proteomics",
"glycobiology",
"drug",
"discovery"
] | 2011 | Structural and Functional Analysis of Laninamivir and its Octanoate Prodrug Reveals Group Specific Mechanisms for Influenza NA Inhibition |
Insulin-like signalling is a conserved mechanism that coordinates animal growth and metabolism with nutrient status . In Drosophila , insulin-producing median neurosecretory cells ( IPCs ) regulate larval growth by secreting insulin-like peptides ( dILPs ) in a diet-dependent manner . Previous studies have shown that n... | Ribosome biogenesis is a major consumer of cellular energy and a rate-limiting process during cell growth . The ribosome biogenesis pathway is tightly connected with signaling pathways that regulate tissue growth . For example , nutrient-regulated signaling cues adjust the rate of ribosome biogenesis . On the other han... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"animal",
"genetics",
"model",
"organisms",
"genetic",
"screens",
"gene",
"identification",
"and",
"analysis",
"genetics",
"biology",
"and",
"life",
"sciences",
"research",
"and",
"analysis",
"methods",
"gene",
"function"
] | 2014 | p53- and ERK7-Dependent Ribosome Surveillance Response Regulates Drosophila Insulin-Like Peptide Secretion |
Adenylyl cyclase ( AC ) is an important messenger involved in G-protein-coupled-receptor signal transduction pathways , which is a well-known target for drug development . AC is regulated by activated stimulatory ( Gαs ) and inhibitory ( Gαi ) G proteins in the cytosol . Although experimental studies have shown that th... | Communication between cells is essential for the survival of any multicellular organism . When these mechanisms cannot function properly , diseases can occur such as heart failure or Parkinson’s disease . Understanding cell communication is therefore crucial for drug development . Important proteins in cellular signall... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"and",
"discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"molecular",
"dynamics",
"diagnostic",
"radiology",
"crystal",
"structure",
"enzymes",
"condensed",
"matter",
"physics",
"enzymology",
"protein",
"structure",
"lyases",
"crystallography",
"g",
"protein",
"coupled",
"receptors",
"... | 2017 | Exploring the inhibition mechanism of adenylyl cyclase type 5 by n-terminal myristoylated Gαi1 |
Single-cell RNA sequencing ( scRNA-seq ) has become a powerful tool for the systematic investigation of cellular diversity . As a number of computational tools have been developed to identify and visualize cell populations within a single scRNA-seq dataset , there is a need for methods to quantitatively and statistical... | Single-cell technologies generate hundreds to thousands of data points per sample , presenting a conundrum in determining similarities and differences across multiple samples . Currently , similarity is determined by the degree of “intermixing” of data points among samples , a local approach , but this approach cannot ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"infographics",
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"methods",
"and",
"resources",
"immune",
"cells",
"cluster",
"analysis",
"statistics",
"hierarchical",
"clustering",
"immunology",
"mathematics",
"g... | 2018 | Quantitative assessment of cell population diversity in single-cell landscapes |
The establishment of HIV-1 latency gives rise to persistent chronic infection that requires life-long treatment . To reverse latency for viral eradiation , the HIV-1 Tat protein and its associated ELL2-containing Super Elongation Complexes ( ELL2-SECs ) are essential to activate HIV-1 transcription . Despite efforts to... | To cure chronic HIV-1 infection requires reversal of HIV-1 latency from latently infected CD4+ T cells . A key step in HIV latency reversal is the recruitment of Super Elongation Complexes ( SECs ) that contain ELL2 by an HIV-encoded protein , Tat , to activate proviral transcription . To identify novel drug targets , ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"flow",
"cytometry",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"cancer",
"treatment",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"immunodeficiency",
"viruses",
"... | 2019 | Reiterative Enrichment and Authentication of CRISPRi Targets (REACT) identifies the proteasome as a key contributor to HIV-1 latency |
Toxoplasmic retinochoroiditis appears to be more severe in Brazil , where it is a leading cause of blindness , than in Europe , but direct comparisons are lacking . Evidence is accumulating that more virulent genotypes of Toxoplasma gondii predominate in South America . We compared prospective cohorts of children with ... | Toxoplasma gondii is found throughout the world and is the most common parasitic infection in humans . Infection can cause inflammatory lesions at the back of the eye , which sometimes affect vision . These complications appear to be more common and more severe when people acquire infection in Brazil than in Europe or ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"infectious",
"diseases",
"pediatrics",
"and",
"child",
"health"
] | 2008 | Ocular Sequelae of Congenital Toxoplasmosis in Brazil Compared with Europe |
Tailored therapy aims to cure cancer patients effectively and safely , based on the complex interactions between patients' genomic features , disease pathology and drug metabolism . Thus , the continual increase in scientific literature drives the need for efficient methods of data mining to improve the extraction of u... | Tailored therapy aims to cure cancer patients in a fully personal way . Thus , the continual increase in scientific information and , particularly , in published literature , drives the need for efficient methods of data mining to find unique personal genomic features and their connections . Fusion proteins , which are... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Conclusion"
] | [
"cell",
"physiology",
"protein",
"interactions",
"protein",
"interaction",
"networks",
"data",
"mining",
"text",
"mining",
"artificial",
"intelligence",
"network",
"analysis",
"gene",
"types",
"information",
"technology",
"extraction",
"techniques",
"research",
"and",
"... | 2019 | ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins |
Sensory and cognitive performance decline with age . Neural dysfunction caused by nerve death in senile dementia and neurodegenerative disease has been intensively studied; however , functional changes in neural circuits during the normal aging process are not well understood . Caspases are key regulators of cell death... | The approaching era of an “aging society” is receiving considerable attention amongst biomedical researchers in advanced nations . In order to understand the molecular mechanisms underlying age-related alterations of neural circuitry , we focused on caspase-3 , a cysteine protease that induces apoptotic cell death , us... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"arthropoda",
"animal",
"models",
"cell",
"death",
"invertebrates",
"drosophila",
"melanogaster",
"model",
"organisms",
"cell",
"biology",
"olfactory",
"system",
"biology",
"and",
"life",
"sciences",
"cell",
"processes",
"sensory",
"systems",
"molecular",
"cell",
"bio... | 2014 | Caspase Inhibition in Select Olfactory Neurons Restores Innate Attraction Behavior in Aged Drosophila |
CC2D1A and CC2D1B belong to the evolutionary conserved Lgd protein family with members in all multi-cellular animals . Several functions such as centrosomal cleavage , involvement in signalling pathways , immune response and synapse maturation have been described for CC2D1A . Moreover , the Drosophila melanogaster orth... | The proteins of the Lgd/CC2D1 family are conserved in all multicellular animals . The Drosophila melanogaster ortholog Lgd is involved in the regulation of signalling receptor degradation via the endosomal pathway . Loss of lgd function causes ectopic ligand-independent activation of the Notch signalling pathway due to... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The Mammalian Orthologs of Drosophila Lgd, CC2D1A and CC2D1B, Function in the Endocytic Pathway, but Their Individual Loss of Function Does Not Affect Notch Signalling |
To understand the interplay of residual structures and conformational fluctuations in the interaction of intrinsically disordered proteins ( IDPs ) , we first combined implicit solvent and replica exchange sampling to calculate atomistic disordered ensembles of the nuclear co-activator binding domain ( NCBD ) of transc... | Intrinsically disordered proteins ( IDPs ) are now widely recognized to play fundamental roles in biology and to be frequently associated with human diseases . Although the potential advantages of intrinsic disorder in cellular signaling and regulation have been widely discussed , the physical basis for these proposed ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"physics",
"computational",
"chemistry",
"statistical",
"mechanics",
"chemistry",
"biology",
"computational",
"biology",
"biophysics",
"macromolecular",
"structure",
"analysis"
] | 2012 | Residual Structures, Conformational Fluctuations, and Electrostatic Interactions in the Synergistic Folding of Two Intrinsically Disordered Proteins |
The time-course of the pathological effects induced by the venom of the snake Bothrops asper in muscle tissue was investigated by a combination of histology , proteomic analysis of exudates collected in the vicinity of damaged muscle , and immunodetection of extracellular matrix proteins in exudates . Proteomic assay o... | The local pathology induced by viperid snakes is characterized by a complex of alterations as consequence of direct and indirect effects of the toxins present in the venom , as well as the host response to tissue damage , and constitutes a dynamic process of degenerative and reparative events . The pathogenesis of loca... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"toxins",
"classical",
"mechanics",
"pathology",
"and",
"laboratory",
"medicine",
"enzymes",
"enzymology",
"toxicology",
"collagens",
"toxic",
"agents",
"membrane",
"proteins",
"damage",
"mechanics",
"cellular",
"structures",
"an... | 2016 | Muscle Tissue Damage Induced by the Venom of Bothrops asper: Identification of Early and Late Pathological Events through Proteomic Analysis |
The recent spread of Zika virus ( ZIKV ) and its association with increased rates of Guillain Barre and other neurological disorders as well as congenital defects that include microcephaly has created an urgent need to develop animal models to examine the pathogenesis of the disease and explore the efficacy of potentia... | The recent spread of Zika virus ( ZIKV ) and its association with increased rates of neurological disorders and congenital defects created an urgent need for animal models to examine the pathogenesis of the disease and explore the efficacy of potential therapeutics and vaccines . We describe the first symptomatic PRVAB... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"nervous",
"system",
"pathogens",
"immunology",
"microbiology",
"brain",
"animal",
"models",
"viruses",
"model",
"organisms",
"rna",
"viruses",
... | 2016 | Zika (PRVABC59) Infection Is Associated with T cell Infiltration and Neurodegeneration in CNS of Immunocompetent Neonatal C57Bl/6 Mice |
It has been suggested that some cancer cells rely upon fatty acid oxidation ( FAO ) for energy . Here we show that when FAO was reduced approximately 90% by pharmacological inhibition of carnitine palmitoyltransferase I ( CPT1 ) with low concentrations of etomoxir , the proliferation rate of various cancer cells was un... | Oxidation of long-chain fatty acids inside of the mitochondrial matrix provides an essential source of energy for some cells . Since long-chain fatty acids cannot freely pass into the mitochondrial matrix , they rely on a protein called carnitine palmitoyltransferase I ( CPT1 ) for transport . Prior research has found ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"chemical",
"compounds",
"gene",
"regulation",
"metabolic",
"processes",
"cell",
"processes",
"carbohydrates",
"organic",
"compounds",
"glucose",
"acidic",
"amino",
"acids",
"amino",
"acids",
"mitochondria",
"bioenergetics",
"cellular",
"structures",
"and",
"organelles",
... | 2018 | Identifying off-target effects of etomoxir reveals that carnitine palmitoyltransferase I is essential for cancer cell proliferation independent of β-oxidation |
Estimating the reduction in levels of infection during implementation of soil-transmitted helminth ( STH ) control programmes is important to measure their performance and to plan interventions . Markov modelling techniques have been used with some success to predict changes in STH prevalence following treatment in Vie... | Several million children are periodically dewormed to prevent the impairments to health and the economy caused by soil-transmitted helminths in endemic communities . It is important that managers of STH control programmes be able to anticipate the impact of the control measures on the prevalence of the diseases for two... | [
"Abstract",
"Introduction",
"Material",
"and",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"markov",
"models",
"tropical",
"diseases",
"geographical",
"locations",
"parasitic",
"diseases",
"animals",
"data",
"management",
"ascaris",
"ascaris",
"lumbricoides",
"mathematics",
"tanzania",
"neglected",
"trop... | 2016 | Markov Model Predicts Changes in STH Prevalence during Control Activities Even with a Reduced Amount of Baseline Information |
Alkhurma hemorrhagic fever virus ( AHFV ) and Kyasanur forest disease virus ( KFDV ) cause significant human disease and mortality in Saudi Arabia and India , respectively . Despite their distinct geographic ranges , AHFV and KFDV share a remarkably high sequence identity . Given its emergence decades after KFDV , AHFV... | Alkhurma hemorrhagic fever ( AHF ) and Kyasanur Forest disease ( KFD ) viruses both cause serious and sometimes fatal human disease in their respective ranges , Saudi Arabia and India . AHFV was first identified in the mid-1990s and due to its strong genetic similarity to KFDV it has since been considered the result of... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"rna",
"viruses",
"virology",
"viral",
"classification",
"biology",
"microbiology",
"evolutionary",
"biology",
"public",
"health"
] | 2011 | Ancient Ancestry of KFDV and AHFV Revealed by Complete Genome Analyses of Viruses Isolated from Ticks and Mammalian Hosts |
Knowledge of the foci of Plasmodium species infections is critical for a country with an elimination agenda . Namibia is targeting malaria elimination by 2020 . To support decision making regarding targeted intervention , we examined for the first time , the foci of Plasmodium species infections and regional prevalence... | Namibia is a member of the SADC elimination 8 ( E8 ) group with a target to eliminate malaria by 2020 . This target stems from years of aggressive interventional strategies that has led to significant reductions in morbidity and mortality . The focus of this strategy is mainly on Plasmodium falciparum as the primary pa... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"parasite",
"groups",
"medicine",
"and",
"health",
"sciences",
"namibia",
"education",
"plasmodium",
"angola",
"sociology",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"parasitology",
"apic... | 2019 | Molecular detection of P. vivax and P. ovale foci of infection in asymptomatic and symptomatic children in Northern Namibia |
How chaperones interact with protein chains to assist in their folding is a central open question in biology . Obtaining atomistic insight is challenging in particular , given the transient nature of the chaperone-substrate complexes and the large system sizes . Recent single-molecule experiments have shown that the ch... | Trigger Factor ( TF ) is an ATP-independent chaperone protein that assists in folding and prevents misfolding . Up to now , it is a general unsolved question how chaperones assist in the folding of protein chains . Experimental methods that can probe at the length and timescales of inter-residue interactions are scarce... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"Discussion"
] | [] | 2015 | The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins |
Despite the availability of vaccines , influenza remains a major public health challenge . A key reason is the virus capacity for immune escape: ongoing evolution allows the continual circulation of seasonal influenza , while novel influenza viruses invade the human population to cause a pandemic every few decades . Cu... | Influenza vaccines used today offer good protection , but have limitations: they have to be updated regularly , to remain effective in the face of ongoing virus evolution , and they cannot be used in advance of an influenza pandemic . In this study we considered how such ‘conventional’ vaccines might compare on the pop... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"organismal",
"evolution",
"viral",
"vaccines",
"medicine",
"and",
"health",
"sciences",
"influenza",
"immunology",
"cell-mediated",
"immunity",
"microbiology",
"vaccines",
"preventive",
"medicine",
"microbial",
"evolution",
"vaccination",
"and",
"immunization",
"public",
... | 2016 | Universal or Specific? A Modeling-Based Comparison of Broad-Spectrum Influenza Vaccines against Conventional, Strain-Matched Vaccines |
Foamy macrophages ( FM ) s harbor lipid bodies that not only assist mycobacterial persistence within the granulomas but also are sites for intracellular signaling and inflammatory mediators which are essential for mycobacterial pathogenesis . However , molecular mechanisms that regulate intracellular lipid accumulation... | Foamy macrophages ( FMs ) not only provide a suitable survival niche for the mycobacteria in the granuloma but also are reservoirs for several inflammatory mediators that regulate mycobacterial pathogenesis . Hence , understanding the mechanisms that regulate infection-induced FM generation assumes importance . In this... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"reverse",
"transcriptase-polymerase",
"chain",
"reaction",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"molecular",
"probe",
"techniques",
"granulomas",
"gene",
"regulation",
"immunology",
"immunoblotting",
"notch",
"signaling",
"molecul... | 2016 | MUSASHI-Mediated Expression of JMJD3, a H3K27me3 Demethylase, Is Involved in Foamy Macrophage Generation during Mycobacterial Infection |
The neonatal intestine is a very complex and dynamic organ that must rapidly adapt and remodel in response to a barrage of environmental stimuli during the first few postnatal weeks . Recent studies demonstrate that the zinc finger transcriptional repressor Blimp1/Prdm1 plays an essential role governing postnatal repro... | The transcriptional repressor Blimp1/Prdm1 plays a pivotal role in the metabolic switch that occurs in the small intestine during the suckling to weaning transition . Notably , expression profiling of perinatal Blimp1-deficient small intestine revealed premature activation of metabolic genes normally restricted to post... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Blimp1/Prdm1 Functions in Opposition to Irf1 to Maintain Neonatal Tolerance during Postnatal Intestinal Maturation |
Myopia is one of the most common ocular disorders worldwide . Pathological myopia , also called high myopia , comprises 1% to 5% of the general population and is one of the leading causes of legal blindness in developed countries . To identify genetic determinants associated with pathological myopia in Japanese , we co... | Myopia is one of the most common ocular disorders with elongation of axis of the eyeball . Pathological myopia or high myopia , a subset of myopia which is characterized with excessive axial elongation and degenerative changes of the eye , is a leading cause of visual impairment . Since genetic factors play significant... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"ophthalmology",
"genetics",
"and",
"genomics/complex",
"traits",
"ophthalmology/retinal",
"disorders"
] | 2009 | A Genome-Wide Association Analysis Identified a Novel Susceptible Locus for Pathological Myopia at 11q24.1 |
Innate immune restriction factors represent important specialized barriers to zoonotic transmission of viruses . Significant consideration has been given to their possible use for therapeutic benefit . The apolipoprotein B mRNA editing enzyme catalytic polypeptide 3 ( APOBEC3 ) family of cytidine deaminases are potent ... | The APOBEC3 family of proteins is a potent cellular defense mechanism capable of restricting a broad range of viruses including HIV . HIV requires a critical accessory protein , Vif , which targets APOBEC3 for degradation thereby shielding its genome from lethal mutagenesis . Previous in vitro studies have shown that i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"microbial",
"mutation",
"retrovirology",
"and",
"hiv",
"immunopathogenesis",
"immunology",
"microbiology",
"host-pathogen",
"interaction",
"immunodeficiency",
"viruses",
"animal",
"models",
"of",
"infection",
"infectious",
"diseases",
"virulence",
"factors",
"a... | 2013 | HIV Restriction by APOBEC3 in Humanized Mice |
The PIK3CA gene is one of the most frequently mutated oncogenes in human cancers . It encodes p110α , the catalytic subunit of phosphatidylinositol 3-kinase alpha ( PI3Kα ) , which activates signaling cascades leading to cell proliferation , survival , and cell growth . The most frequent mutation in PIK3CA is H1047R , ... | The PI3Kα protein is involved in cellular processes such as cell growth , division , and formation of new blood vessels ( angiogenesis ) that aid cancer cell survival . In certain types of cancer cells , PI3Kα is found to be altered compared to healthy cells . These PI3Kα alterations , called mutations , are found in 2... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"physics",
"biology",
"and",
"life",
"sciences",
"physical",
"sciences",
"biophysics",
"biophysical",
"simulations"
] | 2014 | Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant |
Rer1 is a retrieval receptor for endoplasmic reticulum ( ER ) retention of various ER membrane proteins and unassembled or immature components of membrane protein complexes . However , its physiological functions during mammalian development remain unclear . This study aimed to investigate the role of Rer1-mediated qua... | We showed that Rer1 functions as an early-Golgi quality control pathway that maintains γ-secretase activity by maintaining sufficient cell surface expression of γ-secretase complex during cerebral cortex development , thereby modulating Notch signaling . | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"lysosomes",
"molecular",
"probe",
"techniques",
"brain",
"notch",
"signaling",
"membrane",
"proteins",
"molecular",
"biology",
"techniques",
"immunologic",
"techniques",
"cellular",
"structures",
"and",
"organelles",
"research",
... | 2018 | Rer1-mediated quality control system is required for neural stem cell maintenance during cerebral cortex development |
Aplasia cutis congenita ( ACC ) manifests with localized skin defects at birth of unknown cause , mostly affecting the scalp vertex . Here , genome-wide linkage analysis and exome sequencing was used to identify the causative mutation in autosomal dominant ACC . A heterozygous Arg-to-His missense mutation ( p . R930H )... | Elucidating the pathomechanisms in congenital diseases of the skin provides the opportunity to learn what cellular processes are important during embryonic development of the skin structures . Aplasia cutis congenita ( ACC ) manifests with localized skin defects , most commonly affecting the scalp skin . Here , global ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"dermatology",
"genetics",
"biology",
"human",
"genetics",
"genetics",
"of",
"disease"
] | 2013 | BMS1 Is Mutated in Aplasia Cutis Congenita |
Because physical form and function are intimately linked , mechanisms that maintain cell shape and size within strict limits are likely to be important for a wide variety of biological processes . However , while intrinsic controls have been found to contribute to the relatively well-defined shape of bacteria and yeast... | Because many physical processes change with scale , size control is a fundamental problem for living systems . While in some instances the size of a structure is directly determined by the dimensions of its individual constituents , many biological structures are dynamic , self-organising assemblies of relatively small... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/cell",
"growth",
"and",
"division",
"cell",
"biology",
"computer",
"science/systems",
"and",
"control",
"theory",
"cell",
"biology/cell",
"adhesion",
"cell",
"biology/cytoskeleton"
] | 2010 | A Polarised Population of Dynamic Microtubules Mediates Homeostatic Length Control in Animal Cells |
Chemotherapy is still a critical issue in the management of leishmaniasis . Until recently , pentavalent antimonials , amphotericin B or pentamidine compounded the classical arsenal of treatment . All these drugs are toxic and have to be administered by the parenteral route . Tamoxifen has been used as an antiestrogen ... | Leishmaniasis is an antropozoonotic disease with a wide range of clinical manifestations . In humans , signs of disease vary from skin and mucosal ulcers to enlargement of internal organs such as the liver and spleen . The unicellular parasite Leishmania amazonensis is able to infect humans and cause localized or diffu... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/protozoal",
"infections",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"infectious",
"diseases/antimicrobials",
"and",
"drug",
"resistance"
] | 2008 | Tamoxifen Is Effective in the Treatment of Leishmania amazonensis Infections in Mice |
Cholesterol Dependent Cytolysins ( CDCs ) are important bacterial virulence factors that form large ( 200–300 Å ) membrane embedded pores in target cells . Currently , insights from X-ray crystallography , biophysical and single particle cryo-Electron Microscopy ( cryo-EM ) experiments suggest that soluble monomers fir... | Pore formation is central to the ability of cholesterol dependent cytolysins ( CDCs ) to act as important bacterial virulence factors . Secreted by numerous pathogens the toxins assemble into a circular ring and then perforate the target membrane to form the largest self-assembling proteinaceous pores known . In this p... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Methods"
] | [
"stereochemistry",
"molecular",
"dynamics",
"molecular",
"conformation",
"chemistry",
"physical",
"sciences",
"computational",
"chemistry"
] | 2014 | A New Model for Pore Formation by Cholesterol-Dependent Cytolysins |
The human pathogen Candida albicans can assume either of two distinct cell types , designated “white” and “opaque . ” Each cell type is maintained for many generations; switching between them is rare and stochastic , and occurs without any known changes in the nucleotide sequence of the genome . The two cell types diff... | The opportunistic fungal pathogen Candida albicans can switch between two heritable states—the “white” and “opaque” states . These two cell types differ in many characteristics , including cell structure , mating competence , and virulence . Recent studies of the molecular mechanism of regulating the white-opaque switc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"microbiology",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2007 | Interlocking Transcriptional Feedback Loops Control White-Opaque Switching in Candida albicans |
The rise of large-scale recordings of neuronal activity has fueled the hope to gain new insights into the collective activity of neural ensembles . How can one link the statistics of neural population activity to underlying principles and theories ? One attempt to interpret such data builds upon analogies to the behavi... | Understanding how populations of neurons collectively encode sensory information is one of the central goals of computational neuroscience . In physics , systems are often characterized by identifying and describing critical points ( e . g . the transition between two states of matter ) . The success of this approach h... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"applied",
"mathematics",
"ocular",
"anatomy",
"neuroscience",
"simulation",
"and",
"modeling",
"algorithms",
"probability",
"distribution",
"mathematics",
"ganglion",
"cells",
"computational",
"neuroscience",
"thermodynamics",
"codi... | 2017 | Signatures of criticality arise from random subsampling in simple population models |
Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism , Population flux balance analysis ( Population FBA ) successfully described metabolic heterogeneity in a population of independent Escherichia coli cells growing in a defined medium . W... | No two living cells are exactly the same . Even cells from a clonal population with identical genomes living in the same environment will express proteins in different numbers simply due to the random nature of the chemistry involved in gene expression . The consequences of this stochastic gene expression are complex a... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"discussion"
] | [
"cell",
"physiology",
"protein",
"metabolism",
"chemical",
"compounds",
"aliphatic",
"amino",
"acids",
"enzymes",
"enzymology",
"carbohydrates",
"cell",
"metabolism",
"organic",
"compounds",
"glucose",
"threonine",
"fungi",
"model",
"organisms",
"experimental",
"organism"... | 2017 | Population FBA predicts metabolic phenotypes in yeast |
The mean conditional fixation time of a mutant is an important measure of stochastic population dynamics , widely studied in ecology and evolution . Here , we investigate the effect of spatial randomness on the mean conditional fixation time of mutants in a constant population of cells , N . Specifically , we assume th... | We study the influence of randomness on evolutionary dynamics , assuming that a newly arising mutant may experience a different set of environments compared to the wild type . We calculate the mean conditional fixation time of the mutant under different assumptions on spatial interactions , and show that randomness has... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"bacteriology",
"infographics",
"biofilms",
"population",
"dynamics",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"microbiology",
"probability",
"distribution",
"mathematics",
"population",
"biology",
"skewness",
"computer",
"and",
"information",
"sci... | 2017 | The effect of spatial randomness on the average fixation time of mutants |
Aspergillus fumigatus causes invasive pulmonary disease in immunocompromised hosts and allergic asthma in atopic individuals . We studied the contribution of lung eosinophils to these fungal diseases . By in vivo intracellular cytokine staining and confocal microscopy , we observed that eosinophils act as local sources... | The opportunistic fungus , Aspergillus fumigatus , causes a spectrum of diseases ranging from invasive aspergillosis in the severely immunosuppressed to allergic asthma in atopic individuals . Here we explored the contribution of eosinophils , a type of white blood cell , to host defenses and pathogenesis in murine mod... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"aspergillus",
"fumigatus",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"cytokines",
"aspergillus",
"pathogens",
"immunology",
"microbio... | 2017 | Central Role of IL-23 and IL-17 Producing Eosinophils as Immunomodulatory Effector Cells in Acute Pulmonary Aspergillosis and Allergic Asthma |
Visceral leishmaniasis ( VL ) is an important neglected disease caused by a protozoan parasite , and represents a serious public health problem in many parts of the world . It is zoonotic in Europe and Latin America , where infected dogs constitute the main domestic reservoir for the parasite and play a key role in VL ... | Visceral leishmaniasis [VL] is an important but neglected tropical disease that occurs worldwide . In areas where the disease is zoonotic , it is considered a serious public and animal health problem . In Brazil , despite the existing prevention and control programs , the disease is spreading , and in São Paulo State i... | [
"Abstract",
"Introduction",
"Methodology",
"Results",
"Discussion",
"Conclusion"
] | [
"medicine",
"and",
"health",
"sciences",
"vector-borne",
"diseases",
"tropical",
"diseases",
"vertebrates",
"geographical",
"locations",
"sand",
"flies",
"parasitic",
"diseases",
"dogs",
"animals",
"mammals",
"mathematics",
"neglected",
"tropical",
"diseases",
"infectious... | 2017 | Risk analysis and prediction of visceral leishmaniasis dispersion in São Paulo State, Brazil |
An open question in human genetics is what underlies the tissue-specific manifestation of hereditary diseases , which are caused by genomic aberrations that are present in cells across the human body . Here we analyzed this phenomenon for over 300 hereditary diseases by using comparative network analysis . We created a... | An open question in human genetics is what underlies the tissue-specific manifestation of hereditary diseases , which are caused by genomic aberrations that are present in cells across the entire human body . In order to answer this question , we created an extensive resource of protein expression and interactions acro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"biochemistry",
"genetic",
"networks",
"genomics",
"functional",
"genomics",
"protein",
"interactions",
"proteins",
"genome",
"analysis",
"genetics",
"biology",
"and",
"life",
"sciences",
"proteomics",
"computational",
"biology"
] | 2014 | Comparative Analysis of Human Tissue Interactomes Reveals Factors Leading to Tissue-Specific Manifestation of Hereditary Diseases |
Reptile-associated Salmonella bacteria are a major , but often neglected cause of both gastrointestinal and bloodstream infection in humans globally . The diversity of Salmonella enterica has not yet been determined in venomous snakes , however other ectothermic animals have been reported to carry a broad range of Salm... | Salmonella enterica is a remarkable bacterial species that causes Neglected Tropical Diseases globally . The burden of disease is greatest in some of the most poverty-afflicted regions of Africa , where salmonellosis frequently causes bloodstream infection with fatal consequences . The bacteria have the ability to colo... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"discussion"
] | [
"taxonomy",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"vertebrates",
"animals",
"salmonellosis",
"bacterial",
"diseases",
"reptile",
"genomics",
"phylogenetics",
"data",
"management",
"enterobacteriac... | 2019 | The diversity, evolution and ecology of Salmonella in venomous snakes |
Malaria is a global health concern caused by infection with Plasmodium parasites . With rising insecticide and drug resistance , there is a critical need to develop novel control strategies , including strategies to block parasite sporogony in key mosquito vector species . MAPK signaling pathways regulated by extracell... | Malaria is a global health concern caused by infection with Plasmodium parasites . With rising insecticide and drug resistance , there is a critical need to develop novel control strategies . One strategy is to develop a Plasmodium-resistant mosquito through the manipulation of key signaling pathways and processes in t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"parasite",
"groups",
"body",
"fluids",
"plasmodium",
"parasitic",
"diseases",
"animals",
"parasitic",
"protozoans",
"parasitology",
"cell",
"signaling",
"c-jun",
"n-terminal",
"kinase",
"signali... | 2018 | Inhibition of JNK signaling in the Asian malaria vector Anopheles stephensi extends mosquito longevity and improves resistance to Plasmodium falciparum infection |
The C . elegans ortholog of mammalian calsyntenins , CASY-1 , is an evolutionarily conserved type-I transmembrane protein that is highly enriched in the nervous system . Mammalian calsyntenins are strongly expressed at inhibitory synapses , but their role in synapse development and function is still elusive . Here , we... | GABA acts as a major inhibitory neurotransmitter in both vertebrate and invertebrate nervous systems . Despite the potential deregulation of GABA signaling in several neurological disorders , our understanding of the genetic factors that regulate GABAergic synaptic transmission has just started to evolve . Here , we id... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"fluorescence",
"imaging",
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"caenorhabditis",
"nervous",
"system",
"immunology",
"electrophysiology",
"neuroscience",
"animals",
"motor",
"neurons",
"animal",
"models",
"caenorhabditis",
"elegans",
"... | 2018 | The C-terminal of CASY-1/Calsyntenin regulates GABAergic synaptic transmission at the Caenorhabditis elegans neuromuscular junction |
Rapid place encoding by hippocampal neurons , as reflected by place-related firing , has been intensely studied , whereas the substrates that translate hippocampal place codes into behavior have received little attention . A key point relevant to this translation is that hippocampal organization is characterized by fun... | The ability to remember locations in space is dependent on an area of the brain called the hippocampus . A much-studied property of neurons in the hippocampus is that they rapidly come to represent or code for specific places—i . e . , the hippocampus “learns” places—as animals or humans move through an environment . H... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience",
"physiology"
] | 2009 | From Rapid Place Learning to Behavioral Performance: A Key Role for the Intermediate Hippocampus |
Cysteine residues have a rich chemistry and play a critical role in the catalytic activity of a plethora of enzymes . However , cysteines are susceptible to oxidation by Reactive Oxygen and Nitrogen Species , leading to a loss of their catalytic function . Therefore , cysteine oxidation is emerging as a relevant physio... | Cysteine oxidation is emerging as a relevant regulatory mechanism of enzymatic function in the cell . Many proteins are protected from over oxidation by reactive oxygen species by the formation of a cyclic sulfenyl amide . Understanding how cyclic sulfenyl amide is formed and its dependence on protein structure is not ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"QM/MM",
"methods",
"Results",
"Discussion"
] | [] | 2015 | Protein Topology Determines Cysteine Oxidation Fate: The Case of Sulfenyl Amide Formation among Protein Families |
Head and Neck Squamous Cell Carcinoma ( HNSCC ) is a heterogeneous disease of significant mortality and with limited treatment options . Recent genomic analysis of HNSCC tumors has identified several distinct molecular classes , of which the mesenchymal subtype is associated with Epithelial to Mesenchymal Transition ( ... | The expression of the transcriptional regulator , E26 transformation-specific 1 ( ETS1 ) , is elevated in many epithelial cancers and portends aggressive tumor behavior and poor survival . Within these carcinomas , ETS1 function has been shown to be associated with a wide range of cellular responses that include increa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"gene",
"regulation",
"carcinomas",
"cancers",
"and",
"neoplasms",
"oncology",
"regulator",
"genes",
"head",
"and",
"neck",
"tumors",
"gene",
"types",
"head",
"and",
"neck",
"squamous",
"cell",
"carcinoma",
"small",
"interf... | 2019 | Molecular dissection of the oncogenic role of ETS1 in the mesenchymal subtypes of head and neck squamous cell carcinoma |
Chronic schistosomiasis is associated with T cell hypo-responsiveness and immunoregulatory mechanisms , including induction of regulatory T cells ( Tregs ) . However , little is known about Treg functional capacity during human Schistosoma haematobium infection . CD4+CD25hiFOXP3+ cells were characterized by flow cytome... | Schistosomiasis , a parasitic worm infection , affects over 240 million people worldwide , especially children in sub-Saharan Africa . It is associated with immune hypo-responsiveness which results in an inability of the immune system to eliminate parasites . Animal models suggest that helminths induce regulatory T cel... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | CD4+CD25hiFOXP3+ Regulatory T Cells and Cytokine Responses in Human Schistosomiasis before and after Treatment with Praziquantel |
Stressful life events are major environmental risk factors for anxiety disorders , although not all individuals exposed to stress develop clinical anxiety . The molecular mechanisms underlying the influence of environmental effects on anxiety are largely unknown . To identify biological pathways mediating stress-relate... | Genetic and environmental factors contribute to the etiology of psychiatric diseases but the underlying mechanisms are poorly understood . Chronic psychosocial stress is a well-known risk factor for anxiety disorders . To identify biological pathways involved in psychosocial stress-induced anxiety and resilience to it ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"neuropsychiatric",
"disorders",
"medicine",
"and",
"health",
"sciences",
"anxiety",
"disorders",
"natural",
"antisense",
"transcripts",
"gene",
"regulation",
"vertebrates",
"social",
"sciences",
"mice",
"animals",
"mammals",
"micrornas",
"genome",
"an... | 2019 | Multi-omics analysis identifies mitochondrial pathways associated with anxiety-related behavior |
We computationally determined miRs that are significantly connected to molecular pathways by utilizing gene expression profiles in different cancer types such as glioblastomas , ovarian and breast cancers . Specifically , we assumed that the knowledge of physical interactions between miRs and genes indicated subsets of... | We assume that a network of physical interactions between miRs and genes allows us to determine miRs that influence the expression of whole pathways in different tumor types . Specifically , we represented each pathway by an enrichment score and an array of miRs counting the number of genes in the pathway a given miR c... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"systems",
"biology",
"regulatory",
"networks",
"biology",
"computational",
"biology"
] | 2013 | Important miRs of Pathways in Different Tumor Types |
Spontaneous emergence of synchronized population activity is a characteristic feature of developing brain circuits . Recent experiments in the developing neo-cortex showed the existence of driver cells able to impact the synchronization dynamics when single-handedly stimulated . We have developed a spiking network mode... | There is timely interest on the impact of peculiar neurons ( driver cells ) and of small neuronal sub-networks ( cliques ) on operational brain dynamics . We first provide experimental data concerning the effect of stimulated driver cells on the bursting activity observable in the developing entorhinal cortex . Secondl... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"nervous",
"system",
"population",
"dynamics",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"network",
"analysis",
"computational",
"neuroscience",
"population",
"biology... | 2018 | Modeling driver cells in developing neuronal networks |
Risk factors associated with L . donovani visceral leishmaniasis ( VL; kala azar ) relapse are poorly characterized . We investigated patient characteristics and drug regimens associated with VL relapse using data from Médecins Sans Frontières - Holland ( MSF ) treatment centres in Southern Sudan . We used MSF operatio... | Visceral leishmaniasis ( kala-azar ) caused by Leishmania donovani is spread from person to person by Phlebotomus sandflies . Major epidemics of visceral leishmaniasis have occurred in Southern Sudan during the 20th century . The worst of these killed 100 , 000 people in the western Upper Nile area of Southern Sudan fr... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"public",
"health",
"and",
"epidemiology/epidemiology",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"infectious",
"diseases/protozoal",
"infections",
"infectious",
"diseases/epidemiology",
"and",
... | 2010 | Visceral Leishmaniasis Relapse in Southern Sudan (1999–2007): A Retrospective Study of Risk Factors and Trends |
The Ori region of bacterial genomes is segregated early in the replication cycle of bacterial chromosomes . Consequently , Ori region positioning plays a pivotal role in chromosome dynamics . The Ori region of the E . coli chromosome is organized as a macrodomain with specific properties concerning DNA mobility , segre... | The Ori region from bacterial chromosomes plays a pivotal role in chromosome organization and segregation as it is replicated and segregated early in cell division cycle and its positioning impacts the cellular organization of the chromosome in the cell . The E . coli chromosome is divided into four macrodomains ( MD )... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"medicine",
"and",
"health",
"sciences",
"chromosome",
"structure",
"and",
"function",
"microbiology",
"chromosome",
"mapping",
"dna",
"replication",
"bacterial",
"genetics",
"forms",
"of",
"dna",
"dna",
"molecular",
"biology",
"techniques",
"microbial",... | 2016 | The MaoP/maoS Site-Specific System Organizes the Ori Region of the E. coli Chromosome into a Macrodomain |
In northern Tunisia , the co-circulation of two related sand fly-borne phleboviruses , Toscana virus ( TOSV ) and Punique virus ( PUNV ) was previously demonstrated . In contrast to TOSV , a prominent human pathogen , there is no data supporting that PUNV is capable to infect and cause disease to humans . We studied th... | In northern Tunisia , two different pheboviruses are known to circulate in sand fly population , Toscana virus ( TOSV ) and Punique virus ( PUNV ) . In contrast to TOSV , a prominent human pathogen , there is no data supporting that PUNV is capable to infect humans and to cause a disease . We studied the respective inv... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Co-Circulation of Toscana Virus and Punique Virus in Northern Tunisia: A Microneutralisation-Based Seroprevalence Study |
No ideal vaccine exists to control plague , a deadly dangerous disease caused by Yersinia pestis . In this context , we cloned , expressed and purified recombinant F1 , LcrV antigens of Y . pestis and heat shock protein70 ( HSP70 ) domain II of M . tuberculosis in E . coli . To evaluate the protective potential of each... | Efforts are in progress by various scientific groups towards the development of plague vaccines . However , lack of better understanding about the Y . pestis infection mechanisms and pathogenesis prevents the development of an effective vaccine . In our effort to develop a more efficacious plague vaccine , we evaluated... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"bacteriology",
"immune",
"cells",
"immunology",
"microbiology",
"vaccines",
"infectious",
"disease",
"immunology",
"immunologic",
"adjuvants",
"vaccination",
"and",
"immunization",
"bacterial",
"genes",
"immunomodulation",
"animal",
"cells",
"molecular",
"biology",
"immune... | 2014 | HSP70 Domain II of Mycobacterium tuberculosis Modulates Immune Response and Protective Potential of F1 and LcrV Antigens of Yersinia pestis in a Mouse Model |
Tissue macrophages are derived exclusively from blood monocytes , which as monocyte-derived macrophages support HIV-1 replication . However , among human tissue macrophages only intestinal macrophages are non-permissive to HIV-1 , suggesting that the unique microenvironment in human intestinal mucosa renders lamina pro... | Human intestinal macrophages , unlike lymphoid tissue macrophages , brain microglia and genital ( vaginal ) macrophages , are profoundly incapable of supporting productive HIV-1 infection . Intriguingly , all macrophages are derived exclusively from blood monocytes , which are HIV-1 permissive after differentiation int... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"virology",
"hiv",
"biology",
"microbiology",
"viral",
"diseases"
] | 2011 | Stromal Down-Regulation of Macrophage CD4/CCR5 Expression and NF-κB Activation Mediates HIV-1 Non-Permissiveness in Intestinal Macrophages |
Vascular endothelial growth factor ( VEGF ) is a potent cytokine that binds to specific receptors on the endothelial cells lining blood vessels . The signaling cascade triggered eventually leads to the formation of new capillaries , a process called angiogenesis . Distributions of VEGF receptors and VEGF ligands are th... | Angiogenesis is the growth of new blood vessels from pre-existing vasculature that occurs in physiological ( e . g . , exercise ) and pathological contexts ( e . g . , cancer ) . This process is often triggered by a signaling cascade that occurs upon ligand-receptor binding between vascular endothelial growth factor ( ... | [
"Abstract",
"Introduction",
"Discussion",
"Acknowledgments"
] | [
"computational",
"biology/systems",
"biology"
] | 2009 | The Presence of VEGF Receptors on the Luminal Surface of Endothelial Cells Affects VEGF Distribution and VEGF Signaling |
Genome-wide association studies ( GWAS ) have identified hundreds of associated loci across many common diseases . Most risk variants identified by GWAS will merely be tags for as-yet-unknown causal variants . It is therefore possible that identification of the causal variant , by fine mapping , will identify alleles w... | Genome-wide association studies ( GWAS ) exploit the correlation in genetic diversity along chromosomes in order to detect effects on disease risk without having to type causal loci directly . The inevitable downside of this approach is that , when the correlation between the marker and the causal variant is imperfect ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics",
"and",
"genomics/disease",
"models",
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"genetics",
"and",
"genomics/complex",
"traits"
] | 2011 | Quantifying the Underestimation of Relative Risks from Genome-Wide Association Studies |
Epidemiological modelling has a vital role to play in policy planning and prediction for the control of vectors , and hence the subsequent control of vector-borne diseases . To decide between competing policies requires models that can generate accurate predictions , which in turn requires accurate knowledge of vector ... | The basic reproductive ratio ( R0 ) is a crucial measure of transmission intensity , lying at the interface between mathematical modelling and policy decision making . If control measures can induce a situation where R0 ≤ 1 for a sustained period of time then the pathogen must be eradicated . For diseases spread by sho... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"death",
"rates",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"infectious",
"disease",
"epidemiology",
"demography",
"pathogens",
"immunology",
"vector-borne",
"diseases",
"culicoides",
"microbiology",
"animals",
... | 2016 | The Interaction between Vector Life History and Short Vector Life in Vector-Borne Disease Transmission and Control |
Biological rhythms play a fundamental role in the physiology and behavior of most living organisms . Rhythmic circadian expression of clock-controlled genes is orchestrated by a molecular clock that relies on interconnected negative feedback loops of transcription regulators . Here we show that the circadian clock exer... | Most living organisms on earth present biological rhythms that play a fundamental role in the coordination of their physiology and behavior . The discovery of the molecular circadian clock gives important insight into the mechanisms involved in the generation of these rhythms . Indeed , this molecular clock orchestrate... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"systems",
"biology",
"biochemistry",
"biology",
"genomics",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2013 | The Circadian Clock Coordinates Ribosome Biogenesis |
The combination of deworming and improved sanitation or hygiene may result in greater reductions in soil-transmitted helminth ( STH ) infection than any single intervention on its own . We measured STH prevalence in rural Bangladesh and assessed potential interactions among deworming , hygienic latrines , and household... | Soil-transmitted helminth infections remain prevalent in many low-resource areas of the world . The World Health Organization recommends that schoolchildren in countries where these infections remain common receive deworming medication two times a year . However , previous research has shown that people who live in cou... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | The Interaction of Deworming, Improved Sanitation, and Household Flooring with Soil-Transmitted Helminth Infection in Rural Bangladesh |
Human T cell lymphotropic virus-1 ( HTLV-1 ) primarily infects CD4+ T cells , causing inflammatory disorders or a T cell malignancy in 5% to 10% of carriers . The cytotoxic T lymphocyte ( CTL ) response is a key factor that controls the viral load and thus the risk of disease . The ability to detect the viral protein T... | Human T cell lymphotropic virus-1 ( HTLV-1 ) infects white blood cells ( CD4+ T cells ) for the lifetime of the host . The immune response limits viral spread , and people with a weak immune response have a high risk of developing an aggressive blood cancer , or a condition involving irreversible spinal cord damage . V... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"flow",
"cytometry",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"cloning",
"retroviruses",
"viruses",
"rna",
"viruses",
... | 2016 | CADM1/TSLC1 Identifies HTLV-1-Infected Cells and Determines Their Susceptibility to CTL-Mediated Lysis |
Human cancer genomes are highly complex , making it challenging to identify specific drivers of cancer growth , progression , and tumor maintenance . To bypass this obstacle , we have applied array comparative genomic hybridization ( array CGH ) to zebrafish embryonal rhabdomyosaroma ( ERMS ) and utilized cross-species... | Cancer is a complex genetic disease that is often associated with regional gains and losses of genomic DNA segments . These changes result in aberrant gene expression and drive continued tumor growth . Because amplified and deleted DNA segments tend to span large regions of chromosomes , it has been challenging to iden... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | Cross-Species Array Comparative Genomic Hybridization Identifies Novel Oncogenic Events in Zebrafish and Human Embryonal Rhabdomyosarcoma |
The Grb2-associated binding protein 1 ( GAB1 ) integrates signals from different signaling pathways and is over-expressed in many cancers , therefore representing a new therapeutic target . In the present study , we aim to target the pleckstrin homology ( PH ) domain of GAB1 for cancer treatment . Using homology models... | In this paper , we described the identification and evaluation of a set of first-in-class potent inhibitors targeting a new cancer target , Grb2-associated binder-1 ( GAB1 ) , which integrates signals from different signaling pathways , and is frequently over-expressed in cancer cells . To achieve our goals , we have e... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"and",
"life",
"sciences",
"computational",
"biology"
] | 2015 | Novel Inhibitors Induce Large Conformational Changes of GAB1 Pleckstrin Homology Domain and Kill Breast Cancer Cells |
The leptospiral LigA protein consists of 13 bacterial immunoglobulin-like ( Big ) domains and is the only purified recombinant subunit vaccine that has been demonstrated to protect against lethal challenge by a clinical isolate of Leptospira interrogans in the hamster model of leptospirosis . We determined the minimum ... | Leptospirosis is the most widespread bacterial infection transmitted to humans from host animals that harbor the bacteria in their kidneys . Human infections caused by the bacterium , Leptospira interrogans , frequently result in a life-threatening illness characterized by jaundice and kidney failure . Vaccines are urg... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"adaptive",
"immunity",
"immunity",
"biology",
"microbiology",
"bacterial",
"pathogens"
] | 2011 | A LigA Three-Domain Region Protects Hamsters from Lethal Infection by Leptospira interrogans |
To measure the activity of neurons using whole-brain activity imaging , precise detection of each neuron or its nucleus is required . In the head region of the nematode C . elegans , the neuronal cell bodies are distributed densely in three-dimensional ( 3D ) space . However , no existing computational methods of image... | To reach the ultimate goal of neuroscience to understanding how each neuron functions in the brain , whole-brain activity imaging techniques with single-cell resolution have been intensively developed . There are many neurons in the whole-brain images and manual detection of the neurons is very time-consuming . However... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"fluorescence",
"imaging",
"engineering",
"and",
"technology",
"caenorhabditis",
"neuroscience",
"animals",
"animal",
"models",
"caenorhabditis",
"elegans",
"human",
"factors",
"engineering",
"model",
"organisms",
"neuroimaging",
"research",
"and",
"analysi... | 2016 | Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space |
Histone ubiquitinations are critical for the activation of the DNA damage response ( DDR ) . In particular , RNF168 and RING1B/BMI1 function in the DDR by ubiquitinating H2A/H2AX on Lys-13/15 and Lys-118/119 , respectively . However , it remains to be defined how the ubiquitin pathway engages chromatin to provide regul... | Post-translational modifications of histones play important roles in regulating both the structure and function of chromatin . As all DNA based processes , including transcription , DNA replication and DNA repair , occur within the context of chromatin , the actual in vivo substrate of these reactions is chromatin . Th... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"cellular",
"stress",
"responses",
"genetic",
"mutation",
"chromosome",
"biology",
"gene",
"expression",
"genetics",
"biology",
"molecular",
"cell",
"biology",
"chromatin",
"histone",
"modification"
] | 2014 | Nucleosome Acidic Patch Promotes RNF168- and RING1B/BMI1-Dependent H2AX and H2A Ubiquitination and DNA Damage Signaling |
Tetanus is a vaccine-preventable , neglected disease that is life threatening if acquired and occurs most frequently in regions where vaccination coverage is incomplete . Challenges in vaccination coverage contribute to the occurrence of non-neonatal tetanus in sub-Saharan countries , with high case fatality rates . Th... | Tetanus is a disease characterized by violent , repetitive muscular spasms that are frequently lethal . It rarely occurs in high-income countries due to a highly effective vaccine coupled with a strong immunisation system . Tanzania is a large low-income country in East Africa . Its size and rapidly growing population ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"death",
"rates",
"medicine",
"and",
"health",
"sciences",
"tracheostomy",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"health",
"care",
"preventive",
"medicine",
"bacterial",
"diseases",
"sepsis",
... | 2018 | Pre-post effects of a tetanus care protocol implementation in a sub-Saharan African intensive care unit |
Breast cancer is the most common malignancy in women worldwide . With the increasing awareness of heterogeneity in breast cancers , better prediction of breast cancer prognosis is much needed for more personalized treatment and disease management . Towards this goal , we have developed a novel computational model for b... | With the increasing awareness of heterogeneity in breast cancers , better prediction of breast cancer prognosis is much needed early on for more personalized treatment and management . Towards this goal we propose in this study a novel pathway-based prognosis prediction model , which emphasizes on individualized pathwa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"bioinformatics",
"epidemiology",
"database",
"and",
"informatics",
"methods",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"disease",
"informatics",
"research",
"and",
"analysis",
"methods"
] | 2014 | A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer |
The master circadian clock in fish has been considered to reside in the pineal gland . This dogma is challenged , however , by the finding that most zebrafish tissues contain molecular clocks that are directly reset by light . To further examine the role of the pineal gland oscillator in the zebrafish circadian system ... | Most physiological and behavioral processes exhibit daily rhythms which are driven by an internal timing mechanism known as the circadian clock . Circadian systems are thought to be organized in a hierarchical manner , with a central pacemaker in the brain regulating peripheral clocks throughout the body . In fish spec... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pineal",
"gland",
"vertebrates",
"animals",
"biomechanics",
"biological",
"locomotion",
"hormones",
"circadian",
"oscillators",
"animal",
"models",
"osteichthyes",
"developmental",
"biology",
"model",
"organisms",
"chronobiology",
... | 2016 | Genetically Blocking the Zebrafish Pineal Clock Affects Circadian Behavior |
In vivo fluorescence microscopy and electron cryo-tomography have revealed that chemoreceptors self-assemble into extended honeycomb lattices of chemoreceptor trimers with a well-defined relative orientation of trimers . The signaling response of the observed chemoreceptor lattices is remarkable for its extreme sensiti... | The chemotaxis system allows bacteria to respond to minute changes in chemical concentration , and serves as a paradigm for biological signal processing and the self-assembly of large protein lattices in living cells . The sensitivity of the chemotaxis system relies crucially on cooperative interactions among chemorece... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"physics",
"cell",
"signaling",
"biochemistry",
"cell",
"motility",
"signal",
"transduction",
"cell",
"biology",
"membrane",
"receptor",
"signaling",
"proteins",
"biophysics",
"theory",
"transmembrane",
"receptors",
"biology",
"and",
"life",
"sciences",
"physical",
"sci... | 2014 | The Role of Membrane-Mediated Interactions in the Assembly and Architecture of Chemoreceptor Lattices |
The protozoan parasite Leishmania donovani ( LD ) reduces cellular cholesterol of the host possibly for its own benefit . Cholesterol is mostly present in the specialized compartment of the plasma membrane . The relation between mobility of membrane proteins and cholesterol depletion from membrane continues to be an im... | The protozoan parasites , Leishmania donovani , replicate within the macrophages of the mammalian hosts . During its intracellular lifecycle , the parasite induces a wide variety of defects in the membrane homeostasis . Membrane bound receptor molecules are important for interacting with external stimuli . Our study ve... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"biology",
"and",
"life",
"sciences",
"parasitology",
"medicine",
"and",
"health",
"sciences"
] | 2014 | Leishmania donovani Infection Enhances Lateral Mobility of Macrophage Membrane Protein Which Is Reversed by Liposomal Cholesterol |
Taste is the primary sensory system for detecting food quality and palatability . Drosophila detects five distinct taste modalities that include sweet , bitter , salt , water , and the taste of carbonation . Of these , sweet-sensing neurons appear to have utility for the detection of nutritionally rich food while bitte... | The gustatory system is largely responsible for interpreting the nutritional value and potential toxicity of food compounds prior to ingestion . The receptors and neural circuits mediating the detection of sweet and bitter compounds have been identified in fruit fly , but neural mechanisms underlying detection of other... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Drosophila Fatty Acid Taste Signals through the PLC Pathway in Sugar-Sensing Neurons |
Open reading frame ( ORF ) 45 of Kaposi's sarcoma-associated herpesvirus ( KSHV ) is a tegument protein . A genetic analysis with a null mutant suggested a possible role for this protein in the events leading to viral egress . In this study , ORF45 was found to interact with KIF3A , a kinesin-2 motor protein that trans... | Kaposi's sarcoma–associated herpesvirus ( KSHV ) is a tumor virus associated with Kaposi's sarcoma ( KS ) and a spectrum of other lymphomas . These tumor cells are usually latently infected with this virus . The inactive virus in cells can get reactivated , whereupon there is viral DNA replication and viral protein syn... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/virion",
"structure,",
"assembly,",
"and",
"egress",
"cell",
"biology",
"virology"
] | 2009 | Kaposi's Sarcoma-Associated Herpesvirus ORF45 Interacts with Kinesin-2 Transporting Viral Capsid-Tegument Complexes along Microtubules |
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