Split (3)

train · 24.8k rows

headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development	journal.pgen.1002277	null	[ [ "The development of a multicellular organism requires the formation of functionally distinct cell types through the differential activation of gene expression .", "Such gene expression programs are enabled by transcription factors that endow the progenitors with the competence to differentiate under the i...	[ "Understanding how silent genes can be competent for activation provides insight into development as well as cellular reprogramming and pathogenesis .", "We performed genomic location analysis of the pioneer transcription factor FoxA in the adult mouse liver and found that about one-third of the FoxA bound sites ...	[ "FoxA transcriptional regulatory proteins are “pioneer factors” that engage silent genes , helping to endow the competence for activation .", "About a third of the DNA sites we found to be occupied by FoxA in the adult liver are at genes that are silent .", "Analysis of transcription factor binding motifs near ...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "immunodeficiency viruses", "immune cells", "cytokines", "viral persistence and latency", "virology", "t cells", "immunology", "biology", "microbiology", "immune system" ]	Homeostatic Proliferation Fails to Efficiently Reactivate HIV-1 Latently Infected Central Memory CD4+ T Cells	journal.ppat.1002288	null	[ [ "The existence of latent reservoirs of HIV-infected cells constitutes a major impediment to viral eradication .", "HIV-1 latent reservoirs are small , but extremely long-lived .", "Latent infection is associated with undetectable levels of viral gene expression and appears to be non-cytopathic .", ...	[ "Homeostatic proliferation ensures the longevity of central memory T-cells by inducing cell proliferation in the absence of cellular differentiation or activation .", "This process is governed mainly by IL-7 .", "Central memory T-cells can also be stimulated via engagement of the T-cell receptor , leading to ce...	[ "HIV-1 latently infected cells are considered the last barrier towards viral eradication and cure .", "However , the low number of latently infected cells found in patients makes studies extremely difficult .", "Here , using a model of primary CD4 T-cells we study the behavior of latently infected central memor...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome expression analysis", "genomics", "genome evolution", "genome analysis", "transcriptome analysis", "genetics", "biology and life sciences", "computational biology", "evolutionary biology", "evolutionary genetics" ]	Meiotic Drive Impacts Expression and Evolution of X-Linked Genes in Stalk-Eyed Flies	journal.pgen.1004362	null	[ [ "Meiosis typically results in an equal transmission probability of each allele from parent to gamete .", "This seemingly cooperative outcome masks an inherent genetic conflict .", "Alleles on any one chromosome would increase in frequency more rapidly if that chromosome passed to all , instead of half...	[ "Although sex chromosome meiotic drive has been observed in a variety of species for over 50 years , the genes causing drive are only known in a few cases , and none of these cases cause distorted sex-ratios in nature .", "In stalk-eyed flies ( Teleopsis dalmanni ) , driving X chromosomes are commonly found at fr...	[ "Sex chromosome meiotic drive causes changes in the sex-ratios of natural populations , and may even lead to extinction if the driving element reaches high frequency .", "However , very little is known about the genes that cause sex-ratio drive , and no causal gene has been identified in a species that consistent...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Type I and Type II Interferon Coordinately Regulate Suppressive Dendritic Cell Fate and Function during Viral Persistence	journal.ppat.1005356	null	[ [ "Unlike immune responses against most infections , the response against persisting viruses rapidly becomes dysfunctional and unable to purge infection .", "The prolonged virus replication progressively induces a deterioration of the T cell response , a phenomenon termed exhaustion [1] .", "T cell exha...	[ "Persistent viral infections are simultaneously associated with chronic inflammation and highly potent immunosuppressive programs mediated by IL-10 and PDL1 that attenuate antiviral T cell responses .", "Inhibiting these suppressive signals enhances T cell function to control persistent infection; yet , the under...	[ "Persistent virus infections induce host derived immunosuppressive factors that attenuate the immune response and prevent control of infection .", "Although the mechanisms of T cell exhaustion are being defined , we know surprisingly little about the underlying mechanisms that induce the immunosuppressive state a...	2016
[ "Introduction", "Modeling Coevolution", "Results", "Discussion" ]	[]	Coevolution and the Effects of Climate Change on Interacting Species	journal.pbio.1001685	The effects on survival of species-species interaction in the face of a changing climate depend on whether the species' interests are conflicting or non-conflicting.	[ [ "Climatic changes , or indeed any change in the environment , have the potential to cause the local extinction of species , and to alter community composition and ecosystem functioning [1] .", "Numerous models have been used to predict how the density and geographical range of species will be affected by ...	[ "Recent studies suggest that environmental changes may tip the balance between interacting species , leading to the extinction of one or more species .", "While it is recognized that evolution will play a role in determining how environmental changes directly affect species , the interactions among species force ...	[ "Recent studies suggest that environmental changes may tip the balance between species that interact with each other , leading to the extinction of one or more species .", "While it is recognized that evolution will alter the way environmental changes directly affect individual species , the interactions between ...	2013
[ "Introduction", "Results", "Discussion", "Models" ]	[]	Computational Models Describing Possible Mechanisms for Generation of Excessive Beta Oscillations in Parkinson’s Disease	journal.pcbi.1004609	null	[ [ "On the basis of published computational models , several theories for generation of beta oscillations have been formulated .", "McCarthy et al . [27] propose that beta oscillations originate in the striatum and spread to the rest of the circuit .", "On the basis of this theory one could expect the fo...	[ "In Parkinson’s disease , an increase in beta oscillations within the basal ganglia nuclei has been shown to be associated with difficulty in movement initiation .", "An important role in the generation of these oscillations is thought to be played by the motor cortex and by a network composed of the subthalamic ...	[ "The collective firing of neurons is an essential mechanism for communicating information in the brain .", "However , in Parkinson’s disease there is a disruption of healthy brain dynamics , which interrupts the processing of normal movement .", "In particular , the neurons become overly synchronized and produc...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "virology", "microbial pathogens", "microbial control", "host-pathogen interaction", "viral replication complex", "biology", "microbiology", "viral replication", "pathogenesis" ]	CIB1 Synergizes with EphrinA2 to Regulate Kaposi's Sarcoma-Associated Herpesvirus Macropinocytic Entry in Human Microvascular Dermal Endothelial Cells	journal.ppat.1003941	null	[ [ "Kaposi's sarcoma-associated herpes virus or human herpes virus 8 ( HHV-8 ) , a member of the lymphotrophic ( γ2 ) herpesvirus subfamily , is etiologically linked to endothelial cell neoplasm Kaposi's sarcoma ( KS ) , and B-cell neoplasms primary effusion lymphoma ( PEL ) or body cavity based B-cell lymphoma ...	[ "KSHV envelope glycoproteins interact with cell surface heparan sulfate and integrins , and activate FAK , Src , PI3-K , c-Cbl , and Rho-GTPase signal molecules in human microvascular dermal endothelial ( HMVEC-d ) cells .", "c-Cbl mediates the translocation of virus bound α3β1 and αVβ3 integrins into lipid rafts...	[ "KSHV infection of endothelial cells in humans leads into the development of Kaposi's sarcoma ( KS ) .", "Hence , understanding of in vitro KSHV entry in endothelial cells is critical to develop strategies to control KSHV infection and KS .", "The de novo KSHV infection of endothelial HMVEC-d cells is initiated...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "gene regulation", "messenger rna", "animals", "dna transcription", "circadian oscillators", "animal models", "drosophila melanogaster", "model organisms", "chronobiology", "epigenetics", "dna", "chromatin", "drosophila", "promoter regions", "research and analysis meth...	Linking Core Promoter Classes to Circadian Transcription	journal.pgen.1006231	null	[ [ "In many metazoans , transcription of numerous genes in most cell types occurs in a rhythmic fashion with a period of ~24 hours , also if the organism is held under constant conditions; these rhythms are termed circadian transcriptional rhythms [1] .", "They are to a large extent orchestrated by the cellu...	[ "Circadian rhythms in transcription are generated by rhythmic abundances and DNA binding activities of transcription factors .", "Propagation of rhythms to transcriptional initiation involves the core promoter , its chromatin state , and the basal transcription machinery .", "Here , I characterize core promoter...	[ "Circadian rhythms switch gene expression on and off with a daily rhythm in most tissues in mammals and other animals .", "Typically , thousands of genes are affected , and the functions of these rhythms include preparing and adjusting various physiological functions in tissues to meet time-of-day dependent requi...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Diagnostic Accuracy of Recombinant Immunoglobulin-like Protein A-Based IgM ELISA for the Early Diagnosis of Leptospirosis in the Philippines	journal.pntd.0003879	null	[ [ "Leptospirosis is a ubiquitous zoonosis caused by over a hundred serovars of the pathogenic spirochetes , Leptospira spp .", "The disease is an important public health problem in low- and middle-income countries in the tropics , especially in Southeast Asia and Latin America , including the Philippines [1...	[ "Leptospirosis is an important but largely under-recognized public health problem in the tropics .", "Establishment of highly sensitive and specific laboratory diagnosis is essential to reveal the magnitude of problem and to improve treatment .", "This study aimed to evaluate the diagnostic accuracy of a recomb...	[ "Leptospirosis is an important but largely under-recognized public health problem in the tropics .", "A sensitive , specific and practical point-of-care laboratory test is needed to improve clinical management in resource-limited settings .", "We developed a recombinant LigA protein based IgM assay ( IgM ELISA ...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry/molecular evolution", "computational biology/macromolecular structure analysis", "biochemistry", "genetics and genomics/microbial evolution and genomics", "computational biology/sequence motif analysis", "computational biology/comparative sequence analysis", "biochemistry/chemical biology ...	Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis	journal.pcbi.1000351	null	[ [ "It is well known that polyketide synthase ( PKS ) gene clusters can generate enormously diverse array of polyketide products by making use of various biosynthetic paradigms like , modular organization of sets of catalytic domains or iterative catalysis of condensation steps using single set of catalytic doma...	[ "Sequence data arising from an increasing number of partial and complete genome projects is revealing the presence of the polyketide synthase ( PKS ) family of genes not only in microbes and fungi but also in plants and other eukaryotes .", "PKSs are huge multifunctional megasynthases that use a variety of biosyn...	[ "Polyketide synthases ( PKSs ) form a large family of multifunctional proteins involved in the biosynthesis of diverse classes of therapeutically important natural products .", "These enzymes biosynthesize natural products with enormous diversity in chemical structures by combinatorial use of a limited number of ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "nervous system components", "drosophila melanogaster", "model organisms", "cognitive neuroscience", "behavioral neuroscience", "decision making", "physiology", "biology", "anatomy and physiology", "neurological system", "neuroscience" ]	The Origin of Behavioral Bursts in Decision-Making Circuitry	journal.pcbi.1002075	null	[ [ "Bursts in behavior are common [1]–[10] , but only recently have there been modeling efforts to understand its origin from a behavioral point of view [11]–[14] .", "The queued priority list model was first proposed by Barabási [11] , [12] to explain why inter-event times in human activities such as e-mail...	[ "From ants to humans , the timing of many animal behaviors comes in bursts of activity separated by long periods of inactivity .", "Recently , mathematical modeling has shown that simple algorithms of priority-driven behavioral choice can result in bursty behavior .", "To experimentally test this link between d...	[ "It has long been observed that animal movement tends to come in bursts of activity .", "This has been seen in many animal species , ranging from small insects to even human activity patterns .", "The underlying mechanisms remain unknown , but recently a mathematical model showed that it could be due to priorit...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "systems biology", "rna", "nucleic acids", "synthetic biology", "biology", "computational biology", "biophysics" ]	Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization	journal.pcbi.1003172	null	[ [ "Small non-coding RNA ( sRNA ) has raised a big interest because of the predictability and modularity of its binding with a large variety of molecules and macromolecules [1] .", "Given this functional potential , the use of sRNAs to control protein expression has triggered a new way to engineer integrated...	[ "Small RNAs ( sRNAs ) can operate as regulatory agents to control protein expression by interaction with the 5′ untranslated region of the mRNA .", "We have developed a physicochemical framework , relying on base pair interaction energies , to design multi-state sRNA devices by solving an optimization problem wit...	[ "Is our current knowledge of in vivo RNA-RNA interactions and thermodynamics enough to perform the unsupervised computational design of fully synthetic sequences encoding functional RNAs in living cells ?", "Recent work gave a positive answer for the challenging problem of designing activating riboregulators .", ...	2013
[ "Introduction", "Methods", "Results", "Discussion", "Strengths and limitations", "Conclusion" ]	[ "health promotion", "children", "medicine and health sciences", "face", "education", "sociology", "tropical diseases", "geographical locations", "social sciences", "australia", "health care", "bacterial diseases", "age groups", "eye diseases", "neglected tropical diseases", "families",...	The impact of health promotion on trachoma knowledge, attitudes and practice (KAP) of staff in three work settings in remote Indigenous communities in the Northern Territory	journal.pntd.0005503	null	[ [ "Trachoma is the world’s leading cause of infectious blindness .", "Globally , trachoma is linked to poverty , household crowding , limited access to water and poor hygiene [1 , 2] .", "Active infection with Chlamydia trachomatis is usually found in young children and transmitted by infected eye and n...	[ "Globally , trachoma is the leading cause of infectious blindness and Australia is the only developed country with endemic trachoma .", "It is found in remote Indigenous communities burdened with poverty , overcrowding and poor hygiene .", "Lack of culturally appropriate health promotion , a small trachoma work...	[ "Australia is the only high-income nation with endemic trachoma .", "It is prevalent in remote Indigenous communities , although it was eliminated from wider society in Australia over one hundred years ago .", "Trachoma elimination across vast areas of remote Australia is an enormous challenge .", "Community ...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "statistical mechanics", "neural networks", "computational neuroscience", "biophysics theory", "biology", "biophysics", "neuroscience" ]	Dynamic Finite Size Effects in Spiking Neural Networks	journal.pcbi.1002872	null	[ [ "Realistic models of neural networks in the central nervous system are analytically and computationally intractable , presenting a challenge to our understanding of the highly complex spiking dynamics of neurons .", "Consequently , some degree of simplification is necessary for theoretical progress and th...	[ "We investigate the dynamics of a deterministic finite-sized network of synaptically coupled spiking neurons and present a formalism for computing the network statistics in a perturbative expansion .", "The small parameter for the expansion is the inverse number of neurons in the network .", "The network dynami...	[ "One avenue towards understanding how the brain functions is to create computational and mathematical models .", "However , a human brain has on the order of a hundred billion neurons with a quadrillion synaptic connections .", "Each neuron is a complex cell comprised of multiple compartments hosting a myriad o...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "helminths", "parasitic diseases", "invertebrate genomics", "animals", "genomic library construction", "organisms", "genome analysis", "dna construction", "molecular biology techniques", "r...	A Genome Wide Comparison to Identify Markers to Differentiate the Sex of Larval Stages of Schistosoma haematobium, Schistosoma bovis and their Respective Hybrids	journal.pntd.0005138	null	[ [ "Flatworm parasites of the genus Schistosoma are well known trematodes for their serious threat to human and animal health .", "These blood flukes cause schistosomiasis , a neglected disease which ranks second to malaria , in terms of morbidity and mortality [1] .", "More than 200 million people are i...	[ "For scientists working on gonochoric organisms , determining sex can be crucial for many biological questions and experimental studies , such as crossbreeding , but it can also be a challenging task , particularly when no sexual dimorphism is visible or cannot be directly observed .", "In metazoan parasites of t...	[ "Current global changes ( environmental and anthropogenic ) are expected to promote the spread and transmission of infectious diseases .", "One of the direct consequences of such changes is the modification of the geographical distribution of species , enabling natural hybridization .", "Such hybridization is a...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "light", "neuroscience", "electromagnetic radiation", "circadian oscillators", "chronobiology", "crystallographic techniques", "research and analysis methods", "animal cells", "gene expression", "luminescence", "light pulses", "physics", "biochemistry", "genetic oscillators", "circadian ...	Weak coupling between intracellular feedback loops explains dissociation of clock gene dynamics	journal.pcbi.1007330	null	[ [ "Circadian clocks are omnipresent in almost all living organisms as a consequence of adaptation to 24 h environmental fluctuations , leading to convergent evolution across different kingdoms of life [1] .", "Interlocked transcriptional-translational feedback loops ( TTFLs ) have been identified as a commo...	[ "Circadian rhythms are generated by interlocked transcriptional-translational negative feedback loops ( TTFLs ) , the molecular process implemented within a cell .", "The contributions , weighting and balancing between the multiple feedback loops remain debated .", "Dissociated , free-running dynamics in the ex...	[ "Circadian clocks are endogenous pacemakers that generate gene expression oscillations with a period of approximately 24h .", "They enable an organism to anticipate daily changes in light and temperature and allow to align physiological properties to the most beneficial time around the solar day .", "The suprac...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Epigenome of Evolving Drosophila Neo-Sex Chromosomes: Dosage Compensation and Heterochromatin Formation	journal.pbio.1001711	This study shows how young sex chromosomes have altered their chromatin structure in Drosophila, and what genomic changes have led to silencing of the Y, and hyper-transcription of the X.	[ [ "Sex chromosomes evolve from ordinary autosomes [1] .", "Degeneration of the Y chromosome is a general facet of sex chromosome evolution , and old Y chromosomes are gene poor , often contain high amounts of repetitive DNA , and in Drosophila the Y is entirely heterochromatic [2] .", "The euchromatic ,...	[ "Sex chromosomes originated from autosomes but have evolved a highly specialized chromatin structure .", "Drosophila Y chromosomes are composed entirely of silent heterochromatin , while male X chromosomes have highly accessible chromatin and are hypertranscribed as a result of dosage compensation .", "Here , w...	[ "Sex chromosomes differ from non-sex chromosomes ( “autosomes” ) at the genomic , transcriptomic , and epigenomic level , yet the X and Y share a common evolutionary origin .", "The Drosophila Y chromosome is gene-poor and associated with a compact and transcriptionally inactive form of genetic material called he...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements	journal.pgen.1005383	null	[ [ "Recent progress in high-throughput transcriptome analysis has led to a constantly growing catalog of non-coding transcripts ( ncRNAs , for review see [1 , 2] ) .", "The prevalence of a variety of short ( ~20–35 nt; sRNAs ) and long ncRNAs ( >~200 nt; lncRNAs ) has been reported in numerous organisms .", ...	[ "Because of their nuclear dimorphism , ciliates provide a unique opportunity to study the role of non-coding RNAs ( ncRNAs ) in the communication between germline and somatic lineages .", "In these unicellular eukaryotes , a new somatic nucleus develops at each sexual cycle from a copy of the zygotic ( germline )...	[ "Paramecium tetraurelia provides an excellent model for studying the mechanisms involved in the production of non-coding transcripts and their mode of action .", "Different types of non-coding RNAs ( ncRNAs ) were shown to be implicated in the programmed DNA elimination process that occurs in this organism .", ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "research design", "infectious diseases", "medicine and health sciences", "clinical research design", "biology and life sciences", "microbiology", "research and analysis methods" ]	Safety and Efficacy Assessment of Two New Leprosy Skin Test Antigens: Randomized Double Blind Clinical Study	journal.pntd.0002811	null	[ [ "Despite the success of the widely applied multidrug therapy ( MDT ) in reducing the prevalence of leprosy , transmission continues with new case detection maintaining a steady rate in endemic regions of high burden areas , further emphasizing the importance of early detection [1] .", "A sensitive and spe...	[ "New tools are required for the diagnosis of pre-symptomatic leprosy towards further reduction of disease burden and its associated reactions .", "To address this need , two new skin test antigens were developed to assess safety and efficacy in human trials .", "A Phase I safety trial was first conducted in a n...	[ "Clinically useful skin test reagents should be safe and sufficiently sensitive to detect infection prior to physical manifestations of leprosy disease .", "While in these small scale human studies , leprosy reagents were safe for use in humans , they failed in respect of sensitivity at a rate of 20–25% in the ke...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "systems biology", "medicine", "infectious diseases", "viral hemorrhagic fevers", "gene expression", "neglected tropical diseases", "biology", "microbiology", "molecular cell biology" ]	Transcriptome Analysis of Human Peripheral Blood Mononuclear Cells Exposed to Lassa Virus and to the Attenuated Mopeia/Lassa Reassortant 29 (ML29), a Vaccine Candidate	journal.pntd.0002406	null	[ [ "Lassa Fever ( LF ) is one of the most neglected tropical diseases and has the second highest global incidence of any viral hemorrhagic fever ( VHF ) , after Dengue HF .", "The estimated “at risk” population in Sierra Leone , Guinea , and Nigeria , may be as high as 59 million .", "The number of sympt...	[ "Lassa virus ( LASV ) is the causative agent of Lassa Fever and is responsible for several hundred thousand infections and thousands of deaths annually in West Africa .", "LASV and the non-pathogenic Mopeia virus ( MOPV ) are both rodent-borne African arenaviruses .", "A live attenuated reassortant of MOPV and ...	[ "The virulent Lassa fever virus ( LASV ) and the non-pathogenic Mopeia virus ( MOPV ) infect rodents and , incidentally , people in West Africa .", "The mechanism of LASV damage in human beings is unclear .", "There is no licensed Lassa fever vaccine and therapeutic intervention is usually too late .", "The M...	2013
[ "Introduction", "Discussion", "Materials and Methods" ]	[ "gastroenterology and hepatology/gastrointestinal cancers", "cell biology/cell signaling", "cell biology/cell growth and division", "biophysics/theory and simulation", "cell biology/cell adhesion", "gastroenterology and hepatology/small intestine" ]	A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt	journal.pcbi.1001045	null	[ [ "The epithelium of the small intestine is the most rapidly regenerating tissue of adult mammals .", "Cell production starts near the crypt base , producing numerous progeny which move up the crypt-villus axis .", "Cells moving up the crypt continue proliferating while in parallel becoming committed ei...	[ "We introduce a novel dynamic model of stem cell and tissue organisation in murine intestinal crypts .", "Integrating the molecular , cellular and tissue level of description , this model links a broad spectrum of experimental observations encompassing spatially confined cell proliferation , directed cell migrati...	[ "In the murine small intestine there are more than a million organized groups of proliferating cells , the crypts , each of which contains about 250–300 cells .", "About 60% of these cells are in rapid cycle .", "The functional stem cells of this tissue have been demonstrated to reside at defined positions at t...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide association studies", "medicine", "genetics", "genetics and genomics", "biology", "hematology", "clinical genetics" ]	Genome-Wide Association Study of White Blood Cell Count in 16,388 African Americans: the Continental Origins and Genetic Epidemiology Network (COGENT)	journal.pgen.1002108	null	[ [ "Proliferation and differentiation of hematopoietic stem cells into mature white blood cells ( WBC ) in the bone marrow , followed by release into the circulation of mature WBC , is a highly regulated process [1] .", "WBC comprise several subtypes including neutrophils , lymphocytes , monocytes , eosinoph...	[ "Total white blood cell ( WBC ) and neutrophil counts are lower among individuals of African descent due to the common African-derived “null” variant of the Duffy Antigen Receptor for Chemokines ( DARC ) gene .", "Additional common genetic polymorphisms were recently associated with total WBC and WBC sub-type lev...	[ "Although recent genome-wide association studies have identified common genetic variants associated with total white blood cell ( WBC ) and WBC sub-type counts in European and Japanese ancestry populations , whether these or other loci account for differences in WBC count among African Americans is unknown .", "B...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "african trypanosomiasis", "tropical diseases", "parasitic diseases", "parasitic protozoans", "animals", "glossina", "protozoans", "neglected tropical diseases", "molecular biology techniques", "tsetse fly", "infectious diseas...	Illuminating the Prevalence of Trypanosoma brucei s.l. in Glossina Using LAMP as a Tool for Xenomonitoring	journal.pntd.0004441	null	[ [ "Human African trypanosomiasis ( HAT ) , commonly known as sleeping sickness , is a parasitic disease caused by two sub-species of trypanosome , Trypanosoma brucei gambiense in West and Central Africa , which causes a chronic disease and T . b . rhodesiense in East and southern Africa which causes an acute di...	[ "As the reality of eliminating human African trypanosomiasis ( HAT ) by 2020 draws closer , the need to detect and identify the remaining areas of transmission increases .", "Here , we have explored the feasibility of using commercially available LAMP kits , designed to detect the Trypanozoon group of trypanosome...	[ "Recent control efforts have reduced the global incidence of Gambiense human African trypanosomiasis ( HAT ) to <5 , 000 cases per year , strengthening the prospect of eliminating the disease as a public health problem by 2020 .", "To meet this goal , new methods for identifying transmission must be explored to p...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "empirical methods", "computer applications", "computer science", "computational chemistry", "protein structure", "chemistry", "biology", "computational biology", "computer-aided design", "macromolecular structure analysis" ]	Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping	journal.pcbi.1002288	null	[ [ "Protein phosphorylation is one of the most abundant posttranslational modifications .", "It is catalyzed by protein kinases , a large group of enzymes that account for approximately 2% of the human genome [1] .", "Phosphorylation involves the regulation of almost every process in the cell , and numer...	[ "Protein kinases are key signaling enzymes that catalyze the transfer of γ-phosphate from an ATP molecule to a phospho-accepting residue in the substrate .", "Unraveling the molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor is important for understanding...	[ "Protein kinases are key signaling enzymes and major drug targets that catalyze the transfer of phosphate group to a phospho-accepting residue in the substrate .", "Unraveling molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor ( substrate consensus sequen...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics/macromolecular assemblies and machines", "biophysics/protein folding", "biophysics/theory and simulation", "cell biology/neuronal signaling mechanisms", "biophysics/membrane proteins and energy transduction" ]	Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel	journal.pcbi.1000289	null	[ [ "Potassium channels are the single most common type of ion channels in nature .", "The", "subclass of voltage-dependent potassium channels enable controlled ion transport", "over the cell membrane and are hence pivotal for a wide range of functions such as", "nerve impulse action potentials , ...	[ "Structure and dynamics of voltage-gated ion channels , in particular the motion of", "the S4 helix , is a highly interesting and hotly debated topic in current", "membrane protein research .", "It has critical implications for insertion and", "stabilization of membrane proteins as well as for finding how t...	[ "Proteins that transport ions across the cellular membrane are essential for", "cellular life .", "The proteins conducting positively charged potassium ions are key", "players in heart beat and nerve impulse generation because they are regulating", "the electrical excitability of the cell ( together with pr...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chemical bonding", "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "gene regulation", "pathogens", "microbiology", "organic compounds", "plasmid construction", "regulator genes", "fungi", "plant science", "experimental organism systems", "gene ty...	Wor1 establishes opaque cell fate through inhibition of the general co-repressor Tup1 in Candida albicans	journal.pgen.1007176	null	[ [ "Candida albicans is a common opportunistic fungal pathogen of humans .", "Found in the mouth , gastrointestinal tract , vagina and skin , C . albicans is harmless to the healthy , but in immunocompromised individuals C . albicans can cause serious infection , with a mortality rate of up to 40% in dissemi...	[ "The pathogenic fungus Candida albicans can undergo phenotypic switching between two heritable states: white and opaque .", "This phenotypic plasticity facilitates its colonization in distinct host niches .", "The master regulator WOR1 is exclusively expressed in opaque phase cells .", "Positive feedback regu...	[ "The opportunistic fungal pathogen Candida albicans is a common member of the human gut microbiota , but can also cause serious infections in immune-compromised individuals .", "Morphological plasticity is essential for its ability to adapt to and colonize a varied array of diverse host niches .", "One such mor...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/microbial evolution and genomics", "virology/virus evolution and symbiosis", "virology", "computational biology/evolutionary modeling", "infectious diseases/viral infections", "virology/immune evasion" ]	Glycosylation Focuses Sequence Variation in the Influenza A Virus H1 Hemagglutinin Globular Domain	journal.ppat.1001211	null	[ [ "The influenza A virus ( IAV ) hemagglutinin ( HA ) is a homotrimeric glycoprotein that initiates infection by attaching virus to host cell sialic acids and mediating fusion of viral and endosomal membranes [1] .", "HA consists of a fibrous stem inserted into the viral membrane supporting a globular domai...	[ "Antigenic drift in the influenza A virus hemagglutinin ( HA ) is responsible for seasonal reformulation of influenza vaccines .", "Here , we address an important and largely overlooked issue in antigenic drift: how does the number and location of glycosylation sites affect HA evolution in man ?", "We analyzed ...	[ "Influenza A virus is highly susceptible to neutralizing antibodies specific for the viral hemagglutinin glycoprotein ( HA ) , and is easily controlled by standard vaccines .", "Influenza A virus remains an important human pathogen , however , due to its ability to rapidly evade antibody responses .", "This pro...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/epigenetics" ]	Genetic Identification of a Network of Factors that Functionally Interact with the Nucleosome Remodeling ATPase ISWI	journal.pgen.1000089	null	[ [ "Eukaryotic cells store their genetic information in the form of chromatin , a complex of DNA packed with structural and regulatory proteins .", "The functional repeating unit of chromatin is the nucleosome , 146 base pairs of DNA wrapped around an octamer of histone proteins .", "While this packaging...	[ "Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function .", "However , much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and ...	[ "The eukaryotic genome is organized in a highly dynamic structure called chromatin .", "Access to DNA in the context of chromatin is granted by enzymatic activities that use the energy of hydrolysis of ATP to slide or covalently modify nucleosomes .", "ISWI is an evolutionarily conserved nucleosome-sliding fact...	2008
[ "Introduction", "Results/Discussion", "Materials and Methods", "Supporting Information" ]	[ "viruses", "mammals", "virology" ]	A Point Mutation in a Herpesvirus Polymerase Determines Neuropathogenicity	journal.ppat.0030160	null	[ [ "Equid herpesvirus type 1 ( EHV-1 ) is an aerosol-transmitted alphaherpesvirus , which causes rhinopneumonitis , abortion , and paralysis .", "Devastating outbreaks of the paralytic form of the disease occurred recently worldwide , resulting in its classification as a potentially emerging disease by the U...	[ "Infection with equid herpesvirus type 1 ( EHV-1 ) leads to respiratory disease , abortion , and neurologic disorders in horses .", "Molecular epidemiology studies have demonstrated that a single nucleotide polymorphism resulting in an amino acid variation of the EHV-1 DNA polymerase ( N752/D752 ) is significantl...	[ "Equid herpesvirus type 1 ( EHV-1 ) , a close relative of varicella-zoster virus and herpes simplex virus of humans , is spread by aerosol and is the causative agent of the most common neurologic disease of horses .", "Outbreaks of the neurologic form of EHV-1 can be devastating to individual animals and entire h...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "aneuploidy", "stem cells", "induced pluripotent stem cells", "chromosomal disorders", "genetics", "biology", "human genetics", "genetics and genomics" ]	Reprogramming to Pluripotency Can Conceal Somatic Cell Chromosomal Instability	journal.pgen.1002913	null	[ [ "The potential to restore pluripotency to mature somatic cells has generated new prospects in the establishment of patient-specific regenerative therapies and has also offered new options for more advanced and specific modeling of human disease [1] , [2] .", "However , several obstacles remain prior to th...	[ "The discovery that somatic cells are reprogrammable to pluripotency by ectopic expression of a small subset of transcription factors has created great potential for the development of broadly applicable stem-cell-based therapies .", "One of the concerns regarding the safe use of induced pluripotent stem cells ( ...	[ "iPSC technology has the potential to revolutionize stem-cell based regenerative medicine and would also allow for the production of patient-specific cells for disease modeling and drug discovery .", "One of the primary safety concerns of iPSCs is genetic instability , which is associated with cancer and various ...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "computational biology/transcriptional regulation", "genetics and genomics/bioinformatics", "computational biology" ]	Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions	journal.pcbi.1000039	null	[ [ "Several experimental advances in the study of gene regulation have highlighted the fact that transcription factors have a certain affinity to all DNA regions , as evidenced by many experimental techniques , such as DNAse footprinting [1] , gel-shift assays [2] , SELEX [3] , and more recently genome-wide chro...	[ "Recent experimental and theoretical efforts have highlighted the fact that binding of transcription factors to DNA can be more accurately described by continuous measures of their binding affinities , rather than a discrete description in terms of binding sites .", "While the binding affinities can be predicted ...	[ "The binding of proteins to DNA is a key molecular mechanism , which can regulate the expression of genes in response to different cellular and environmental conditions .", "The extensive research on gene regulation has generated binding models for many transcription factors , but the prediction of new binding si...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "veterinary diseases", "veterinary parasitology", "giardiasis", "zoonotic diseases", "biology", "microbiology", "zoology", "parasitic diseases", "veterinary science", "parasitology" ]	Genetic Characterizations of Giardia duodenalis in Sheep and Goats in Heilongjiang Province, China and Possibility of Zoonotic Transmission	journal.pntd.0001826	null	[ [ "Giardia duodenalis ( syn . Giardia lamblia , Giardia intestinalis ) is one of the most common protozoa in humans and animals .", "Giardiasis of humans and animals has a wide spectrum of clinical signs , including the onset of diarrhea , abdominal pain , bloating , vomiting , nausea and/or weight loss .",...	[ "Giardia duodenalis is a widespread intestinal protozoan of both humans and mammals .", "To date , few epidemiological studies have assessed the potential and importance of zoonotic transmission; and the human giardiasis burden attributable to G . duodenalis of animal origin is unclear .", "No information about...	[ "Giardiasis is a kind of zoonotic disease with global distribution .", "Due to the great number of asymptomatic giardiasis cases , human giardiasis is often underreported .", "The sources of infection of giardiasis are feces of humans and mammals with the pathogen being transmitted by the fecal-oral route .", ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "parastic protozoans", "protein kinase signaling cascade", "signal transduction", "molecular cell biology", "toxoplasma gondii", "parasitology", "protozoology", "biology", "microbiology", "signaling pathways", "signaling cascades" ]	TgCDPK3 Regulates Calcium-Dependent Egress of Toxoplasma gondii from Host Cells	journal.ppat.1003066	null	[ [ "Toxoplasma gondii , the causative agent of toxoplasmosis , is a member of the phylum Apicomplexa , a group of unicellular eukaryotes consisting chiefly of obligate intracellular parasites .", "Among these medically and agriculturally important parasites are the Eimeria spp .", ", causing enteritis in...	[ "The phylum Apicomplexa comprises a group of obligate intracellular parasites of broad medical and agricultural significance , including Toxoplasma gondii and the malaria-causing Plasmodium spp .", "Key to their parasitic lifestyle is the need to egress from an infected cell , actively move through tissue , and r...	[ "The phylum Apicomplexa includes a number of medically and agriculturally relevant parasites .", "These include the Plasmodium species , agents of malaria and estimated to cause over 1 million deaths per year , and Toxoplasma gondii , which infects 30–80% of any human population .", "These parasites rely on a u...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "retrotransposons", "dna transcription", "animal models", "genome sequencing", "developmental biology", "model organisms", "molecular genetics", "embryology", "transposons", "gene expression", "biology", "molecular biology", "gene identification and analysis", "genetics", "genomics", "...	Next-Generation Sequencing Identifies the Danforth's Short Tail Mouse Mutation as a Retrotransposon Insertion Affecting Ptf1a Expression	journal.pgen.1003205	null	[ [ "The Danforth's short tail ( Sd ) mouse mutation arose spontaneously in the early 1920s in an inbred mouse colony maintained in the laboratory of C . H . Danforth [1] , [2] .", "The inbred line in which the Sd mutation arose was being maintained for study of a dominant but incompletely penetrant posterior...	[ "The semidominant Danforth's short tail ( Sd ) mutation arose spontaneously in the 1920s .", "The homozygous Sd phenotype includes severe malformations of the axial skeleton with an absent tail , kidney agenesis , anal atresia , and persistent cloaca .", "The Sd mutant phenotype mirrors features seen in human c...	[ "Birth defects are the leading cause of infant mortality in the United States , accounting for 1 in 5 infant deaths annually .", "Birth defects that affect development of the caudal portion of the embryo can include malformations of the spine , such as spina bifida , and malformations of the kidneys and lower gas...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	The Causes and Consequences of Changes in Virulence following Pathogen Host Shifts	journal.ppat.1004728	null	[ [ "Virulence—which we define as the harm a pathogen does to its host—can sometimes dramatically increase when pathogens shift to infect new host species , resulting in new and devastating outbreaks and epidemics [1 , 2] .", "For example , in bats , Ebola virus appears to be largely asymptomatic , but it is ...	[ "Emerging infectious diseases are often the result of a host shift , where the pathogen originates from a different host species .", "Virulence—the harm a pathogen does to its host—can be extremely high following a host shift ( for example Ebola , HIV , and SARs ) , while other host shifts may go undetected as th...	[ "Many emerging infectious diseases are the result of a host shift , with the pathogen jumping into the new host from another species .", "Virulence—the harm a pathogen does to its host—can be extremely high following a host shift ( for example HIV , SARs and Ebola ) , while other host shifts may go undetected as ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "model organisms", "genetics", "biology", "molecular cell biology", "genetics and genomics" ]	Cooperative and Antagonistic Contributions of Two Heterochromatin Proteins to Transcriptional Regulation of the Drosophila Sex Determination Decision	journal.pgen.1002122	null	[ [ "Eukaryotic genomes are organized into two distinct classes of chromatin [1] .", "The major class ( euchromatin ) can undergo decondensation to enable transcription during interphase , whereas a minor fraction ( heterochromatin ) remains compact and mostly transcriptionally silent throughout the cell cycl...	[ "Eukaryotic nuclei contain regions of differentially staining chromatin ( heterochromatin ) , which remain condensed throughout the cell cycle and are largely transcriptionally silent .", "RNAi knockdown of the highly conserved heterochromatin protein HP1 in Drosophila was previously shown to preferentially reduc...	[ "Eukaryotic genomes are organized into two distinct classes of chromatin , euchromatin and heterochromatin .", "The former is less condensed to enable transcription , whereas heterochromatin , which is marked by Heterochromatin Protein 1 ( HP1 ) , remains compact and mostly transcriptionally silent throughout the...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary modeling", "biology and life sciences", "computational biology", "biophysics", "biophysical simulations" ]	Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel	journal.pcbi.1003976	null	[ [ "Cyclic nucleotide-gated ( CNG ) ion channels are nonselective cation channels , essential for visual and olfactory sensory transduction in vertebrates [1]–[4] .", "Like other members of the voltage-gated-like ion channel superfamily [2] , the CNG channels are composed of four ( identical or similar ) mon...	[ "Cyclic nucleotide-gated ( CNG ) ion channels are nonselective cation channels , essential for visual and olfactory sensory transduction .", "Although the channels include voltage-sensor domains ( VSDs ) , their conductance is thought to be independent of the membrane potential , and their gating regulated by cyt...	[ "Cyclic nucleotide-gated ( CNG ) channels mediate the passage of cations through the cytoplasmic membrane .", "They are involved in sensory transduction and cellular development in the rod and cone photoreceptors , as well as in brain , kidney , heart and other cells , and are linked to achromatopsia and other ra...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "epigenetics", "biology", "genomics", "genetics and genomics" ]	Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome	journal.pgen.1002036	null	[ [ "The chromatin of mature sperm differs dramatically from that of other cell types .", "Most of the sperm genome is packaged by small basic proteins called protamines , with only a few genomic sites remaining bound by nucleosomes [1] , [2] , [3] , [4] , [5] .", "This change in DNA packaging takes place...	[ "Chromatin in sperm is different from that in other cells , with most of the genome packaged by protamines not nucleosomes .", "Nucleosomes are , however , retained at some genomic sites , where they have the potential to transmit paternal epigenetic information .", "It is not understood how this retention is s...	[ "In most cells , DNA is packaged by protein complexes called nucleosomes .", "In sperm , however , nucleosomes are only retained at a small fraction of the genome , particularly at the start sites of genes .", "In this work , we show that the sites at which nucleosomes are retained in sperm are specified by var...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "taxonomy", "medicine and health sciences", "engineering and technology", "statistics", "drugs", "microbiology", "decision tree learning", "decision analysis", "antibiotic resistance", "phylogenetics", "data management", "mathematics", "forecasting", "antibiotics", "a...	Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data	journal.pcbi.1006258	null	[ [ "Antibiotic resistance has turned into an acute global threat .", "The rise of bacterial strains resistant to multiple antibiotics is expected to dramatically limit treatment effectiveness [1] , leading to potentially incurable outbreaks .", "In addition to new drug development efforts , there is an u...	[ "The emergence of microbial antibiotic resistance is a global health threat .", "In clinical settings , the key to controlling spread of resistant strains is accurate and rapid detection .", "As traditional culture-based methods are time consuming , genetic approaches have recently been developed for this task ...	[ "One of the major health threats of 21st century is emergence of antibiotic resistance .", "To manage its human health and economic impact , efforts are made to develop novel diagnostic tools that rapidly detect resistant strains in clinical settings .", "In our study , we employed a range of powerful machine l...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics and genomics/gene expression", "genetics and genomics/functional genomics", "genetics and genomics/complex traits", "genetics and genomics/genetics of disease", "neurological disorders/neurogenetics" ]	A Common Variant Associated with Dyslexia Reduces Expression of the KIAA0319 Gene	journal.pgen.1000436	null	[ [ "Dyslexia , or reading disability ( RD ) , is a condition that affects an individual's ability to read and spell in the absence of any obvious sensory or neurological impairment and despite adequate intelligence and educational opportunity [1] .", "RD is one of the most common learning disabilities in sch...	[ "Numerous genetic association studies have implicated the KIAA0319 gene on human chromosome 6p22 in dyslexia susceptibility .", "The causative variant ( s ) remains unknown but may modulate gene expression , given that ( 1 ) a dyslexia-associated haplotype has been implicated in the reduced expression of KIAA0319...	[ "Dyslexia , or reading disability , is a common disorder caused by both genetic and environmental factors .", "Genetic studies have implicated a number of genes as candidates for playing a role in dyslexia .", "We functionally characterized one such gene ( KIAA0319 ) to identify variant ( s ) that might affect ...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "engineering and technology", "bacteriophages", "symbiosis", "manufacturing processes", "parasitic diseases", "wolbachia", "germ cells", "viruses", "developmental biology", "pupae", "heat treatment", "bacteria", "sperm", "animal cells", "life cycles", ...	Exposure to opposing temperature extremes causes comparable effects on Cardinium density but contrasting effects on Cardinium-induced cytoplasmic incompatibility	journal.ppat.1008022	null	[ [ "Temperature has profound effects on the biology of ectothermic organisms as well as on the microbiota inhabiting these organisms [1–4] .", "The heritable symbionts of arthropods , which are primarily vertically transmitted from mother to offspring , are closely integrated with host biology [5] , and may ...	[ "Terrestrial arthropods , including insects , commonly harbor maternally inherited intracellular symbionts that confer benefits to the host or manipulate host reproduction to favor infected female progeny .", "These symbionts may be especially vulnerable to thermal stress , potentially leading to destabilization ...	[ "Insects often harbor heritable symbiotic bacteria that infect their cells and/or bodily fluids .", "These heritable bacteria are passed from mother to offspring and can have substantial effects on host insect biology , and include bacteria like Cardinium that cause mating incompatibilities between symbiont-infec...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "veterinary science" ]	Epidemiological and Genetic Data Supporting the Transmission of Ancylostoma ceylanicum among Human and Domestic Animals	journal.pntd.0001522	null	[ [ "Hookworms are one of the most common parasitic nematodes that inhabit the small intestine of humans and animals such as dogs and cats .", "The two primary species of hookworm infecting humans are Ancylostoma duodenale and Necator americanus [1] , with A . duodenale occurring mainly in the Middle East , N...	[ "Currently , information on species-specific hookworm infection is unavailable in Malaysia and is restricted worldwide due to limited application of molecular diagnostic tools .", "Given the importance of accurate identification of hookworms , this study was conducted as part of an ongoing molecular epidemiologic...	[ "Parasitic zoonoses pose a continuing public health problem , especially in endemic developing countries where the majority of populations live in poor , overcrowded conditions , lack education , and practice poor standards of hygiene and improper sanitary disposal of feces .", "Close contact with domestic animal...	2012
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "inflammatory diseases", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "cytokines", "fungal genetics", "pathogens", "immunology", "microbiology", "developmental biology", "signs and symptoms"...	Modulation of the immune response by Fonsecaea pedrosoi morphotypes in the course of experimental chromoblastomycosis and their role on inflammatory response chronicity	journal.pntd.0005461	null	[ [ "A common theme observed across multiple fungal pathogens is their ability to impair the establishment of a protective immune response .", "Although early inflammation is beneficial in containing the infection , an uncontrolled inflammatory response is detrimental and may eventually oppose disease eradica...	[ "A common theme across multiple fungal pathogens is their ability to impair the establishment of a protective immune response .", "Although early inflammation is beneficial in containing the infection , an uncontrolled inflammatory response is detrimental and may eventually oppose disease eradication .", "Chrom...	[ "Pathogenic fungi often present two distinct forms , which are correlated to the host’s inflammatory response and eventual disease outcome .", "Chromoblastomycosis is a fungal disease occurring especially in tropical areas , and it is most often caused by the dimorphic fungus Fonsecaea pedrosoi .", "Although it...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "shigellosis infections", "infectious disease epidemiology", "pediatrics", "bacterial diseases", "clinical epidemiology", "global health", "infectious disease control", "infectious diseases", "disease ecology", "epidemiology", "travel-associated diseases", "infectious disease mod...	Housefly Population Density Correlates with Shigellosis among Children in Mirzapur, Bangladesh: A Time Series Analysis	journal.pntd.0002280	null	[ [ "Shigella , a human host-restricted pathogen that invades and damages gut mucosa , persists as a public health problem in developing and transitional countries because of its high transmissibility via direct fecal-oral contact , the severe clinical disease it causes , widespread drug resistance that limits th...	[ "Shigella infections are a public health problem in developing and transitional countries because of high transmissibility , severity of clinical disease , widespread antibiotic resistance and lack of a licensed vaccine .", "Whereas Shigellae are known to be transmitted primarily by direct fecal-oral contact and ...	[ "Whereas previous researchers have noted that seasonal peaks in the numbers of houseflies and patients suffering from Shigella diarrheal infection seemed to coincide , this is the first research to quantify the association using time-series statistical methods .", "The results show that houseflies could account f...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "meiosis", "homologous chromosomes", "spermatocytes", "chromosome structure and function", "anaphase", "cell cycle and cell division", "cell processes", "germ cells", "mitosis", "sperm", "spermatids", "sex chromosomes", "animal cells", "chromosome biology", "cell biology", "biology and...	MNM and SNM maintain but do not establish achiasmate homolog conjunction during Drosophila male meiosis	journal.pgen.1008162	null	[ [ "In preparation for the first meiotic division , homologous chromosomes are paired up into bivalent chromosomes .", "Pairing into bivalents is required for their bi-polar orientation within the spindle during prometaphase of meiosis I ( MI ) .", "However , once all bivalents have reached bi-orientatio...	[ "The first meiotic division reduces genome ploidy .", "This requires pairing of homologous chromosomes into bivalents that can be bi-oriented within the spindle during prometaphase I . Thereafter , pairing is abolished during late metaphase I , and univalents are segregated apart onto opposite spindle poles durin...	[ "Meiosis is a special cell division that occurs in two steps , meiosis I and II .", "It converts diploid into haploid cells which can be used as gametes for sexual reproduction where two gametes from opposite sexes , a sperm and an oocyte , fuse to generate the zygote , the first diploid cell of the next generati...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "resonance frequency", "action potentials", "medicine and health sciences", "engineering and technology", "signal processing", "membrane potential", "electrophysiology", "neuroscience", "signal filtering", "systems science", "mathematics", "neuronal tuning", "computer and information science...	High-Frequency Resonance in the Gerbil Medial Superior Olive	journal.pcbi.1005166	null	[ [ "The intrinsic frequency preference of neurons for oscillatory inputs , otherwise known as subthreshold resonance , has been associated with the efficient extraction of auditory information .", "While turtle hair cells are highly tuned to pure tones up to 400Hz thanks to their intrinsic resonant propertie...	[ "A high-frequency , subthreshold resonance in the guinea pig medial superior olive ( MSO ) was recently linked to the efficient extraction of spatial cues from the fine structure of acoustic stimuli .", "We report here that MSO neurons in gerbil also have resonant properties and , based on our whole-cell recordin...	[ "Principal neurons of the medial superior olive ( MSO ) are fast and precise coincidence detectors involved in the neuronal computation of sound localization .", "We show that they exhibit resonance properties in vitro , responding to small oscillatory inputs , maximally at preferred frequencies .", "Their reso...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "computational neuroscience", "sensory systems", "biology", "neuroscience", "coding mechanisms" ]	Population Decoding in Rat Barrel Cortex: Optimizing the Linear Readout of Correlated Population Responses	journal.pcbi.1003415	null	[ [ "A goal of systems neuroscience is to achieve a quantitative understanding of how cortical neurons report sensory events in their population activity .", "The interlaced synaptic architecture of neuronal networks provides anatomical evidence for population decoding by downstream neuronal structures .", ...	[ "Sensory information is encoded in the response of neuronal populations .", "How might this information be decoded by downstream neurons ?", "Here we analyzed the responses of simultaneously recorded barrel cortex neurons to sinusoidal vibrations of varying amplitudes preceded by three adapting stimuli of 0 , 6...	[ "In the natural environment , animals are constantly exposed to sensory stimulation .", "A key question in systems neuroscience is how attributes of a sensory stimulus can be “read out” from the activity of a population of brain cells .", "We chose to investigate this question in the whisker-mediated touch syst...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/sensory systems" ]	What a Plant Sounds Like: The Statistics of Vegetation Echoes as Received by Echolocating Bats	journal.pcbi.1000429	null	[ [ "The filtering characteristics of a reflecting object are known as its frequency response and mainly depend on its acoustical cross-section .", "In a plant covered with leaves , the leaves will reflect most of the energy emitted by the bats [9] .", "The cross section of the leaves will have a major in...	[ "A critical step on the way to understanding a sensory system is the analysis of the input it receives .", "In this work we examine the statistics of natural complex echoes , focusing on vegetation echoes .", "Vegetation echoes constitute a major part of the sensory world of more than 800 species of echolocatin...	[ "More than 800 species of bats perceive their surroundings through echolocation .", "They emit ultrasonic pulses and analyze the information conveyed in the echoes returning from objects in their surroundings .", "This enables bats to orient in space , to acquire food and to perfectly function in complete darkn...	2009
[ "Introduction", "Results/Discussion", "Materials and Methods", "Supporting Information" ]	[ "infectious diseases", "genetics and genomics", "cryptococcus neoformans", "molecular biology" ]	A Link between Virulence and Homeostatic Responses to Hypoxia during Infection by the Human Fungal Pathogen Cryptococcus neoformans	journal.ppat.0030022	null	[ [ "Microbial pathogens must overcome numerous obstacles to infection to successfully colonize a host .", "It has been hypothesized that one of these barriers is hypoxia .", "Oxygen levels in mammalian tissues are found to be considerably below atmospheric levels [1–3] .", "Moreover , inflammation , ...	[ "Fungal pathogens of humans require molecular oxygen for several essential biochemical reactions , yet virtually nothing is known about how they adapt to the relatively hypoxic environment of infected tissues .", "We isolated mutants defective in growth under hypoxic conditions , but normal for growth in normoxic...	[ "Opportunistic environmental pathogens adapt to hostile conditions within the host to cause disease .", "We describe two pathways in the pathogenic fungus Cryptococcus neoformans that are both necessary for adaptation to hypoxia and required for its virulence .", "One pathway uses a pathway homologous to the ma...	2007
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "fish", "reproductive system", "gonads", "messenger rna", "vertebrates", "animals", "germ cells", "osteichthyes", "developmental biology", "sequence motif analysis", "embryos", "research and analysis methods", "sequence analysis", "embryology", "animal c...	A novel evolutionary conserved mechanism of RNA stability regulates synexpression of primordial germ cell-specific genes prior to the sex-determination stage in medaka	journal.pbio.3000185	In medaka a duplicate of dmrt1 acts as master sex-determining gene, with tightly controlled expression pattern in the gonads. This study shows that two RNA-binding proteins with antagonistic properties target a sequence motif in the 3’-UTR (D3U-box), promoting either RNA stabilization in germ cells or degradation in th...	[ [ "The gonads of vertebrates are characterized by the intimate association of germ cells and supporting somatic cells [1–4] .", "The precursor cells of the soma are derived from the embryonic lateral plate mesoderm , whereas germ cells originate from the germline lineage [5–9] .", "To carry out their hi...	[ "Dmrt1 is a highly conserved transcription factor , which is critically involved in regulation of gonad development of vertebrates .", "In medaka , a duplicate of dmrt1—acting as master sex-determining gene—has a tightly timely and spatially controlled gonadal expression pattern .", "In addition to transcriptio...	[ "The development of the gonads in vertebrates is mainly regulated by dmrt1 , a master sex-determining gene that has a timely and spatially controlled gonadal expression pattern .", "In addition to transcriptional regulation , a sequence motif located in the 3′ UTR ( D3U-box ) mediates transcript stability of dmrt...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Dampening the Signals Transduced through Hedgehog via MicroRNA miR-7 Facilitates Notch-Induced Tumourigenesis	journal.pbio.1001554	Analysis of tumorigenesis in Drosophila reveals a tumor-suppressor role for Hedgehog signaling in the context of oncogenic Notch signaling.	[ [ "A fundamental question in biology is what instructs cells to stop growing when the proper size is attained to commence terminal differentiation .", "Indeed , this issue is relevant not only to size regulation but also to cancer .", "One strategy that organisms use to promote the growth of organs invo...	[ "Fine-tuned Notch and Hedgehog signalling pathways via attenuators and dampers have long been recognized as important mechanisms to ensure the proper size and differentiation of many organs and tissues .", "This notion is further supported by identification of mutations in these pathways in human cancer cells .",...	[ "Growth control mechanisms ensure that organs attain the correct final size , generally averting tumour growth .", "This control is often linked to spatially confined domains known as organizers ( conserved signalling centres ) , established along the dorsal-ventral and anterior-posterior axes of the organ by the...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "cell signaling", "biochemistry", "signal transduction", "nuclear membrane", "cell biology", "post-translational modification", "proteins", "signaling molecules", "biology and life sciences", "cell nucleus", "cellular structures and organelles", "cytosol", "mapk signalin...	Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction	journal.pcbi.1006075	null	[ [ "Cells need to respond to a large variety of external stimuli such as environmental changes or extracellular communication signals .", "Signals transmitted from cell surface receptors to target genes in the nucleus are frequently transduced by cascades of covalent protein modifications .", "These modi...	[ "The spatial architecture of signaling pathways and the interaction with cell size and morphology are complex , but little understood .", "With the advances of single cell imaging and single cell biology , it becomes crucial to understand intracellular processes in time and space .", "Activation of cell surface...	[ "Frequently , cells detect signals at their surface , which are transmitted to the nucleus .", "The influence of cell shape and size is often neglected and cells are regarded as well-mixed compartments .", "However , the advance of modern microscopy has unraveled heterogeneous distribution of signaling molecule...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "humoral immunity", "immune cells", "immunity", "immunity to infections", "immunology", "biology" ]	Rapidly Boosted Plasma IL-5 Induced by Treatment of Human Schistosomiasis haematobium Is Dependent on Antigen Dose, IgE and Eosinophils	journal.pntd.0002149	null	[ [ "Schistosoma haematobium infection is the most prevalent form of human schistosomiasis and a major public health problem .", "Schistosomiasis haematobium is associated with bladder calcification , hydronephrosis , kidney failure , lesions of the genital tract and bladder carcinoma .", "S . haematobium...	[ "IgE specific to worm antigen ( SWA ) and pre-treatment eosinophil number , are associated with human immunity to re-infection with schistosomes after chemotherapeutic treatment .", "Treatment significantly elevates circulating IL-5 24-hr post-treatment of Schistosoma mansoni .", "Here we investigate if praziqu...	[ "Partial human immunity to infection with trematode worms of the genus Schistosoma is associated with IgE specific to adult worm-derived antigens and eosinophils .", "Treatment studies of Schistosoma infection allow us to examine the temporal features of the immune response post-antigen exposure , their inter-dep...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "genome-wide association studies", "medicine and health sciences", "gene regulation", "coronary heart disease", "genome analysis", "cardiology", "small interfering rnas", "genomics", "gene expression", "smad signaling", "genetic loci", "biochemistry", "signal transduction", "rna", "cell ...	Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk	journal.pgen.1007681	null	[ [ "Coronary artery disease ( CAD ) is the worldwide leading cause of death [1] .", "Numerous genetic loci have been associated with CAD with genome-wide association studies ( GWAS ) [2–8] and point to common inherited variation that mediates the genetic risk for this disease .", "Unfortunately , a major...	[ "Although numerous genetic loci have been associated with coronary artery disease ( CAD ) with genome wide association studies , efforts are needed to identify the causal genes in these loci and link them into fundamental signaling pathways .", "Recent studies have investigated the disease mechanism of CAD associ...	[ "Coronary artery disease ( CAD ) is the worldwide leading cause of death .", "The majority of risk for CAD is genetic in nature , i . e . , a feature of the genetic information that is transmitted to each individual from both parents , and primarily affects the disease processes in the blood vessel wall that regu...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "systems biology", "genome analysis tools", "caenorhabditis elegans", "animal genetics", "model organisms", "cellular stress responses", "genetic screens", "gene expression", "genetics", "gene regulation", "molecular genetics", "biology", "genomics", "molecular cell biol...	Identification of a Tissue-Selective Heat Shock Response Regulatory Network	journal.pgen.1003466	null	[ [ "The heat shock response ( HSR ) has been studied extensively as a cellular response to acute stress such as elevated temperature [1] .", "The master regulator of the HSR is Heat Shock Factor 1 ( HSF1 ) , a stress responsive transcription factor that regulates the inducible transcription of a family of ge...	[ "The heat shock response ( HSR ) is essential to survive acute proteotoxic stress and has been studied extensively in unicellular organisms and tissue culture cells , but to a lesser extent in intact metazoan animals .", "To identify the regulatory pathways that control the HSR in Caenorhabditis elegans , we perf...	[ "The heat shock response ( HSR ) is an essential stress response that functions to maintain protein folding homeostasis , or proteostasis , and whose critical role in human diseases is recently becoming apparent .", "Previously , most of our understanding of the HSR has come from cultured cells and unicellular or...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "biology", "molecular cell biology" ]	A Combination of H2A.Z and H4 Acetylation Recruits Brd2 to Chromatin during Transcriptional Activation	journal.pgen.1003047	null	[ [ "H2A . Z is a variant of the canonical histone H2A .", "Amongst the different variants of core histones that have been identified to date , H2A . Z is unique in being the only variant that is essential for viability and development in a number of organisms [1] , [2] , [3] , [4] .", "H2A . Z has been i...	[ "H2A . Z is an essential histone variant that has been implicated to have multiple chromosomal functions .", "To understand how H2A . Z participates in such diverse activities , we sought to identify downstream effector proteins that are recruited to chromatin via H2A . Z .", "For this purpose , we developed a ...	[ "Within the cell's nucleus , DNA closely associates with histone proteins , forming a structure known as chromatin .", "Packaging DNA into chromatin allows for efficient storage of the genome , and it also provides an additional means of regulating processes , such as gene expression , that require access to DNA ...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immunology", "immunology/immune response", "immunology/immunity to infections" ]	HLA Class I-T Cell Epitopes from trans-Sialidase Proteins Reveal Functionally Distinct Subsets of CD8+ T Cells in Chronic Chagas Disease	journal.pntd.0000288	null	[ [ "Trypanosoma cruzi , the causative agent of Chagas disease , constitutes a prominent human health problem in Central and South America [1] .", "It is estimated that approximately 4 million individuals have chagasic heart disease , making Chagas disease the most frequent cause of infectious cardiomyopathy ...	[ "Previously , we identified a set of HLA-A020 . 1-restricted trans-sialidase peptides as targets of CD8+ T cell responses in HLA-A0201+ individuals chronically infected by T . cruzi .", "Herein , we report the identification of peptides encoded by the same trans-sialidase gene family that bind alleles representat...	[ "At present , 16–20 million people in Central and South America are infected with Trypanosoma cruzi , the causative agent of Chagas disease in humans .", "The primary clinical consequence of the infection is a cardiomyopathy , which manifests in approximately 30% of infected individuals , many years after the ini...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Model-based Traction Force Microscopy Reveals Differential Tension in Cellular Actin Bundles	journal.pcbi.1004076	null	[ [ "Adherent cells continuously probe the mechanical properties of their environment by exerting forces through integrin-based sites of adhesions ( focal adhesions , FAs ) [1 , 2] .", "These cellular forces are mainly generated by myosin II motors that interact with different types of actin networks and bund...	[ "Adherent cells use forces at the cell-substrate interface to sense and respond to the physical properties of their environment .", "These cell forces can be measured with traction force microscopy which inverts the equations of elasticity theory to calculate them from the deformations of soft polymer substrates ...	[ "Adherent cells respond very sensitively not only to biochemical , but also to physical properties of their environment .", "For example , it has been shown that stem cell differentiation can be guided by substrate rigidity , which is sensed by cells by actively pulling on their environment with actomyosin-genera...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Understanding Heterogeneity in the Impact of National Neglected Tropical Disease Control Programmes: Evidence from School-Based Deworming in Kenya	journal.pntd.0004108	null	[ [ "Soil transmitted helminths ( STH: Ascaris lumbricoides , Trichuris trichiura , and the hookworms Necator americanus and Ancylostoma duodenale ) are among the diseases classified by the World Health Organization as neglected tropical diseases ( NTDs ) [1] .", "STHs are endemic in 166 countries worldwide [...	[ "The implementation of soil-transmitted helminth ( STH ) treatment programmes occurs in varied environmental , social and economic contexts .", "Programme impact will be influenced by factors that affect the reduction in the prevalence and intensity of infections following treatment , as well as the subsequent ra...	[ "Most countries with endemic soil-transmitted helminth ( STH ) infections have started implementing deworming programmes in recent years .", "However , the achievable impact on the prevalence and intensity of infections will depend on the socioeconomic and environmental context in which the programme is implement...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "deletion mutation", "chromosome structure and function", "engineering and technology", "metabolic processes", "synthetic biology", "microbiology", "mutation", "genome analysis", "genetic elements", "bacterial genetics", "microbial genetics", "microbial genomics", "syntheti...	Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti	journal.pgen.1007357	null	[ [ "The prediction of genotype-phenotype relationships is a fundamental goal of genetic , biomedical , and eco-evolutionary research , and this problem underpins the design of synthetic microbial systems for biotechnological applications [1] .", "Recently , there has been a shift away from the functional cha...	[ "Bacterial genome evolution is characterized by gains , losses , and rearrangements of functional genetic segments .", "The extent to which large-scale genomic alterations influence genotype-phenotype relationships has not been investigated in a high-throughput manner .", "In the symbiotic soil bacterium Sinorh...	[ "S . meliloti , which has traditionally facilitated ground-breaking insights into symbiotic communication , is also emerging as an excellent model for studying the evolution of functional relationships between bacterial chromosomes and anciently acquired accessory replicons .", "Multi-replicon genome architecture...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biology" ]	Inter-Allelic Prion Propagation Reveals Conformational Relationships among a Multitude of [PSI] Strains	journal.pgen.1002297	null	[ [ "Independent prion isolates that exhibit distinct biological characteristics are identified as prion strains .", "Successful propagation of yeast [PSI] prion strains in pure protein solutions unambiguously established that [PSI] strains were amyloid conformers of the same Sup35 protein [1]–[3] .", "Us...	[ "Immense diversity of prion strains is observed , but its underlying mechanism is less clear .", "Three [PSI] prion strains—named VH , VK , and VL—were previously isolated in the wild-type yeast genetic background .", "Here we report the generation and characterization of eight new [PSI] isolates , obtained by ...	[ "A prion is a host-encoded infectious protein that can usually adopt many distinct self-propagating conformations , referred to as prion strains .", "Upon interspecies transmission , a prion isolate can mutate and give rise to novel strains .", "It is not well understood how the strain diversity is created .", ...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "organismal evolution", "medicine and health sciences", "gut bacteria", "multiplex networks", "metabolic networks", "microbiology", "diet", "social sciences", "habits", "nutrition", "happiness", "network analysis", "microbial evolution", "bacteria", "computer and information sciences", ...	Social dynamics modeling of chrono-nutrition	journal.pcbi.1006714	null	[ [ "Recently , the human gut microbiota has emerged as a major research topic in many fields , from biology to neuroscience and medicine [1–5] .", "One of the main targets is to find out and explain how it may influence different aspects of physiology , such as gut-brain communication and human behaviors [1 ...	[ "Gut microbiota and human relationships are strictly connected to each other .", "What we eat reflects our body-mind connection and synchronizes with people around us .", "However , how this impacts on gut microbiota and , conversely , how gut bacteria influence our dietary behaviors has not been explored yet ....	[ "Human gut microbiota is able to influence different aspects of physiology , such as human behaviors .", "Our close social connections , in turn , impact on eating behaviors and diets , which play a key role in driving the gut microbial composition and its metabolic processes .", "To quantify the dynamic interp...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/comparative sequence analysis", "computational biology/macromolecular sequence analysis", "computational biology/sequence motif analysis" ]	Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines	journal.pcbi.1000338	null	[ [ "RNA is remarkably versatile [1] , [2] , acting not only as messengers to transfer genetic information from DNA to protein , but also as critical structural components [3] and catalytic enzymes [4] , [5] in the cell .", "More intriguingly , non-coding RNAs ( ncRNA ) have been found to play important regul...	[ "An increasing number of cis-regulatory RNA elements have been found to regulate gene expression post-transcriptionally in various biological processes in bacterial systems .", "Effective computational tools for large-scale identification of novel regulatory RNAs are strongly desired to facilitate our exploration...	[ "RNA is remarkably versatile , acting not only as messengers to transfer genetic information from DNA to protein but also as critical structural components and catalytic enzymes in the cell .", "More intriguingly , RNA elements in messenger RNAs have been widely found in bacteria to control the expression of thei...	2009
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biochemistry", "evolutionary ecology", "ecology", "phenotypes", "evolutionary processes", "ecological economics", "genetics", "biology and life sciences", "dna", "population genetics", "evolutionary biology", "evolutionary genetics", "genetic loci" ]	Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila	journal.pgen.1004775	null	[ [ "All organisms live in environments that vary through time and such environmental heterogeneity can impose highly variable selection pressures on populations .", "In this situation , an allele may be beneficial during one environmental regime and subsequently deleterious during another .", "Such an al...	[ "In many species , genomic data have revealed pervasive adaptive evolution indicated by the fixation of beneficial alleles .", "However , when selection pressures are highly variable along a species' range or through time adaptive alleles may persist at intermediate frequencies for long periods .", "So called “...	[ "Herein , we investigate the genomic basis of rapid adaptive evolution in response to seasonal fluctuations in the environment .", "We identify hundreds of polymorphisms ( seasonal SNPs ) that undergo dramatic shifts in allele frequency – on average between 40 and 60% – and oscillate between seasons repeatedly ov...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "genomics", "genetics", "biology", "computational biology", "genetics and genomics" ]	Rewiring of PDZ Domain-Ligand Interaction Network Contributed to Eukaryotic Evolution	journal.pgen.1002510	null	[ [ "PDZ domains are linear motif-mediated protein-protein interaction modules .", "PDZ domain-ligand interactions have been greatly expanded in metazoans and are widely used to assemble signaling complexes , including those found in neuronal synapses [1] .", "Thus , an understanding of how PDZ domain-lig...	[ "PDZ domain-mediated interactions have greatly expanded during metazoan evolution , becoming important for controlling signal flow via the assembly of multiple signaling components .", "The evolutionary history of PDZ domain-mediated interactions has never been explored at the molecular level .", "It is of grea...	[ "Rewiring of interactions is a powerful tool for the evolution of organism complexity .", "Rewiring among preexisting proteins provides a simple mechanism for the development of new signaling circuits by redirecting information flows without a gain or loss of genes .", "Particularly , interactions mediated by s...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "markov models", "population genetics", "invertebrate genomics", "animals", "animal models", "drosophila melanogaster", "model organisms", "mathematics", "experimental organism systems", "energy-producing organelles", "mitochondria", "bioenergetics", "population biology", ...	Fine scale mapping of genomic introgressions within the Drosophila yakuba clade	journal.pgen.1006971	null	[ [ "When two species hybridize , produce fertile hybrids and persist , three outcomes are possible .", "First , genes from one of the species might be selected against in their hybrids thus removing “foreign” genes from the gene pool , with the rate of removal being proportional to the product of the populat...	[ "The process of speciation involves populations diverging over time until they are genetically and reproductively isolated .", "Hybridization between nascent species was long thought to directly oppose speciation .", "However , the amount of interspecific genetic exchange ( introgression ) mediated by hybridiza...	[ "Even though hybridization is thought to be pervasive among animal species , the frequency of introgression , the transfer of genetic material between species , remains largely unknown .", "In this report we quantify the magnitude and genomic distribution of introgression among three species of Drosophila that en...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health and epidemiology", "population genetics", "microbiology", "parasitology", "parastic protozoans", "leishmania", "population biology", "zoology", "epidemiology", "biology", "protozoology", "evolutionary biology", "genetics and genomics" ]	Multifaceted Population Structure and Reproductive Strategy in Leishmania donovani Complex in One Sudanese Village	journal.pntd.0001448	null	[ [ "Leishmaniases are worldwide vector-borne diseases of humans and domestic animals , caused by protozoan parasites of the genus Leishmania .", "These parasitic infections are a serious public health problem , with about 350 million persons at risk and 2 , 357 , 000 new cases per year [1] .", "The genus...	[ "Leishmania species of the subgenus Leishmania and especially L . donovani are responsible for a large proportion of visceral leishmaniasis cases .", "The debate on the mode of reproduction and population structure of Leishmania parasites remains opened .", "It has been suggested that Leishmania parasites could...	[ "Leishmaniases are a serious public health problem , especially in developing countries , caused by Leishmania parasites and transmitted by sandfly bites .", "More information is needed on the population biology of these pathogens for diagnostic and epidemiological inquiries and for drug and vaccine elaboration ....	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases", "medicine and health sciences", "diagnostic medicine", "women's health", "obstetrics and gynecology" ]	The Colposcopic Atlas of Schistosomiasis in the Lower Female Genital Tract Based on Studies in Malawi, Zimbabwe, Madagascar and South Africa	journal.pntd.0003229	null	[ [ "Urogenital schistosomiasis is most commonly caused by S . haematobium; however , cases of urogenital infections with other schistosome species have been reported .", "S . haematobium is particularly common in Africa , but may also occur in the Middle East .", "Previously , S . haematobium infection h...	[ "Schistosoma ( S . ) haematobium is a neglected tropical disease which may affect any part of the genital tract in women .", "Female genital schistosomiasis ( FGS ) may cause abnormal vaginal discharge , contact bleeding , genital tumours , ectopic pregnancies and increased susceptibility to HIV .", "Symptoms m...	[ "Female genital schistosomiasis commonly remains undiagnosed due to its unacknowledged clinical manifestations .", "Millions of women in endemic areas are infected , and many suffer from abnormal vaginal discharge , contact bleeding , genital tumours , ectopic pregnancies , and an increased susceptibility to HIV ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "body fluids", "pathology and laboratory medicine", "immune activation", "immunology", "cell differentiation", "developmental biology", "signs and symptoms", "cytotoxic t cells", "white blood cells", "inflammation", "animal cel...	P2X7 Receptor Inhibition Improves CD34 T-Cell Differentiation in HIV-Infected Immunological Nonresponders on c-ART	journal.ppat.1005571	null	[ [ "Combined antiretroviral treatment ( c-ART ) has greatly improved the outcome of HIV infection .", "The key objective of c-ART is to suppress viral replication and to induce the production of sufficient numbers of CD4+ T cells to prevent AIDS-defining ( CD4+ T-cell counts below 200 cells/mm3 ) , and non-A...	[ "Peripheral CD4+ T-cell levels are not fully restored in a significant proportion of HIV+ individuals displaying long-term viral suppression on c-ART .", "These immunological nonresponders ( INRs ) have a higher risk of developing AIDS and non-AIDS events and a lower life expectancy than the general population , ...	[ "Combined antiretroviral therapy ( c-ART ) has dramatically decreased AIDS-related mortality and morbidity .", "Nevertheless increased morbidity is still present in HIV+ patients namely among those who experience poor immune CD4+ T-cell restoration under c-ART ( i . e . CD4 <500 cells/mm3 ) .", "The mechanisms ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "reproductive system", "markov models", "gene regulation", "invertebrate genomics", "mutation", "mathematics", "gene types", "hidden markov models", "gene expression", "molecular evolution", "chimeric genes", "animal genomics", "probability theory", "teste...	Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba	journal.pgen.1006795	null	[ [ "Tandem duplications are known as a source of genetic novelty that can contribute new genes with novel functions [1 , 2] .", "For example , duplication of homeobox loci has been associated developmental changes across vertebrates [3] .", "The globin gene families have achieved functional differences v...	[ "One common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes .", "Here , we use genome wide RNA-seq data from a population sample of Drosophila yakuba to test this ‘gene dosage’ hypothesis .", ...	[ "The enclosed work shows that whole gene duplications rarely affect gene expression , in contrast to widely held views that the adaptive value of duplicate genes is related to additive changes in gene expression due to gene copy number .", "We further explain how tandem duplications that create shuffled gene stru...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Role for Host Activation-Induced Cytidine Deaminase in Innate Immune Defense against KSHV	journal.ppat.1003748	null	[ [ "Herpesviruses have co-evolved with their hosts for millions of years , acquiring means to evade and manipulate host immune responses [1] .", "Evolutionary success of these viruses is highlighted by their life-long persistence , high prevalence and minimal pathological burden in immunocompetent hosts .", ...	[ "Activation-induced cytidine deaminase ( AID ) is specifically induced in germinal center B cells to carry out somatic hypermutation and class-switch recombination , two processes responsible for antibody diversification .", "Because of its mutagenic potential , AID expression and activity are tightly regulated t...	[ "Immune responses to pathogens rely heavily on the ability of B cells to generate a unique set of antibodies that can bind and eliminate the pathogen .", "Activation-induced cytidine deaminase ( AID ) is the enzyme specifically upregulated in activated B cells to diversify the antibody repertoire by introducing m...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cancer genetics", "protein interactions", "model organisms", "cell division", "dna", "chromatin", "protein kinase signaling cascade", "stress signaling cascade", "chromosome biology", "proteins", "biology", "biochemistry", "signal transduction", "nucleic acids", "genetics", "yeast and...	Site-Specific Phosphorylation of the DNA Damage Response Mediator Rad9 by Cyclin-Dependent Kinases Regulates Activation of Checkpoint Kinase 1	journal.pgen.1003310	null	[ [ "Eukaryotic cells have developed highly conserved surveillance pathways known as the DNA damage response ( DDR ) to preserve genome integrity after genotoxic insult .", "These pathways inhibit replication and segregation of damaged DNA by activating checkpoints and regulating transcription , replication a...	[ "The mediators of the DNA damage response ( DDR ) are highly phosphorylated by kinases that control cell proliferation , but little is known about the role of this regulation .", "Here we show that cell cycle phosphorylation of the prototypical DDR mediator Saccharomyces cerevisiae Rad9 depends on cyclin-dependen...	[ "Human cells activate the DNA damage response ( DDR ) to repair DNA damage and to prevent cells with DNA damage from proliferating .", "Alterations to the DDR are strongly implicated in the development of cancer .", "Using the budding yeast model system , we have studied how the regulation of the key DDR compon...	2013
[ "Introduction", "Results", "Discussion" ]	[ "cardiovascular disorders/arrhythmias, electrophysiology, and pacing", "physiology/cell signaling", "physiology/integrative physiology", "cardiovascular disorders/myocardial infarction", "computational biology/systems biology" ]	Oxidized Calmodulin Kinase II Regulates Conduction Following Myocardial Infarction: A Computational Analysis	journal.pcbi.1000583	null	[ [ "Calmodulin kinase II ( CaMKII ) mediates diverse roles in the heart , including excitation-contraction coupling , sinus node automaticity , apoptosis , hypertrophy , and gene transcription [1] , [2] .", "Mounting experimental evidence demonstrates an important role for CaMKII in heart disease and arrhyth...	[ "Calmodulin kinase II ( CaMKII ) mediates critical signaling pathways responsible for divergent functions in the heart including calcium cycling , hypertrophy and apoptosis .", "Dysfunction in the CaMKII signaling pathway occurs in heart disease and is associated with increased susceptibility to life-threatening ...	[ "Calmodulin kinase II ( CaMKII ) is a multifunctional serine/threonine kinase that regulates diverse functions in heart .", "Recently , a novel pathway for CaMKII activation was discovered where oxidation of the kinase at specific methionine residues produces persistent activity .", "This alternative oxidation-...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[]	A model of chronic, transmissible Otitis Media in mice	journal.ppat.1007696	null	[ [ "Acute otitis media ( AOM ) an inflammation of the middle ear caused by bacterial infections [1] affects a large portion of the human population every year and is a source of considerable morbidity and societal burden [2 , 3] .", "The majority of those afflicted are infants and children , and the conditio...	[ "Infection and inflammation of the middle ears that characterizes acute and chronic otitis media ( OM ) , is a major reason for doctor visits and antibiotic prescription , particularly among children .", "Nasopharyngeal pathogens that are commonly associated with OM in humans do not naturally colonize the middle ...	[ "Bacterial infections of the middle ears ( otitis media ) , particularly among children , is a global problem , causing fever , pain , conductive hearing loss and possible complications due to persistence/recurrence .", "Current understanding is poor , and advances are slowed by limitations of experimental system...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "chitin", "vesicles", "g1 phase", "cell cycle and cell division", "cell processes", "membrane proteins", "fungi", "model organisms", "materials science", "experimental organism systems", "cytokinesis", "cellular structures and organelles", "macromolecules", "extraction techniques", "mate...	Cell polarity protein Spa2 coordinates Chs2 incorporation at the division site in budding yeast	journal.pgen.1007299	null	[ [ "Before the end of mitosis , eukaryotic cells need to redirect the secretory machinery towards the site of division to ensure cells deposit additional plasma membrane between the two daughter cells .", "In addition , secretory vesicles transport key factors to enable cells to perform cytokinesis successfu...	[ "Deposition of additional plasma membrane and cargoes during cytokinesis in eukaryotic cells must be coordinated with actomyosin ring contraction , plasma membrane ingression and extracellular matrix remodelling .", "The process by which the secretory pathway promotes specific incorporation of key factors into th...	[ "Eukaryotic cells require division of all their cellular components before finally giving rise to two independent cells in a process named cytokinesis .", "Eukaryotic cells must build a physical barrier of plasma membrane , which is coupled with the remodelling of the extracellular matrix between the dividing cel...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "agriculture", "biology" ]	Surface α-1,3-Glucan Facilitates Fungal Stealth Infection by Interfering with Innate Immunity in Plants	journal.ppat.1002882	null	[ [ "The fungal cell wall , the outermost layer of the cell , is a physically rigid structure responsible for protecting the cell from environmental stresses and maintaining cell morphology .", "The fungal cell wall is primarily composed of polysaccharides , such as β- and α-glucans , chitin and mannans; howe...	[ "Plants evoke innate immunity against microbial challenges upon recognition of pathogen-associated molecular patterns ( PAMPs ) , such as fungal cell wall chitin .", "Nevertheless , pathogens may circumvent the host PAMP-triggered immunity .", "We previously reported that the ascomycete Magnaporthe oryzae , a f...	[ "Magnaporthe oryzae , Cochlioborus miyabeanus , and Rhizoctonia solani are the top three fungal pathogens that are responsible for devastating damage to the production of rice , a staple cereal for half of the world's population .", "These fungal pathogens infect host plants despite the plants' innate immunity , ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/innate immunity" ]	Virus-Infection or 5′ppp-RNA Activates Antiviral Signal through Redistribution of IPS-1 Mediated by MFN1	journal.ppat.1001012	null	[ [ "Type I and III interferons ( IFNs ) play central roles in innate immune responses to viral infections [1] , [2] , [3] , [4] .", "In a variety of tissues , IFN production is triggered by a cytoplasmic sensor , retinoic acid inducible gene I ( RIG-I ) -like Receptor ( RLR ) , which specifically senses vira...	[ "In virus-infected cells , RIG-I-like receptor ( RLR ) recognizes cytoplasmic viral RNA and triggers innate immune responses including production of type I and III interferon ( IFN ) and the subsequent expression of IFN-inducible genes .", "Interferon-β promoter stimulator 1 ( IPS-1 , also known as MAVS , VISA an...	[ "Virus-infections , such as influenza and chronic hepatitis C , are prominent diseases and outbreaks of newly emerging viruses are serious problems for modern society .", "Higher animals , including humans , are genetically equipped with mechanisms , collectively known as innate immunity , to counteract viral inf...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "condensation", "condensed matter physics", "animals", "blastulas", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "experimental organism systems", "embryos", "drosophila", "research and analysis meth...	A revised understanding of Tribolium morphogenesis further reconciles short and long germ development	journal.pbio.2005093	null	[ [ "Insects are the most speciose phylum of animals and display remarkable diversity in adult morphology [1] .", "Insect embryo development is also very diverse , particularly in the stages leading to the formation of the elongated , segmented embryo ( called the germband ) [2] .", "The molecular and mor...	[ "In Drosophila melanogaster , the germband forms directly on the egg surface and solely consists of embryonic tissue .", "In contrast , most insect embryos undergo a complicated set of tissue rearrangements to generate a condensed , multilayered germband .", "The ventral side of the germband is embryonic , whil...	[ "In many animals , certain groups of cells in the embryo do not directly contribute to the formation of adult structures .", "Instead , these so-called ‘extraembryonic tissues’ that support and facilitate development are discarded and degenerate prior to birth/hatching .", "Embryos of most insect species are th...	2018
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "spleen", "immunology", "vaccines", "preventive medicine", "mathematics", "forecasting", "statistics (mathematics)", "genome analysis", "bioassays and physiological analysis", "vaccination and immunization"...	Early Transcriptome Signatures from Immunized Mouse Dendritic Cells Predict Late Vaccine-Induced T-Cell Responses	journal.pcbi.1004801	null	[ [ "The development of vaccines against complex chronic diseases such as HIV or cancer has been largely unsuccessful so far .", "Novel vaccine technologies are rationally designed to generate appropriate protective immune responses [1] , notably efficient T-cell responses .", "Such vaccine vectors includ...	[ "Systems biology offers promising approaches for identifying response-specific signatures to vaccination and assessing their predictive value .", "Here , we designed a modelling strategy aiming to predict the quality of late T-cell responses after vaccination from early transcriptome analysis of dendritic cells ....	[ "Vaccines are designed to elicit effective immune responses against antigens .", "The various vector platforms used in vaccine development are diverse and complex , rendering the selection of promising vaccines vector challenging .", "We have designed a modeling strategy that predicts the propensity of vaccine ...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell death", "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "enzymes", "293t cells", "endoplasmic reticulum", "cell processes", "microbiology", "enzymology", "biological cultures", "hepacivirus", "pathogens", "viruses", "rna viruses", "cellular...	Enterovirus 71 protease 2Apro and 3Cpro differentially inhibit the cellular endoplasmic reticulum-associated degradation (ERAD) pathway via distinct mechanisms, and enterovirus 71 hijacks ERAD component p97 to promote its replication	journal.ppat.1006674	null	[ [ "Enterovirus 71 ( EV71 ) , which belongs to the Picornaviridae family Enterovirus genus , is a single-stranded positive-sense RNA virus [1] .", "This pathogen is the causative agent of hand , foot and mouth disease ( HFMD ) , and is especially the major cause of severe HFMD .", "Since the first report...	[ "Endoplasmic reticulum-associated degradation ( ERAD ) is an important function for cellular homeostasis .", "The mechanism of how picornavirus infection interferes with ERAD remains unclear .", "In this study , we demonstrated that enterovirus 71 ( EV71 ) infection significantly inhibits cellular ERAD by targe...	[ "Understanding of viral-host interactions is important for learning about viral pathogenesis and providing potential anti-viral targets .", "The protein quality control system , which consists of ERAD and autophagic degradation , is necessary for cellular homeostasis .", "Our previous studies and others have de...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "alkaloids", "medicine and health sciences", "chemical compounds", "drugs", "immunology", "microbiology", "vertebrates", "animals", "parasitic protozoans", "antimalarials", "xenopus", "germ cells", "animal models", "oocytes", "clinical medicine", "model organisms", "amphibians", "p...	Molecular Mechanisms for Drug Hypersensitivity Induced by the Malaria Parasite’s Chloroquine Resistance Transporter	journal.ppat.1005725	null	[ [ "Originally identified as the protein responsible for conferring resistance to the ‘wonder-drug’ chloroquine ( CQ ) [1 , 2] , the Plasmodium falciparum ‘chloroquine resistance transporter’ ( PfCRT ) has become a key player in the malaria parasite’s steadily expanding resistance to drugs [3–5] .", "The iso...	[ "Mutations in the Plasmodium falciparum ‘chloroquine resistance transporter’ ( PfCRT ) confer resistance to chloroquine ( CQ ) and related antimalarials by enabling the protein to transport these drugs away from their targets within the parasite’s digestive vacuole ( DV ) .", "However , CQ resistance-conferring i...	[ "In acquiring resistance to one drug , many pathogens and cancer cells become hypersensitive to other drugs .", "This phenomenon could be exploited to combat existing drug resistance and to delay the emergence of resistance to new drugs .", "However , much remains to be understood about the mechanisms that unde...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/nucleolus and nuclear bodies", "biochemistry/protein folding", "virology", "cell biology/nuclear structure and function" ]	Virus-Induced Chaperone-Enriched (VICE) Domains Function as Nuclear Protein Quality Control Centers during HSV-1 Infection	journal.ppat.1000619	null	[ [ "Protein quality control ( PQC ) is essential for maintaining active and properly folded proteins and for degrading aberrantly folded proteins that would otherwise interfere with vital cellular processes .", "PQC systems consist of a balance between protein refolding machinery ( molecular chaperones ) and...	[ "Virus-Induced Chaperone-Enriched ( VICE ) domains form adjacent to nuclear viral replication compartments ( RC ) during the early stages of HSV-1 infection .", "Between 2 and 3 hours post infection at a MOI of 10 , host protein quality control machinery such as molecular chaperones ( e . g . Hsc70 ) , the 20S pr...	[ "Protein quality control is a protective cellular mechanism by which damaged proteins are refolded or degraded so that they cannot interfere with essential cellular processes .", "In the event that protein quality control machinery cannot refold or degrade damaged proteins , sequestration of misfolded protein is ...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "cell biology/microbial physiology and metabolism", "immunology/cellular microbiology and pathogenesis", "genetics and genomics/gene expression", "infectious diseases/fungal infections", "genetics and genomics/gene function", "microbiology", "microbiology/microbial physiology and metabolism", "molecul...	Importance of Mitochondria in Survival of Cryptococcus neoformans Under Low Oxygen Conditions and Tolerance to Cobalt Chloride	journal.ppat.1000155	null	[ [ "Cryptococcus neoformans is an opportunistic fungal pathogen that causes life-threatening meningoencephalitis primarily in immunocompromised patients [1] .", "C . neoformans is an obligate aerobe and its natural environment includes pigeon droppings , soil contaminated with avian guano [1] and decaying tr...	[ "Cryptococcus neoformans is an environmental fungal pathogen that requires atmospheric levels of oxygen for optimal growth .", "For the fungus to be able to establish an infection , it must adapt to the low oxygen concentrations in the host environment compared to its natural habitat .", "In order to investigat...	[ "Cryptococcus neoformans is an obligate aerobic fungus that requires atmospheric levels of oxygen ( 21% ) for optimal growth .", "However , the fungus is able to cause life-threatening brain infections in humans , where the oxygen tension is significantly lower than 21% .", "To understand the pathobiology of Cr...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "computational biology/population genetics", "computational biology/macromolecular structure analysis", "computer science/applications", "genetics and genomics/comparative genomics", "computational biology/sequence motif analysis", "evolutionary biology/evolutionary and comparative genetics", "computati...	Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences	journal.pcbi.1000421	null	[ [ "Analysis of discrete linear sequences has played an increasingly important role in biology .", "In particular , the detection of heterogeneous regions among sequences can aid in understanding the heterogeneous processes that act upon those regions [1] , [2] .", "Therefore , determining whether specif...	[ "A major analytical challenge in computational biology is the detection and description of clusters of specified site types , such as polymorphic or substituted sites within DNA or protein sequences .", "Progress has been stymied by a lack of suitable methods to detect clusters and to estimate the extent of clust...	[ "The invention and application of high-throughput technologies for DNA sequencing have resulted in an increasing abundance of biological sequence data .", "DNA or protein sequence data are naturally arranged as discrete linear sequences , and one of the fundamental challenges of analysis of sequence data is the d...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology/behavioral ecology" ]	Human Probing Behavior of Aedes aegypti when Infected with a Life-Shortening Strain of Wolbachia	journal.pntd.0000568	null	[ [ "Insect transmitted diseases such as malaria and dengue occur in more than 100 countries worldwide , placing at risk around half the world's population .", "The disease burden is high with more than 500 million cases each year .", "Despite various vector control measures , there continues to be emerge...	[ "Mosquitoes are vectors of many serious pathogens in tropical and sub-tropical countries .", "Current control strategies almost entirely rely upon insecticides , which increasingly face the problems of high cost , increasing mosquito resistance and negative effects on non-target organisms .", "Alternative strat...	[ "Mosquitoes transmit diseases when they are actively searching for a source of blood .", "This so called probing behavior comprises the “searching” time , the beginning of the feeding process until the first sign of blood can be seen within the insect body .", "The manipulation of this behavior can have importa...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "organ transplantation", "cardiac transplantation", "biopsy", "cardiovascular anatomy", "variant genotypes", "genetic mapping", "surgical and invasive medical procedures", "molecular biology techniques", "genotyping", "heart-lung transplantation", "research and ...	Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype	journal.pcbi.1005629	null	[ [ "Solid-organ transplantation is now a common practice [1] .", "However , the clinical outcomes remain poor with median survival rate of 5 . 3 years for lung and 11 years for heart [2–4] .", "Accurate monitoring of allograft health is essential for long-term survival of the transplant recipient .", ...	[ "Quantification of cell-free DNA ( cfDNA ) in circulating blood derived from a transplanted organ is a powerful approach to monitoring post-transplant injury .", "Genome transplant dynamics ( GTD ) quantifies donor-derived cfDNA ( dd-cfDNA ) by taking advantage of single-nucleotide polymorphisms ( SNPs ) distribu...	[ "More than 180 , 000 people live with organ transplants in the US .", "Monitoring the health of the allograft is a critically important component of post-transplant therapy .", "Recently , we have demonstrated that cell-free DNA ( cfDNA ) enables diagnosis of post-transplant rejection .", "In this approach , ...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	A Sero-epidemiological Approach to Explore Transmission of Mycobacterium ulcerans	journal.pntd.0004387	null	[ [ "Buruli ulcer ( BU ) is a neglected tropical skin disease presenting with a wide range of cutaneous manifestations , from non-ulcerated nodules , plaques or oedema to characteristic necrotizing ulcers [1] .", "While BU cases have been reported in more than 30 countries worldwide , most patients are from i...	[ "The debilitating skin disease Buruli ulcer ( BU ) is caused by infection with Mycobacterium ulcerans .", "While various hypotheses on potential reservoirs and vectors of M . ulcerans exist , the mode of transmission has remained unclear .", "Epidemiological studies have indicated that children below the age of...	[ "Buruli ulcer is a debilitating skin disease caused by Mycobacterium ulcerans .", "Although the understanding of this enigmatic pathogen has improved after decades of research , the mode of transmission is yet to be fully elucidated .", "Recent epidemiological studies have shown an underrepresentation of Buruli...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "disabilities", "pathology and laboratory medicine", "pathogens", "microbiology", "social sciences", "viruses", "age groups", "rna viruses", "anxiety", "mood disorders", "families", "public and occupational health", "emotions", "medical micro...	The association of depression, anxiety, and stress with caring for a child with Congenital Zika Syndrome in Brazil; Results of a cross-sectional study	journal.pntd.0007768	null	[ [ "Brazil hit international headlines in late 2015 with the birth of thousands of babies with microcephaly , which was soon linked to congenital infection with the Zika Virus ( ZIKV ) .", "It was quickly apparent that babies born after congenital ZIKV infection experience a range of severe conditions beyond...	[ "Zika virus ( ZIKV ) infection in pregnancy can cause microcephaly and a wide spectrum of severe adverse outcomes , collectively called “Congenital Zika Syndrome” ( CZS ) .", "Parenting a child with disabilities can have adverse mental health impacts , but these associations have not been fully explored in the co...	[ "The 2015 Zika epidemic in Brazil gained international attention with the birth of thousands of babies with severe adverse outcomes , collectively called “Congenital Zika Syndrome” ( CZS ) .", "Parenting a child with disabilities can be extremely stressful , and in other settings is linked to depression , anxiety...	2019
[ "Introduction", "Models and methods", "Results", "Discussion" ]	[ "resonance frequency", "action potentials", "medicine and health sciences", "vesicles", "nervous system", "membrane potential", "electrophysiology", "neuroscience", "cellular structures and organelles", "mood disorders", "crystallographic techniques", "research and analysis methods", "animal...	Phase changes in neuronal postsynaptic spiking due to short term plasticity	journal.pcbi.1005634	null	[ [ "Chemical synapses between neurons in the brain exhibit short-term plasticity ( STP ) such that the postsynaptic signal produced by the arrival of an action potential at a presynaptic terminal is not identical for each action potential , but varies stochastically and functionally with respect to the presynapt...	[ "In the brain , the postsynaptic response of a neuron to time-varying inputs is determined by the interaction of presynaptic spike times with the short-term dynamics of each synapse .", "For a neuron driven by stochastic synapses , synaptic depression results in a quite different postsynaptic response to a large ...	[ "The synapses that connect neurons in the brain are far from being simple relay points that pass a signal from one neuron to another .", "There is now much evidence that long term changes in the strength of such connections , which determines the amplitude of the received signal , underpin learning and memory in ...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "auditory cortex", "medicine and health sciences", "diagnostic radiology", "functional magnetic resonance imaging", "experimental design", "brain", "social sciences", "neuroscience", "learning and memory", "magnetic resonance imaging", "research design", "hemodynamics", "cognition", "brain...	Differential sustained and transient temporal processing across visual streams	journal.pcbi.1007011	null	[ [ "How do high-level visual areas encode the temporal characteristics of our visual experience ?", "The temporal sensitivity of early visual areas has been studied with electrophysiology in non-human primates [1–4] and recently using fMRI in humans [5 , 6] .", "However , the nature of temporal processin...	[ "How do high-level visual regions process the temporal aspects of our visual experience ?", "While the temporal sensitivity of early visual cortex has been studied with fMRI in humans , temporal processing in high-level visual cortex is largely unknown .", "By modeling neural responses with millisecond precisio...	[ "How does the brain encode the timing of our visual experience ?", "Using functional magnetic resonance imaging ( fMRI ) and a generative temporal model with millisecond resolution , we discovered that visual regions in the lateral and ventral processing streams fundamentally differ in their temporal processing o...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Optimal Census by Quorum Sensing	journal.pcbi.1004238	null	[ [ "To successfully colonize an environment , many bacteria engage in collective tasks , for instance the synthesis of a biofilm matrix or the secretion of enzymes or virulence factors .", "In general , such tasks can only be performed efficiently in a prescribed temporal order and at high enough cell densit...	[ "Quorum sensing is the regulation of gene expression in response to changes in cell density .", "To measure their cell density , bacterial populations produce and detect diffusible molecules called autoinducers .", "Individual bacteria internally represent the external concentration of autoinducers via the leve...	[ "Bacteria regulate gene expression in response to changes in cell density in a process called quorum sensing .", "To synchronize their gene-expression programs , these bacteria need to glean as much information as possible about their cell density .", "Our study is the first to physically model the flow of info...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "proteins", "virology", "protein structure", "viral enzymes", "biology", "microbiology", "viral replication" ]	Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5 Reveals a Conserved Methyltransferase-Polymerase Interface	journal.ppat.1003549	null	[ [ "As a genus of viruses in the family Flaviviridae among positive-strand RNA viruses , flaviviruses have more than 70 members , often causing human encephalitis and hemorrhagic diseases .", "Among these , the mosquito-borne species include important human pathogens such as dengue ( DENV ) , yellow fever ( ...	[ "The flavivirus NS5 harbors a methyltransferase ( MTase ) in its N-terminal ≈265 residues and an RNA-dependent RNA polymerase ( RdRP ) within the C-terminal part .", "One of the major interests and challenges in NS5 is to understand the interplay between RdRP and MTase as a unique natural fusion protein in viral ...	[ "Due to limited coding capacity , RNA viruses often generate proteins that contain more than one enzyme module to fulfill their rather complicated life cycle .", "Among those , the flavivirus nonstructural protein NS5 comprises an N-terminal methyltransferase ( MTase ) and a C-terminal RNA-dependent RNA polymeras...	2013
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "schistosoma", "invertebrates", "helminths", "gene regulation", "messenger rna", "dna-binding proteins", "animals", "micrornas", "bioassays and physiological analysis", "research and analysis methods", "schistosoma japonicum", "proteins", "gene expression", "microarrays", "biochemistry",...	Comprehensive Transcriptome Analysis of Sex-Biased Expressed Genes Reveals Discrete Biological and Physiological Features of Male and Female Schistosoma japonicum	journal.pntd.0004684	null	[ [ "Schistosomiasis , caused by infection with blood flukes ( digenetic trematodes ) of the genus Schistosoma , remains one of the most serious parasitic diseases worldwide , afflicting more than 200 million people , with close to 800 million at risk [1 , 2] .", "This debilitating disease causes an annual nu...	[ "Schistosomiasis is a chronic and debilitating disease caused by blood flukes ( digenetic trematodes ) of the genus Schistosoma .", "Schistosomes are sexually dimorphic and exhibit dramatic morphological changes during a complex lifecycle which requires subtle gene regulatory mechanisms to fulfil these complex bi...	[ "Schistosomiasis is a persistent but neglected parasitic disease , afflicting more than 200 million people worldwide .", "Complex gene regulatory mechanisms are equipped by its causative reagents , parasites of the genus Schistosoma .", "Dissecting these mechanisms thus will be beneficial for better control of ...	2016
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[]	Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton	journal.pgen.1005724	null	[ [ "DNA methylation , a conserved epigenetic mark in most eukaryotes , is essential for growth and development and is associated with many epigenetic phenomena , including imprinting and transposon silencing [1–5] .", "In plants , DNA is methylated in CG , CHG and CHH ( H = A , T , or C ) sites through disti...	[ "DNA methylation is essential for plant and animal development .", "In plants , methylation occurs at CG , CHG , and CHH ( H = A , C or T ) sites via distinct pathways .", "Cotton is an allotetraploid consisting of two progenitor genomes .", "Each cotton fiber is a rapidly-elongating cell derived from the ovu...	[ "Cotton is the world’s largest source of renewable textile fiber and is an allotetraploid crop consisting of two progenitor genomes .", "In plants , de novo CHH ( H = A , T , or C ) methylation depends on RNA-directed DNA methylation ( RdDM ) and CHROMOMETHYLASE2 ( CMT2 ) -mediated pathways .", "The biological ...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "skin", "medicine and health sciences", "keratinocytes", "reproductive system", "integumentary system", "classical mechanics", "geometry", "aspect ratio", "epithelial cells", "mathematics", "damage mechanics", "basal cells", "digestive system", "research and analysis methods", "bending",...	Invagination of Ectodermal Placodes Is Driven by Cell Intercalation-Mediated Contraction of the Suprabasal Tissue Canopy	journal.pbio.1002405	A study of teeth, hair follicles, and mammary ducts reveals that the superficial layer of the initial tissue thickening, or placode, contracts by a novel form of cell intercalation. This exerts a bending force to pinch the underlying layer into a fold.	[ [ "Understanding how tissues form physically ( morphogenesis ) is a major frontier , both in developmental biology and organ regeneration using stem cells [1 , 2] .", "Epithelial bending , especially invagination , is a recurrent morphogenetic event in development [3–12] , but our knowledge of the underlyin...	[ "Ectodermal organs such as teeth , hair follicles , and mammary glands begin their development as placodes .", "These are local epithelial thickenings that invaginate into mesenchymal space .", "There is currently little mechanistic understanding of the cellular processes driving the early morphogenesis of thes...	[ "Teeth , hair follicles , and skin ducts ( including mammary and sweat glands ) are initially formed in the embryo as slight thickenings of a flat epithelium that are called placodes .", "These then invaginate to form dimples or pits that make the characteristic structures found in the adult .", "While some inv...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "luciferase", "nucleic acid synthesis", "medicine and health sciences", "crystal structure", "enzymes", "condensed matter physics", "dna-binding proteins", "enzymology", "microbiology", "limbs (anatomy)", "thumbs", "ribozymes", "polymerases", "rna synthesis", "crystallography", "chemic...	Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling	journal.ppat.1005737	null	[ [ "Several flaviviruses , such as DENV , Japanese Encephalitis virus ( JEV ) , West Nile virus ( WNV ) , Yellow Fever virus ( YFV ) or Tick-borne encephalitis virus ( TBEV ) are major human pathogens , whilst Zika ( ZIKV ) is an emerging flavivirus of global significance causing severe neurological conditions i...	[ "Flaviviruses comprise major emerging pathogens such as dengue virus ( DENV ) or Zika virus ( ZIKV ) .", "The flavivirus RNA genome is replicated by the RNA-dependent-RNA polymerase ( RdRp ) domain of non-structural protein 5 ( NS5 ) .", "This essential enzymatic activity renders the RdRp attractive for antivir...	[ "Dengue virus ( DENV ) is the world’s most prevalent mosquito-borne viral disease and nearly 40% of the world’s population is at risk of infection .", "Currently , no specific drugs are available to treat dengue or other flaviviral diseases .", "DENV NS5 is a large protein of 900 amino acids composed of two dom...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Nitric Oxide Regulated Small RNA Controls Expression of Genes Involved in Redox Homeostasis in Bacillus subtilis	journal.pgen.1004957	null	[ [ "Small regulatory RNAs ( sRNA ) have been shown to play key roles in the regulation of a wide variety of cellular processes in bacteria , including stress responses , environmental signaling and virulence [1 , 2] .", "They generally regulate at the post-transcriptional level by altering mRNA translation o...	[ "RsaE is the only known trans-acting small regulatory RNA ( sRNA ) besides the ubiquitous 6S RNA that is conserved between the human pathogen Staphylococcus aureus and the soil-dwelling Firmicute Bacillus subtilis .", "Although a number of RsaE targets are known in S . aureus , neither the environmental signals t...	[ "Bacteria have evolved various strategies to continually monitor the redox state of the internal and external environments to prevent cell damage and/or to protect them from host defense mechanisms .", "These signals modify the expression of genes , allowing bacteria to adapt to altered redox environments and to ...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "genome-wide association studies", "medicine and health sciences", "statistics", "metaanalysis", "coronary heart disease", "mathematics", "probability distribution", "genome analysis", "molecular genetics", "research and analysis methods", "cardiology", "mathematical and statistical techniques...	Bayesian multiple logistic regression for case-control GWAS	journal.pgen.1007856	null	[ [ "Common , noninfectious diseases are responsible for over ⅔ of the deaths worldwide .", "Genome wide association studies ( GWAS ) have opened up a fundamentally new approach to identify novel regions of the genome which are associated with these complex human diseases .", "In the past decade , GWAS id...	[ "Genetic variants in genome-wide association studies ( GWAS ) are tested for disease association mostly using simple regression , one variant at a time .", "Standard approaches to improve power in detecting disease-associated SNPs use multiple regression with Bayesian variable selection in which a sparsity-enforc...	[ "In recent years , genome wide association studies ( GWAS ) have become the primary approach for identifying genetic variants associated with the origination of complex diseases .", "In case-control GWAS , the genotypes of roughly equal number of diseased ( “cases” ) and healthy ( “controls” ) people are compared...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "horizontal gene transfer", "organismal evolution", "medicine and health sciences", "toxins", "pathology and laboratory medicine", "evolutionary biology", "pathogens", "plasmids", "microbiology", "gene transfer", "toxicology", "toxic agents", "secretion systems", "microbi...	A bacterial toxin-antitoxin module is the origin of inter-bacterial and inter-kingdom effectors of Bartonella	journal.pgen.1007077	null	[ [ "The virulence of many bacterial pathogens depends on effector proteins that are translocated by dedicated secretion systems into eukaryotic host cells where they manipulate various processes in favor of the bacterium [1] .", "Previous work established that these host-targeting secretion systems have evol...	[ "Host-targeting type IV secretion systems ( T4SS ) evolved from conjugative T4SS machineries that mediate interbacterial plasmid transfer .", "However , the origins of effectors secreted by these virulence devices have remained largely elusive .", "Previous work showed that some effectors exhibit homology to to...	[ "Many bacterial pathogens use secretion systems to translocate effector proteins into host cells where they manipulate cell functions in favor of the pathogen .", "It is well-known that these secretion systems evolved from ancestors with functions in genuine bacterial contexts , but the origins of their secreted ...	2017
[ "Introduction", "Keep your data correct", "Correctly interpret your data", "Present your data in a useful way" ]	[ "data acquisition", "education", "statistics", "enzymology", "mathematics", "information technology", "enzyme kinetics", "data processing", "research and analysis methods", "computer and information sciences", "mathematical and statistical techniques", "monte carlo method", "biochemistry", ...	Ten quick tips for getting the most scientific value out of numerical data	journal.pcbi.1006141	null	[ [ "In many studies in the life sciences and other fields , findings are derived from some type of experiment via the analysis of numerical data in one form or another .", "The typical workflow , cf .", "Fig 1 , involves multiple steps where good scientific practice needs to be followed so that sound res...	[ "Most studies in the life sciences and other disciplines involve generating and analyzing numerical data of some type as the foundation for scientific findings .", "Working with numerical data involves multiple challenges .", "These include reproducible data acquisition , appropriate data storage , computationa...	[ "Data expressed as numbers are ubiquitous in research in the life sciences and other fields .", "The typical scientific workflow using such numerical data consists of analyzing the raw data to obtain numerical results , followed by interpreting the results and presenting derived findings .", "In this article , ...	2018

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.