bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatitis E in southern Vietnam: Seroepidemiology in humans and molecular epidemiology in pigs
Authors: Berto A. , Pham H. A. , Thao T. T. N. , Vy N. H. T. , Caddy S. L. , Hiraide R. , Tue N. T. , Goodfellow I. , Carrique‐Mas J. J. , Thwaites G. E. , Baker S. , Boni M. F. ,   the VIZIONS consortium
Published: June 2017

SummaryViral pathogens account for a significant proportion of the burden of emerging infectious diseases in humans. The Wellcome Trust‐Vietnamese Initiative on Zoonotic Infections (WT‐VIZIONS) is aiming to understand the circulation of viral zoonotic pathogens in animals that pose a potential risk to human health. Evidence suggests that human exposure and infections with hepatitis E virus (HEV) genotypes (GT) 3 and 4 results from zoonotic transmission. Hypothesising that HEV GT3 and GT4 are circulating in the Vietnamese pig population and can be transmitted to humans, we aimed to estimate the seroprevalence of HEV exposure in a population of farmers and the general population. We additionally performed sequence analysis of HEV in pig populations in the same region to address knowledge gaps regarding HEV circulation and to evaluate if pigs were a potential source of HEV exposure. We found a high prevalence of HEV GT3 viral RNA in pigs (19.1% in faecal samples and 8.2% in rectal swabs) and a high HEV seroprevalence in pig farmers (16.0%) and a hospital‐attending population (31.7%) in southern Vietnam. The hospital population was recruited as a general‐population proxy even though this particular population subgroup may introduce bias. The detection of HEV RNA in pigs indicates that HEV may be a zoonotic disease risk in this location, although a larger sample size is required to infer an association between HEV positivity in pigs and seroprevalence in humans.
Epidemiology of campylobacteriosis in Denmark 2000–2015
Authors: Kuhn K. G. , Nielsen E. M. , Mølbak K. , Ethelberg S. 
Published: June 2017

SummaryCampylobacter is the most frequently occurring cause of bacterial gastroenteritis in Europe. Unlike other zoonotic diseases, European‐wide incidences of Campylobacter infections have increased during the past decade, resulting in a significant disease burden. In Denmark, campylobacteriosis is notifiable by laboratory and a unique registration system of electronic transfer and storage of notified Campylobacter cases linked to the national person register of age, gender and geographical location allows collection of comprehensive case data. Using national surveillance data, we describe Campylobacter infections in Denmark from 2000 to 2015, focusing on age‐specific incidences, geography, seasonality and outbreaks. During the observed period, a total of 60,725 Campylobacter infections were registered with a mean annual incidence of 69.3 cases/100,000 population. From 2000 to 2014, the incidence of campylobacteriosis decreased by 20%, followed by an apparent increase of 20% from 2014 to 2015. Approximately one‐third of cases were travel‐related. Incidences were highest in males, young adults aged 20–29 years and children under 5 years of age. Generally, children under 10 years of age living in rural areas were at higher risk of infection. Infection patterns were seasonal with an increase from May to October, peaking in August. Outbreaks were identified each year, including four large waterborne outbreaks which all occurred following heavy rainfall events. For the most part, patterns of Campylobacter infection in Denmark during 2000 to 2015 remained remarkably constant and followed what is known about the disease with respect to demographic, temporal and spatial characteristics. To establish better targeted prevention and control measures, the current knowledge gaps regarding both Campylobacter microbiology (degree of clonal diversity and clustering) and the importance of different risk factors (food versus environment/climate) need to be filled.
Skeletal myofiber vascular endothelial growth factor is required for the exercise training‐induced increase in dentate gyrus neuronal precursor cells
Authors: Rich Benjamin , Scadeng Miriam , Yamaguchi Masahiro , Wagner Peter D. , Breen Ellen C. 
Published: June 2017

Key points
Peripheral vascular endothelial growth factor (VEGF) is necessary for exercise to stimulate hippocampal neurogenesis.
Here we report that skeletal myofiber VEGF directly or indirectly regulates exercise‐signalled proliferation of neuronal precursor cells.
Our results found skeletal myofiber VEGF to be necessary for maintaining blood flow through hippocampal regions independent of exercise training state.
This study demonstrates that skeletal myofiber VEGF is required for the hippocampal VEGF response to acute exercise.
These results help to establish the mechanisms by which exercise, through skeletal myofiber VEGF, affects the hippocampus.
AbstractExercise signals neurogenesis in the dentate gyrus of the hippocampus. This phenomenon requires vascular endothelial growth factor (VEGF) originating from outside the blood–brain barrier, but no cellular source has been identified. Thus, we hypothesized that VEGF produced by skeletal myofibers plays a role in regulating hippocampal neuronal precursor cell proliferation following exercise training. This was tested in adult conditional skeletal myofiber‐specific VEGF gene‐ablated mice (VEGFHSA−/−) by providing VEGFHSA−/− and non‐ablated (VEGFf/f) littermates with running wheels for 14 days. Following this training period, hippocampal cerebral blood flow (CBF) was measured by functional magnetic resonance imaging (fMRI), and neuronal precursor cells (BrdU+/Nestin+) were detected by immunofluorescence. The VEGFf/f trained group showed improvements in both speed and endurance capacity in acute treadmill running tests (P < 0.05). The VEGFHSA−/− group did not. The number of proliferating neuronal precursor cells was increased with training in VEGFf/f (P < 0.05) but not in VEGFHSA−/− mice. Endothelial cell (CD31+) number did not change in this region with exercise training or skeletal myofiber VEGF gene deletion. However, resting blood flow through the hippocampal region was lower in VEGFHSA−/− mice, both untrained and trained, than untrained VEGFf/f mice (P < 0.05). An acute hypoxic challenge decreased CBF (P < 0.05) in untrained VEGFf/f, untrained VEGFHSA−/− and trained VEGFHSA−/− mice, but not trained VEGFf/f mice. VEGFf/f, but not VEGFHSA−/−, mice were able to acutely run on a treadmill at an intensity sufficient to increase hippocampus VEGF levels. These data suggest that VEGF expressed by skeletal myofibers may directly or indirectly regulate both hippocampal blood flow and neurogenesis.
Draft Genome Sequences of Eight Crimean-Congo Hemorrhagic Fever Virus Strains
Authors: Koehler J. W. , Delp K. L. , Kearney B. J. , Conrad T. A. , Schoepp R. J. , Garrison A. R. , Altamura L. A. , Rossi C. A. , Minogue T. D. 
Published: June 2017

ABSTRACT
Crimean-Congo hemorrhagic fever virus (CCHFV) is a geographically widespread RNA virus with a high degree of genomic diversity that complicates sequence-based diagnostics. Here, we sequenced eight CCHFV strains for improved assay design and deposition into FDA-ARGOS, the FDA’s pathogen database for development and verification of next generation sequencing assays.
Draft Genome of
Halomonas lionensis
RHS90
T
, a Stress-Tolerant Gammaproteobacterium Isolated from Mediterranean Sea Sediments
Authors: Gaboyer Frédéric , Maignien Loïs , Jebbar Mohamed , Alain Karine 
Published: June 2017

ABSTRACT

Members of the genus
Halomonas
are physiologically versatile and harbor ecological adaptations enabling the colonization of contrasted environments. We present here the draft genome of
Halomonas lionensis
RHS90
T
, isolated from Mediterranean Sea sediments. Numerous genes related to stress tolerance, DNA repair, or external signal-sensing systems were predicted, which could represent selective advantages of this marine bacterium.
Draft Genome Report of Bacillus altitudinis SORB11, Isolated from the Indian Sector of the Southern Ocean
Authors: Halder Urmi , Banerjee Aparna , Chaudhry Vasvi , Varshney Rajeev K. , Mantri Shrikant , Bandopadhyay Rajib 
Published: June 2017

ABSTRACT

Here, we present the draft genome sequence of
Bacillus altitudinis
SORB11, which is tolerant to UV radiation. The strain was isolated from the Indian sector of the Southern Ocean at a depth of 3.8 km. The genome sequence information reported here for
B. altitudinis
SORB11 gives the basis of its UV resistance mechanism and provides data for further comparative studies with other bacteria resistant to UV radiation.
Complete Genome Sequence of Vibrio coralliilyticus 58, Isolated from Pacific Oyster (
Crassostrea gigas
) Larvae
Authors: Kim Hyoun Joong , Kim Ji Hyung , Jun Jin Woo , Giri Sib Sankar , Chi Cheng , Yun Saekil , Kim Sang Guen , Kim Sang Wha , Kang Jeong Woo , Jeong Dae Gwin , Park Se Chang 
Published: June 2017

ABSTRACT

We report here the complete genome of
Vibrio coralliilyticus
strain 58, which was originally isolated from inactive Pacific oyster (
Crassostrea gigas
) larvae in Japan. The assembled genome consisted of two chromosomes and one plasmid. These data will provide valuable information and important insights into the biodiversity of this organism.
Metagenomic 16S rRNA Sequencing Analysis of Pacific Oyster (
Crassostrea gigas
) Microbiota from the Puget Sound Region in the United States
Authors: Li Zhen , Wang Leyi 
Published: June 2017

ABSTRACT

This is the first study analyzing Pacific oyster microbiota in the Puget Sound estuarine system using a next-generation sequencing method. Taxonomic analysis indicated that
Tenericutes, Chlamydiae
,
Proteobacteria
, and
Firmicutes
were the most abundant phyla. Small numbers of operational taxonomic units (OTUs) belonging to the
Vibrio
genus were detected in all the oyster microbiome samples.
Complete Genome Sequences of Five Representative Staphylococcus aureus ST398 Strains from Five Major Sequence Heterogeneity Groups of a Diverse Isolate Collection
Authors: McClure Jo-Ann , Zhang Kunyan 
Published: June 2017

ABSTRACT

Staphylococcus aureus
sequence type 398 (ST398) is a rapidly emerging livestock-associated strain causing zoonotic disease in humans. The course of pathogen evolution remains unclear, prompting whole-genome comparative studies in attempts to elucidate this issue. We present the full, annotated genomes of five newly isolated representative ST398 strains from five major sequence heterogeneity groups of our diverse isolate collection.
Genome Sequence of Paracoccus contaminans LMG 29738
T
, Isolated from a Water Microcosm
Authors: Aurass Philipp , Karste Susanne , Trost Eva , Glaeser Stefanie P. , Kämpfer Peter , Flieger Antje 
Published: June 2017

ABSTRACT

We announce here the complete genome sequence of
Paracoccus contaminans
LMG 29738
T
, which we recently isolated from a contaminated water microcosm. The genome consists of a 2.94-Mb chromosome and a 94-kb plasmid. To our knowledge, we provide the first DNA methylation analysis of a
Paracoccus
species.
Draft Genome Sequence of Serratia proteamaculans MFPA44A14-05, a Model Organism for the Study of Meat and Seafood Spoilage
Authors: Fougy Lysiane , Coeuret Gwendoline , Champomier-Vergès Marie-Christine , Chaillou Stéphane 
Published: June 2017

ABSTRACT

In this study, we present a draft genome sequence of
Serratia proteamaculans
MFPA44A14-05. This strain was isolated from a spoiled organic modified-atmosphere-packed beef carpaccio. The draft genome sequence will contribute to the understanding of the role of the
S. proteamaculans
species in meat and seafood spoilage.
Microbial Impact on Host Metabolism: Opportunities for Novel Treatments of Nutritional Disorders?
Authors: Plovier Hubert , Cani Patrice D. 
Published: June 2017

ABSTRACT
Malnutrition is the cause of major public health concerns worldwide. On the one hand, obesity and associated pathologies (also known as the metabolic syndrome) affect more than 10% of the world population. Such pathologies might arise from an elevated inflammatory tone. We have discovered that the inflammatory properties of high-fat diets were linked to the translocation of lipopolysaccharide (LPS). We proposed a mechanism associating the gut microbiota with the onset of insulin resistance and low-grade inflammation, a phenomenon that we called “metabolic endotoxemia.” We and others have shown that bacteria as well as host-derived immune-related elements control microbial communities and eventually contribute to the phenotype observed during diet-induced obesity, diabetes, and metabolic inflammation. On the other hand, undernutrition is one of the leading causes of death in children. A diet poor in energy and/or nutrients causes incomplete development of the gut microbiota and may profoundly affect energy absorption, initiating stunted growth, edema, and diarrhea. In this review, we discuss how changes in microbiota composition are associated with obesity and undernutrition. We also highlight that opposite consequences exist in terms of energy absorption from the diet (obesity versus undernutrition), but interestingly the two situations share similar defects in term of diversity, functionality, and inflammatory potential.
Fungi as a Source of Food
Authors: Dupont Joëlle , Dequin Sylvie , Giraud Tatiana , Le Tacon François , Marsit Souhir , Ropars Jeanne , Richard Franck , Selosse Marc-André 
Published: June 2017

ABSTRACTIn this article, we review some of the best-studied fungi used as food sources, in particular, the cheese fungi, the truffles, and the fungi used for drink fermentation such as beer, wine, and sake. We discuss their history of consumption by humans and the genomic mechanisms of adaptation during artificial selection.
Sex and the Imperfect Fungi
Authors: Dyer Paul S. , Kück Ulrich 
Published: June 2017

ABSTRACT

Approximately 20% of species in the fungal kingdom are only known to reproduce by asexual means despite the many supposed advantages of sexual reproduction. However, in recent years, sexual cycles have been induced in a series of emblematic “asexual” species. We describe how these discoveries were made, building on observations of evidence for sexual potential or “cryptic sexuality” from population genetic analyses; the presence, distribution, and functionality of mating-type genes; genome analyses revealing the presence of genes linked to sexuality; the functionality of sex-related genes; and formation of sex-related developmental structures. We then describe specific studies that led to the discovery of mating and sex in certain
Candida
,
Aspergillus
,
Penicillium
, and
Trichoderma
species and discuss the implications of sex including the beneficial exploitation of the sexual cycle. We next consider whether there might be any truly asexual fungal species. We suggest that, although rare, imperfect fungi may genuinely be present in nature and that certain human activities, combined with the genetic flexibility that is a hallmark of the fungal kingdom, might favor the evolution of asexuality under certain conditions. Finally, we argue that fungal species should not be thought of as simply asexual or sexual, but rather as being composed of isolates on a continuum of sexual fertility.
The Mycobiome: Impact on Health and Disease States
Authors: El-Jurdi Najla , Ghannoum Mahmoud A. 
Published: June 2017

ABSTRACT
The term “microbiome” refers to microorganisms (microbiota) and their genomes (metagenome) coexisting with their hosts. Some researchers coined the term “second genome” to underscore the importance of the microbiota and its collective metagenome on their host’s health and/or disease. It is now undeniable that the commensal fungal microorganisms, alongside the other components of the microbiota, play a central role in association with the human host. In recognition, projects were launched nationally and internationally to unify efforts to characterize the microbiome and elucidate the functional role of the microbiota and the mechanism(s) by which these organisms and their metabolites (metabolome) may affect health and disease states. In this article, we will highlight the role of the fungal community as an indispensable component of the microbiome.
Fungal Sex: The Basidiomycota
Authors: Coelho Marco A. , Bakkeren Guus , Sun Sheng , Hood Michael E. , Giraud Tatiana 
Published: June 2017

ABSTRACT
Fungi of the Basidiomycota, representing major pathogen lineages and mushroom-forming species, exhibit diverse means to achieve sexual reproduction, with particularly varied mechanisms to determine compatibilities of haploid mating partners. For species that require mating between distinct genotypes, discrimination is usually based on both the reciprocal exchange of diffusible mating pheromones, rather than sexes, and the interactions of homeodomain protein signals after cell fusion. Both compatibility factors must be heterozygous in the product of mating, and genetic linkage relationships of the mating pheromone/receptor and homeodomain genes largely determine the complex patterns of mating-type variation. Independent segregation of the two compatibility factors can create four haploid mating genotypes from meiosis, referred to as tetrapolarity. This condition is thought to be ancestral to the basidiomycetes. Alternatively, cosegregation by linkage of the two mating factors, or in some cases the absence of the pheromone-based discrimination, yields only two mating types from meiosis, referred to as bipolarity. Several species are now known to have large and highly rearranged chromosomal regions linked to mating-type genes. At the population level, polymorphism of the mating-type genes is an exceptional aspect of some basidiomycete fungi, where selection under outcrossing for rare, intercompatible allelic variants is thought to be responsible for numbers of mating types that may reach several thousand. Advances in genome sequencing and assembly are yielding new insights by comparative approaches among and within basidiomycete species, with the promise to resolve the evolutionary origins and dynamics of mating compatibility genetics in this major eukaryotic lineage.
Pathology of Tuberculosis: How the Pathology of Human Tuberculosis Informs and Directs Animal Models
Authors: Basaraba Randall J. , Hunter Robert L. 
Published: June 2017

ABSTRACT

Tuberculosis (TB) is a chronic inflammatory disease caused by the pathogenic bacterium
Mycobacterium tuberculosis
. A wide variety of host- and pathogen-associated variables influence the clinical manifestation of TB in different individuals within the human population. As a consequence, the characteristic granulomatous lesions that develop within the lung are heterogeneous in size and cellular composition. Due to the lack of appropriate tissues from human TB patients, a variety of animal models are used as surrogates to study the basic pathogenesis and to test experimental vaccines and new drug therapies. Few animal models mimic the clinical course and pathological response of
M. tuberculosis
seen in the naturally occurring disease in people. In particular, post-primary TB, which accounts for the majority of cases of active TB and is responsible for transmission between individuals via aerosol exposers, cannot be reproduced in animals and therefore cannot be adequately modeled experimentally. This article describes a new paradigm that explains the pathogenesis of post-primary TB in humans. This new evidence was derived from histological examination of tissues from patients with different stages of
M. tuberculosis
infection and that had not been treated with antimicrobial drugs. Gaining a better understanding of this unique stage of TB disease will lead to more effective treatment, diagnostic, and prevention strategies.
Mycobacterium tuberculosis
in the Face of Host-Imposed Nutrient Limitation
Authors: Berney Michael , Berney-Meyer Linda 
Published: June 2017

ABSTRACT

Coevolution of pathogens and host has led to many metabolic strategies employed by intracellular pathogens to deal with the immune response and the scarcity of food during infection. Simply put, bacterial pathogens are just looking for food. As a consequence, the host has developed strategies to limit nutrients for the bacterium by containment of the intruder in a pathogen-containing vacuole and/or by actively depleting nutrients from the intracellular space, a process called nutritional immunity. Since metabolism is a prerequisite for virulence, such pathways could potentially be good targets for antimicrobial therapies. In this chapter, we review the current knowledge about the
in vivo
diet of
Mycobacterium tuberculosis
, with a focus on amino acid and cofactors, discuss evidence for the bacilli’s nutritionally independent lifestyle in the host, and evaluate strategies for new chemotherapeutic interventions.
Comparison of the Chronic Kidney Disease Epidemiology Collaboration, the Modification of Diet in Renal Disease study and the Cockcroft-Gault equation in patients with heart failure
Authors: Szummer Karolina , Evans Marie , Carrero Juan Jesus , Alehagen Urban , Dahlström Ulf , Benson Lina , Lund Lars H 
Published: June 2017

BackgroundIt is unknown how the creatinine-based renal function estimations differ for dose adjustment cut-offs and risk prediction in patients with heart failure.Method and resultsThe renal function was similar with the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) (median 59 mL/min/1.73 m2, IQR 42 to 77) and Modification of Diet in Renal Disease Study (MDRD) (59 mL/min/1.73 m2, IQR 43 to 75) and slightly lower with the Cockcroft-Gault (CG) equation (57 mL/min, IQR 39 to 82). Across the commonly used renal function stages, the CKD-EPI and the MDRD classified patients into the same stage in 87.2% (kappa coefficient 0.83, p<0.001); the CKD-EPI and the CG equation agreed in 52.3% (kappa coefficient 0.39, p<0.001). Hence, a differing number of patients will receive dose adjustment depending on which formula is used as cut-off. The CG equation predicted worse prognosis better (c-statistics 0.740, 95% CI 0.734 to 0.746) than CKD-EPI (0.697, 95% CI 0.690 to 0.703, p<0.001) and MDRD (0.680, 95% CI 0.734 to 0.746). Using net reclassification improvement (NRI), the CG identified 12.8% more patients at higher risk of death as compared with the CKD-EPI equation.Patients registered in the Swedish Heart Failure Registry (n= 40 736) with standardised creatinine values between 2000 and 2012 had their renal function estimated with the CKD-EPI, the MDRD and the CG. Agreement between the formulas was compared for categories. Prediction of death was assessed with c-statistics and with NRI.ConclusionThe choice of renal function estimation formula has clinical implications and differing results at various cut-off levels. For prognosis, the CG predicts mortality better than the CKD-EPI and MDRD.
Imaging of strong field dissociative single and double ionization channels of N2O
Authors: Afaneh Feras , Schmidt-Böcking Horst 
Published: June 2017

In this paper, we study single and double ionizations of N2O in a short elliptically polarized 800 nm laser pulse using the COLTRIMS technique. The molecular-frame photoelectron angular distribution and the ion sum-momentum distribution of single and double ionizations of N2O molecules are reported for the single ionization dissociative channel NO[Formula: see text] + N and the double ionization dissociative channel NO[Formula: see text] + N[Formula: see text]. The ionizations of multiple orbitals for the two studied dissociative channels were identified via studying the orientation dependent ionization rates for their KERs. The results show that the shape of the ionizing orbitals governs the single and double ionization processes of N2O.