bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Quality Draft Genome Sequence of an Endophytic Pseudomonas viridiflava Strain with Herbicidal Properties against Its Host, the Weed
Lepidium draba
L
Authors: Samad Abdul , Trognitz Friederike , Antonielli Livio , Compant Stéphane , Sessitsch Angela 
Published: October 2016

ABSTRACT

Here, we report the draft genome sequence of
Pseudomonas viridiflava
strain CDRTc14 a pectinolytic bacterium showing herbicidal activity, isolated from the root of
Lepidium draba
L. growing as a weed in an Austrian vineyard. The availability of this genome sequence allows us to investigate the genetic basis of plant–microbe interactions.
Complete Genome Sequences of Multidrug-Resistant Campylobacter jejuni Strain 14980A (Turkey Feces) and Campylobacter coli Strain 14983A (Housefly from a Turkey Farm), Harboring a Novel Gentamicin Resistance Mobile Element
Authors: Miller William G. , Huynh Steven , Parker Craig T. , Niedermeyer Jeffrey A. , Kathariou Sophia 
Published: October 2016

ABSTRACT

Multidrug resistance (MDR) in foodborne pathogens is a major food safety and public health issue. Here we describe whole-genome sequences of two MDR strains of
Campylobacter jejuni
and
Campylobacter coli
from turkey feces and a housefly from a turkey farm
.
Both strains harbor a novel chromosomal gentamicin resistance mobile element.
Draft Genome Sequence of
Vibrio
(
Listonella
)
anguillarum
ATCC 14181
Authors: Grim Christopher J. , Schreier Harold J. 
Published: October 2016

ABSTRACT

We report the draft genome sequence of
Vibrio anguillarum
ATCC 14181, a Gram-negative, hemolytic, O2 serotype marine bacterium that causes mortality in mariculture species. The availability of this genome sequence will add to our knowledge of diversity and virulence mechanisms of
Vibrio anguillarum
as well as other pathogenic
Vibrio
spp.
Complete Genome Sequences of Three Important Methicillin-Resistant Clinical Isolates of Staphylococcus pseudintermedius
Authors: Riley Matthew C. , Perreten Vincent , Bemis David A. , Kania Stephen A. 
Published: October 2016

ABSTRACT

We report the first complete genome sequences of three predominant clones (ST68, ST71, and ST84) of methicillin-resistant
Staphylococcus pseudintermedius
in North America. All strains were isolated from canine infections and have different SCC
mec
elements and antibiotic resistance gene patterns.
Complete Genome Sequence of Spiroplasma helicoides TABS-2
T
(DSM 22551), a Bacterium Isolated from a Horsefly (
Tabanus abactor
)
Authors: Shen Wei-Yi , Lo Wen-Sui , Lai Yi-Ching , Kuo Chih-Horng 
Published: October 2016

ABSTRACT

Spiroplasma helicoides
TABS-2
T
(DSM 22551) was isolated from the gut of a horsefly (
Tabanus abactor
) collected near Ardmore, Oklahoma, USA, in 1987. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among
Spiroplasma
species.
Structural geology of the Baraboo District
Authors: Marshak Stephen , Wilkerson M. Scott , DeFrates Joshua 
Published: October 2016

Abstract
A field trip to the Baraboo District provides an amazing opportunity to teach (or learn) many important aspects of structural geology. For example, students can define the regional-scale shape of the Proterozoic-age south-verging Baraboo Syncline from data on bedding attitudes and facing indicators and then can compare this shape to a digital elevation model of the district to see relationships between the dip of a stratigraphic unit and the width of its outcrop belt. Key outcrops of the Baraboo District, which we describe in detail, allow students to identify and sketch mesoscopic tectonic structures (joints, spaced and phyllitic cleavage, veins, faults, slip lineations, parasitic folds, boudinage, crenulation cleavage, and kink folds) and to interpret the kinematic significance of these structures. Students will leave Baraboo with a clear image of how progressive crustal shortening can be accommodated under lower-greenschist conditions.
Triassic chrysophyte cyst fossils discovered in the Ordos Basin, China
Authors: Zhang Wenzheng , Yang Hua , Xia Xinyu , Xie Liqin , Xie Guwei 
Published: October 2016

Abstract
Algae with siliceous structures are proposed to have originated following the Permian-Triassic extinction or even earlier, but there have been no robust fossil records to indicate their existence before the Jurassic–Cretaceous Periods. Recently, abundant chrysophyte (classes Chrysophyceae and Synurophyceae) cyst fossils were discovered in a Late Triassic lacustrine stratum deposited ∼228–235 m.y. ago in the Ordos Basin, China. The high morphological variety of the discovered cyst fossils suggests that the chrysophytes were remarkably diversified, and that their common ancestors emerged even earlier. This discovery provided fossil records of the early evolution of algae with siliceous structures. The cyst fossils formed thin laminations in organic-rich shale, reflecting variable environmental conditions in the ancient lake basin.
Economic impact of early intervention in psychosis services: results from a longitudinal retrospective controlled study in England
Authors: Tsiachristas Apostolos , Thomas Tony , Leal Jose , Lennox Belinda R 
Published: October 2016

ObjectivesTo demonstrate the costs, outcomes and economic impact of early intervention in psychosis (EIP) services.DesignLongitudinal retrospective observational study of service usage and outcome data from mental health and acute care services for all those with a diagnosis of psychosis in contact with mental health services over a 3-year period (April 2010–March 2013).SettingThames Valley and South Midlands region in England (region covered by Oxford Academic Health Science Network).Participants3674 people with psychosis, aged 16–35 years.InterventionsEIP team or other community mental health teams.Main outcome measuresChange in housing status, change in employment status and improvement on each of the four domains of the Health of the Nation Outcome Scale (HONOS) questionnaire. Costs of mental and acute health inpatient, outpatient and community service use were also included in the study.ResultsPatients in EIP services were 116% more likely (95% CI 1.263 to 3.708) to gain employment, 52% more likely to become accommodated in a mainstream house (95% CI 0.988 to 2.326) and 17% more likely to have an improvement in the emotional well-being domain of the HONOS questionnaire (95% CI 1.067 to 1.285), as compared to those in non-EIP services. Annual National Health Service (NHS) costs were also significantly lower for patients using EIP services compared to non-users. The mean annual NHS cost savings associated with EIP were £4031 (95% CI £1281 to £6780). These mostly came from lower mental health inpatient costs (£4075, 95% CI £1164 to £6986), lower acute hospital outpatient costs (£59, 95% CI £9 to £109), lower accident and emergency costs (£31, 95% CI £12 to £51), and higher mental health community costs (£648, 95% CI £122 to £1175). If all people with a first-episode psychosis across England were to be treated by EIP services, the savings in societal costs would be an estimated £63.3 million per year, of which £33.5 million would be in NHS costs.ConclusionsTreatment within an EIP service is associated with better health and social outcomes, and reduced costs.
Dual Roles for Regulatory T-cell Depletion and Costimulatory Signaling in Agonistic GITR Targeting for Tumor Immunotherapy
Authors: Mahne Ashley E. , Mauze Smita , Joyce-Shaikh Barbara , Xia Jane , Bowman Edward P. , Beebe Amy M. , Cua Daniel J. , Jain Renu 
Published: October 2016

AbstractAgonistic monoclonal antibodies (mAb) targeting the T-cell receptor coregulatory molecule GITR exert potent therapeutic activities in preclinical tumor models. Although anti-GITR mAb are thought to act by depleting and destabilizing the intratumoral T regulatory cell (Treg) population, the precise mechanism of action is obscure. Here, we addressed this issue using a Treg fate-mapping approach, which revealed that Treg loss was primarily due to cell depletion, with minimal evidence of Treg conversion to a non–Foxp3-expressing population. Further characterization of persisting Tregs following anti-GITR mAb treatment showed that a highly activated subpopulation of CD44hiICOShi intratumoral Tregs were preferentially targeted for elimination, with the remaining Tregs exhibiting a less suppressive phenotype. With these changes in the Treg population, intratumoral CD8+ T cells acquired a more functional phenotype characterized by downregulation of the exhaustion markers PD-1 and LAG-3. This reversal of CD8+ T-cell exhaustion was dependent on both agonistic GITR signaling and Treg depletion, as neither mechanism by itself could fully rescue the exhaustion phenotype. Tests of anti-human GITR antibody MK-4166 in a humanized mouse model of cancer mimicked many of the effects of anti-mouse GITR mAb in syngeneic tumor models, decreasing both Treg numbers and immune suppressor phenotype while enhancing effector responsiveness. Overall, our results show how anti-GITR mAb shifts Treg populations to enable immune attack on tumors, with clinical implications for molecular markers to modify emerging treatments. Cancer Res; 77(5); 1108–18. ©2016 AACR.
A Study of TP53 RNA Splicing Illustrates Pitfalls of RNA-seq Methodology
Authors: Mehta Sunali , Tsai Peter , Lasham Annette , Campbell Hamish , Reddel Roger , Braithwaite Antony , Print Cristin 
Published: October 2016

Abstract
TP53 undergoes multiple RNA-splicing events, resulting in at least nine mRNA transcripts encoding at least 12 functionally different protein isoforms. Antibodies specific to p53 protein isoforms have proven difficult to develop, thus researchers must rely on the transcript information to infer isoform abundance. In this study, we used deep RNA-seq, droplet digital PCR (ddPCR), and real-time quantitative reverse transcriptase PCR (RT-qPCR) from nine human cell lines and RNA-seq data available for tumors in The Cancer Genome Atlas to analyze TP53 splice variant expression. All three methods detected expression of the FL/40TP53α_T1 variant in most human tumors and cell lines. However, other less abundant variants were only detected with PCR-based methods. Using RNA-seq simulation analysis, we determined why RNA-seq is unable to detect less abundant TP53 transcripts and discuss the implications of these findings for the general interpretation of RNA-seq data. Cancer Res; 76(24); 7151–9. ©2016 AACR.
Geoquímica do magmatismo Ediacarano Serra do Caramuru, NE da Província Borborema, RN, Brasil
Authors: Macêdo Filho Antomat Avelino de , Souza Zorano Sérgio de 
Published: October 2016

Os stocks Serra do Caramuru e Tapuio (magmatismo Serra do Caramuru), localizados no extremo NE do Domínio Rio Piranhas-Seridó (RN), são representantes do plutonismo ediacarano a cambriano da Província Borborema. Análises químicas de rocha total (elementos maiores e traço, incluindo elementos terras raras) em amostras provenientes principalmente do stock Serra do Caramuru permitiram efetuar a caracterização geoquímica deste magmatismo. Foram identificadas as fácies diorítica, granítica porfirítica, granítica equigranular I e granítica equigranular II, além de diques e sheets graníticos. A fácies diorítica é leucocrática a melanocrática, rica em biotita e hornblenda. As fácies graníticas são hololeucocráticas a leucocráticas, com biotita e eventualmente hornblenda. A variação no conteúdo de óxidos e elementos traço sugere o fracionamento de zircão, apatita, titanita, clinopiroxênio (em dioritos), biotita, hornblenda, allanita, plagioclásio, microclina e granada (em diques tardios). O comportamento de Zr, La e Yb indica que dioritos não constituem o magma parental dos granitos. Por outro lado, as fácies graníticas parecem ser cogenéticas, apresentando trends de diferenciação e espectros de elementos terras raras (ETR) análogos [12,3≤(La/Yb)N≤190,8; Eu/Eu*=0,30-0,68]. O padrão de ETR de diques e sheets graníticos [6,96≤(La/Yb)N≤277,84; Eu/Eu*=0,18-0,58] sugere não cogeneticidade ao magmatismo Serra do Caramuru. A fácies diorítica é metaluminosa, shoshonítica, enquanto os granitos são metaluminosos a ligeiramente peraluminosos, cálcio-alcalinos de alto potássio. Diagramas envolvendo óxidos e elementos traço corroboram um ambiente pós-colisional. Os dados aportados permitem correlacionar o magmatismo Serra do Caramuru ao grupo de granitoides pós-colisionais, cálcio-alcalinos de alto potássio com eventuais associações shoshoníticas, do Domínio Rio Piranhas-Seridó.
Novos dados geológicos e isotópicos para o Domínio Iriri-Xingu, Província Amazônia Central: implicações para a idade do Grupo Iriri
Authors: Semblano Flávio Robson Dias , Pereira Nayan Cezar S. , Vasquez Marcelo Lacerda , Macambira Moacir José Buenano 
Published: October 2016

O Domínio Iriri-Xingu, sul da Província Amazônia Central, é uma das regiões geologicamente menos conhecidas do Cráton Amazônico. Nela predominam rochas vulcânicas e granitóides paleoproterozoicos e o embasamento regional raramente aflora. Estudos petrográficos e feições de campo possibilitaram identificar três conjuntos de rochas: Granitos Tipo A (sienogranitos e quartzo-sienitos), Granitos Tipo I (monzogranitos, quartzo-monzodioritos, quartzo-monzonitos e granodioritos) e rochas vulcânicas e vulcanoclásticas do Grupo Iriri (riolitos e dacitos, e ignimbritos dacíticos, respectivamente). As idades Pb‑Pb em zircão confirmam a ocorrência de pelo menos dois eventos magmáticos orosirianos nessa região: 1992-1986 Ma e 1889 Ma. Dados isotópicos Sm-Nd das rochas estudadas forneceram idades-modelo Nd TDM de 2,43 a 3,13 Ga com εNd(t) de –10 a –3, o que permitiu confirmar uma fonte crustal antiga para esses magmas, típica da Província Amazônia Central. Esses resultados indicam que os eventos magmáticos de 1,99 Ga e 1,89 Ga, que são comuns no Domínio Tapajós, também ocorrem no Domínio Iriri-Xingu. Contudo, apresentam fontes crustais arqueanas contrastantes com as fontes paleoproterozoicas características do Domínio Tapajós. Além disso, as idades obtidas em cristais de zircão das rochas vulcânicas do Domínio Iriri-Xingu são mais antigas que ca. 1880 Ma, habitualmente correlatas ao Grupo Iriri. Assim, este trabalho propõe uma redefinição litoestratigráfica dessa unidade, com base na ocorrência de rochas vulcânicas de ca. 1988 Ma na sua área-tipo.
A faixa de dobramentos do Rio Salgado, norte-noroeste da Zona Transversal-Província Borborema (PB-CE)
Authors: Neves Benjamim Bley de Brito , Campos Neto Mario da Costa 
Published: October 2016

O sistema de Dobramentos Piancó-Alto Brígida (SPAB) foi definido como um branching system of orogens neoproterozoico na parte centro-ocidental da Zona Transversal-Província Borborema. A discriminação de Faixa de Dobramentos do Rio Salgado (FDRS) está sendo proposta para o ramo mais setentrional deste sistema. Esta faixa (FDRS) está cortada ao norte pelo Lineamento Patos (aqui considerado como um boundary transform continental) e margeada por uma série de basement inliers paleoproterozoicos ao sul (Riacho São Pedro, Icaiçara, S. José do Caiano, Coremas etc.), estando em parte encoberta por sedimentos fanerozoicos do Araripe. Os ramos mais ao sul e sudeste do SPAB estão cortados por dezenas de stocks e batólitos intrusivos (tipo “I”) de um arco magmático continental que se estende da costa paraibana ao sertão do Piauí (ca. 800 km). A FDRS está situada entre este arco magmático e o Lineamento de Patos e é constituída principalmente por sequências siliciclásticas finas de grande ritmicidade, com intercalações locais de sheets de vulcânicas félsicas, intermediárias e básicas. O metamorfismo regional corresponde à fácies xisto verde baixo (sericita-clorita-biotita). Foram realizadas três seções litoestratigráficas e estruturais completas, transversais à FDRS, sendo identificadas preliminarmente cinco distintas unidades paraestratigráficas. Estudos geocronológicos (U-Pb) preliminares indicam uma sedimentação pós-650 Ma. Três fases de deformação foram identificadas e serão discutidas. As características geológicas gerais, a posição tectônica e a natureza do embasamento da FDRS apontam para o desenvolvimento orogênico de uma bacia de antearco no Neocriogeniano.
Compartimentação fisiográfica aplicada ao mapeamento em detalhamento progressivo do núcleo urbano central de Ilhabela-SP
Authors: Diniz Tales de Deus , Zaine José Eduardo , Rodrigues Flávio Henrique 
Published: October 2016

O processo de urbanização no Brasil ocorre, predominantemente, de maneira desordenada, sem a correta consideração das potencialidades e limitações do meio físico, o que se traduz numa forma de ocupação que pode expor a população e o equipamento urbano a processos de superfície, tais como inundações e movimentos de massa. Isso é observado no município de Ilhabela - SP, onde a alta taxa de crescimento populacional, somada ao relevo acidentado, intensifica esse problema, evidenciando a necessidade de uma orientação adequada da expansão urbana. Dentro deste contexto, o mapeamento baseado na compartimentação fisiográfica pode fornecer instrumentos apropriados para o planejamento da ocupação ordenada do meio físico. Assim, o objetivo da presente pesquisa foi a elaboração de mapas da região mais densamente urbanizada de Ilhabela, utilizando a compartimentação fisiográfica baseada na análise integrada de imagens aéreas da área de estudo. A fotoanálise e fotointerpretação das mesmas, somadas às informações obtidas em campo, subsidiaram a divisão e classificação da área de estudo em unidades que apresentam uniformidade em relação à morfologia e propriedades geotécnicas. Esse procedimento resultou na identificação de unidades mapeadas em três escalas (1:50.000, 1:20.000 e 1:10.000), com diferentes níveis de detalhes, acompanhada da descrição de suas principais características físicas e principais processos exógenos atuantes. As cartas obtidas permitiram uma compreensão detalhada acerca das características do meio físico da Ilha de São Sebastião, bem como dos principais fatores condicionantes da ocupação antrópica na mesma, mostrando-se ferramentas eficazes e adequadas ao planejamento territorial urbano do município-arquipélago.
Circulating Ceramides Predict Cardiovascular Outcomes in the Population-Based FINRISK 2002 Cohort
Authors: Havulinna Aki S. , Sysi-Aho Marko , Hilvo Mika , Kauhanen Dimple , Hurme Reini , Ekroos Kim , Salomaa Veikko , Laaksonen Reijo 
Published: October 2016

Objective—
Ceramides are molecular lipids implicated in apoptosis, inflammation, obesity, and insulin resistance. An earlier study reported that ceramides were associated with fatal outcome among patients with coronary heart disease. Here, we examined whether ceramides are associated with major adverse cardiovascular events (MACEs) among apparently healthy individuals.

Approach and Results—

FINRISK 2002 is a population-based risk factor survey, which recruited men and women aged 25 to 74 years. The cohort was followed up until the end of 2014. We quantified 4 circulating ceramides, Cer(d18:1/16:0), Cer(d18:1/18:0), Cer(d18:1/24:0), and Cer(d18:1/24:1), in 8101 serum samples by a targeted liquid chromatography–tandem mass spectrometry assay. Primary outcome of interest was incident MACE (n=813). Secondary analyses were performed for MACE death (n=116) without previous nonfatal MACE and for recurrent MACE (n=226) among survivors of a previous incident MACE. We used Cox proportional hazard models adjusted for the Framingham covariates to determine the association of ceramides with the outcomes. Of the ceramide species, Cer(d18:1/18:0) had the strongest association with incident MACE and the highest unadjusted hazard ratio of 1.31 (95% confidence interval, 1.21–1.41), which remained significant at 1.21 (95% confidence interval, 1.11–1.33) after Framingham risk factor adjustments. The hazard ratios were generally stronger for recurrent and fatal events than for first events. Clinical net reclassification improvement was 7.5% (
P
=6.9×10
−
5
) for Cer(d18:1/18:0).

Conclusions—
Distinct serum ceramides are associated with the risk of incident MACE in apparently healthy individuals. These results should encourage more detailed analyses of ceramides in cardiovascular pathobiology and suggest new biomarkers of MACE risk.
Microvascular Endothelial Dysfunction in Sedentary, Obese Humans Is Mediated by NADPH Oxidase
Authors: La Favor Justin D. , Dubis Gabriel S. , Yan Huimin , White Joseph D. , Nelson Margaret A.M. , Anderson Ethan J. , Hickner Robert C. 
Published: October 2016

Objective—
The objectives of this study were to determine the impact of in vivo reactive oxygen species (ROS) on microvascular endothelial function in obese human subjects and the efficacy of an aerobic exercise intervention on alleviating obesity-associated dysfunctionality.

Approach and Results—

Young, sedentary men and women were divided into lean (body mass index 18–25; n=14), intermediate (body mass index 28–32.5; n=13), and obese (body mass index 33–40; n=15) groups. A novel microdialysis technique was utilized to detect elevated interstitial hydrogen peroxide (H
2
O
2
) and superoxide levels in the vastus lateralis of obese compared with both lean and intermediate subjects. Nutritive blood flow was monitored in the vastus lateralis via the microdialysis-ethanol technique. A decrement in acetylcholine-stimulated blood flow revealed impaired microvascular endothelial function in the obese subjects. Perfusion of apocynin, an NADPH oxidase inhibitor, lowered (normalized) H
2
O
2
and superoxide levels, and reversed microvascular endothelial dysfunction in obese subjects. After 8 weeks of exercise, H
2
O
2
levels were decreased in the obese subjects and microvascular endothelial function in these subjects was restored to levels similar to lean subjects. Skeletal muscle protein expression of the NADPH oxidase subunits p22
phox
, p47
phox
, and p67
phox
was increased in obese relative to lean subjects, where p22
phox
and p67
phox
expression was attenuated by exercise training in obese subjects.

Conclusions—
This study implicates NADPH oxidase as a source of excessive ROS production in skeletal muscle of obese individuals and links excessive NADPH oxidase–derived ROS to microvascular endothelial dysfunction in obesity. Furthermore, aerobic exercise training proved to be an effective strategy for alleviating these maladies.