bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of an
Enterococcus thailandicus
Strain Isolated from Bovine Feces
Authors: Beukers Alicia G. , Zaheer Rahat , Goji Noriko , Cook Shaun R. , Amoako Kingsley K. , Chaves Alexandre V. , Ward Michael P. , McAllister Tim A. 
Published: July 2016

ABSTRACT

Here, we report the first draft genome sequence of
Enterococcus thailandicus
isolated from the feces of feedlot cattle in Southern Alberta.
Complete Genome Sequence of
Diaphorina citri-associated C virus
, a Novel Putative RNA Virus of the Asian Citrus Psyllid,
Diaphorina citri
Authors: Nouri Shahideh , Salem Nidà , Falk Bryce W. 
Published: July 2016

ABSTRACT

We present here the complete nucleotide sequence and genome organization of a novel putative RNA virus identified in field populations of the Asian citrus psyllid,
Diaphorina citri
, through sequencing of the transcriptome followed by reverse transcription-PCR (RT-PCR). We tentatively named this virus
Diaphorina citri-associated C virus
(DcACV). DcACV is an unclassified positive-sense RNA virus.
Draft Genome Sequence of
Rhizobium
sp. GHKF11, Isolated from Farmland Soil in Pecan Grove, Texas
Authors: Iyer Rupa , Damania Ashish 
Published: July 2016

ABSTRACT

Rhizobium
sp. GHKF11 is an organophosphate-degrading bacterial strain that was isolated from farmland soil in Pecan Grove, Texas, USA. In addition to a capacity for pesticide degradation, GHKF11 shares conserved traits with other
Rhizobium
spp., including heavy metal resistance and transport genes that may have significant agricultural biotechnology applications.
Draft Genome Sequence and Complete Plasmid Sequence of
Acinetobacter lwoffii
F78, an Isolate with Strong Allergy-Protective Properties
Authors: Fritzenwanker Moritz , Hain Torsten , Kesper Dörthe A. , Harb Hani , Renz Harald , Domann Eugen 
Published: July 2016

ABSTRACT

The hygiene hypothesis states that the tremendous increase in atopic diseases correlates significantly with less contact to microbes in childhood. Here, we report the draft genome sequence of
Acinetobacter lwoffii
F78, a rural cowshed isolate with strong allergy-protective properties that contains an 8,579-bp plasmid.
Complete Genome Sequence of
Herbinix luporum
SD1D, a New Cellulose-Degrading Bacterium Isolated from a Thermophilic Biogas Reactor
Authors: Koeck Daniela E. , Maus Irena , Wibberg Daniel , Winkler Anika , Zverlov Vladimir V. , Liebl Wolfgang , Pühler Alfred , Schwarz Wolfgang H. , Schlüter Andreas 
Published: July 2016

ABSTRACT

A novel cellulolytic bacterial strain was isolated from an industrial-scale biogas plant. The 16S rRNA gene sequence of the strain SD1D showed 96.4% similarity to
Herbinix hemicellulosilytica
T3/55
T
, indicating a novel species within the genus
Herbinix
(family
Lachnospiraceae
). Here, the complete genome sequence of
Herbinix luporum
SD1D is reported.
Whole-Genome Sequence of
Chlamydia gallinacea
Type Strain 08-1274/3
Authors: Hölzer Martin , Laroucau Karine , Creasy Heather Huot , Ott Sandra , Vorimore Fabien , Bavoil Patrik M. , Marz Manja , Sachse Konrad 
Published: July 2016

ABSTRACT

The recently introduced bacterial species
Chlamydia gallinacea
is known to occur in domestic poultry and other birds. Its potential as an avian pathogen and zoonotic agent is under investigation. The whole-genome sequence of its type strain, 08-1274/3, consists of a 1,059,583-bp chromosome with 914 protein-coding sequences (CDSs) and a plasmid (p1274) comprising 7,619 bp with 9 CDSs.
Genome Sequence of
Bibersteinia trehalosi
Strain Y31 Isolated from the Pneumonic Lung of a Bighorn Sheep
Authors: Kugadas Abirami , Humann Jodi L. , Pierlé Sebastián Aguilar , Srikumaran Subramaniam , Brayton Kelly A. 
Published: July 2016

ABSTRACT

Here, we report the genome sequence for
Bibersteinia trehalosi
strain Y31, isolated from the lungs of a bighorn sheep (
Ovis canadensis
) that had succumbed to pneumonia, which exhibits proximity-dependent inhibition (PDI) of
Mannheimia haemolytica
. The sequence will be used to understand the mechanism of PDI for these organisms.
American Ginseng Attenuates Colitis-Associated Colon Carcinogenesis in Mice: Impact on Gut Microbiota and Metabolomics
Authors: Wang Chong-Zhi , Yu Chunhao , Wen Xiao-Dong , Chen Lina , Zhang Chun-Feng , Calway Tyler , Qiu Yunping , Wang Yunwei , Zhang Zhiyu , Anderson Samantha , Wang Yitao , Jia Wei , Yuan Chun-Su 
Published: July 2016

Abstract
Inflammatory bowel disease is a risk factor for colorectal cancer initiation and development. In this study, the effects of American ginseng on chemically induced colitis and colon carcinogenesis were evaluated using an azoxymethane (AOM)/dextran sulfate sodium (DSS) mouse model. During the acute phase on day 15, the oral administration of ginseng (15 and 30 mg/kg/day) significantly suppressed AOM/DSS–induced colitis, as demonstrated by the disease activity index and colon tissue histology. During the chronic phase in week 13, AOM/DSS–induced tumor multiplicity was significantly suppressed by ginseng. Ginseng significantly attenuated the increase of inflammatory cytokines, such as IL1α, IL1β, IL6, G-CSF, and GM-CSF. Serum metabolomics data in the PCA plots showed good separation between the AOM/DSS model and ginseng-treated mice, and the most important endogenous metabolite changes were identified. The 16S rRNA data showed that after AOM/DSS, the microbiome community in the model group was obviously changed, and ginseng inhibited these changes. Fecal metabolomics analysis supported these findings. In conclusion, oral ginseng significantly decreased AOM/DSS–induced colitis and colon carcinogenesis by inhibiting inflammatory cytokines and restoring the metabolomics and microbiota profiles accordingly. Selective endogenous small molecules could be used as biomarkers to elucidate the effects of ginseng treatment. Cancer Prev Res; 9(10); 803–11. ©2016 AACR.
Aptamer-Based Proteomic Profiling Reveals Novel Candidate Biomarkers and Pathways in Cardiovascular Disease
Authors: Ngo Debby , Sinha Sumita , Shen Dongxiao , Kuhn Eric W. , Keyes Michelle J. , Shi Xu , Benson Mark D. , O’Sullivan John F. , Keshishian Hasmik , Farrell Laurie A. , Fifer Michael A. , Vasan Ramachandran S. , Sabatine Marc S. , Larson Martin G. , Carr Steven A. , Wang Thomas J. , Gerszten Robert E. 
Published: July 2016

Background:
Single-stranded DNA aptamers are oligonucleotides of ≈50 base pairs in length selected for their ability to bind proteins with high specificity and affinity. Emerging DNA aptamer-based technologies may address limitations of existing proteomic techniques, including low sample throughput, which have hindered proteomic analyses of large cohorts.

Methods:
To identify early biomarkers of myocardial injury, we applied an aptamer-based proteomic platform that measures 1129 proteins to a clinically relevant perturbational model of planned myocardial infarction (PMI), patients undergoing septal ablation for hypertrophic cardiomyopathy. Blood samples were obtained before and at 10 and 60 minutes after PMI, and protein changes were assessed by repeated-measures analysis of variance. The generalizability of our PMI findings was evaluated in a spontaneous myocardial infarction cohort (Wilcoxon rank-sum). We then tested the platform’s ability to detect associations between proteins and Framingham Risk Score components in the Framingham Heart Study, performing regression analyses for each protein versus each clinical trait.

Results:

We found 217 proteins that significantly changed in the peripheral vein blood after PMI in a derivation cohort (n=15;
P
<5.70E-5). Seventy-nine of these proteins were validated in an independent PMI cohort (n=15;
P
<2.30E-4); >85% were directionally consistent and reached nominal significance. We detected many protein changes that are novel in the context of myocardial injury, including Dickkopf-related protein 4, a WNT pathway inhibitor (peak increase 124%,
P
=1.29E-15) and cripto, a growth factor important in cardiac development (peak increase 64%,
P
=1.74E-4). Among the 40 validated proteins that increased within 1 hour after PMI, 23 were also elevated in patients with spontaneous myocardial infarction (n=46;
P
<0.05). Framingham Heart Study analyses revealed 156 significant protein associations with the Framingham Risk Score (n=899), including aminoacylase 1 (β=0.3386,
P
=2.54E-22) and trigger factor 2 (β=0.2846,
P
=5.71E-17). Furthermore, we developed a novel workflow integrating DNA-based immunoaffinity with mass spectrometry to analytically validate aptamer specificity.

Conclusions:
Our results highlight an emerging proteomics tool capable of profiling >1000 low-abundance analytes with high sensitivity and high precision, applicable both to well-phenotyped perturbational studies and large human cohorts, as well.
Incidence and Predictors of Complications During Cryoballoon Pulmonary Vein Isolation for Atrial Fibrillation
Authors: Guhl Emily N. , Siddoway Donald , Adelstein Evan , Bazaz Raveen , Mendenhall George S. , Nemec Jan , Saba Samir , Schwartzman David , Voigt Andrew , Wang Norman C. , Jain Sandeep K. 
Published: July 2016

Background

Cryoballoon pulmonary vein isolation (
PVI
) has emerged as an alternative to radiofrequency
PVI
for atrial fibrillation (
AF
). Data are lacking to define the rates and predictors of complications, particularly phrenic nerve injury (
PNI
).

Methods and Results

We evaluated a single‐center prospective registry of 450 consecutive patients undergoing cryoballoon
PVI
between 2011 and 2015. Patients were 59±10 years old, 26% were women, 58% had hypertension, their mean
CHA
2
DS
2
VAS
c score was 1.7±1.3, 30% had persistent atrial fibrillation, and 92% received a second‐generation 28‐mm balloon. Predefined major complications were persistent
PNI
, pericardial effusion, deep vein thrombosis, arteriovenous fistula, atrioesophageal fistula, bleeding requiring transfusion, stroke, and death.
PNI
was categorized as persistent if it persisted after discharge from the laboratory. Logistic regression was performed to identify predictors of complications and specifically
PNI
. We identified a major complication in 10 (2.2%) patients. In 49 (10.8%) patients, at least transient
PNI
was observed; only 5 persisted beyond the procedure (1.1%). All cases of
PNI
resolved eventually, with the longest time to resolution being 48 days. We also describe 2 cases of
PNI
manifesting after the index hospitalization. Regression analysis identified 23‐mm balloon use (16.3% versus 5.2%, odds ratio 2.94,
P
=0.011) and increased age (62.8±7.7 versus 58.7±0.12 years, odds ratio 1.058,
P
=0.014) as independent significant predictors of
PNI
. There were no significant predictors of major complications.

Conclusions

In a large contemporary cohort, cryoballoon
PVI
is associated with low procedural risk, including lower rates of
PNI
than previously reported. Older age and 23‐mm balloon use were associated with
PNI
. Our low rate of
PNI
may reflect more sensitive detection methods, including compound motor action potential monitoring and forced double‐deflation.
Endothelin‐1 Drives Epithelial‐Mesenchymal Transition in Hypertensive Nephroangiosclerosis
Authors: Seccia Teresa M. , Caroccia Brasilina , Gioco Francesca , Piazza Maria , Buccella Valentina , Guidolin Diego , Guerzoni Eugenia , Montini Barbara , Petrelli Lucia , Pagnin Elisa , Ravarotto Verdiana , Belloni Anna S. , Calò Lorenzo A. , Rossi Gian Paolo 
Published: July 2016

Background
Tubulointerstitial fibrosis, the final outcome of most kidney diseases, involves activation of epithelial mesenchymal transition (EMT). Endothelin‐1 (ET‐1) activates EMT in cancer cells, but it is not known whether it drives EMT in the kidney. We therefore tested the hypothesis that tubulointerstitial fibrosis involves EMT driven by ET‐1.

Methods and Results

Transgenic TG[mRen2]27 (TGRen2) rats developing fulminant angiotensin II–dependent hypertension with prominent cardiovascular and renal damage were submitted to drug treatments targeted to ET‐1 and/or angiotensin II receptor or left untreated (controls). Expressional changes of E‐cadherin and α‐smooth muscle actin (αSMA) were examined as markers of renal EMT. In human kidney HK‐2 proximal tubular cells expressing the ET
B
receptor subtype, the effects of ET‐1 with or without ET‐1 antagonists were also investigated. The occurrence of renal fibrosis was associated with EMT in control TGRen2 rats, as evidenced by decreased E‐cadherin and increased αSMA expression. Irbesartan and the mixed ET‐1 receptor antagonist bosentan prevented these changes in a blood pressure–independent fashion (
P
< 0.001 for both versus controls). In HK‐2 cells ET‐1 blunted E‐cadherin expression, increased αSMA expression (both
P
< 0.01), collagen synthesis, and metalloproteinase activity (
P
< 0.005, all versus untreated cells). All changes were prevented by the selective ET
B
receptor antagonist BQ‐788. Evidence for involvement of the Rho‐kinase signaling pathway and dephosphorylation of Yes‐associated protein in EMT was also found.

Conclusions

In angiotensin II–dependent hypertension, ET‐1 acting via ET
B
receptors and the Rho‐kinase and Yes‐associated protein induces EMT and thereby renal fibrosis.
Sources of Uncertainty in Future Projections of the Carbon Cycle
Authors: Hewitt Alan J. , Booth Ben B. B. , Jones Chris D. , Robertson Eddy S. , Wiltshire Andy J. , Sansom Philip G. , Stephenson David B. , Yip Stan 
Published: July 2016

Abstract
The inclusion of carbon cycle processes within CMIP5 Earth system models provides the opportunity to explore the relative importance of differences in scenario and climate model representation to future land and ocean carbon fluxes. A two-way analysis of variance (ANOVA) approach was used to quantify the variability owing to differences between scenarios and between climate models at different lead times. For global ocean carbon fluxes, the variance attributed to differences between representative concentration pathway scenarios exceeds the variance attributed to differences between climate models by around 2025, completely dominating by 2100. This contrasts with global land carbon fluxes, where the variance attributed to differences between climate models continues to dominate beyond 2100. This suggests that modeled processes that determine ocean fluxes are currently better constrained than those of land fluxes; thus, one can be more confident in linking different future socioeconomic pathways to consequences of ocean carbon uptake than for land carbon uptake. The contribution of internal variance is negligible for ocean fluxes and small for land fluxes, indicating that there is little dependence on the initial conditions. The apparent agreement in atmosphere–ocean carbon fluxes, globally, masks strong climate model differences at a regional level. The North Atlantic and Southern Ocean are key regions, where differences in modeled processes represent an important source of variability in projected regional fluxes.
Impact of Assimilating Dropsonde Observations from MPEX on Ensemble Forecasts of Severe Weather Events
Authors: Romine Glen S. , Schwartz Craig S. , Torn Ryan D. , Weisman Morris L. 
Published: July 2016

AbstractOver the central Great Plains, mid- to upper-tropospheric weather disturbances often modulate severe storm development. These disturbances frequently pass over the Intermountain West region of the United States during the early morning hours preceding severe weather events. This region has fewer in situ observations of the atmospheric state compared with most other areas of the United States, contributing toward greater uncertainty in forecast initial conditions. Assimilation of supplemental observations is hypothesized to reduce initial condition uncertainty and improve forecasts of high-impact weather.During the spring of 2013, the Mesoscale Predictability Experiment (MPEX) leveraged ensemble-based targeting methods to key in on regions where enhanced observations might reduce mesoscale forecast uncertainty. Observations were obtained with dropsondes released from the NSF/NCAR Gulfstream-V aircraft during the early morning hours preceding 15 severe weather events over areas upstream from anticipated convection. Retrospective data-denial experiments are conducted to evaluate the value of dropsonde observations in improving convection-permitting ensemble forecasts. Results show considerable variation in forecast performance from assimilating dropsonde observations, with a modest but statistically significant improvement, akin to prior targeted observation studies that focused on synoptic-scale prediction. The change in forecast skill with dropsonde information was not sensitive to the skill of the control forecast. Events with large positive impact sampled both the disturbance and adjacent flow, akin to results from past synoptic-scale targeting studies, suggesting that sampling both the disturbance and adjacent flow is necessary regardless of the horizontal scale of the feature of interest.
Depth of Cochlear Implant Array Within the Cochlea and Performance Outcome
Authors: Hilly Ohad , Smith Leah , Hwang Euna , Shipp David , Symons Sean , Nedzelski Julian M. , Chen Joseph M. , Lin Vincent Y.W. 
Published: July 2016

Objective: To evaluate whether the depth of cochlear implant array within the cochlea affects performance outcomes 1 year following cochlear implantation. Methods: A retrospective case review of 120 patients who were implanted with the Advanced Bionics HiFocus 1J. Post-implantation plain-radiographs were retrospectively reviewed, and the depth of insertion was measured in degrees from the round window to the electrode tip. Correlation between the depth of insertion and 1-year post-activation Hearing in Noise Test (HINT) scores was analyzed. Intrascala position was not assessed. Results: Depth of electrode insertion ranged from 180° to 720°, and HINT scores ranged from 0% to 100%. A Mann-Whitney U test demonstrated significantly improved 1-year post-activation HINT scores in patients with an insertion depth of 360° or more in comparison with patients with insertion depth of less than 360° (81% vs 61%, P = .048). Patients with 13 to 15 contacts within cochlear turns performed as well as patients with full insertion of all 16 contacts, while patients with only 12 contacts performed poorly. Conclusions: Insertion depth of the AB HiFocus 1J electrode of less than 360° is associated with reduced 1-year post-activation HINT scores when compared with deeper insertions. Partial insertion of 13 active contacts or more led to similar results as full insertion.
Low prevalence of the use of the Chinese term for ‘psychiatry’ in the names of community psychiatry clinics: A nationwide study in Taiwan
Authors: Dai Ying-Xiu , Chen Mu-Hong , Chen Tzeng-Ji 
Published: July 2016

Background: Relabeling has been proposed as a strategy to reduce the stigma associated with mental illnesses. Previous studies have shown that changing the names of psychiatry clinics has led to reduced feelings of being stigmatized among patients. In Taiwan, terms other than ‘psychiatry’ (in Chinese, jīng shén kē) are more commonly used in the names of psychiatry clinics. The term ‘psychosomatic clinics’ is widely used instead. Aims: This study investigated the characteristics of psychiatry clinic names in order to better understand the role of clinic names in primary care settings. Methods: Relevant data were extracted from an open database maintained by the government of Taiwan. These data included the names of community psychiatry clinics and hospital-based psychiatry clinics, population size and the degree of urbanization in the area served by each clinic. Results: At the time of this study, there were 254 community psychiatry clinics and 190 hospital-based psychiatry clinics in Taiwan. Only 18.9% of the community clinic names included the term ‘psychiatry’. Additionally, 14.6% of community clinic names and 28.4% of hospital-based clinic names included the term ‘psychosomatics’. The regions in which clinics without ‘psychiatry’ in their names were located had significantly larger populations and higher levels of urbanization than the regions in which clinics with ‘psychiatry’ in their names were located. Conclusion: A low prevalence of the term ‘psychiatry’ in community psychiatry clinic names was found in Taiwan. The stigma associated with psychiatry and other socio-cultural factors are hypothesized to explain this phenomenon.
Is There a Moral Right to Nonmedical Vaccine Exemption?
Authors: Emhoff Isha Ann , Fugate Ellen , Eyal Nir 
Published: July 2016

A recent measles outbreak in the United States was linked to a single source, yet it spanned eighteen jurisdictions and infected 121 people. Forty-seven states currently allow legal exemption from vaccination on religious grounds, eighteen of which also allow it on philosophical grounds. Recent research usually accepts a fundamental right to vaccine exemption and primarily seeks ways to protect herd immunity while also respecting that right, for example, by keeping the exemption available yet harder to procure or by imposing torts for infection-related injury. We argue that when herd immunity is at risk, any moral claim to exemption from vaccination on conscientious, philosophical, or religious grounds is overridden.Our argument rests on an analogy to a series of situations in which a person puts others at risk through philosophically or religiously motivated choices. In these situations, intuitively, there is no claim-right to compromise the safety of others. Similarly, we propose, there is no claim-right to refuse vaccination, regardless of one's conscience, when refusal is sufficiently likely to seriously affect herd immunity and the safety of others. We also address several counterarguments. The lack of a claim-right to exemption when herd immunity is at risk does not mean, however, that it is always prudent for the state to force vaccination, or even that forcing vaccinations must be legal. Alternatives to forced vaccination may prove wiser and more conducive to high vaccination rates.
Validation of an Argentine version of Lupus Quality of Life questionnaire
Authors: Machado Escobar M A , Yacuzzi M S , Martinez R N , González Lucero L , Bellomio V I , Santana M , Galindo L , Mayer M M , Barreira J C , Sarano J , Gomez G , Collado M V , Martinez A , Orozco M C , Betancur G , Dal Pra F , Sanchez A , Juarez V , Lucero E V 
Published: July 2016

Objective To determine reproducibility and validity of an Argentine version of the Lupus Quality of Life questionnaire (LupusQoL) and to determine cut-off values in the questionnaire. Materials and methods One hundred and forty-seven systemic lupus erythematosus patients (American College of Rheumatology 1982/1997) were assessed from April 2014 to July 2014. Demographic and socioeconomic variables were collected, as well as SELENA/SLEDAI, Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index Score, comorbidities and treatment data. Patients completed LupusQoL-Argentine version and European Quality of Life Questionnaire (EuroQoL-5D). Internal consistency and reliability were examined. Convergent validity with EuroQoL-5D was assessed through analysis of latent classes, which established homogeneous categories from the responses of each domain of LupusQoL and for the total. Results Out of 147 patients, 93.2% were female, mean age 36.4 ± 11.1 years, mean disease duration 2.7 ± 9 years, mean SELENA/SLEDAI 2.7 ± 3 points. The cut-off point that defined good or bad quality of life was 0.739 for EuroQoL 5D and 63 for LupusQoL. Cut-off values for each LupusQoL domain were also defined, creating two classes in each of them. There was moderate to high concordance to classify quality of life (Kappa = 0.74, 95% confidence interval = 0.54, 0.95). Conclusion The Argentine version of LupusQoL is a valid, reliable and reproducible instrument to assess quality of life. In this study, cut-off points that allow the classification of patients regarding whether they have good or bad quality of life are established for the first time.