bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of a Psychrotolerant Denitrifying Bacterium,
Janthinobacterium svalbardensis
PAMC 27463
Authors: Cho Yong-Joon , Jung You-Jung , Hong Soon Gyu , Kim Ok-Sun 
Published: November 2017

ABSTRACT

We report here the complete genome sequence of
Janthinobacterium svalbardensis
PAMC 27463 isolated from a freshwater lake on Barton Peninsula on King George Island, Antarctica. The genome consists of a chromosome with 6,274,078 bp which contains 5,585 genes, including 121 RNA genes.
Draft Genome Sequence and Annotation of the Apicomplexan Parasite
Besnoitia besnoiti
Authors: Schares Gereon , Venepally Pratap , Lorenzi Hernán A. 
Published: November 2017

ABSTRACT

The apicomplexan parasite
Besnoitia besnoiti
is the causative agent of bovine besnoitiosis that affects livestock, particularly cattle. The definitive host of
B. besnoiti
is unknown and its transmission only partially understood. Here, we report the first draft genome sequence, assembly, and annotation of this parasite.
Draft Genome Sequence of Agrobacterium tumefaciens Biovar 1 Strain 186, Isolated from Walnut
Authors: Poret-Peterson Amisha T. , Bhatnagar Srijak , McClean Ali E. , Kluepfel Daniel A. 
Published: November 2017

ABSTRACT

Agrobacterium tumefaciens
biovar 1 strain 186 was isolated from a walnut tree expressing crown gall symptoms. The draft genome sequence of this strain harbored genes for crown gall formation and will be useful for understanding its virulence on Paradox, the predominant hybrid rootstock used for the cultivation of English walnut in California.
Complete Genome Sequence of Xanthomonas campestris pv.
viticola
Strain CCRMXCV 80 from Brazil
Authors: Lima Nelson B. , Gama Marco A. S. , Mariano Rosa L. R. , Silva Wilson J. , Farias Antônio R. G. , Falcão Raul M. , Sousa-Paula Lucas C. , Benko-Iseppon Ana M. , Paiva Sérgio S. L. , Balbino Valdir Q. , Souza Elineide B. 
Published: November 2017

ABSTRACT

Here, we report the complete 5.3-Mb genome sequence of
Xanthomonas campestris
pv.
viticola
(CCRMXCV 80), which causes grapevine (
Vitis vinifera
L.) bacterial canker. Genome data will improve our understanding of the strain’s comparative genomics and epidemiology, and help to further define plant protection and quarantine procedures.
Draft Genome Sequence of
Saccharomycopsis fodiens
CBS 8332, a Necrotrophic Mycoparasite with Biocontrol Potential
Authors: Junker Klara , Hesselbart Ana , Wendland Jürgen 
Published: November 2017

ABSTRACT

Saccharomycopsis fodiens
is an ascomycetous necrotrophic mycoparasite. Predator-prey interaction leads to killing of the host cell by a penetration peg and utilization of cell content by the predator. Here, we report the 14.9-Mb
S. fodiens
draft genome sequence assembled into 9 large scaffolds and 13 minor scaffolds (<20 kb).
Whole-Genome Sequence of
Pantoea americana
Strain VS1, an Extended-Spectrum β-Lactamase-Producing Epibiont Isolated from
Magnolia grandiflora
Authors: Lata Pushpa , Govindarajan Subramaniam S. , Qi Feng , Li Jian-Liang , Maurya Santosh K. , Sahoo Malaya K. 
Published: November 2017

ABSTRACT

Pantoea americana
strain VS1, an extended-spectrum β-lactamase-producing epibiont, was isolated from
Magnolia grandiflora
in central Florida, USA. Here, we report the
de novo
whole-genome sequence of this strain, which consists of a total of 191 contigs spanning 5,412,831 bp, with a GC content of 57.3% and comprising 4,836 predicted coding sequences.
Draft Genome Sequence of the Mucoid Pseudomonas aeruginosa Clinical Isolate PA34
Authors: Harrison Lucas B. , Hanson Nancy D. 
Published: November 2017

ABSTRACT

Pseudomonas aeruginosa
is a serious threat to patients suffering from cystic fibrosis. These organisms are exposed to a unique set of selective pressures within the lung. Here, we report the draft genome sequence of a mucoid
P. aeruginosa
clinical isolate obtained from a cystic fibrosis patient colonized with
P. aeruginosa
.
Interventions to improve adherence to reporting guidelines in health research: a scoping review protocol
Authors: Blanco David , Kirkham Jamie J , Altman Douglas G , Moher David , Boutron Isabelle , Cobo Erik 
Published: November 2017

IntroductionThere is evidence that the use of some reporting guidelines, such as the Consolidated Standards for Reporting Trials, is associated with improved completeness of reporting in health research. However, the current levels of adherence to reporting guidelines are suboptimal. Over the last few years, several actions aiming to improve compliance with reporting guidelines have been taken and proposed. We will conduct a scoping review of interventions to improve adherence to reporting guidelines in health research that have been evaluated or suggested, in order to inform future interventions.Methods and analysisOur review will follow the Joanna Briggs Institute scoping review methods manual. We will search for relevant studies in MEDLINE, EMBASE and Cochrane Library databases. Moreover, we will carry out lateral searches from the reference lists of the included studies, as well as from the lists of articles citing the included ones. One reviewer will screen the full list, which will be randomly split into two halves and independently screened by the other two reviewers. Two reviewers will perform data extraction independently. Discrepancies will be solved through discussion. In addition, this search strategy will be supplemented by a grey literature search. The interventions found will be classified as assessed or suggested, as well as according to different criteria, in relation to their target (journal policies, journal editors, authors, reviewers, funders, ethical boards or others) or the research stage at which they are performed (design, conducting, reporting or peer review). Descriptive statistical analysis will be performed.Ethics and disseminationA paper summarising the findings from this review will be published in a peer-reviewed journal. This scoping review will contribute to a better understanding and a broader perspective on how the problem of adhering better to reporting guidelines has been tackled so far. This could be a major first step towards developing future strategies to improve compliance with reporting guidelines in health research.
Prevalence and recognition of obesity and its associated comorbidities: cross-sectional analysis of electronic health record data from a large US integrated health system
Authors: Pantalone Kevin M , Hobbs Todd M , Chagin Kevin M , Kong Sheldon X , Wells Brian J , Kattan Michael W , Bouchard Jonathan , Sakurada Brian , Milinovich Alex , Weng Wayne , Bauman Janine , Misra-Hebert Anita D , Zimmerman Robert S , Burguera Bartolome 
Published: November 2017

ObjectiveTo determine the prevalence of obesity and its related comorbidities among patients being actively managed at a US academic medical centre, and to examine the frequency of a formal diagnosis of obesity, via International Classification of Diseases, Ninth Revision (ICD-9) documentation among patients with body mass index (BMI) ≥30 kg/m2.DesignThe electronic health record system at Cleveland Clinic was used to create a cross-sectional summary of actively managed patients meeting minimum primary care physician visit frequency requirements. Eligible patients were stratified by BMI categories, based on most recent weight and median of all recorded heights obtained on or before the index date of 1July 2015. Relationships between patient characteristics and BMI categories were tested.SettingA large US integrated health system.ResultsA total of 324 199 active patients with a recorded BMI were identified. There were 121 287 (37.4%) patients found to be overweight (BMI ≥25 and <29.9), 75 199 (23.2%) had BMI 30–34.9, 34 152 (10.5%) had BMI 35–39.9 and 25 137 (7.8%) had BMI ≥40. There was a higher prevalence of type 2 diabetes, pre-diabetes, hypertension and cardiovascular disease (P value<0.0001) within higher BMI compared with lower BMI categories. In patients with a BMI >30 (n=134 488), only 48% (64 056) had documentation of an obesity ICD-9 code. In those patients with a BMI >40, only 75% had an obesity ICD-9 code.ConclusionsThis cross-sectional summary from a large US integrated health system found that three out of every four patients had overweight or obesity based on BMI. Patients within higher BMI categories had a higher prevalence of comorbidities. Less than half of patients who were identified as having obesity according to BMI received a formal diagnosis via ICD-9 documentation. The disease of obesity is very prevalent yet underdiagnosed in our clinics. The under diagnosing of obesity may serve as an important barrier to treatment initiation.
Frequency of 6-week follow-up appointment scheduling after intrauterine device insertion
Authors: Bernard Abigail , Satterwhite Catherine L , Reddy Madhuri 
Published: November 2017

IntroductionLong-acting reversible contraception (LARC) is widely recommended to reduce unintended pregnancy in the USA. As intrauterine device (IUD) use increases, evaluating the role of post-insertion follow-up is important.MethodsA retrospective patient record review was conducted to assess the follow-up experience of women who had an IUD placed at the University of Kansas Medical Center from 1 January to 30 June 2015. Data were collected on patient demographics, IUD placement, follow-up visit attendance, and outcomes in the 12 months following placement. The primary outcome of interest was the proportion of patients who attended a 6-week follow-up visit. Secondary outcomes included adverse events detected at the 6-week visit and IUD removal within a year of placement.ResultsAmong 380 women who had an IUD inserted, physician documentation of a recommended 6-week follow-up visit was present in 91.3% of patient medical records. Two-thirds (66.6%) of patients receiving a recommendation returned for a follow-up visit. Of the 380 women who had an IUD placed, 66 (17.4%) had their IUD removed within 1 year of placement. Of those, 50 women attended the 6-week follow-up visit and 16 did not (19.8% vs 12.6%, p=0.08). Of the IUD removals, 14 occurred at the 6-week visit. After excluding IUD removals which occurred at the 6-week visit, attending a 6-week follow-up visit was not associated with IUD removal or retention (p=0.52).ConclusionDespite recommendations to forgo the 6-week follow-up visit, visits were still common, with no demonstrated value added.
Nocturnal serum melatonin levels in sulfur mustard exposed patients with sleep disorders
Authors: Mousavi Seyyedeh Soghra , Vahedi E , Shohrati M , Panahi Y , Parvin S 
Published: November 2017

BackgroundSulfur mustard (SM) exposure causes respiratory disorders, progressive deterioration in lung function and mortality in injured victims and poor sleep quality is one of the most common problems among SM-exposed patients. Since melatonin has a critical role in regulation of sleep and awareness, this study aimed to evaluate the serum melatonin levels in SM-injured subjects.MethodsA total of 30 SM-exposed male patients and 10 controls was evaluated. Sleep quality was evaluated by the Pittsburgh Sleep Quality Index (PSQI); daytime sleepiness was measured by the Epworth Sleepiness Scale (ESS), and the risk of obstructive sleep apnoea was determined by the STOP-Bang questionnaire. Polysomnography (PSG) and pulmonary function tests (PFTs) were also available. Nocturnal serum melatonin levels were measured using an ELISA kit.ResultsThe mean of PSQI, ESS and STOP-Bang scores in patients (11.76±3.56, 12.6±3.03 and 5.03±1.09, respectively) were significantly (p<0.01) higher than those in the controls (2.78±0.83, 4.69±1.15 and 1.18±0.82, respectively). PFTs also showed declined respiratory quality in SM-patients. There was a significant difference regarding the PSG results between patients and controls (p<0.01). The mean of nocturnal serum melatonin levels in patients (29.78±19.31 pg/mL) was significantly (p=0.005) lower than that in the controls (78.53±34.41 pg/mL).ConclusionsReduced nocturnal serum melatonin and respiratory disorders can be the reasons for poor sleep quality among these patients.Trial registration numberIRCT2015092924267N1, Pre-results.
Stent-assisted coiling of cerebral aneurysms: a single-center clinical and angiographic analysis
Authors: Wang Jun , Vargas Jan , Spiotta Alejandro , Chaudry Imran , Turner Raymond D , Lena Jonathan , Turk Aquilla 
Published: November 2017

ObjectiveThis study retrospectively compared the clinical and angiographic outcomes of treating cerebral aneurysms with Neuroform (NEU), Enterprise (EP), and Low-profile Visualized Intraluminal Support (LVIS/LVIS Jr) stents.Materials and methodsWe conducted a retrospective analysis of a procedural database. All aneurysm procedures using any of the three types of self-expanding nitinol stents (NEU, EP and LVIS/LVIS Jr) were included. Intra-procedure complications, post-procedure complications, and angiographic results (Raymond–Roy grade scale, RRGS) were analyzed retrospectively. A multivariate logistic regression analysis was conducted to identify predictors of intra-procedure and post-procedure complications.ResultsTwo hundred and forty-three aneurysms in 229 patients treated with stent-assisted coiling were included (NEU group: 109 aneurysms; EP group: 61 aneurysms; LVIS/LVIS Jr: 73 aneurysms). The LVIS/LVIS Jr group was associated with the lowest rate of initial complete occlusion (RRGS I: 47.9%; 35/73). Follow-up showed the proportion of RRGS I increased for all stent groups but was greatest in the LVIS/LVIS Jr group. Overall, 17 intra-procedural complications were seen in 229 patients (7.4%) and 15 post-procedural complications were found in 198 patients at follow-up (7.6%), with no differences between stent groups. Thrombotic events were the most common complications and occurred in 13 patients (13/229, 5.7%).ConclusionsAll three types of stents used to treat cerebral aneurysms with unfavorable neck were safe and effective, providing suitable support for the coil mass. LVIS/LVIS Jr promotes better progressive aneurysm complete occlusion than the other two stents but seems to cause more common intra-procedural stent-related thrombotic events and fewer post-procedural complications.
Is bridging therapy still required in stroke due to carotid artery terminus occlusions?
Authors: Bourcier Romain , Alexandre Pierre-Louis , Eugène François , Delasalle-Guyomarch Béatrice , Guillon Benoit , Kerleroux Basile , Saleme Suzana , Marnat Gaultier , Boucebci Samy , Mirza Mahmood , Ferré Jean-Christophe , Papagiannaki Chrysanthi , Desal Hubert 
Published: November 2017

IntroductionStudies comparing endovascular stroke treatment using mechanical thrombectomy (MT) with or without prior IV tissue plasminogen activator (tPa) have included only 30% of internal carotid artery terminus occlusions (ICA-O), a known predictor of recanalization failure with IV tPa.ObjectiveTo carry out a retrospective multicenter analysis of prospectively collected data of consecutive patients to investigate the impact of intravenous thrombolysis on ICA-O by comparing patients treated with MT alone or bridging therapy (BT).Material and methodsPatients with ICA-O treated with MT alone or BT were retrospectively examined and compared. Demographic data, vascular risk factors, treatment modalities, complications, technical and clinical outcomes were recorded. A propensity score (PS) analysis was used to compare modified Rankin Scale (mRS) score at 3 months and intracerebral hemorrhage (ICH) between groups.Results141 consecutive patients (60% BT/40% MT) were included between January 2014 and June 2016. Baseline characteristics did not differ between the groups. There was no significant difference in the rate of Thrombolysis in Cerebral Infarction 2b/3, distal emboli, and median number of passes between the groups. There was a significant difference between BT and MT groups in the median time between imaging and groin puncture (median 97 min vs 75, p=0.007), the rate of ICH (44% vs 27%, p=0.05), but not for symptomatic ICH (18% vs 13%, p=0.49). With PS, there was a trend towards a higher rate of ICH (OR=2.3, 95% CI 0.9 to 5.9, p=0.09) in the BT group compared with the MT alone group, with no difference in mRS score ≤2 at 3 months (OR=1.6, 95% CI 0.7 to 3.7, p=0.29).ConclusionThere was no significant difference in clinical outcomes between patients receiving bridging therapy versus direct thrombectomy. Bridging therapy delayed time to groin puncture and increased ICH rate.
GCMix
Authors: Kim Sang-Hoon , Lee Jinhyuk , Kim Jin-Soo 
Published: November 2017

In multi-level cell (MLC) NAND flash memory, two logical pages are overlapped on a single physical page. Even after a logical page is programmed, the data can be corrupted if the programming of the coexisting logical page is interrupted. This phenomenon is called paired page interference.
This article proposes a novel software technique to deal with the paired page interference without any additional hardware or extra page write. The proposed technique utilizes valid pages in the victim block during garbage collection (GC) as the backup against the interference, and pairs them with incoming pages written by the host. This approach eliminates undesirable page copy to backup pages against the interference. However, such a strategy has an adverse effect on the hot/cold separation policy, which is essential to improve the efficiency of GC. To limit the downside, we devise a metric to estimate the benefit of GCMix on-the-fly so that GCMix can be adaptively utilized only when the benefit outweighs the overhead. Evaluations using synthetic and real workloads show GCMix can effectively deal with the paired page interference, reducing the write amplification factor by up to 17.5%compared to the traditional technique, while providing comparable I/O performance.
Interferon-γ Signaling in Melanocytes and Melanoma Cells Regulates Expression of CTLA-4
Authors: Mo Xuan , Zhang Hanghang , Preston Sarah , Martin Kayla , Zhou Bo , Vadalia Nish , Gamero Ana M. , Soboloff Jonathan , Tempera Italo , Zaidi M. Raza 
Published: November 2017

AbstractCTLA4 is a cell surface receptor on T cells that functions as an immune checkpoint molecule to enforce tolerance to cognate antigens. Anti–CTLA4 immunotherapy is highly effective at reactivating T-cell responses against melanoma, which is postulated to be due to targeting CTLA4 on T cells. Here, we report that CTLA4 is also highly expressed by most human melanoma cell lines, as well as in normal human melanocytes. Interferon-γ (IFNG) signaling activated the expression of the human CTLA4 gene in a melanocyte and melanoma cell–specific manner. Mechanistically, IFNG activated CTLA4 expression through JAK1/2-dependent phosphorylation of STAT1, which bound a specific gamma-activated sequence site on the CTLA4 promoter, thereby licensing CBP/p300-mediated histone acetylation and local chromatin opening. In melanoma cell lines, elevated baseline expression relied upon constitutive activation of the MAPK pathway. Notably, RNA-seq analyses of melanoma specimens obtained from patients who had received anti–CTLA4 immunotherapy (ipilimumab) showed upregulation of an IFNG-response gene expression signature, including CTLA4 itself, which correlated significantly with durable response. Taken together, our results raise the possibility that CTLA4 targeting on melanoma cells may contribute to the clinical immunobiology of anti–CTLA4 responses.Significance: These findings show that human melanoma cells express high levels of the immune checkpoint molecule CTLA4, with important possible implications for understanding how anti-CTLA4 immunotherapy mediates its therapeutic effects. Cancer Res; 78(2); 436–50. ©2017 AACR.
β-Adrenergic Signaling Impairs Antitumor CD8+ T-cell Responses to B-cell Lymphoma Immunotherapy
Authors: Nissen Michael D. , Sloan Erica K. , Mattarollo Stephen R. 
Published: November 2017

Abstractβ-Adrenergic receptor (βAR) signaling regulates many physiological processes, including immune system responses. There is growing evidence also for βAR-induced modulation of cancer growth and metastasis. In the Eμ-myc mouse model of B-cell lymphoma, we investigated the effects of chronically elevated βAR signaling on lymphoma progression and antitumor immunity, as well as the impact on cancer immunotherapy. Chronic treatment with the nonselective β-agonist isoprenaline promoted lymphoma development in a manner dependent on signaling within the hematopoietic compartment. βAR signaling significantly suppressed the proliferation, IFNγ production, and cytolytic killing capacity of antigen-specific CD8+ T cells. This inhibited CD8+ T-cell responses to immune modulating antibodies, including anti–PD-1 and anti–4-1BB, resulting in less effective control of lymphoma. The inhibitory effects on CD8+ T cells occurred independently of changes to DC function and included direct suppression of CD8+ T-cell stimulation. The suppressive effects of chronic βAR signaling on antitumor effector cells was selective to T cells, as it did not perturb the innate lymphocyte response to an experimental NKT cell-targeting vaccine, in a setting where innate immune control is dependent on NKT cell and NK cell activation. These findings demonstrate that chronic βAR signaling has an immunosuppressive effect on CD8+ T cells, which decreases the efficacy of CD8+ T cell-targeting immunotherapies. These findings identify βAR signaling as a target for modulation during cancer immunotherapy that may increase therapeutic response and improve patient outcomes. Cancer Immunol Res; 6(1); 98–109. ©2017 AACR.
Predictors and Long-Term Clinical Outcome of Longitudinal Stent Deformation
Authors: Rhee Tae-Min , Park Kyung Woo , Lee Joo Myung , Lee Michael S. , Jeon Ki-Hyun , Kang Hyun-Jae , Koo Bon-Kwon , Rhew Jay Young , Cha Kwang Soo , Bae Jang-Ho , Han Kyoo-Rok , Park Si-Hoon , Park Woo-Jung , Rha Seung-Woon , Oh Seok-Kyu , Kwon Hyuck Moon , Seung Ki-Bae , Ahn Taehoon , Kim Sang-Hyun , Kim Hyo-Soo 
Published: November 2017

Background—
There are limited data on the frequency of and factors associated with quantitative coronary angiography (QCA)–defined longitudinal stent deformation (LSD) in various contemporary drug-eluting stents platforms. This study sought to evaluate the predictors of LSD and its long-term clinical implication.

Methods and Results—

A patient-level pooled analysis was performed with 7350 lesions in 5871 patients treated with platinum-chromium–based everolimus-eluting stent (Promus Element), cobalt-chromium–based everolimus-eluting stent (Promus/Xience V), or cobalt-chromium–based zotarolimus-eluting stent (Endeavor Resolute). QCA was performed to analyze differences of stent length between immediate post-deployment and final post-procedure. Independent factors associated with LSD were identified. Clinical outcomes at 3 years were compared between those with and without QCA-based LSD. The frequency of QCA-based LSD was 1.12% (82 cases). Nine of these cases were angiographically overt. Left main or ostial lesion, bifurcation treatment with provisional side branch stenting or ballooning, additional downstream intervention of a distal lesion, intravascular ultrasound use, and adjunctive post-dilatation were independently associated with QCA-based LSD. The type of stent was not associated with QCA-based LSD. Rates of target lesion failure were nominally higher in lesions with QCA-based LSD than in those without (8.97% versus 5.88%; hazard ratio, 1.415; 95% confidence interval, 0.631–3.175;
P
=0.399).

Conclusions—
LSD is uncommon with contemporary drug-eluting stents, regardless of the type of stent platform. LSD is mainly associated with procedural factors, especially with additional downstream procedures which require the passage of devices through the stent. Careful manipulation of poststent imaging or procedural devices is required to prevent LSD. More data are needed to clarify the impact of LSD on clinical events.