bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequences of Four Novel Escherichia coli Bacteriophages Belonging to New Phage Groups
Authors: Carstens Alexander B. , Kot Witold , Hansen Lars H. 
Published: July 2015

ABSTRACT

Here, we describe the sequencing and genome annotations of a set of four
Escherichia coli
bacteriophages (phages) belonging to newly discovered groups previously consisting of only a single phage and thus expand our knowledge of these phage groups.
Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain 12C
Authors: Sousa Thiago Jesus , Mariano Diego , Parise Doglas , Parise Mariana , Viana Marcus Vinicius Canário , Guimarães Luis Carlos , Benevides Leandro Jesus , Rocha Flávia , Bagano Priscilla , Ramos Rommel , Silva Artur , Figueiredo Henrique , Almeida Sintia , Azevedo Vasco 
Published: July 2015

ABSTRACT

We present here the complete genome sequence of
Corynebacterium pseudotuberculosis
strain 12C, isolated from a sheep abscess in the Brazil. The sequencing was performed with the Ion Torrent Personal Genome Machine (PGM) system, a fragment library, and a coverage of ~48-fold. The genome presented is a circular chromosome with 2,337,451 bp in length, 2,119 coding sequences, 12 rRNAs, 49 tRNAs, and a G+C content of 52.83%.
Genome Sequence of the Urethral Isolate Pseudomonas aeruginosa RN21
Authors: Wibberg Daniel , Tielen Petra , Narten Maike , Schobert Max , Blom Jochen , Schatschneider Sarah , Meyer Ann-Kathrin , Neubauer Rüdiger , Albersmeier Andreas , Albaum Stefan , Jahn Martina , Goesmann Alexander , Vorhölter Frank-Jörg , Pühler Alfred , Jahn Dieter 
Published: July 2015

ABSTRACT

Pseudomonas aeruginosa
is known to cause complicated urinary tract infections (UTI). The improved 7.0-Mb draft genome sequence of
P. aeruginosa
RN21, isolated from a patient with an acute UTI, was determined. It carries three (pro)phage genomes, genes for two restriction/modification systems, and a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system.
Complete Genome Sequence of Chikungunya Virus Isolated from an Aedes aegypti Mosquito during an Outbreak in Yemen, 2011
Authors: Fahmy Nermeen T. , Klena John D. , Mohamed Amr S. , Zayed Alia , Villinski Jeffrey T. 
Published: July 2015

ABSTRACT

Chikungunya virus is recognized as a serious public health problem. The complete genome was sequenced for a chikungunya virus isolated from the mosquito
Aedes aegypti
during a 2011 outbreak in Al Hodayda, Yemen, which resulted in significant human fatalities. Phylogenetic analysis demonstrated that this Yemeni isolate is most closely related to Indian Ocean strains of the east/central/south African genotype.
Genome Sequence of
Halomonas
sp. Strain MCTG39a, a Hydrocarbon-Degrading and Exopolymeric Substance-Producing Bacterium
Authors: Gutierrez Tony , Whitman William B. , Huntemann Marcel , Copeland Alex , Chen Amy , Kyrpides Nikos , Markowitz Victor , Pillay Manoj , Ivanova Natalia , Mikhailova Natalia , Ovchinnikova Galina , Andersen Evan , Pati Amrita , Stamatis Dimitrios , Reddy T. B. K. , Ngan Chew Yee , Chovatia Mansi , Daum Chris , Shapiro Nicole , Cantor Michael N. , Woyke Tanja 
Published: July 2015

ABSTRACT

Halomonas
sp. strain MCTG39a was isolated from coastal sea surface water based on its ability to utilize
n
-hexadecane. During growth in marine medium the strain produces an amphiphilic exopolymeric substance (EPS) amended with glucose, which emulsifies a variety of oil hydrocarbon substrates. Here, we present the genome sequence of this strain, which is 4,979,193 bp with 4,614 genes and an average G+C content of 55.0%.
First Complete Genome Sequences of Staphylococcus aureus subsp.
aureus
Rosenbach 1884 (DSM 20231
T
), Determined by PacBio Single-Molecule Real-Time Technology
Authors: Shiroma Akino , Terabayashi Yasunobu , Nakano Kazuma , Shimoji Makiko , Tamotsu Hinako , Ashimine Noriko , Ohki Shun , Shinzato Misuzu , Teruya Kuniko , Satou Kazuhito , Hirano Takashi 
Published: July 2015

ABSTRACT

The first complete genome sequences of
Staphylococcus aureus
subsp.
aureus
Rosenbach 1884 strain DSM 20231
T
, the type strain of the bacterium causing staphylococcal disease, were determined using PacBio RS II. The sequences represent the chromosome (2,755,072 bp long; G+C content, 32.86%) and a plasmid (27,490 bp long; G+C content, 30.69%).
Sociodemographic and health behavioural factors associated with access to and utilisation of eye care in Korea: Korea Health and Nutrition Examination Survey 2008–2012
Authors: Rim Tyler Hyungtaek , Choi Moonjung , Yoon Jin Sook , Kim Sung Soo 
Published: July 2015

ObjectiveTo determine the sociodemographic and health behavioural factors associated with access to and utilisation of eye care in Korea.DesignNationwide cross-sectional studyMethods25 752 Koreans over the age of 30 were assessed from a national representative survey. We analysed independent variables of self-reporting eye clinic visits through multivariable analyses of sociodemographic factors. The time since the last visit to an eye clinic was used to assess access to and utilisation of eye care.ResultsOf the 25 752 respondents, 8237 (32.0%) visited an eye clinic in the past year, 11 028 (42.8%) were seen more than 1 year ago, while 6487 (25.2%) had never seen an ophthalmologist. Eye clinic utilisation was statistically associated with older age, female sex, higher household income, higher education levels, living in an urban area, and having comorbidities including diabetes and hypertension. Middle-aged men between 30 and 49 years were found to be less likely to receive eye care compared to the rest of the population, and the proportion that did plummeted after the financial crisis of 2007.ConclusionsThere is a substantial sociodemographic disparity in eye care utilisation in Korea, and men with low financial income and education level are especially at risk. Use of eye care among middle-aged men has decreased since the global financial crisis that began in 2007, and therefore healthcare policies and public interventions should be targeted at vulnerable groups to promote access to medical care.
Reducing the incidence of oxyhaemoglobin desaturation during rapid sequence intubation in a paediatric emergency department
Authors: Kerrey Benjamin T , Mittiga Matthew R , Rinderknecht Andrea S , Varadarajan Kartik R , Dyas Jenna R , Geis Gary Lee , Luria Joseph W , Frey Mary E , Jablonski Tamara E , Iyer Srikant B 
Published: July 2015

ObjectivesRapid sequence intubation (RSI) is the standard for definitive airway management in emergency medicine. In a video-based study of RSI in a paediatric emergency department (ED), we reported a high degree of process variation and frequent adverse effects, including oxyhaemoglobin desaturation (SpO2<90%). This report describes a multidisciplinary initiative to improve the performance and safety of RSI in a paediatric ED.MethodsWe conducted a local improvement initiative in a high-volume academic paediatric ED. We simultaneously tested: (1) an RSI checklist, (2) a pilot/copilot model for checklist execution, (3) the use of a video laryngoscope and (4) the restriction of laryngoscopy to specific providers. Data were collected primarily by video review during the testing period and the historical period (2009–2010, baseline). We generated statistical process control charts (G-charts) to measure change in the performance of six key processes, attempt failure and the occurrence of oxyhaemoglobin desaturation during RSI. We iteratively revised the four interventions through multiple plan-do-study-act cycles within the Model for Improvement.ResultsThere were 75 cases of RSI during the testing period (July 2012–September 2013). Special cause variation occurred on the G-charts for three of six key processes, attempt failure and desaturation, indicating significant improvement. The frequency of desaturation was 50% lower in the testing period than the historical (16% vs 33%). When all six key processes were performed, only 6% of patients experienced desaturation.ConclusionsFollowing the simultaneous introduction of four interventions in a paediatric ED, RSI was performed more reliably, successfully and safely.
Living actively in the face of impending death: constantly adjusting to bodily decline at the end-of-life
Authors: Morgan Deidre D , Currow David C , Denehy Linda , Aranda Sanchia A 
Published: July 2015

ContextPeople with advanced cancer experience bodily change resulting in debilitating functional decline. Although inability to participate in everyday activities (occupation) contributes to profound suffering, limited research has examined the relationship between altered bodily experience (embodiment) and functional ability.ObjectivesThe purpose of this study was to better understand the lived experience of functional decline for people with advanced cancer living at home.MethodsIndepth interviews were conducted with 10 community dwelling people with advanced cancer about their bodily experiences of functional decline. This study employed a pragmatic qualitative approach, informed by hermeneutic phenomenology.ResultsPeople described living with rapidly disintegrating bodies and how this affected their ability to participate in everyday activities. Analysis identified themes which were evaluated against conceptual frameworks of ‘occupation’ and ‘embodiment’. People experienced a shifting sense of self. They had to continuously reinterpret changing bodies. Previously automatic movements became disjointed and effortful. Simple actions like standing or getting out of bed required increasing concentration. Relentless bodily breakdown disrupted peoples’ relationship with time, hindering their ability, but not their desire, to participate in everyday activities. Contending with this deterioration is the work of adaptation to functional decline at the end-of-life.ConclusionsThis study highlights the role active participation in everyday activities plays in mediating adjustment to functional decline. These findings challenge us to look beyond palliation of physical symptoms and psychospiritual care as ends in themselves. Symptom control and palliation should be viewed as mechanisms to optimise active participation in essential and valued activities.
Evaluation of promoter hypomethylation and expression ofp73as a diagnostic and prognostic biomarker in Wilms’ tumour
Authors: Song Dongjian , Yue Lifang , Wu Gang , Ma Shanshan , Yang Heying , Liu Qiuliang , Zhang Da , Xia Ziqiang , Jia Jia , Wang Jiaxiang 
Published: July 2015

AimsA member of the p53 family, thep73gene is essential for the maintenance of genomic stability, DNA repair and apoptosis regulation. This study was designed to evaluate the utility of expression and DNA methylation patterns of thep73gene in the early diagnosis and prognosis of Wilms’ tumour (WT).MethodsMethylation-specific PCR, semi-quantitative (sq-PCR), real-time quantitative PCR (qRT–PCR), receiver operating characteristic (ROC), and survival and hazard function curve analyses were utilised to measure the expression and DNA methylation patterns ofp73in WT tissue samples with a view to assessing diagnostic and prognostic value.ResultsThe relative expression ofp73mRNA was higher, while the promoter methylation level was lower in the WT than the control group (p<0.05) and closely associated with poor survival prognosis in children with WT (p<0.05). Increased expression and decreased methylation ofp73were correlated with increasing tumour size, clinical stage and unfavourable histological differentiation (p<0.05). ROC curve analysis showed areas under the curve of 0.544 for methylation and 0.939 for expression in WT venous blood, indicating the higher diagnostic yield of preoperativep73expression.ConclusionsPreoperative venous bloodp73level serves as an underlying biomarker for the early diagnosis of WT.p73overexpression and concomitantly decreased promoter methylation are significantly associated with poor survival in children with WT.
Auscultating heart and breath sounds through patients’ gowns: who does this and does it matter?
Authors: Rankin Alastair J , Rankin Stephen H , Rankin Andrew C 
Published: July 2015

ABSTRACT

Background
Doctors are taught to auscultate with the stethoscope applied to the skin, but in practice may be seen applying the stethoscope to the gown.

Objectives
To determine how often doctors auscultate heart and breath sounds through patients’ gowns, and to assess the impact of this approach on the quality of the sounds heard.

Methods
A sample of doctors in the west of Scotland were sent an email in 2014 inviting them to answer an anonymous questionnaire about how they auscultated heart and breath sounds. Normal heart sounds from two subjects were recorded through skin, through skin and gown, and through skin, gown and dressing gown. These were played to doctors, unaware of the origin of each recording, who completed a questionnaire about the method and quality of the sounds they heard.

Results
206 of 445 (46%) doctors completed the questionnaire. 124 (60%) stated that they listened to patients’ heart sounds, and 156 (76%) to patients’ breath sounds, through patients’ gowns. Trainees were more likely to do this compared with consultants (OR 3.39, 95% CI 1.74 to 6.65). Doctors of all grades considered this practice affected the quality of the sounds heard. 32 doctors listened to the recorded heart sounds. 23 of the 64 (36%) skin and 23 of the 64 (36%) gown recordings were identified. The majority of doctors (74%) could not differentiate between skin or gown recordings, but could tell them apart from the double layer recordings (p=0.02). Trainees were more likely to hear artefactual added sounds (p=0.04).

Conclusions
Many doctors listen to patients’ heart and breath sounds through hospital gowns, at least occasionally. In a short test, most doctors could not distinguish between sounds heard through a gown or skin. Further work is needed to determine the impact of this approach to auscultation on the identification of murmurs and added sounds.
Implication of a Chromosome 15q15.2 Locus in Regulating UBR1 and Predisposing Smokers to MGMT Methylation in Lung
Authors: Leng Shuguang , Wu Guodong , Collins Leonard B. , Thomas Cynthia L. , Tellez Carmen S. , Jauregui Andrew R. , Picchi Maria A. , Zhang Xiequn , Juri Daniel E. , Desai Dhimant , Amin Shantu G. , Crowell Richard E. , Stidley Christine A. , Liu Yushi , Swenberg James A. , Lin Yong , Wathelet Marc G. , Gilliland Frank D. , Belinsky Steven A. 
Published: July 2015

Abstract
O6-Methylguanine-DNA methyltransferase (MGMT) is a DNA repair enzyme that protects cells from carcinogenic effects of alkylating agents; however, MGMT is silenced by promoter hypermethylation during carcinogenesis. A single-nucleotide polymorphism (SNP) in an enhancer in the MGMT promoter was previously identified to be highly significantly associated with risk for MGMT methylation in lung cancer and sputum from smokers. To further genetic investigations, a genome-wide association and replication study was conducted in two smoker cohorts to identify novel loci for MGMT methylation in sputum that were independent of the MGMT enhancer polymorphism. Two novel trans-acting loci (15q15.2 and 17q24.3) that were identified acted together with the enhancer SNP to empower risk prediction for MGMT methylation. We found that the predisposition to MGMT methylation arising from the 15q15.2 locus involved regulation of the ubiquitin protein ligase E3 component UBR1. UBR1 attenuation reduced turnover of MGMT protein and increased repair of O6-methylguanine in nitrosomethylurea-treated human bronchial epithelial cells, while also reducing MGMT promoter activity and abolishing MGMT induction. Overall, our results substantiate reduced gene transcription as a major mechanism for predisposition to MGMT methylation in the lungs of smokers, and support the importance of UBR1 in regulating MGMT homeostasis and DNA repair of alkylated DNA adducts in cells. Cancer Res; 75(15); 3108–17. ©2015 AACR.
Nicotine Induces Tumor Growth and Chemoresistance through Activation of the PI3K/Akt/mTOR Pathway in Bladder Cancer
Authors: Yuge Kazuyuki , Kikuchi Eiji , Hagiwara Masayuki , Yasumizu Yota , Tanaka Nobuyuki , Kosaka Takeo , Miyajima Akira , Oya Mototsugu 
Published: July 2015

Abstract
Continued smoking is highly associated with not only a higher incidence but also greater risk of tumor recurrence, progression, and acquired chemoresistance of urothelial carcinoma. We investigated whether nicotine affects urothelial carcinoma, and the detailed mechanism by which nicotine could induce tumor growth and any associated chemoresistance. Cell viability was evaluated in the human bladder cancer cell line T24 exposed to nicotine with or without cisplatin (CDDP) and NVP-BEZ235 as a PI3K/mTOR dual inhibitor by the WST-1 assay. Protein expression of the PI3K/Akt/mTOR pathway was investigated by Western blotting or immunohistochemical analysis. The influence of nicotine on tumor growth was also evaluated with or without CDDP and/or NVP-BEZ235 in a subcutaneous bladder tumor model. The result demonstrated that cell proliferation was increased in T24 cells after exposure to nicotine. Phospho-specific Akt (pAkt) and phospho-specific p70 S6 kinase (pS6) were significantly upregulated by nicotine exposure. Tumor growth in vivo was significantly induced by nicotine exposure in accordance with increased pS6 expression. Nicotine attenuated inhibition of T24 cell growth by CDDP and further upregulated pS6 expression in vitro and in vivo. NVP-BZE235 inhibited T24 cell proliferation and pAkt and pS6 expression induced after exposure to nicotine and/or CDDP. In conclusion, nicotine increases tumor growth and induces acquired chemoresistance through activation of the PI3K/Akt/mTOR pathway in bladder cancer. Mol Cancer Ther; 14(9); 2112–20. ©2015 AACR.
Anti-Endosialin Antibody–Drug Conjugate: Potential in Sarcoma and Other Malignancies
Authors: Rouleau Cecile , Gianolio Diego A. , Smale Robert , Roth Stephanie D. , Krumbholz Roy , Harper Jay , Munroe Kenneth J. , Green Tessa L. , Horten Bruce C. , Schmid Steven M. , Teicher Beverly A. 
Published: July 2015

Abstract
Endosialin/TEM1/CD248 is a cell surface protein expressed at high levels by the malignant cells of about 50% of sarcomas and neuroblastomas. The antibody–drug conjugate (ADC) anti-endosialin-MC-VC-PABC-MMAE was selectively cytotoxic to endosialin-positive cells in vitro and achieved profound and durable antitumor efficacy in preclinical human tumor xenograft models of endosialin-positive disease. MC-VC-PABC-MMAE was conjugated with anti-endosialin with 3–4 MMAE molecules per ADC. The anti-endosialin-MC-VC-PABC-MMAE conjugate was tested for activity in four human cell lines with varied endosialin levels. The HT-1080 fibrosarcoma cells do not express endosialin, A-673 Ewing sarcoma cells and SK-N-AS neuroblastoma cells are moderate expressers of endosialin, and SJSA-1 osteosarcoma cells express very high levels of endosialin. To determine whether endosialin expression was maintained in vivo, A-673 Ewing sarcoma, SK-N-AS neuroblastoma, and SJSA-1 osteosarcoma cells were grown as xenograft tumors in nude mice. The SK-N-AS neuroblastoma and the A-673 Ewing sarcoma lines were selected for in vivo efficacy testing of the anti-endosialin-MC-VC-PABC-MMAE conjugate. The treatment groups included a vehicle control, unconjugated anti-endosialin, an admix control consisting of anti-endosialin and a dose of free MMAE equivalent to the dose administered as the ADC, and the anti-endosialin-MC-VC-PABC-MMAE conjugate. The unconjugated anti-endosialin had no antitumor activity and resulted in similar tumor growth as the vehicle control. The admix control produced a modest tumor growth delay. Administration of the anti-endosialin-MC-VC-PABC-MMAE conjugate resulted in a marked prolonged tumor response of both xenograts. These proof-of-concept results break new ground and open a promising drug discovery approach to these rare and neglected tumors. Mol Cancer Ther; 14(9); 2081–9. ©2015 AACR.
CDKN2B Loss Promotes Progression from Benign Melanocytic Nevus to Melanoma
Authors: McNeal Andrew S. , Liu Kevin , Nakhate Vihang , Natale Christopher A. , Duperret Elizabeth K. , Capell Brian C. , Dentchev Tzvete , Berger Shelley L. , Herlyn Meenhard , Seykora John T. , Ridky Todd W. 
Published: July 2015

Abstract
Deletion of the entire CDKN2B–CDKN2A gene cluster is among the most common genetic events in cancer. The tumor-promoting effects are generally attributed to loss of CDKN2A-encoded p16 and p14ARF tumor suppressors. The degree to which the associated CDKN2B-encoded p15 loss contributes to human tumorigenesis is unclear. Here, we show that CDKN2B is highly upregulated in benign melanocytic nevi, contributes to maintaining nevus melanocytes in a growth-arrested premalignant state, and is commonly lost in melanoma. Using primary melanocytes isolated directly from freshly excised human nevi naturally expressing the common BRAFV600E-activating mutation, nevi progressing to melanoma, and normal melanocytes engineered to inducibly express BRAFV600E, we show that BRAF activation results in reversible, TGFβ-dependent, p15 induction that halts proliferation. Furthermore, we engineer human skin grafts containing nevus-derived melanocytes to establish a new, architecturally faithful, in vivo melanoma model, and demonstrate that p15 loss promotes the transition from benign nevus to melanoma.
Significance: Although BRAFV600E mutations cause melanocytes to initially proliferate into benign moles, mechanisms responsible for their eventual growth arrest are unknown. Using melanocytes from human moles, we show that BRAF activation leads to a CDKN2B induction that is critical for restraining BRAF oncogenic effects, and when lost, contributes to melanoma. Cancer Discov; 5(10); 1072–85. ©2015 AACR.
This article is highlighted in the In This Issue feature, p. 1005
Low Impact of Traditional Risk Factors on Carotid Intima-Media Thickness
Authors: Santos Itamar S. , Alencar Airlane P. , Rundek Tatjana , Goulart Alessandra C. , Barreto Sandhi M. , Pereira Alexandre C. , Benseñor Isabela M. , Lotufo Paulo A. 
Published: July 2015

Objective—
There is little information about how much traditional cardiovascular risk factors explain common carotid artery intima-media thickness (CCA-IMT) variance. We aimed to study to which extent CCA-IMT values are determined by traditional risk factors and which commonly used measurements of blood pressure, glucose metabolism, lipid profile, and adiposity contribute the most to this determination in the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil) cohort baseline.

Approach and Results—

We analyzed 9792 individuals with complete data and CCA-IMT measurements. We built multiple linear regression models using mean left and right CCA-IMT as the dependent variable. All models were stratified by sex. We also analyzed individuals stratified by 10-year coronary heart disease risk and, in separate, those with no traditional risk factors. Main models’
R
2
varied between 0.141 and 0.373. The major part of the explained variance in CCA-IMT was because of age and race. Indicators of blood pressure, lipid profile, and adiposity that most frequently composed the best models were pulse pressure, low-density lipoprotein/high-density lipoprotein ratio, and neck circumference. The association between neck circumference and CCA-IMT persisted significant even after further adjustment for vessel sizes and body mass index. Indicators of glucose metabolism had smaller contribution.

Conclusions—
We found that >60% of CCA-IMT were not explained by demographic and traditional cardiovascular risk factors, which highlights the need to study novel risk factors. Pulse pressure, low-density lipoprotein/high-density lipoprotein ratio, and neck circumference were the most consistent contributors.