bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of a Rabies Virus Isolated from a Human in Central African Republic
Authors: Tricou Vianney , Berthet Nicolas , Nakouné Emmanuel , Kazanji Mirdad 
Published: June 2014

ABSTRACT
To validate the feasibility of using next-generation sequencing in an African context, the complete genome of a rabies virus isolated from a human patient was obtained by high-throughput sequencing after virus isolation in mice and random unbiased amplification. Phylogenetic analysis suggested that this virus belongs to the Africa II clade.
Characterization of an Avian Influenza Virus H9N2 Strain Isolated from a Wild Bird in Southern China
Authors: Xu Qian , Xie Zhixun , Xie Liji , Xie Zhiqin , Deng Xianwen , Liu Jiabo , Luo Sisi 
Published: June 2014

ABSTRACT
We isolated an avian influenza virus H9N2 strain from a wild bird in the Guangxi Province of southern China in 2013 named A/turtledove/Guangxi/49B6/2013(H9N2) (GX49B6). We aimed to understand the genetic characters of the GX49B6 strain by analyzing the complete genome sequence. The results showed that our isolated strain has features of low pathogenic avian influenza viruses and viruses that infect humans. The discovery of the complete genome sequence of the GX49B6 strain may be helpful to further the understanding of the epidemiology and surveillance of avian influenza viruses in the field.
Draft Genome Sequence of Bacillus subtilis strain KATMIRA1933
Authors: Karlyshev Andrey V. , Melnikov Vyacheslav G. , Chikindas Michael L. 
Published: June 2014

ABSTRACT

In this report, we present a draft sequence of
Bacillus subtilis
KATMIRA1933. Previous studies demonstrated probiotic properties of this strain partially attributed to production of an antibacterial compound, subtilosin. Comparative analysis of this strain's genome with that of a commercial probiotic strain,
B. subtilis
Natto, is presented.
Draft Genome Sequences of
Geomicrobium
sp. Strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, Isolated from Aquatic Samples
Authors: Kudo Toshiaki , Nakahara Tomomi , Zhang Xiaochi , Taniyama Shigeto , Arakawa Osamu , Murase Shinji , Nakata Hideaki , Oshima Kenshiro , Suda Wataru , Kitamura Keiko , Iida Toshiya , Oshida Yumi , Inoue Tetsushi , Hongoh Yuichi , Hattori Masahira , Ohkuma Moriya 
Published: June 2014

ABSTRACT

Haloalkaliphilic strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, closely related to
Geomicrobium sediminis
, were isolated from aquatic samples, and their draft genome sequences were determined. The genome information of these four strains will be useful for studies of their physiology and ecology.
Draft Genome Sequence of Bacillus amyloliquefaciens B-1895
Authors: Karlyshev Andrey V. , Melnikov Vyacheslav G. , Chistyakov Vladimir A. 
Published: June 2014

ABSTRACT

In this report, we present a draft genome sequence of
Bacillus amyloliquefaciens
strain B-1895. Comparison with the genome of a reference strain demonstrated similar overall organization, as well as differences involving large gene clusters.
Draft Genome Sequence of
Penicillium expansum
Strain R19, Which Causes Postharvest Decay of Apple Fruit
Authors: Yu Jiujiang , Jurick Wayne M. , Cao Huansheng , Yin Yanbin , Gaskins Verneta L. , Losada Liliana , Zafar Nikhat , Kim Maria , Bennett Joan W. , Nierman William C. 
Published: June 2014

ABSTRACT

Among the species that cause blue mold, isolates of
Penicillium expansum
are the most prevalent and virulent species, causing more than 50 percent of postharvest decay. We report the draft genome sequence of
P. expansum
R19 in order to identify fungal virulence factors and to understand the mechanism of infection.
Differences in socioeconomic position, lifestyle and health-related pregnancy characteristics between Pakistani and White British women in the Born in Bradford prospective cohort study: the influence of the woman's, her partner's and their parents’ place of birth
Authors: West J , Lawlor D A , Fairley L , Wright J 
Published: June 2014

ObjectiveTo examine differences between Pakistani and White British women in relation to socioeconomic position, lifestyle and health-related pregnancy characteristics, and to determine whether these differences vary depending on the woman's, her partner's and both of their parents’ place of birth.DesignProspective cohort study.SettingBradford, UKParticipants3656 Pakistani and 3503 White British women recruited to the Born in Bradford study.Main outcome measuresSocioeconomic position (employment status; level of education; receipt of benefits; housing tenure), lifestyle characteristics (body mass index (BMI) at the start of pregnancy; smoking during pregnancy) and health-related pregnancy characteristics (hypertensive disorders of pregnancy; gestational diabetes; fasting glucose, postload glucose and fasting insulin at ∼27 weeks gestation).ResultsFewer Pakistani women were employed (OR 0.17, 95% CI 0.15 to 0.19), the difference being markedly less for UK born women. UK born Pakistani women were more likely, and South Asian born less likely, to be educated post 16 than White British women. Smoking was uncommon among Pakistani women, though the difference comparing UK born Pakistani women to White British women was less than for other groups. BMI was lower among Pakistani compared to White British women (adjusted mean difference −1.12, 95% CI −1.43 to −0.81), the difference being greatest when partners were UK born irrespective of the woman’s place of birth. Pakistani women had higher fasting and postload glucose (mean difference 0.20 mmol/L, 95% CI 0.17 to 0.24; 0.37, 95% CI 0.28 to 0.45), higher fasting insulin and were more likely to have gestational diabetes (GDM).ConclusionsOur results suggest that some socioeconomic, lifestyle and pregnancy characteristics could be beginning to change in response to migration to the UK, with generally beneficial changes, that is, improving education and employment prospects, lower BMI and no evidence that being UK born has further increased the risk of GDM, but some negative, that is, slight increases in smoking.
Epidemiology of injuries in hurling: a prospective study 2007–2011
Authors: Blake Catherine , O'Malley Edwenia , Gissane Conor , Murphy John C 
Published: June 2014

ObjectivesHurling is a stick handling game which, although native to Ireland, has international reach and presence. The aim of this study was to report incidence and type of injuries incurred by elite male hurling players over five consecutive playing seasons.DesignProspective cohort study.SettingMale intercounty elite sports teams participating in the National GAA Injury Database, 2007–2011.ParticipantsA total of 856 players in 25 county teams were enrolled.Primary and secondary outcomesIncidence, nature and mechanism of injury were recorded by team physicians or physiotherapists to a secure online data collection portal. Time-loss injury rates per 1000 training and match play hours were calculated and injury proportions were expressed.ResultsIn total 1030 injuries were registered, giving a rate of 1.2 injuries per player. These were sustained by 71% (n=608) of players. Injury incidence rate was 2.99 (95% CI 2.68 to 3.30) per 1000 training hours and 61.75 (56.75 to 66.75) per 1000 match hours. Direct player-to-player contact was recorded in 38.6% injuries, with sprinting (24.5%) and landing (13.7%) the next most commonly reported injury mechanisms. Median duration of time absent from training or games, where the player was able to return in the same season, was 12 days (range 2–127 days). The majority (68.3%) of injuries occurred in the lower limbs, with 18.6% in the upper limbs. The trunk and head/neck regions accounted for 8.6% and 4.1% injuries, respectively. The distribution of injury type was significantly different (p<0.001) between upper and lower extremities: fractures (upper 36.1%, lower 1.5%), muscle strain (upper 5.2%, lower 45.8%).ConclusionsThese data provide stable, multiannual data on injury patterns in hurling, identifying the most common injury problems. This is the first step in applying a systematic, theory-driven injury prevention model in the sport.
Are statin trials in diabetes representative of real-world diabetes care: a population-based study on statin initiators in Finland
Authors: Ruokoniemi Päivi , Sund Reijo , Arffman Martti , Helin-Salmivaara Arja , Huupponen Risto , Keskimäki Ilmo , Vehko Tuulikki , Korhonen Maarit Jaana 
Published: June 2014

ObjectiveTo assess the representativeness of the Heart Protection Study (HPS) and the Collaborative Atorvastatin Diabetes Study (CARDS) for incident statin users.DesignA population-based analysis with linked register data.SettingFinland.Population56 963 patients with diabetes initiating statin use from 2005 to 2008.Main outcome measuresWe determined the proportions of real-world patients who fulfilled the eligibility criteria for HPS and CARDS trials and assessed the cardiovascular disease (CVD) event rates, assumed to reflect the background CVD risk, for those eligible and ineligible. We used descriptive statistics to identify the patient characteristics, lipid-lowering interventions and adherence to statin therapy.ResultsOf the real-world patients, 57% (N=32 582) fulfilled the eligibility criteria for HPS (DM) and 49% (N=20 499) of those without CVD for CARDS. The patients ineligible for HPS (DM) had a higher cumulative risk for CVD events than those eligible, whereas regarding CARDS the cumulative risks were of similar magnitude. The overall CVD event rates seemed to be comparable to those in the reviewed trials. Both trials were under-representative of women and users of antihypertensive agents and metformin. 27% and 29% of real-world patients had an initial statin dose corresponding to <20 mg of simvastatin. The proportions of patients who were deemed adherent were 57% in the real world and 85% in both trials.ConclusionsOnly half of the real-world patients would have qualified for the HPS (DM) and CARDS, limiting their representativeness for clinical practice. Women and users of antihypertensive agents and metformin were under-represented in both trials. These deviations reflect the changes in diabetes treatment over the years and are not expected to modify the average treatment effects of statins on CVD. Prescribing of lower statin doses in clinical practice than used in the trials and lower adherence may, however, attenuate the benefits in the real world.
Analgesic use, pain and daytime sedation in people with and without dementia in aged care facilities: a cross-sectional, multisite, epidemiological study protocol
Authors: Tan Edwin C K , Visvanathan Renuka , Hilmer Sarah N , Vitry Agnes I , Quirke Tara , Emery Tina , Robson Leonie , Shortt Terry , Sheldrick Simon , Lee Sunny (Soon Won) , Clothier Robyn , Reeve Emily , Gnjidic Danijela , Ilomäki Jenni , Bell J Simon 
Published: June 2014

IntroductionPeople living with dementia may experience and express pain in different ways to people without dementia. People with dementia are typically prescribed fewer analgesics than people without dementia indicating a potential difference in how pain is identified and treated in these populations. The objectives of this study are to (1) investigate the prevalence of analgesic load, pain and daytime sedation in people with and without dementia in Australian residential aged care facilities (RACFs), and (2) investigate the clinical and diagnostic associations between analgesic load, pain and daytime sedation in people with and without dementia in Australian RACFs.Methods/analysisThis will be a cross-sectional study of 300 permanent residents of up to 10 low-level and high-level RACFs in South Australia with and without dementia. Trained study nurses will administer validated and dementia-specific assessments of self-reported and clinician-observed pain, sedation and other clinical and humanistic outcomes. Medicine-use data will be extracted directly from each resident's medication administration chart. Binary and multinominal logistic regression will be used to compute unadjusted and adjusted ORs and 95% CIs for factors associated with pain, analgesic load and daytime sedation. These factors will include dementia severity, behavioural and psychological symptoms, quality of life, resident satisfaction, attitudes towards medicines, activities of daily living and nutritional status.Ethics and disseminationInstitutional ethics approval has been granted. The findings will be disseminated through public lectures, professional and scientific conferences and in peer-reviewed journal articles. The findings of this study will allow for a better understanding of the prevalence and factors associated with analgesic use, pain and other outcomes in residential care. The findings of this study will be used to inform the development and implementation of strategies to improve the quality of life of people with dementia.
PBX1 Is a Favorable Prognostic Biomarker as It Modulates 13-cis Retinoic Acid–Mediated Differentiation in Neuroblastoma
Authors: Shah Nilay , Wang Jianjun , Selich-Anderson Julia , Graham Garrett , Siddiqui Hasan , Li Xin , Khan Javed , Toretsky Jeffrey 
Published: June 2014

Abstract
Purpose: Neuroblastoma is an embryonic childhood cancer with high mortality. 13-cis retinoic acid (13-cisRA) improves survival for some patients, but many recur, suggesting clinical resistance. The mechanism of resistance and the normal differentiation pathway are poorly understood. Three–amino-acid loop extension (TALE) family genes are master regulators of differentiation. Because retinoids promote differentiation in neuroblastoma, we evaluated TALE family gene expression in neuroblastoma.
Experimental Design: We evaluated expression of TALE family genes in RA-sensitive and -resistant neuroblastoma cell lines, with and without 13-cisRA treatment, identifying genes whose expression correlates with retinoid sensitivity. We evaluated the roles of one gene, PBX1, in neuroblastoma cell lines, including proliferation and differentiation. We evaluated PBX1 expression in primary human neuroblastoma samples by qRT-PCR, and three independent clinical cohort microarray datasets.
Results: We confirmed that induction of PBX1 expression, and no other TALE family genes, was associated with 13-cisRA responsiveness in neuroblastoma cell lines. Exogenous PBX1 expression in neuroblastoma cell lines, mimicking induced PBX1 expression, significantly impaired proliferation and anchorage-independent growth, and promoted RA-dependent and -independent differentiation. Reduced PBX1 protein levels produced an aggressive growth phenotype and RA resistance. PBX1 expression correlated with histologic neuroblastoma subtypes, with highest expression in benign ganglioneuromas and lowest in high-risk neuroblastomas. High PBX1 expression is prognostic of survival, including in multivariate analysis, in the three clinical cohorts.
Conclusions: PBX1 is an essential regulator of differentiation in neuroblastoma and potentiates retinoid-induced differentiation. Neuroblastoma cells and tumors with low PBX1 expression have an immature phenotype with poorer prognosis, independent of other risk factors. Clin Cancer Res; 20(16); 4400–12. ©2014 AACR.
Association of EGFR Expression Level and Cetuximab Activity in Patient-Derived Xenograft Models of Human Non–Small Cell Lung Cancer
Authors: Amendt Christiane , Staub Eike , Friese-Hamim Manja , Störkel Stephan , Stroh Christopher 
Published: June 2014

Abstract
Purpose: To explore in a panel of patient-derived xenograft models of human non–small cell lung cancer (NSCLC) whether high EGFR expression, was associated with cetuximab activity.
Experimental Design: NSCLC patient-derived xenograft models (n = 45) were implanted subcutaneously into panels of nude mice and randomization cohorts were treated with either cetuximab, cisplatin, cisplatin plus cetuximab, vehicle control, or else were left untreated. Responses according to treatment were assessed at week 3 by analyzing the relative change in tumor volume and an experimental analogue of the Response Evaluation Criteria in Solid Tumors (RECIST) guidelines. An EGFR IHC score was calculated for each patient-derived xenograft model and response was assessed according to EGFR expression level.
Results: When tumors were stratified into high and low EGFR expression groups (IHC score threshold 200; scale 0–300), a stronger antitumor activity was seen in the high EGFR expression group compared with the low EGFR expression group in both the cetuximab monotherapy and cisplatin plus cetuximab combination therapy settings. For tumors treated with cisplatin plus cetuximab, the objective response rate was significantly higher in the high EGFR expression group compared with the low EGFR expression group (68% vs. 29%). Objective response rates were similar in high and low expression groups for tumors treated with cisplatin alone (27% vs. 24%, respectively).
Conclusion: Cetuximab activity in NSCLC patient-derived xenograft models was demonstrated clearly only in tumors that expressed high levels of EGFR, as defined by an IHC score of ≥200. Clin Cancer Res; 20(17); 4478–87. ©2014 AACR.
Sonic Hedgehog Paracrine Signaling Activates Stromal Cells to Promote Perineural Invasion in Pancreatic Cancer
Authors: Li Xuqi , Wang Zheng , Ma Qingyong , Xu Qinhong , Liu Han , Duan Wanxing , Lei Jianjun , Ma Jiguang , Wang Xiu , Lv Shifang , Han Liang , Li Wei , Guo Jian , Guo Kun , Zhang Dong , Wu Erxi , Xie Keping 
Published: June 2014

Abstract
Purpose: Pancreatic cancer is characterized by stromal desmoplasia and perineural invasion (PNI). We sought to explore the contribution of pancreatic stellate cells (PSC) activated by paracrine Sonic Hedgehog (SHH) in pancreatic cancer PNI and progression.
Experimental Design: In this study, the expression dynamics of SHH were examined via immunohistochemistry, real-time PCR, and Western blot analysis in a cohort of carcinomatous and nonneoplastic pancreatic tissues and cells. A series of in vivo and in vitro assays was performed to elucidate the contribution of PSCs activated by paracrine SHH signaling in pancreatic cancer PNI and progression.
Results: We show that SHH overexpression in tumor cells is involved in PNI in pancreatic cancer and is an important marker of biologic activity of pancreatic cancer. Moreover, the overexpression of SHH in tumor cells activates the hedgehog pathway in PSCs in the stroma instead of activating tumor cells. These activated PSCs are essential for the promotion of pancreatic cancer cell migration along nerve axons and nerve outgrowth to pancreatic cancer cell colonies in an in vitro three-dimensional model of nerve invasion in cancer. Furthermore, the coimplantation of PSCs activated by paracrine SHH induced tumor cell invasion of the trunk and nerve dysfunction along sciatic nerves and also promoted orthotropic xenograft tumor growth, metastasis, and PNI in in vivo models.
Conclusions: These results establish that stromal PSCs activated by SHH paracrine signaling in pancreatic cancer cells secrete high levels of PNI-associated molecules to promote PNI in pancreatic cancer. Clin Cancer Res; 20(16); 4326–38. ©2014 AACR.
Screening for Cardiac Dysfunction in Anthracycline-Exposed Childhood Cancer Survivors
Authors: Armenian Saro H. , Gelehrter Sarah K. , Vase Tabitha , Venkatramani Rajkumar , Landier Wendy , Wilson Karla D. , Herrera Claudia , Reichman Leah , Menteer John-David , Mascarenhas Leo , Freyer David R. , Venkataraman Kalyanasundaram , Bhatia Smita 
Published: June 2014

Abstract
Purpose: To examine the utility and reliability of obtaining early echocardiographic measurements of left ventricular (LV) remodeling as well as blood biomarkers of cardiac injury in asymptomatic childhood cancer survivors at risk for LV dysfunction and congestive heart failure due to past exposure to anthracycline chemotherapy.
Experimental Design: Using a cross-sectional design, anthracycline-exposed childhood cancer survivors with preserved ejection fraction (EF; ≥50%) were evaluated using early echocardiographic indices and blood biomarkers of LV dysfunction. Survivors treated with ≥300 mg/m2 anthracyclines [high risk (HR): n = 100] were compared with those treated with &lt;300 mg/m2 anthracyclines [low risk (LR): n = 50] and matched healthy controls (HC: n = 50). All echocardiograms were interpreted by an institutional cardiologist and a study cardiologist blinded to risk status.
Results: Time from diagnosis was comparable for HR (12.0 years) and LR (13.2 years, P = 0.8) survivors. Echocardiograms: HR had lower LV thickness-dimension ratio (Z-score: HR: −0.62, LR: −0.03, HC: −0.02; P &lt; 0.001), increased LV wall stress (HR: 66.7 g/cm2, LR: 56.6 g/cm2, HC: 54.2 g/cm2; P &lt; 0.01), and higher myocardial performance index (HR: 0.51, LR: 0.46, HC: 0.46; P &lt; 0.01). Interobserver correlation (clinical/blinded reading) for all echocardiographic indices was excellent (range: R = 0.76–0.97, P &lt; 0.001). Blood biomarkers: With the exception of NT-proBNP (r = 0.28, P &lt; 0.01), there was no correlation between blood biomarkers (B-type natriuretic peptide, Troponin-T, ST-2, Galectin-3) and LV dysfunction.
Conclusion: Childhood cancer survivors with preserved EF 10+ years from anthracycline exposure had dose-dependent changes in echocardiographic markers of LV dysfunction. Clin Cancer Res; 20(24); 6314–23. ©2014 AACR.
ID1 Promotes Breast Cancer Metastasis by S100A9 Regulation
Authors: Gumireddy Kiranmai , Li Anping , Kossenkov Andrew V. , Cai Kathy Q. , Liu Qin , Yan Jinchun , Xu Hua , Showe Louise , Zhang Lin , Huang Qihong 
Published: June 2014

AbstractMetastasis is a major factor responsible for mortality in patients with breast cancer. Inhibitor of DNA binding 1 (Id1) has been shown to play an important role in cell differentiation, tumor angiogenesis, cell invasion, and metastasis. Despite the data establishing Id1 as a critical factor for lung metastasis in breast cancer, the pathways and molecular mechanisms of Id1 functions in metastasis remain to be defined. Here, we show that Id1 interacts with TFAP2A to suppress S100A9 expression. We show that expression of Id1 and S100A9 is inversely correlated in both breast cancer cell lines and clinical samples. We also show that the migratory and invasive phenotypes in vitro and metastasis in vivo induced by Id1 expression are rescued by reestablishment of S100A9 expression. S100A9 also suppresses the expression of known metastasis-promoting factor RhoC activated by Id1 expression. Our results suggest that Id1 promotes breast cancer metastasis by the suppression of S100A9 expression.Implications: Novel pathways by Id1 regulation in metastasis. Mol Cancer Res; 12(9); 1334–43. ©2014 AACR.