bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Adaptation of Porcine Circovirus Type 1 to Cultured Porcine Kidney Cells Revealed by Single-Molecule Long-Read Sequencing Technology
Authors: Tombácz Dóra , Moldován Norbert , Balázs Zsolt , Csabai Zsolt , Snyder Michael , Boldogkői Zsolt 
Published: February 2017

ABSTRACT
Porcine circovirus type 1 (PCV1) is a nonpathogenic circovirus, and a contaminant of the porcine kidney (PK-15) cell line. We present the complete and annotated genome sequence of strain Szeged of PCV1, determined by Pacific Biosciences RSII long-read sequencing platform.
Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group
Authors: Guinebretière Marie-Hélène , Loux Valentin , Martin Véronique , Nicolas Pierre , Sanchis Vincent , Broussolle Véronique 
Published: February 2017

ABSTRACT

Bacteria from the
Bacillus cereus
group exhibit genetic and physiological diversity through different ecotypes. Here, we present the draft genome sequences of 20 bacterial strains belonging to the contrasted psychrotolerant and thermotolerant ecotypes.
Concordance of Barthel Index, ECOG-PS, and Palliative Performance Scale in the assessment of functional status in patients with advanced medical diseases
Authors: Hernández-Quiles C , Bernabeu-Wittel M , Pérez-Belmonte L M , Macías-Mir P , Camacho-González D , Massa B , Maiz-Jiménez M , Ollero-Baturone M 
Published: January 2017

ObjectiveAnalysing most relevant clinical features and concordance between different functional scales in patients with advanced medical diseases (PAMD).MethodsCross-sectional multicentre study that included PAMD (heart, lung, kidney, liver, and neurological diseases) in hospital settings from February 2009 to October 2010. We analysed clinical, biological and functional features in performing activities of daily living (ADL) by medians of Barthel Index (BI); additionally we assessed their performance status by medians of Eastern Cooperative Oncology Group-Performance Status (ECOG-PS) and Palliative Performance Scale (PPS) scores. We evaluated the concordance of these instruments in assessing functional impairment by κ and intraclass correlation coefficient tests.Results1847 patients were included (average age 79 years, 50.1% men). Most common symptoms were dyspnoea (62.31%), asthenia (23%) and delirium (20.14%). Functional assessment showed a high prevalence of severe or total impairment in performing basic ADL by medians of used instruments (BI median=35 (IQR=70), and 52.1% of patients with severe–total impairment; ECOG-PS median=2 (IQR 30), and 44% of patients with severe–total impairment; and PPS median=50 (IQR 30), and 32% of patients with severe–total impairment). Concordance among these instruments was acceptably good (κindexes ranging from 0.653 to 0.745 (p<0.0001)).ConclusionsPAMD represent a population with severe functional impairment, which requires a multidisciplinary approach for proper management. Assessment of functional ability in this population by BI, ECOG-PS, and PPS showed good concordance.
The use of whole-body computed tomography in major trauma: variations in practice in UK trauma hospitals
Authors: Sammy Ian Ayenga , Chatha Hridesh , Bouamra Omar , Fragoso-Iñiguez Marisol , Lecky Fiona , Edwards Antoinette 
Published: January 2017

IntroductionWhole-body CT (WBCT) use in patients with trauma in England and Wales is not well documented. WBCT in trauma can reduce time to definitive care, thereby increasing survival. However, its use varies significantly worldwide.MethodsWe performed a retrospective observational study of Trauma Audit and Research Network (TARN) data from 2012 to 2014. The proportion of adult patients receiving WBCT during initial resuscitation at major trauma centres (MTCs) and trauma units/non-designated hospitals (TUs/NDHs) was compared. A model was developed that included factors associated with WBCT use, and centre effects within the model were explored to determine variation in usage beyond that expected from the model.ResultsOf the 115 664 study participants, 16.5% had WBCT. WBCT was performed five times more frequently in MTCs than in TUs/NDHs (31% vs 6.6%). In the multivariate model, increased injury severity, low GCS, shock, comorbidities and triage category increased the chances of having a WBCT, but there was no consistent relation with age. High falls and motor vehicle collisions also increased WBCT usage. Adjusting for casemix, there was a 13-fold intrahospital variation in the use of WBCT between MTCs and a 30-fold variation between TUs/NDHs. The amount of variability between individual hospitals that could not be accounted for by the factors shown to impact on WBCT use was 26% (95% CI 17% to 39%) for MTCs and 17% (95% CI 13% to 21%) for TUs/NDHs.ConclusionThere are significant variations in WBCT use between different hospitals in England and Wales, which require further investigation.
levels and sociodemographic correlates of accelerometer-based physical activity in Irish children: a cross-sectional study
Authors: Li Xia , Kearney Patricia M , Keane Eimear , Harrington Janas M , Fitzgerald Anthony P 
Published: January 2017

BackgroundThe aim of this study was to explore levels and sociodemographic correlates of physical activity (PA) over 1 week using accelerometer data.MethodsAccelerometer data was collected over 1 week from 1075 8–11-year-old children in the cross-sectional Cork Children's Lifestyle Study. Threshold values were used to categorise activity intensity as sedentary, light, moderate or vigorous. Questionnaires collected data on demographic factors. Smoothed curves were used to display minute by minute variations. Binomial regression was used to identify factors correlated with the probability of meeting WHO 60 min moderate to vigorous PA guidelines.ResultsOverall, 830 children (mean (SD) age: 9.9(0.7) years, 56.3% boys) were included. From the binomial multiple regression analysis, boys were found more likely to meet guidelines (probability ratio 1.17, 95% CI 1.06 to 1.28) than girls. Older children were less likely to meet guidelines than younger children (probability ratio 0.91, CI 0.87 to 0.95). Normal weight children were more likely than overweight and obese children to meet guidelines (probability ratio 1.25, CI 1.16 to 1.34). Children in urban areas were more likely to meet guidelines than those in rural areas (probability ratio 1.19, CI 1.07 to 1.33). Longer daylight length days were associated with greater probability of meeting guidelines compared to shorter daylight length days.ConclusionsPA levels differed by individual factors including age, gender and weight status as well as by environmental factors including residence and daylight length. Less than one-quarter of children (26.8% boys, 16.2% girls) meet guidelines. Effective intervention policies are urgently needed to increase PA.
Optimal first coil selection to avoid aneurysmal recanalization in endovascular intracranial aneurysmal coiling
Authors: Neki Hiroaki , Kohyama Shinya , Otsuka Toshihiro , Yonezawa Azusa , Ishihara Shoichiro , Yamane Fumitaka 
Published: January 2017

BackgroundAneurysmal recanalization is a problem with endovascular coiling and one of its risk factors is the low volume embolization ratio (VER). The first coil VER (1st VER) is believed to be critical for obtaining a high VER. The main objective of this study was to evaluate factors potentially useful for selecting the optimal 1st VER for endovascular coiling.Methods609 initial saccular aneurysmal treatments performed between January 2010 and December 2014 at our institution were included in this retrospective study. Attempted procedures, retreatment cases, intraoperative rupture cases, and stent-assisted coiling cases were excluded. Age, sex, aneurysm location, ruptured aneurysm, aneurysm shape, neck size, maximum aneurysm size, dome-to-neck ratio, aneurysm volume, procedure, immediate Raymond scale score, 1st VER, and VER between the recanalization groups and non-recanalization groups were compared.ResultsThe factors related to recanalization were ruptured aneurysms, neck width, maximum aneurysm size, aneurysm volume, procedure, 1st VER, and VER. The cut-off values for aneurysm recanalization were a 1st VER of 10.0% and a VER of 33.0%. The maximum average VER of normal size aneurysms was found in the groups with a 1st VER of 17.5–20.0%.Conclusions1st VER was found to be a helpful index for estimating aneurysmal recanalization after coil embolization. The target 1st VER was 17.5–20.0% for obtaining a higher VER and avoiding recanalization.
Trauma advanced practice provider programme development in an academic setting to optimize care coordination
Authors: Woodfall Michelle C , Browder Timothy D , Alfaro Jesus M , Claudius Meghan A , Chan Garrett K , Robinson Denise Greci , Spain David A 
Published: January 2017

BackgroundBenchmark data from the Trauma Quality Improvement Program (TQIP) identified an opportunity for improvement in our trauma programme. Our unexpected return to the intensive care unit (ICU) was found to be higher than the national averages and we also noticed that our readmission rate had increased. We chose to address these complications as continuous quality improvement projects. It was hypothesized that restructuring the workflow of the trauma advanced practice providers (APPs) to focus on the delivery of comprehensive clinical care would decrease return to ICU and readmission rates of trauma patients.MethodsThe development of the APP programme occurred from 2012 to 2014. First, APP daily shifts were extended to mirror the resident physicians’ coverage. Second, the APPs’ original job description was expanded from ‘task-oriented’ workflow to providing comprehensive clinical care. Third, the APPs were involved in the evaluation and decision-making process for transferring trauma patients from the ICU. Finally, the APPs implemented a new discharge process that included all information in a standardized format and a follow-up phone call 24–48 hours after discharge. The trauma registry at our verified, academic level I trauma center was use to assess our ICU and hospital readmission rates during the time we instituted the new APP workflow programme.ResultsIn 2012, our ICU readmission rate was 5.7% (TQIP=1.9%) but then decreased to 4.4% in 2013 (TQIP=2.5%) and 2.1% in 2014 (TQIP=2.8%). Our hospital readmission rate was 2.0% in 2012 but then decreased to 1.38% and 0.96% over the next 2 years.ConclusionsAfter extending the APP service coverage, implementing a comprehensive clinical care model and standardizing the discharge process, our unplanned return to ICU rates have decreased to below the TQIP national average and hospital readmission rates have also decreased by half.Level of evidenceIII.
Distinctive Histogenesis and Immunological Microenvironment Based on Transcriptional Profiles of Follicular Dendritic Cell Sarcomas
Authors: Laginestra Maria Antonella , Tripodo Claudio , Agostinelli Claudio , Motta Giovanna , Hartmann Sylvia , Döring Claudia , Rossi Maura , Melle Federica , Sapienza Maria Rosaria , Tabanelli Valentina , Pileri Alessandro , Fuligni Fabio , Gazzola Anna , Mannu Claudia , Sagramoso Carlo Alberto , Lonardi Silvia , Lorenzi Luisa , Bacci Francesco , Sabattini Elena , Borges Anita , Simonitsch-Klupp Ingrid , Cabecadas Jose , Campo Elias , Rosai Juan , Hansmann Martin-Leo , Facchetti Fabio , Pileri Stefano Aldo 
Published: January 2017

Abstract
Follicular dendritic cell (FDC) sarcomas are rare mesenchymal tumors with variable clinical, morphologic, and phenotypic characteristics. Transcriptome analysis was performed on multiple FDC sarcomas and compared with other mesenchymal tumors, microdissected Castleman FDCs, and normal fibroblasts. Using unsupervised analysis, FDC sarcomas clustered with microdissected FDCs, distinct from other mesenchymal tumors and fibroblasts. The specific endowment of FDC-related gene expression programs in FDC sarcomas emerged by applying a gene signature of differentially expressed genes (n = 1,289) between microdissected FDCs and fibroblasts. Supervised analysis comparing FDC sarcomas with microdissected FDCs and other mesenchymal tumors identified 370 and 2,927 differentially expressed transcripts, respectively, and on the basis of pathway enrichment analysis ascribed to signal transduction, chromatin organization, and extracellular matrix organization programs. As the transcriptome of FDC sarcomas retained similarity with FDCs, the immune landscape of FDC sarcoma was investigated by applying the CIBERSORT algorithm to FDC sarcomas and non-FDC mesenchymal tumors and demonstrated that FDC sarcomas were enriched in T follicular helper (TFH) and T regulatory (TREG) cell populations, as confirmed in situ by immunohistochemistry. The enrichment in specific T-cell subsets prompted investigating the mRNA expression of the inhibitory immune receptor PD-1 and its ligands PD-L1 and PD-L2, which were found to be significantly upregulated in FDC sarcomas as compared with other mesenchymal tumors, a finding also confirmed in situ. Here, it is demonstrated for the first time the transcriptional relationship of FDC sarcomas with nonmalignant FDCs and their distinction from other mesenchymal tumors.
Implications: The current study provides evidence of a peculiar immune microenvironment associated with FDC sarcomas that may have clinical utility. Mol Cancer Res; 15(5); 541–52. ©2017 AACR.
Genome-Wide Analysis Identifies MEN1 and MAX Mutations and a Neuroendocrine-Like Molecular Heterogeneity in Quadruple WT GIST
Authors: Pantaleo Maria A. , Urbini Milena , Indio Valentina , Ravegnini Gloria , Nannini Margherita , De Luca Matilde , Tarantino Giuseppe , Angelini Sabrina , Gronchi Alessandro , Vincenzi Bruno , Grignani Giovanni , Colombo Chiara , Fumagalli Elena , Gatto Lidia , Saponara Maristella , Ianni Manuela , Paterini Paola , Santini Donatella , Pirini M. Giulia , Ceccarelli Claudio , Altimari Annalisa , Gruppioni Elisa , Renne Salvatore L. , Collini Paola , Stacchiotti Silvia , Brandi Giovanni , Casali Paolo G. , Pinna Antonio D. , Astolfi Annalisa , Biasco Guido 
Published: January 2017

Abstract
Quadruple wild-type (WT) gastrointestinal stromal tumor (GIST) is a genomic subgroup lacking KIT/PDGFRA/RAS pathway mutations, with an intact succinate dehydrogenase (SDH) complex. The aim of this work is to perform a wide comprehensive genomic study on quadruple WT GIST to improve the characterization of these patients. We selected 14 clinical cases of quadruple WT GIST, of which nine cases showed sufficient DNA quality for whole exome sequencing (WES). NF1 alterations were identified directly by WES. Gene expression from whole transcriptome sequencing (WTS) and miRNA profiling were performed using fresh-frozen, quadruple WT GIST tissue specimens and compared with SDH and KIT/PDGFRA-mutant GIST. WES identified an average of 18 somatic mutations per sample. The most relevant somatic oncogenic mutations identified were in TP53, MEN1, MAX, FGF1R, CHD4, and CTDNN2. No somatic alterations in NF1 were identified in the analyzed cohort. A total of 247 mRNA transcripts and 66 miRNAs were differentially expressed specifically in quadruple WT GIST. Overexpression of specific molecular markers (COL22A1 and CALCRL) and genes involved in neural and neuroendocrine lineage (ASCL1, Family B GPCRs) were detected and further supported by predicted miRNA target analysis. Quadruple WT GIST show a specific genetic signature that deviates significantly from that of KIT/PDGFRA-mutant and SDH-mutant GIST. Mutations in MEN1 and MAX genes, a neural-committed phenotype and upregulation of the master neuroendocrine regulator ASCL1, support a genetic similarity with neuroendocrine tumors, with whom they also share the great variability in oncogenic driver genes.
Implications: This study provides novel insights into the biology of quadruple WT GIST that potentially resembles neuroendocrine tumors and should promote the development of specific therapeutic approaches. Mol Cancer Res; 15(5); 553–62. ©2017 AACR.
Client-centred home modifications improve daily activity performance of older adults
Authors: Stark Susan , Landsbaum Amanda , Palmer Janice L. , Somerville Emily K. , Morris John C. , Harvey A. , Friedman Dorismae Hacker 
Published: January 2017

Background Remaining at home is a high priority for many older adults, but the capacity to “age in place” often is threatened by environmental barriers. Purpose To describe a client-centred occupational therapy home modification intervention program and examine the impact of the intervention on daily activity performance over time. Methods Using a competence-environmental press framework, a client-centred home modification program for older adults was implemented. In this quasi-experimental, single group prospective study, participants' subjective ratings of daily activity performance were evaluated before and after the intervention (baseline/post/post). Findings After home modification, participants' perception of their daily activity performance at home improved significantly and was maintained 2 years post-modification. Implications Home modification may benefit older adults attempting to age in place.
Global Crossing: A Turnaround
Authors: Nautiyal Anmol , Shastri Suryanarayana 
Published: January 2017

During the 1990s, India saw tremendous changes in the economy and many Indian firms enjoyed the benefits of the Government's open policy. On-going process of relaxation in trade barriers and tariffs and the phasing-out of Quantitative Restrictions (QRs) are and will create many opportunities for growth. Changes in the external environment will impose challenges as well as create many opportunities for Indian firms. The focus of this paper is to identify the challenges and propose strategies for Indian multinationals. This would enable them to counter the challenges, leverage the opportunities and extend their product and service offering beyond the shores of the country. This paper analyses the pre-2010 period on the rationale that the strategies adopted by a firm during the years leading to 2010 will play an important role in judging how competitive it will be in the future. We have developed an Evolution Map and propose the use of a Competitive Map for an analysis of the Firm and its Product and Service offering. These tools will help companies identify and locate their relative position in their industries, assess their resources and capabilities, and help devise a future course of action. Following a methodical approach, we have analysed the market characteristics, and identified the Internal and External challenges that firms will face beyond 2010. We have developed a model to identify the strategies that firms need to implement to counter these challenges and stay competitive. Our strategy model and the Key Action Points provide a roadmap for firms who wish to carry their industry leadership to foreign lands. We give a thorough treatment of the key elements of each core strategy and finally analyse the key sectors of the Indian industry and identify some potential Indian multinationals of 2010.
Effects of Nested Interruptions on Task Resumption: A Laboratory Study With Intensive Care Nurses
Authors: Sasangohar Farzan , Donmez Birsen , Easty Anthony C. , Trbovich Patricia L. 
Published: January 2017

Objective: Interruptions to secondary tasks resulting in multiple tasks to resume may tax working memory. The objective of this research is to study such interruptions experienced by intensive care unit (ICU) nurses. Background: ICU nurses are frequently interrupted, resulting in a switch from primary to secondary tasks. In two recent studies, we observed that some of these secondary tasks also get interrupted, resulting in multiple tasks that have to be resumed, a phenomenon we refer to as nested interruptions. Although completing multiple secondary tasks in a serial fashion during an interruption period can create context-switching costs, we hypothesize that nested interruptions tax the working memory even more than just performing multiple secondary tasks sequentially because the nurse would have to encode in working memory the resumption goals for both the primary and the interrupted secondary tasks. Method: We conducted a laboratory study with 30 ICU nurses, who performed an electronic order-entry task under three interruption conditions: (a) baseline—no secondary task during the interruption period; (2) serial—performance of two tasks one after the other during the interruption period; and (3) nested—performance of two tasks during the interruption period, one of which was also interrupted. Results: Nested interruptions resulted in significantly longer primary-task resumption lag and less accurate task resumption compared with both the serial interruption and baseline conditions. Conclusion: The nested nature of interruptions adds to the resumption lag and diminishes resumption accuracy by likely populating the working memory with goals associated with interrupted secondary tasks.
The Importance of Team Sex Composition in Team-Training Research Employing Complex Psychomotor Tasks
Authors: Jarrett Steven M. , Glaze Ryan M. , Schurig Ira , Arthur Winfred 
Published: January 2017

Objective: The relationship between team sex composition and team performance on a complex psychomotor task was examined because these types of tasks are commonly used in the lab-based teams literature. Background: Despite well-documented sex-based differences on complex psychomotor tasks, the preponderance of studies—mainly lab based—that use these tasks makes no mention of the sex composition of teams across or within experimental conditions. Method: A sample of 123 four-person teams with varying team sex composition learned and performed a complex psychomotor task, Steal Beasts Pro PE. Each team completed a 5-hr protocol whereby they conducted several performance missions. Results: The results indicated significant large mean differences such that teams with larger proportions of males had higher performance scores. Conclusion: These findings demonstrate the potential effect of team sex composition on the validity of studies that use complex psychomotor tasks to explore and investigate team performance–related phenomena when (a) team sex composition is not a focal variable of interest and (b) it is not accounted for or controlled. Application: Given the proclivity of complex psychomotor action-based tasks used in lab-based team studies, it is important to understand and control for the impact of team sex composition on team performance. When team sex composition is not controlled for, either methodologically or statistically, it may affect the validity of the results in teams studies using these types of tasks.
Frequency of Mental Illness Among Jews in Israel
Authors: Halevi H. S. 
Published: January 2017

This is mainly a statistical survey of mental illness in Israel and there was no intention for a medical analysis of the data. The statistical data may and should serve as a basis for a medical interpretation. Demographic and social conditions prevailing in Israel are particularly suitable for a thorough investigation of mental health problems in its heterogeneous and changing population. Statistical techniques and epidemiological methods found their application in most branches of medicine. In our case their full use will depend on the reaction of the psychiatric profession to the statistical survey and on their efforts to integrate the figures in a clinical effort in order to make the epidemiological conclusions a basis for therapeutical progress. Some time ago a leading medical weekly remarked in connection with psychiatric epidemiology(22): “Another problem has been the distressing way in which the results of years of work melt away before the two crucial words ‘so what?’.” Exploitation of all possibilities for research by a proper team may help greatly in understanding dynamics of mental health.