bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian spatiotemporal modelling for identifying unusual and unstable trends in mammography utilisation
Authors: Duncan Earl W , White Nicole M , Mengersen Kerrie 
Published: May 2016

ObjectivesTo compare two Bayesian models capable of identifying unusual and unstable temporal patterns in spatiotemporal data.SettingAnnual counts of mammography screening users from each statistical local area (SLA) in Brisbane, Australia, recorded between 1997 and 2008 inclusive.Primary outcome measuresMammography screening counts.ResultsThe temporal trends of 91 SLAs (58%) were dissimilar from the overall common temporal trend. SLAs that followed the common temporal trend also tended to have stable temporal trends. SLAs with unstable temporal trends tended to be situated farther from the city and farther from mammography screening facilities.ConclusionsThis paper demonstrates the usefulness of the two models in identifying unusual and unstable temporal trends, and the synergy obtained when both models are applied to the same data set. An analysis of these models has provided interesting insights into the temporal trends of mammography screening counts and has shown several possible avenues for further research, such as extending the models to allow for multiple common temporal trends and accounting for additional spatiotemporal heterogeneity.
Effectiveness of a biopsychosocial e-learning intervention on the clinical judgements of medical students and GP trainees regarding future risk of disability in patients with chronic lower back pain: study protocol for a randomised controlled trial
Authors: Dwyer Christopher P , Durand Hannah , MacNeela Pádraig , Reynolds Bronagh , Hamm Robert M , Main Christopher J , O'Connor Laura L , Conneely Sinéad , Taheny Darragh , Slattery Brian W , O'Neill Ciaran , NicGabhainn Saoirse , Murphy Andrew W , Kropmans Thomas , McGuire Brian E 
Published: May 2016

IntroductionChronic lower back pain (CLBP) is a major healthcare problem with wide ranging effects. It is a priority for appropriate management of CLBP to get individuals back to work as early as possible. Interventions that identify biopsychosocial barriers to recovery have been observed to lead to successfully reduced pain-related work absences and increased return to work for individuals with CLBP. Modern conceptualisations of pain adopt a biopsychosocial approach, such as the flags approach. Biopsychosocial perspectives have been applied to judgements about future adjustment, recovery from pain and risk of long-term disability; and provide a helpful model for understanding the importance of contextual interactions between psychosocial and biological variables in the experience of pain. Medical students and general practitioner (GP) trainees are important groups to target with education about biopsychosocial conceptualisations of pain and related clinical implications.AimThe current study will compare the effects of an e-learning intervention that focuses on a biopsychosocial model of pain, on the clinical judgements of medical students and trainees.Methods and analysisMedical student and GP trainee participants will be randomised to 1 of 2 study conditions: (1) a 20 min e-learning intervention focused on the fundamentals of the flags approach to clinical judgement-making regarding risk of future pain-related disability; compared with a (2) wait-list control group on judgement accuracy and weighting (ie, primary outcomes); flags approach knowledge, attitudes and beliefs towards pain, judgement speed and empathy (ie, secondary outcomes). Participants will be assessed at preintervention and postintervention.Ethics and disseminationThe study will be performed in agreement with the Declaration of Helsinki and is approved by the National University of Ireland Galway Research Ethics Committee. The results of the trial will be published according to the CONSORT statement and will be presented at conferences and reported in peer-reviewed journals.Trial registration numberISRCTN53670726; Pre-results.
Diverse, Biologically Relevant, and Targetable Gene Rearrangements in Triple-Negative Breast Cancer and Other Malignancies
Authors: Shaver Timothy M. , Lehmann Brian D. , Beeler J. Scott , Li Chung-I , Li Zhu , Jin Hailing , Stricker Thomas P. , Shyr Yu , Pietenpol Jennifer A. 
Published: May 2016

Abstract
Triple-negative breast cancer (TNBC) and other molecularly heterogeneous malignancies present a significant clinical challenge due to a lack of high-frequency “driver” alterations amenable to therapeutic intervention. These cancers often exhibit genomic instability, resulting in chromosomal rearrangements that affect the structure and expression of protein-coding genes. However, identification of these rearrangements remains technically challenging. Using a newly developed approach that quantitatively predicts gene rearrangements in tumor-derived genetic material, we identified and characterized a novel oncogenic fusion involving the MER proto-oncogene tyrosine kinase (MERTK) and discovered a clinical occurrence and cell line model of the targetable FGFR3–TACC3 fusion in TNBC. Expanding our analysis to other malignancies, we identified a diverse array of novel and known hybrid transcripts, including rearrangements between noncoding regions and clinically relevant genes such as ALK, CSF1R, and CD274/PD-L1. The over 1,000 genetic alterations we identified highlight the importance of considering noncoding gene rearrangement partners, and the targetable gene fusions identified in TNBC demonstrate the need to advance gene fusion detection for molecularly heterogeneous cancers. Cancer Res; 76(16); 4850–60. ©2016 AACR.
МОРФОЛОГІЧНІ ЗМІНИ ТКАНИН ПЕЧІНКИ ПРИ МОДЕЛЮВАННІ ТЯЖКОЇ ТРАВМИ НА ФОНІ ОТРУЄННЯ СОЛЯМИ МІДІ Й ЦИНКУ
Authors: Копач О. Є. 
Published: May 2016

<p>При отруєнні солями важких металів на фоні тяж-кої травми на 1 добу експерименту спостерігали наростання дистрофічно-некротичних змін, низьку регенераторну активність та прогресуючу жирову дистрофію. На 3 добу наростали структурні зміни, порушення балково-радіальної організації, виражена білкова дистрофія та вогнищеві некрози. На 7 добу експерименту формувався виражений жировий гепатоз переважно перипортальних сегментів часточок. Дистрофічно-некротичні зміни в гепатоцитах переважали по всій величині частки.</p>
Characterizing and Understanding Cloud Ice and Radiation Budget Biases in Global Climate Models and Reanalysis
Authors: Li J.-L. F. , Waliser D. E. , Stephens G. , Lee Seungwon 
Published: May 2016

Abstract
The authors present an observationally based evaluation of the vertically resolved cloud ice water content (CIWC) and vertically integrated cloud ice water path (CIWP) as well as radiative shortwave flux downward at the surface (RSDS), reflected shortwave (RSUT), and radiative longwave flux upward at top of atmosphere (RLUT) of present-day global climate models (GCMs), notably twentieth-century simulations from the fifth phase of the Coupled Model Intercomparison Project (CMIP5), and compare these results to those of the third phase of the Coupled Model Intercomparison Project (CMIP3) and two recent reanalyses. Three different CloudSat and/or Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) combined ice water products and two methods are used to remove the contribution from the convective core ice mass and/or precipitating cloud hydrometeors with variable sizes and falling speeds so that a robust observational estimate can be obtained for model evaluations.
The results show that, for annual mean CIWC and CIWP, there are factors of 2–10 (either over- or underestimate) in the differences between observations and models for a majority of the GCMs and for a number of regions. Most of the GCMs in CMIP3 and CMIP5 significantly underestimate the total ice water mass because models only consider suspended cloud mass, ignoring falling and convective core cloud mass. For the annual means of RSDS, RLUT, and RSUT, a majority of the models have significant regional biases ranging from −30 to 30 W m−2. Based on these biases in the annual means, there is virtually no progress in the simulation fidelity of RSDS, RLUT, and RSUT fluxes from CMIP3 to CMIP5, even though there is about a 50% bias reduction improvement of global annual mean CIWP from CMIP3 to CMIP5. It is concluded that at least a part of these persistent biases stem from the common GCM practice of ignoring the effects of precipitating and/or convective core ice and liquid in their radiation calculations.
Cell-Based Therapies Formulations: Unintended components
Authors: Atouf Fouad 
Published: May 2016

AbstractCell-based therapy is the fastest growing segment of regenerative
medicine, a field that promises to cure diseases not treated by other small
molecules or biological drugs. The use of living cells as the active medicinal
ingredient present great opportunities to deliver treatment that can trigger the
body’s own capacity to regenerate damaged or diseased tissue. Some of the challenges
in controlling the quality of the finished cell-therapy product relate to the use of
a variety of raw materials including excipients, process aids, and growth promotion
factors. The quality of these materials is critical for ensuring the safety and
quality of the finished therapeutic products. This review will discuss some of the
challenges and opportunities associated with the qualification of excipients as well
as that of the ancillary materials used in manufacturing.
Genome-wide analysis of auxin response factor gene family members in medicinal model plantSalvia miltiorrhiza
Authors: Xu Zhichao , Ji Aijia , Song Jingyuan , Chen Shilin 
Published: May 2016

ABSTRACTAuxin response factors (ARFs) can function as transcriptional activators or repressors to regulate the expression of auxin response genes by specifically binding to auxin response elements (AuxREs) during plant development. Based on a genome-wide strategy using the medicinal model plant Salvia miltiorrhiza, 25 S. miltiorrhiza ARF (SmARF) gene family members in four classes (class Ia, IIa, IIb and III) were comprehensively analyzed to identify characteristics including gene structures, conserved domains, phylogenetic relationships and expression patterns. In a hybrid analysis of the phylogenetic tree, microRNA targets, and expression patterns of SmARFs in different organs, root tissues, and methyl jasmonate or indole-3-acetic acid treatment conditions, we screened for candidate SmARFs involved in various developmental processes of S. miltiorrhiza. Based on this analysis, we predicted that SmARF25, SmARF7, SmARF16 and SmARF20 are involved in flower, leaf, stem and root development, respectively. With the further insight into the targets of miR160 and miR167, specific SmARF genes in S. miltiorrhiza might encode products that participate in biological processes as described for ARF genes in Arabidopsis. Our results provide a foundation for understanding the molecular basis and regulatory mechanisms of SmARFs in S. miltiorrhiza.
Sipa1l1 is an early biomarker of liver fibrosis in CCl4-treated rats
Authors: Marfà Santiago , Morales-Ruiz Manuel , Oró Denise , Ribera Jordi , Fernández-Varo Guillermo , Jiménez Wladimiro 
Published: May 2016

ABSTRACT
At present, several procedures are used for staging liver fibrosis. However, these methods may involve clinical complications and/or present diagnostic uncertainty mainly in the early stages of the disease. Thus, this study was designed to unveil new non-invasive biomarkers of liver fibrosis in an in vivo model of fibrosis/cirrhosis induction by CCl4 inhalation by using a label-free quantitative LC-MS/MS approach. We analyzed 94 serum samples from adult Wistar rats with different degrees of liver fibrosis and 36 control rats. Firstly, serum samples from 18 CCl4-treated rats were clustered into three different groups according to the severity of hepatic and the serum proteome was characterized by label-free LC-MS/MS. Furthermore, three different pooled serum samples obtained from 16 control Wistar rats were also analyzed. Based on the proteomic data obtained, we performed a multivariate analysis which displayed three main cell signaling pathways altered in fibrosis. In cirrhosis, more biological imbalances were detected as well as multi-organ alterations. In addition, hemopexin and signal-induced proliferation-associated 1 like 1 (SIPA1L1) were selected as potential serum markers of liver fibrogenesis among all the analyzed proteins. The results were validated by ELISA in an independent group of 76 fibrotic/cirrhotic rats and 20 controls which confirmed SIPA1L1 as a potential non-invasive biomarker of liver fibrosis. In particular, SIPA1L1 showed a clear diminution in serum samples from fibrotic/cirrhotic rats and a great accuracy at identifying early fibrotic stages. In conclusion, the proteomic analysis of serum samples from CCl4-treated rats has enabled the identification of SIPA1L1 as a non-invasive marker of early liver fibrosis.
Capturing the dynamic nascent transcriptome during acute cellular responses: The serum response
Authors: Kirkconnell Killeen S. , Paulsen Michelle T. , Magnuson Brian , Bedi Karan , Ljungman Mats 
Published: May 2016

ABSTRACT
Dynamic regulation of gene expression via signal transduction pathways is of fundamental importance during many biological processes such as cell state transitioning, cell cycle progression and stress responses. In this study we used serum stimulation as a cell response paradigm to apply the nascent RNA Bru-seq technique in order to capture early dynamic changes in the nascent transcriptome. Our data provides an unprecedented view of the dynamics of genome-wide transcription during the first two hours of serum stimulation in human fibroblasts. While some genes showed sustained induction or repression, other genes showed transient or delayed responses. Surprisingly, the dynamic patterns of induction and suppression of response genes showed a high degree of similarity, suggesting that these opposite outcomes are triggered by a common set of signals. As expected, early response genes such as those encoding components of the AP-1 transcription factor and those involved in the circadian clock were immediately but transiently induced. Surprisingly, transcription of important DNA damage response genes and histone genes were rapidly repressed. We also show that RNA polymerase II accelerates as it transcribes large genes and this was independent of whether the gene was induced or not. These results provide a unique genome-wide depiction of dynamic patterns of transcription of serum response genes and demonstrate the utility of Bru-seq to comprehensively capture rapid and dynamic changes of the nascent transcriptome.
Cellular dynamics of regeneration reveals role of two distinct Pax7 stem cell populations in larval zebrafish muscle repair
Authors: Pipalia Tapan G. , Koth Jana , Roy Shukolpa D. , Hammond Christina L. , Kawakami Koichi , Hughes Simon M. 
Published: May 2016

ABSTRACT
Heterogeneity of stem cells or their niches is likely to influence tissue regeneration. Here we reveal stem/precursor cell diversity during wound repair in larval zebrafish somitic body muscle using time-lapse 3D confocal microscopy on reporter lines. Skeletal muscle with incision wounds rapidly regenerates both slow and fast muscle fibre types. A swift immune response is followed by an increase in cells at the wound site, many of which express the muscle stem cell marker Pax7. Pax7+ cells proliferate and then undergo terminal differentiation involving Myogenin accumulation and subsequent loss of Pax7 followed by elongation and fusion to repair fast muscle fibres. Analysis of pax7a and pax7b transgenic reporter fish reveals that cells expressing each of the duplicated pax7 genes are distinctly localised in uninjured larvae. Cells marked by pax7a only or by both pax7a and pax7b enter the wound rapidly and contribute to muscle wound repair, but each behaves differently. Low numbers of pax7a-only cells form nascent fibres. Time-lapse microscopy revealed that the more numerous pax7b-marked cells frequently fuse to pre-existing fibres, contributing more strongly than pax7a-only cells to repair of damaged fibres. pax7b-marked cells are more often present in rows of aligned cells that are observed to fuse into a single fibre, but more rarely contribute to nascent regenerated fibres. Ablation of a substantial portion of nitroreductase-expressing pax7b cells with metronidazole prior to wounding triggered rapid pax7a-only cell accumulation, but this neither inhibited nor augmented pax7a-only cell-derived myogenesis and thus altered the cellular repair dynamics during wound healing. Moreover, pax7a-only cells did not regenerate pax7b cells, suggesting a lineage distinction. We propose a modified founder cell and fusion-competent cell model in which pax7a-only cells initiate fibre formation and pax7b cells contribute to fibre growth. This newly discovered cellular complexity in muscle wound repair raises the possibility that distinct populations of myogenic cells contribute differentially to repair in other vertebrates.
Show and tell: disclosure and data sharing in experimental pathology
Authors: Schofield Paul N. , Ward Jerrold M. , Sundberg John P. 
Published: May 2016

ABSTRACT
Reproducibility of data from experimental investigations using animal models is increasingly under scrutiny because of the potentially negative impact of poor reproducibility on the translation of basic research. Histopathology is a key tool in biomedical research, in particular for the phenotyping of animal models to provide insights into the pathobiology of diseases. Failure to disclose and share crucial histopathological experimental details compromises the validity of the review process and reliability of the conclusions. We discuss factors that affect the interpretation and validation of histopathology data in publications and the importance of making these data accessible to promote replicability in research.
TOTAL HEMISPHERICAL EMISSIVITY OF PRE-OXIDIZED AND UN-OXIDIZED ZR-2.5Nb PRESSURE-TUBE MATERIALS AT 600 °C TO 1000 °C UNDER VACUUM
Authors: Fong Randy W.L. , Paine Michael , Nitheanandan Thambiayah 
Published: May 2016

The emissivity of pre-oxidized and un-oxidized pressure-tube specimens has been measured at high temperatures under vacuum. The emissivity values of un-oxidized tube specimens decreased only slightly from 0.34 at 600 °C to 0.30 at 800 °C and changed gradually to 0.25 at 1000 °C. In comparison, the emissivity of pre-oxidized pressure-tube specimens decreased drastically from 0.70 at 600 °C to 0.35 at 800 °C, and gradually decreased to 0.25 at 1000 °C. The oxide layer of the pre-oxidized tube specimens dissolved into the metal matrix when heated to 700 °C and higher. Using these results, 2 linear correlations were obtained for emissivity with the oxide thickness measured by scanning electron microscopy and secondary ion mass spectroscopy analysis.
Insights from mercury stable isotopes into factors affecting the internal body burden of methylmercury in frequent fish consumers
Authors: Li Miling , von Stackelberg Katherine , Rheinberger Christoph M. , Hammitt James K. , Krabbenhoft David P. , Yin Runsheng , Sunderland Elsie M. 
Published: May 2016

Abstract
Methylmercury (MeHg) exposure can cause adverse health effects in children and adults and is predominantly from seafood consumption in the United States (U.S.). Here we examine evidence for differences in MeHg uptake and metabolism in U.S. individuals who consume three or more fish meals per week. We hypothesized based on prior research that some individuals have enhanced capacity to demethylate ingested MeHg and this will be reflected by a greater than typically observed δ202Hg offset in their hair relative to consumed fish (∼2 ‰). We used self-reported seafood intake data to identify individuals with hair Hg concentrations that agree extremely well with reported ingestion and those that do not. Approximately one-third of individuals in our survey population had hair Hg levels below the lower bound of probabilistic exposure modeling based on dietary intake data. The Δ199Hg values measured in the hair of a subset of individuals with the highest and lowest discrepancies between modeled and measured exposures are consistent with self-reported fish intake, validating the reliability of their dietary recall information. The δ202Hg offset between fish and human hair is similar for low- and high-discrepancy individuals, suggesting enhanced in vivo demethylation does not explain some individuals with hair Hg levels equivalent to non-fish consumers (0.10 ug/g). Using the probabilistic exposure model, we find dietary MeHg absorption efficiencies required to explain hair Hg levels in these high-discrepancy individuals are on average lower than 14% (range: 1%–72%). Exposure modeling for MeHg typically assumes a range of 91–97% and our results emphasize much greater inter-individual variability in this value.
Care home managers' knowledge of palliative care: a Northern Irish study
Authors: Mitchell Gary , McGreevy Jessie , Preshaw Deborah HL , Agnelli Joanne , Diamond Monica 
Published: May 2016

Aim: The aim of this study was to determine care home managers' knowledge of palliative care using the palliative care quiz for nursing (PCQN). Background: Palliative care is strongly advocated for all people living with advancing incurable illness. Within a care home setting there should be a particular emphasis on the importance of palliative care, particularly for those residents who, because of their advancing age, are likely to live with non-malignant diseases such as dementia, chronic obstructive pulmonary disease or heart failure to name a few. Methods: Before the beginning of a workshop on optimising palliative care for people living in care homes, 56 care home managers (all nurses) completed the PCQN, a validated questionnaire that is used to assess a nurse's knowledge of palliative care, as part of a learning exercise. Results: The quiz consisted of 20 questions for which participants could answer true, false or don't know. The average score was 12.89 correct answers out of a possible 20 (64.45%). Conclusion: This study highlights the need to develop the knowledge and competence of care home managers in relation to palliative care. This is particularly important given the increasing number of people who are living with non-malignant disease within a care home setting.
Effectiveness and safety of Mobi-C for treatment of single-level cervical disc spondylosis
Authors: Hou Y. , Nie L. , Pan X. , Si M. , Han Y. , Li J. , Zhang H. 
Published: May 2016

Aims In order to evaluate the effectiveness of the Mobi-C implant in cervical disc degeneration, a randomised study was conducted, comparing the Mobi-C prosthesis arthroplasty with anterior cervical disc fusion (ACDF) in patients with single level cervical spondylosis. Patients and Methods From January 2008 to July 2009, 99 patients were enrolled and randomly divided into two groups, those having a Mobi-C implant (n = 51; 30 men, 21 women) and those undergoing ACDF (n = 48; 28 men, 20 women).The patients were followed up for five years, with the primary outcomes being the Japanese Orthopaedic Association score, visual analogue scale for pain and the incidence of further surgery. The secondary outcomes were the Neck Disability Index and range of movement (ROM) of the treated segment. Results The incidence of further surgery was found to be statistically significant between the two groups (p = 0.49), with seven ACDF patients requiring further surgery and only one Mobi-C patient requiring re-operation. There were significant differences (p < 0.001) between the two groups in the ROM of the treated segment. However, both Mobi-C surgery and ACDF surgery were effective in improving the patient’s clinical symptoms. Take home message: Mobi-C implant surgery is a safe alternative to ACDF surgery in cervical disc degeneration. Cite this article: Bone Joint J 2016;98-B:829–3.