bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cohort profile: the Buffalo OsteoPerio microbiome prospective cohort study
Authors: Banack Hailey R , Genco Robert J , LaMonte Michael J , Millen Amy E , Buck Michael J , Sun Yijun , Andrews Christopher A , Hovey Kathleen M , Tsompana Maria , McSkimming Daniel I , Zhao Jiwei , Wactawski-Wende Jean 
Published: December 2018

PurposeThe Buffalo Osteoporosis and Periodontal Disease (OsteoPerio) study is a prospective cohort study focused on the relationship between the microbiome and oral and systemic health outcomes in postmenopausal women. The cohort was established to examine how the oral microbiome is affected by (and how it affects) periodontal disease presence, severity and progression and to characterise the relationship between the microbiome, lifestyle habits and systemic disease outcomes.ParticipantsParticipants (n=1342) were postmenopausal women who were participating in the Women’s Health Initiative observational study at the Buffalo, New York clinical centre. There were 1026 participants at the 5-year follow-up visit and 518 at the 15-year visit.Findings to dateData collected include questionnaires, anthropometric measures, serum blood and saliva samples. At each clinic visit, participants completed a comprehensive oral examination to measure oral health and the oral microbiome. Preliminary findings have contributed to our understanding of risk factors for periodontal disease and the relationship between the oral microbiome and periodontal disease.Future plansThe novel microbiome data collected on a large sample of participants at three time points will be used to answer a variety of research questions focused on temporal changes in the microbiome and the relationship between the oral microbiome and oral and systemic disease outcomes. Little is currently known about the relationship between the oral microbiome and health outcomes in older adults; data from the OsteoPerio cohort will fill this gap. Microbiome samples are currently being analysed using next-generation sequencing technology with an anticipated completion date of late 2018.
Identifying patient-important outcomes in medication-assisted treatment for opioid use disorder patients: a systematic review protocol
Authors: Sanger Nitika , Shahid Hamnah , Dennis Brittany B , Hudson Jackie , Marsh David , Sanger Stephanie , Worster Andrew , Teed Rand , Rieb Launette , Tugwell Peter , Hutton Brian , Shea Beverley , Beaton Dorcas , Corace Kimberly , Rice Danielle , Maxwell Lara , Samaan M Constantine , de Souza Russell J , Thabane Lehana , Samaan Zainab 
Published: December 2018

IntroductionIllicit opioid use has become a national crisis in Canada, with over 65 000 people seeking treatment for opioid use disorder (OUD) in Ontario and British Columbia alone. Medication-assisted treatment (MAT) is a common treatment for OUD. There is substantial variability in treatment outcomes used to evaluate effectiveness of MAT, making it difficult to establish clinically and scientifically relevant treatment effect. Furthermore, patients are often excluded from the process of determining these outcomes. The primary objective of this review is to examine outcomes currently used to measure MAT effectiveness and to identify patient-relevant outcomes to enhance effectiveness of treatment options. This review refers to patient-important outcomes as those outcomes patients consider important to or markers of treatment success.Methods and analysisMEDLINE, EMBASE, PsycINFO, Cumulative Index to Nursing and Allied Health Literature, Web of Science, Cochrane Library, Cochrane Clinical Trials Registry, National Institutes for Health Clinical Trials Registry and WHO International Clinical Trials Registry Platform databases will be searched. We will search databases from inception to the date the search is ran. Studies of interest include those evaluating the effectiveness of MAT for patients with OUD, with or without consultation with patients regarding what they consider to be important as an indicator of treatment success. Results will be analysed using thematic analysis and qualitative analysis where possible. This will result in comprehensive synthesis of all outcomes and measures found related to OUD treatment effectiveness.Ethics and disseminationWe are collaborating with Canadian Addiction Treatment Centres which provide MAT to patients with OUD who will participate in disseminating study results. Dissemination strategies will involve sharing study results through workshops, presentations, peer-reviewed publications, study reports, community presentations and resources in primary care settings.PROSPERO registration numberCRD42018095553.
Nurse staffing, nursing assistants and hospital mortality: retrospective longitudinal cohort study
Authors: Griffiths Peter , Maruotti Antonello , Recio Saucedo Alejandra , Redfern Oliver C , Ball Jane E , Briggs Jim , Dall'Ora Chiara , Schmidt Paul E , Smith Gary B 
Published: December 2018

ObjectiveTo determine the association between daily levels of registered nurse (RN) and nursing assistant staffing and hospital mortality.DesignThis is a retrospective longitudinal observational study using routinely collected data. We used multilevel/hierarchical mixed-effects regression models to explore the association between patient outcomes and daily variation in RN and nursing assistant staffing, measured as hours per patient per day relative to ward mean. Analyses were controlled for ward and patient risk.Participants138 133 adult patients spending >1 days on general wards between 1 April 2012 and 31 March 2015.OutcomesIn-hospital deaths.ResultsHospital mortality was 4.1%. The hazard of death was increased by 3% for every day a patient experienced RN staffing below ward mean (adjusted HR (aHR) 1.03, 95% CI 1.01 to 1.05). Relative to ward mean, each additional hour of RN care available over the first 5 days of a patient’s stay was associated with 3% reduction in the hazard of death (aHR 0.97, 95% CI 0.94 to 1.0). Days where admissions per RN exceeded 125% of the ward mean were associated with an increased hazard of death (aHR 1.05, 95% CI 1.01 1.09). Although low nursing assistant staffing was associated with increases in mortality, high nursing assistant staffing was also associated with increased mortality.ConclusionLower RN staffing and higher levels of admissions per RN are associated with increased risk of death during an admission to hospital. These findings highlight the possible consequences of reduced nurse staffing and do not give support to policies that encourage the use of nursing assistants to compensate for shortages of RNs.
Chair ICO/UVIC-UCC of palliative care at the University of Vic – Central University of Catalonia: an innovative multidisciplinary model of education, research and knowledge transfer
Authors: Gómez-Batiste Xavier , Lasmarías Cristina , Amblàs Jordi , Costa Xavier , Ela Sara , Mir Sarah , Calsina-Berna Agnès , Espaulella Joan , Santaugènia Sebastià , Pujol Ramon , Geli Marina Geli , Calle Candela 
Published: December 2018

ObjectivesGeneration and dissemination of knowledge is a relevant challenge of palliative care (PC). The Chair Catalan Institute of Oncology (ICO)/University of Vic (UVIC) of Palliative Care (CPC) was founded in 2012, as a joint project of the ICO and the University of Vic/Central of Catalonia to promote the development of PC with public health and community-oriented vision and academic perspectives. The initiative brought together professionals from a wide range of disciplines (PC, geriatrics, oncology, primary care and policy) and became the first chair of PC in Spain. We describe the experience of the CPC at its fifth year of implementation.MethodsData collection from annual reports, publications, training and research activities.ResultsResults for period 2012–2017 are classified into three main blocks: (1) Programme: (a) The advanced chronic care model (Palliative needs (NECPAL)); (b) the psychosocial and spiritual domains of care (Psychosocial needs (PSICPAL)); (c) advance care planning and shared decision making (Advance care planning (PDAPAL)); and (d) the compassive communities projects (Society involvement (SOCPAL)). (2) Education and training activities: (a) The master of PC, 13 editions and 550 professionals trained; (b) postgraduate course on psychosocial care, 4 editions and 140 professionals trained; and (c) workshops on specific topics, pregraduate training and online activities with a remarkable impact on the Spanish-speaking community. (3) Knowledge-transfer activities and research projects: (a) Development of 20 PhDs projects; and (b) 59 articles and 6 books published.ConclusionBeing the first initiative of chair in PC in Spain, the CPC has provided a framework of multidisciplinary areas that have generated innovative experiences and projects in PC.
Deep learning for detecting tumour-infiltrating lymphocytes in testicular germ cell tumours
Authors: Linder Nina , Taylor Jenny C , Colling Richard , Pell Robert , Alveyn Edward , Joseph Johnson , Protheroe Andrew , Lundin Mikael , Lundin Johan , Verrill Clare 
Published: December 2018

AimsTo evaluate if a deep learning algorithm can be trained to identify tumour-infiltrating lymphocytes (TILs) in tissue samples of testicular germ cell tumours and to assess whether the TIL counts correlate with relapse status of the patient.MethodsTILs were manually annotated in 259 tumour regions from 28 whole-slide images (WSIs) of H&E-stained tissue samples. A deep learning algorithm was trained on half of the regions and tested on the other half. The algorithm was further applied to larger areas of tumour WSIs from 89 patients and correlated with clinicopathological data.ResultsA correlation coefficient of 0.89 was achieved when comparing the algorithm with the manual TIL count in the test set of images in which TILs were present (n=47). In the WSI regions from the 89 patient samples, the median TIL density was 1009/mm2. In seminomas, none of the relapsed patients belonged to the highest TIL density tertile (>2011/mm2). TIL quantifications performed visually by three pathologists on the same tumours were not significantly associated with outcome. The average interobserver agreement between the pathologists when assigning a patient into TIL tertiles was 0.32 (Kappa test) compared with 0.35 between the algorithm and the experts, respectively. A higher TIL density was associated with a lower clinical tumour stage, seminoma histology and lack of lymphovascular invasion.ConclusionsDeep learning–based image analysis can be used for detecting TILs in testicular germ cell cancer more objectively and it has potential for use as a prognostic marker for disease relapse.
Assessment of in vitro effects of direct thrombin inhibitors and activated factor X inhibitors through clot waveform analysis
Authors: Wakui Masatoshi , Fujimori Yuta , Katagiri Hisako , Nakamura Shoko , Kondo Yoshino , Kuroda Yuko , Nakagawa Terumichi , Shimizu Nobuko , Murata Mitsuru 
Published: December 2018

AimsClot waveform analysis (CWA) has been reported to extend the interpretation of clotting time measurement. The parameters obtained from successive derivatives of the clotting reaction curves reflect the rates of activation of individual coagulation factors, theoretically dissecting the cascade pathway. This study aims to assess the in vitro effects of direct thrombin inhibitors (DTIs) and activated factor X (FXa) inhibitors.MethodsCWA was applied to the activated partial thromboplastin time (APTT) assay of plasma samples spiked with each drug. For CWA of APTT measurement curves (APTT-CWA), the positive mode of clotting reaction curves was defined as the direction towards fibrin generation.ResultsAll the maximum positive values in the successive derivatives were decreased dependently on the concentrations of each drug. Moreover, the negative values in the second and third derivatives appeared putatively due to consumption of thrombin and factor FXa, respectively, to form complexes with plasma serine protease inhibitors. The decrease of the maximum negative values observed dependently on the concentrations of each drug appeared to be consistent with the decreased generation of thrombin and factor FXa. The analysis of Hill coefficients of each drug in the dose–response of changes in the APTT-CWA parameters revealed a difference in anticoagulant cooperativity between DTIs versus FXa inhibitors.ConclusionsThe APTT-CWA demonstrated evidence for the blockade of thrombin-positive feedback by DTIs and FXa inhibitors and that for the differences in anticoagulant cooperativity between them. The results demonstrate the usability of CWA for assessment of anticoagulation and provide insights into direct anticoagulants.
T cell dysfunction in chronic hepatitis B infection and liver cancer: evidence from transcriptome analysis
Authors: Wang Yu-Gang , Zheng Dong-Hui , Shi Min , Xu Xi-Ming 
Published: December 2018

BackgroundT cell dysfunction occurs in many diseases, especially in chronic virus infection and cancers. However, up to now, little is known on the distinctions in T cell exhaustion between cancer and chronic virus infection. The objective of this study is to explore the transcriptional similarities and differences in exhausted CD8 +T cell between chronic hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC).MethodsRNA sequencing was performed to compare the transcriptome of CD8 +T cells isolated from healthy donors’ blood, tumour tissues of patients with HCC and chronic HBV infected HCC patients’ paracancerous tissues. DESeq2 algorithm was used to determine differentially expressed genes. Gene ontology and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted for in-depth analysis of these differentially expressed genes.ResultsA total number of 2109 and 2203 genes were differentially expressed in patients with chronic HBV infection and HCC, respectively. Comparing these two groups of differentially deregulated genes, we found that nearly half of them were shared, and these shared genes were further classified into several functional categories, such as metabolic process, binding and intracellular organelle. KEGG analysis revealed that these shared deregulated genes were involved in many important pathways such as Parkinson’s disease, oxidative phosphorylation and messenger RNA surveillance. Interestingly, we reported that chronic HBV infection specific deregulated genes were mainly enriched in graft versus host disease, allograft rejection, phenylalanine, tyrosine and tryptophan biosynthesis pathways. Whereas, HCC-specific deregulated genes were highly enriched in oxidative phosphorylation, thyroid cancer and endometrial cancer pathways.ConclusionOur study demonstrated that T cell dysfunction associated with HCC and chronic HBV infection shares high similarities, however, each possesses its own features in terms of specific genes and signalling pathways. Uncovering the differences of T cells dysfunction would facilitate our understanding the diseases pathogenesis and developing innovative therapies in the future.
Lower lymphocyte to monocyte ratio is a potential predictor of poor outcome in patients with cerebral venous sinus thrombosis
Authors: Li Shen , Liu Kai , Zhang Rui , Gao Yuan , Fang Hui , Liu Xinjing , Pei Lulu , Chou L-Ying Richard , Guan Sheng , Guo Xinbin , Xu Haowen , Song Bo , Xu Yuming 
Published: December 2018

BackgroundLymphocyte to monocyte ratio (LMR) is associated with functional outcome in patients with stroke. But the relationship between the LMR value and the prognosis of cerebral venous sinus thrombosis (CVST) has not been investigated.MethodsCVST patients, admitted to the First Affiliated Hospital of Zhengzhou University, were retrospectively identified from November 2010 to January 2017. Functional outcomes of patients were evaluated with the modified Rankin Scale (mRS). Patients were divided into good (mRS 0–2) and poor (mRS 3–6) outcomes groups. Univariate and multivariate Cox regression analyses were used to assess the relationship between LMR and the poor survival outcome.ResultsA total of 228 patients were included of which 41 had poor outcomes (18.0%). The duration of follow-up was 22 months (6–66 months). LMR (2.3±1.2 vs 3.2±1.8, p<0.01) was significantly lower in the poor outcome group. Multivariate Cox regression analysis showed that LMR (HR 0.726, 95% CI 0.546 to 0.964, p=0.027) was a independent predictor of poor prognosis.ConclusionsLMR may be a predictor of poor prognosis in CVST patients.
Impact of the NHS stop smoking services on smoking prevalence in England: a simulation modelling evaluation
Authors: Song Fujian , Elwell-Sutton Tim , Naughton Felix 
Published: December 2018

BackgroundThe English National Health Service (NHS) Stop Smoking Services (SSS), established in 2001, were the first such services in the world. An appropriate evaluation of the SSS has national and international significance. This modelling study sought to evaluate the impact of the SSS on changes in smoking prevalence in England.MethodsA discrete time state-transition model was developed to simulate changes in smoking status among the adult population in England during 2001–2016. Input parameters were based on data from national statistics, population representative surveys and published literature. The main outcome was the percentage point reduction in smoking prevalence attributable to the SSS.ResultsSmoking prevalence was reduced by 10.8% in absolute terms during 2001–2016 in England, and 15.1% of the reduction could be attributable to the SSS. The percentage point reduction in smoking prevalence each year was on average 0.72%, and 0.11% could be attributable to the SSS. The proportion of SSS supported quit attempts increased from 5.6% in 2001, to as high as 19.3% in 2011, and then reduced to 8.4% in 2016. Quit attempts with SSS support had a higher success rate than those without SSS support (15.1%vs11.7%). Smoking prevalence in England continued to decline after the SSS was much reduced from 2013 onwards.ConclusionsApproximately 15% of the percentage point reduction in smoking prevalence during 2001–2016 in England may be attributable to the NHS SSS, although uncertainty remains regarding the actual impact of the formal smoking cessation services.
Geomorphological analysis of gullies on the central peak of Lyot Crater, Mars
Authors: Gulick Virginia C. , Glines Natalie , Hart Shawn , Freeman Patrick 
Published: December 2018

Abstract

The central peak region of Lyot Crater provides an intriguing case study of Martian gully formation on local topographic highs. To better understand how these gullies formed, we carried out a detailed morphological analysis using a HiRISE stereo image pair and a digital terrain model. Gully lengths range from
c.
2.2 to 4.3 km, with maximum depths from 17 to 54 m. Alcove slopes range from
c.
20 to 22°, channel slopes range from 12 to 16° and apron slopes range from 10 to 14°. In general, these slopes are much lower than both the angle of repose (
c.
33°) required to initiate dry flows and the apex slope required to keep these flows from depositing (>21°) under Mars gravity. We find that the observed gully morphology and spatial associations are consistent with an origin by liquid flow. Apron volumes are
c.
10–40% of the gully volume, which we suggest indicates significant volatile loss (water and/or CO
2
) in the slope materials in which they formed because apron volumes emplaced by dry gravitational flows would equal or exceed the gully volumes due to their lower packing density. These observations, coupled with the gullies’ unique micro-environmental setting, lead us to favour a fluvial origin. In addition, we find that the gullies formed almost exclusively on the western slope region, which suggests a possible orographic component. Potential water sources may have been supplied locally in the recent geological past by dry winds blowing across an ice-covered lake situated in a low elevation area just west of the central peak or more globally during periods of higher obliquity. In either case, the integration of morphometric and morphological investigations suggests that these gullies probably formed by surface runoff and through-flow from snow- or icepack melting on the central peak of Lyot Crater.
Risk Factors Analysis of Postoperative Pleural Effusion after Liver Resection
Authors: Tsai Kuei-Yen , Chen Hsin-An , Wang Wan-Yu , Huang Ming-Te 
Published: December 2018

<b><i>Background:</i></b><i></i> Pulmonary complications remain relatively high in morbidities that arise after liver surgery and are associated with increased length of hospital stay and higher cost. Identification of possible risk factors in this retrospective analysis may help reduce operative morbidity and achieve better outcomes. <b><i>Methods:</i></b><i></i> In all, 363 consecutive patients underwent elective hepatectomies between July 2008 and November 2013 and these were identified and analyzed retrospectively. Patient demographics and perioperative variables were collected. The main outcome was an analysis of risk factors associated with postoperative pleural effusion (PPE). <b><i>Results:</i></b> Of 363 patients receiving hepatectomies, 80 patients (22.0%) developed pulmonary complications. The predominant pulmonary complication in this series is pleural effusion (76 patients, 95%). Univariate analysis found that older age, higher body mass index (BMI), chronic obstructive lung disease, asthma, heart disease, hepatitis C infection, heavy smoking, American Society of Anesthesiology class III and IV, hepatectomy site, combined surgeries, perioperative blood transfusion, and cirrhosis of liver were associated with PPE. Only older age, higher BMI, asthma, heavy smoker, combined gastrointestinal surgeries, and perioperative blood transfusion were identified as independent risk factors in multivariate analysis. <b><i>Conclusion:</i></b> This study identifies 6 risk factors for PPE. Identification and management of some of these factors could possibly reduce morbidity and improve short-term surgical outcomes.