bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of Gleason score discrepancy for risk stratification in magnetic resonance-ultrasound fusion prostate biopsy
Authors: Kim See Hyung 
Published: December 2019

Background Magnetic resonance imaging (MRI)-ultrasound (US) fusion biopsy remains challenging and highlights the need towards standardization. Purpose To characterize the clinical and MRI features of clinically significant prostate cancer (csPCa) with discrepant Gleason score (GS) in MRI-US fusion biopsy. Material and Methods A total of 400 consecutive patients with suspected cancer lesions who underwent MRI-US fusion biopsy and subsequent prostatectomy were included. In the comparison of biopsy GS with pathology GS, matched lesions were defined as a GS, and discrepant lesions were defined as an upgrade of the GS. Descriptive statistics were used to define clinical characteristics, including age, prostate-specific antigen (PSA), PSA density, and maximal cancer core length (MCCL). Differences between lesions with matched and discrepant GS were determined considering the location and PI-RADS v2 score. A paired comparison of the volumes between the two groups was performed. Results There were 130 lesions with discrepant GS in 124 patients. There was no significant difference in the age, PSA, and PSA density between the two groups, except for the MCCL ( P = 0.028). The lesions were distributed in the peripheral (n = 88) and transition (n = 42) zones; 33, 50, and 47 lesions were at the apex, mid-gland, and base levels, respectively. PI-RADS scores were as follows: 2 (n = 5), 3 (n = 8), 4 (n = 68), and 5 (n = 39). In comparison with matched lesions, discrepant lesions had significantly smaller multiparametric MRI-measured cancer volumes ( P < 0.05). Conclusion Knowledge of discrepant GS in MRI-US fusion biopsy is important, and a careful approach is needed to reduce this discrepancy.
Light Therapy for Patients With Bipolar Depression: Systematic Review and Meta-Analysis of Randomized Controlled Trials
Authors: Lam Raymond W. , Teng Minnie Y. , Jung Young-Eun , Evans Vanessa C. , Gottlieb John F. , Chakrabarty Trisha , Michalak Erin E. , Murphy Jill K. , Yatham Lakshmi N. , Sit Dorothy K. 
Published: December 2019

Objective Bipolar disorder (BD) is challenging to treat, and fewer treatments are available for depressive episodes compared to mania. Light therapy is an evidence-based nonpharmacological treatment for seasonal and nonseasonal major depression, but fewer studies have examined its efficacy for patients with BD. Hence, we reviewed the evidence for adjunctive light therapy as a treatment for bipolar depression. Methods We conducted a systematic review of databases from inception to June 30, 2019, for randomized, double-blind, placebo-controlled trials of light therapy in patients with BD (CRD42019128996). The primary outcome was change in clinician-rated depressive symptom score; secondary outcomes included clinical response, remission, acceptability, and treatment-emergent mood switches. We quantitatively pooled outcomes using meta-analysis with random-effects models. Results We identified seven trials representing 259 patients with BD. Light therapy was associated with a significant improvement in Hamilton Depression Rating Scale score (standardized mean difference = 0.43, 95% confidence interval [CI], 0.04 to 0.82, P = 0.03). There was also a significant difference in favor of light therapy for clinical response (odds ratio [ OR] = 2.32; 95% CI, 1.12 to 4.81; P = 0.024) but not for remission. There was no difference in affective switches between active light and control conditions ( OR = 1.30; 95% CI, 0.38 to 4.44; P = 0.67). Study limitations included different light treatment parameters, small sample sizes, short treatment durations, and variable quality across trials. Conclusion There is positive but nonconclusive evidence that adjunctive light therapy reduces symptoms of bipolar depression and increases clinical response. Light therapy is well tolerated with no increased risk of affective switch.
Antiphospholipid syndrome and infertility
Authors: El Hasbani G , Khamashta M , Uthman I 
Published: December 2019

Antiphospholipid syndrome is a systemic autoimmune disease associated with obstetric complications along with vascular events affecting multiple organ systems in patients having positive titers of antiphospholipid antibodies. Eight to 20% of infertility cases have an unknown cause, part of which could be due to antiphospholipid syndrome. Although still debatable, many studies have addressed the relation between reproductive failure and antiphospholipid antibodies through the relation between antiphospholipid antibodies and unexplained infertility as well as the effect of antiphospholipid antibodies on the outcome of in vitro fertilization–embryo transfer. Few studies and cases have associated the presence of antiphospholipid antibodies with male infertility, describing morphofunctional penile abnormalities and testicular infarction. There are not enough data to support the routine practice of testing antiphospholipid antibodies in patients with infertility.
Professional values and ethical ideology: Perceptions of nursing students
Authors: Arries Ebin J 
Published: December 2019

Background: Moral philosophical positions and professional values have been shown to influence nurses’ practice behaviours. Understanding nursing students’ professional values and ethical ideologies, therefore, is important as they may help inform evidence-informed curriculum decisions and education strategies to develop students’ professional reflective competencies. However, there is a dearth in current empirical data on Canadian nursing students’ perceptions of professional values and ethical positions. Objectives: This study’s purpose was to examine undergraduate nursing student’s perceptions of professional values and ethical ideology and explore relationships in data and selected participant demographic variables. Research design, participants and context: A descriptive cross-sectional research design was conducted with a convenience sample of undergraduate nursing students recruited from a university in Canada. An online encrypted survey consisting of two validated instruments was administered to participants who met study eligibility criteria. Descriptive and inferential statistics were employed to analyse the data and classify nursing students’ ethical ideologies into four categories based on mean scores for idealism and relativism. Ethical considerations: This study received ethical approval from the institutional Behavioural Research Ethics Board and was executed in-line with ethical principles for research involving humans. Findings: Nursing students scored high on professional values and ethical idealism and differed significantly on a measure of ethical relativism in terms of age and year of study. Professional values were significantly associated with ethical idealism. Based on mean scores for idealism and relativism, most nursing students in the study were classified as situationists. Discussion and conclusion: Findings suggest that faculty pay attention to influences of moral philosophical positions in facilitating nursing students’ professional values development. Implications for future research and curriculum are highlighted to strengthen nursing students’ professional values.
A qualitative study of care coordination in community physical rehabilitation
Authors: Symons Jane L , Jamison Julie , Dening Jane , Murray Linda , Pearson Sue 
Published: December 2019

Introduction This study explored the factors influencing effective care coordination in a community physical rehabilitation service. The two research questions answered were “What was effective care coordination?” and “What were the barriers and enablers?” Methods This qualitative study, influenced by an interprofessional skill framework, was conducted in a regional service in Australia. Participants were 35 allied health, nursing, and client administration team members. Individual interviews, group observations, and focus groups generated data. This article will present the descriptive thematic analysis method and results. Results Care coordination resulted from a suite of informal and formal tools that smoothed the client’s rehabilitation journey. Effectiveness and efficiency were sought alongside client-centred, holistic, and flexible yet consistent approaches to care coordination. All staff undertook care coordination relevant to their managerial, clinical, or administration support roles. The involvement of many people and processes required effective teamwork, notably communication, collaboration, coordination, and navigation of stakeholder differences. The barriers to and enablers of care coordination were the service’s resources including integrated workspaces, transport and communication systems, and the individuals’ resources including clinical reasoning skills in, and familiarity and buy in with care coordination and rehabilitation. Discussion Staff viewed care coordination as an integral and valued part of rehabilitation, with some responsibilities shared by all staff. Additional time and support were required for stakeholders to enact their assigned care coordination roles. Effective care coordination required staff to be trained and competent in interprofessional collaboration. Systems that were efficient to use and encouraged accountability were desired.
Identifying people with multiple sclerosis in the Canadian Primary Care Sentinel Surveillance Network
Authors: Marrie Ruth Ann , Kosowan Leanne , Taylor Carole , Singer Alexander 
Published: December 2019

Background We validated a case definition for multiple sclerosis using a clinical cohort linked with the Manitoba Primary Care Research Network of the Canadian Primary Care Sentinel Surveillance Network, and applied this definition to describe multiple sclerosis epidemiology using the Canadian Primary Care Sentinel Surveillance Network repository. Methods We developed candidate case definitions for multiple sclerosis in the Manitoba Primary Care Research Network using diagnoses and medications. We compared these case definitions to multiple sclerosis diagnoses identified by applying a validated definition to population-based administrative data (reference standard 1) and multiple sclerosis diagnoses recorded by the provincial Multiple Sclerosis Clinic (reference standard 2) using sensitivity, specificity, positive predictive value and negative predictive value. We applied the preferred case definition to the national Canadian Primary Care Sentinel Surveillance Network dataset. Results The Manitoba Primary Care Research Network included 160,904 patients. The preferred case definition required ≥2 billing records for multiple sclerosis within 2 years or multiple sclerosis listed as a health condition or ≥1 multiple sclerosis-specific prescription. This definition had a low sensitivity versus administrative (44.25%) and clinic datasets (53.41%) but high specificity versus administrative data (99.95%). Specificity was lower versus clinic data (71.43%), but the positive predictive value was high. Conclusion We developed a case definition for multiple sclerosis that can be applied to the Canadian Primary Care Sentinel Surveillance Network dataset for studies examining primary care of persons with multiple sclerosis.
Biomechanical Comparison of First Tarsometatarsal Arthrodesis Constructs Over Prolonged Cyclic Testing
Authors: Prieto-Diaz Cynthia , Anderle Mathew R. , Brinker Laura Zagrocki , Allard Randall , Leasure Jeremi 
Published: December 2019

Background: Traditionally, a lengthy period of nonweightbearing is required following arthrodesis of the first tarsometatarsal (TMT) joint in order to provide a stable healing environment for the bones. The goal of this research was to determine the resistance to plantar gapping of 2 locked intramedullary devices and a medial plate with crossing screw, all specifically designed for hallux valgus correction, and compare them to traditional 2–crossing screw fixation under a cyclic testing protocol. We hypothesized the locked intramedullary devices and the medial plate with crossing screw would better resist plantar gapping. Methods: Forty cadaver specimens received 1 of 4 operative treatments: a locked intramedullary device with 2 points of fixation in the cuneiform, a locked intramedullary device with 1 point of fixation in the cuneiform, a medial plate with crossing screw, or 2 crossing screws. We applied dorsiflexion bending forces to the first TMT joint using a cadaveric fatigue model for 20 000 cycles. The plantar gap between the metatarsal and cuneiform was measured at the beginning and end of cyclic testing. Thirty-six specimens were included in the final data set. Results: Both locked intramedullary device groups and the medial plate with crossing screw group exhibited significantly less gap widening compared to the 2–crossing screw group (vs 3-hole intramedullary device, P = .014; vs 4-hole intramedullary device, P = .010; and vs medial plate with crossing screw, P = .044). The intramedullary device groups were the most stable during the cyclic fatigue test, exhibiting the smallest gap widening. The medial plate with crossing screw fixation was also more stable than crossing screws in the cyclic fatigue model. Conclusions: The locked intramedullary devices and medial plate with crossing screw resisted plantar gapping better than 2 crossing screws when used for first TMT arthrodesis. Clinical Relevance: These results indicate that locked intramedullary devices and medial plates with crossing screws may promote superior bone healing and may better tolerate early weightbearing compared with 2 crossing screws.
Mediterranean diet during pregnancy and childhood respiratory and atopic outcomes: birth cohort study
Authors: Bédard Annabelle , Northstone Kate , Henderson A. John , Shaheen Seif O. 
Published: December 2019

Evidence for associations between Mediterranean diet during pregnancy and childhood asthma, allergy and related outcomes is conflicting. Few cohorts have followed children to school age, and none have considered lung function.In the Avon Longitudinal Study of Parents and Children, we analysed associations between maternal Mediterranean diet score during pregnancy (estimated by a food frequency questionnaire, using ana prioridefined score adapted to pregnant women; score ranging from 0 (low adherence) to 7 (high adherence)) and current doctor-diagnosed asthma, wheeze, eczema, hay fever, atopy and lung function in 8907 children at 7–9 years. Interaction between maternal Mediterranean diet and maternal smoking in pregnancy was investigated.The maternal Mediterranean diet score was not associated with asthma or other allergic outcomes. Weak positive associations were found between maternal Mediterranean diet score and childhood maximal mid-expiratory flow (forced expiratory flow at 25–75% of forced vital capacity (FEF25–75%)) after controlling for confounders. Higher Mediterranean diet scores were associated with increased FEF25–75%z-scores adjusted for age, height and sex (β 0.06, 95% CI 0.01–0.12; p=0.03, comparing a score of 4–7versusa score of 0–3). Stratifying associations by maternal smoking during pregnancy showed that associations with FEF25–75%were only seen in children of never-/passive-smoking mothers, but no evidence for a statistically significant interaction was found.Results suggest adherence to a Mediterranean diet during pregnancy may be associated with increased small airway function in childhood, but we found no evidence for a reduced risk of asthma or other allergic outcomes.
High-sensitivity troponin I and all-cause mortality in patients with stable COPD: an analysis of the COSYCONET study
Authors: Waschki Benjamin , Alter Peter , Zeller Tanja , Magnussen Christina , Neumann Johannes T. , Twerenbold Raphael , Sinning Christoph , Herr Christian , Kahnert Kathrin , Fähndrich Sebastian , Blankenberg Stefan , Rabe Klaus F. , Welte Tobias , Jörres Rudolf A. , Vogelmeier Claus F. , Bals Robert , Watz Henrik 
Published: December 2019

Chronic obstructive pulmonary disease (COPD) is a leading cause of death with a considerable part of the population dying from cardiovascular diseases. High-sensitivity troponin I (hs-TnI) might help to better identify COPD patients at high risk of mortality. We aimed to study the predictive value of hs-TnI for all-cause mortality beyond established COPD assessments, and after consideration of relevant cardiovascular risk factors and prevalent cardiovascular diseases, in a broad population with stable COPD.Circulating hs-TnI concentrations together with a wide range of respiratory and cardiovascular markers were evaluated in 2085 patients with stable COPD across all severity stages enrolled in the multicentre COSYCONET cohort study. The primary outcome was all-cause mortality over 3 years of follow-up.Hs-TnI was detectable in 2020 (96.9%) patients. The median hs-TnI concentration was 3.8 ng·L−1(interquartile range 2.5–6.6 ng·L−1), with levels above the 99th percentile reference limit of 27 ng·L−1observed in 1.8% of patients. In Cox regression analyses including adjustments for airflow limitation, dyspnoea grade, exercise capacity and history of severe exacerbations, as well as traditional cardiovascular risk factors, estimated glomerular filtration rate, ankle–brachial index, N-terminal pro-brain natriuretic peptides and prevalent cardiovascular diseases, hs-TnI was a significant predictor for all-cause mortality, both as a continuous variable (hazard ratio (HR) for log hs-TnI 1.28, 95% CI 1.01–1.62) and categorised according to the cut-off of 6 ng·L−1(HR 1.63, 95% CI 1.10–2.42).In patients with stable COPD, hs-TnI is a strong predictor of all-cause mortality beyond established COPD mortality predictors, and independent of a broad range of cardiovascular risk factors and prevalent cardiovascular diseases. Hs-TnI concentrations well below the upper reference limit provide further prognostic value for all patients with COPD when added to established risk assessments.
Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads
Authors: Prada-Luengo Iñigo , Krogh Anders , Maretty Lasse , Regenberg Birgitte 
Published: December 2019

Abstract
Background
Circular DNA has recently been identified across different species including human normal and cancerous tissue, but short-read mappers are unable to align many of the reads crossing circle junctions hence limiting their detection from short-read sequencing data.

Results
Here, we propose a new method, Circle-Map that guides the realignment of partially aligned reads using information from discordantly mapped reads to map the short unaligned portions using a probabilistic model. We compared Circle-Map to similar up-to-date methods for circular DNA and RNA detection and we demonstrate how the approach implemented in Circle-Map dramatically increases sensitivity for detection of circular DNA on both simulated and real data while retaining high precision.

Conclusion
Circle-Map is an easy-to-use command line tool that implements the required pipeline to accurately detect circular DNA from circle enriched next generation sequencing experiments. Circle-Map is implemented in python3.6 and it is freely available at https://github.com/iprada/Circle-Map.
uap: reproducible and robust HTS data analysis
Authors: Kämpf Christoph , Specht Michael , Scholz Alexander , Puppel Sven-Holger , Doose Gero , Reiche Kristin , Schor Jana , Hackermüller Jörg 
Published: December 2019

Abstract
Background
A lack of reproducibility has been repeatedly criticized in computational research. High throughput sequencing (HTS) data analysis is a complex multi-step process. For most of the steps a range of bioinformatic tools is available and for most tools manifold parameters need to be set. Due to this complexity, HTS data analysis is particularly prone to reproducibility and consistency issues. We have defined four criteria that in our opinion ensure a minimal degree of reproducible research for HTS data analysis. A series of workflow management systems is available for assisting complex multi-step data analyses. However, to the best of our knowledge, none of the currently available work flow management systems satisfies all four criteria for reproducible HTS analysis.

Results
Here we present , a workflow management system dedicated to robust, consistent, and reproducible HTS data analysis. is optimized for the application to omics data, but can be easily extended to other complex analyses. It is available under the GNU GPL v3 license at https://github.com/yigbt/uap.

Conclusions
is a freely available tool that enables researchers to easily adhere to reproducible research principles for HTS data analyses.
The in vivo impact of MsLAC1, a Miscanthus laccase isoform, on lignification and lignin composition contrasts with its in vitro substrate preference
Authors: He Feng , Machemer-Noonan Katja , Golfier Philippe , Unda Faride , Dechert Johanna , Zhang Wan , Hoffmann Natalie , Samuels Lacey , Mansfield Shawn D. , Rausch Thomas , Wolf Sebastian 
Published: December 2019

Abstract
Background
Understanding lignin biosynthesis and composition is of central importance for sustainable bioenergy and biomaterials production. Species of the genus Miscanthus have emerged as promising bioenergy crop due to their rapid growth and modest nutrient requirements. However, lignin polymerization in Miscanthus is poorly understood. It was previously shown that plant laccases are phenol oxidases that have multiple functions in plant, one of which is the polymerization of monolignols. Herein, we link a newly discovered Miscanthus laccase, MsLAC1, to cell wall lignification. Characterization of recombinant MsLAC1 and Arabidopsis transgenic plants expressing MsLAC1 were carried out to understand the function of MsLAC1 both in vitro and in vivo.

Results
Using a comprehensive suite of molecular, biochemical and histochemical analyses, we show that MsLAC1 localizes to cell walls and identify Miscanthus transcription factors capable of regulating MsLAC1 expression. In addition, MsLAC1 complements the Arabidopsis lac4–2 lac17 mutant and recombinant MsLAC1 is able to oxidize monolignol in vitro. Transgenic Arabidopsis plants over-expressing MsLAC1 show higher G-lignin content, although recombinant MsLAC1 seemed to prefer sinapyl alcohol as substrate.

Conclusions
In summary, our results suggest that MsLAC1 is regulated by secondary cell wall MYB transcription factors and is involved in lignification of xylem fibers. This report identifies MsLAC1 as a promising breeding target in Miscanthus for biofuel and biomaterial applications.