bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the Long-Term Impact of Concussion upon Cognition: A 5-Year Prospective Investigation
Authors: Piantella Stefan , McDonald Stuart J , Maruff Paul , Wright Bradley J 
Published: February 2020

AbstractObjectiveJockeys have high rates of concussion, with 5% of jockeys receiving at least one concussion annually. The impact of acute concussion upon cognition is well understood, but less is known about the long-term effects of concussion upon cognition. Our aim was to assess the impact of concussion upon jockeys who had provided pre-concussion assessments of cognition using a prospective design.MethodIn this study, over a 5-year period, we assessed the cognitive performance of jockeys with ≥1 medically diagnosed concussion (MDC; n = 17, months since concussion, M = 29.18), against those who had not been concussed (NC; n = 41). Jockeys who had not been concussed in the preceding 6 months completed four computer-based cognitive assessments from the CogSport battery.ResultsUnlike the majority of the small existing literature, there was no difference (p ≥ .05) between the MDC and NC groups after controlling for age and baseline performance. Additionally, we used a measure of reliable change to assess for clinically meaningful decrements from baseline in each test and composite score 5 years later. None of the jockeys in the MDC group recorded significant decrements on any CogSport measure from baseline (z &gt; −1.65).ConclusionsThe findings suggest that the presence of concussion does not result in persistent decrements in cognitive performance and that when findings are considered collectively, assessing factors beyond medically diagnosed concussion (e.g., chronic stress, undiagnosed concussion) may improve the interpretation of our current findings.
Eye-Tracking Technology in Plastic and Reconstructive Surgery: A Systematic Review
Authors: Asaad Malke , Dey Jacob K , Al-Mouakeh Ahmad , Manjouna Mohamad Baraa , Nashed Mohammad A , Rajesh Aashish , Boonipat Thanapoom , Bite Uldis 
Published: February 2020

Abstract

Background
The use of eye-tracking technology in plastic surgery has gained popularity over the past decade due to its ability to assess observers’ visual preferences in an objective manner.

Objectives
The goal of this study was to provide a comprehensive review of eye-tracking studies in plastic and reconstructive surgery, which can aid in the design and conduct of high-quality eye-tracking studies.

Methods
Through application of Preferred Reporting Items for Systematic review and Meta-Analysis (PRISMA) guidelines, a comprehensive search of articles published on eye-tracking across several databases was conducted from January 1946 to January 2019. Inclusion criteria included studies evaluating the use of eye-tracking technology in the field of plastic and reconstructive surgery. The resulting publications were screened by 2 independent reviewers.

Results
A total of 595 articles were identified, 23 of which met our inclusion criteria. The most common application of eye-tracking was to assess individuals with cleft lip/palate (9 studies). All 19 studies that evaluated fixation patterns among conditions vs controls reported significant differences between the 2 groups. Five out of 7 studies assessing visual data between preoperative and postoperative patients identified significant differences between the preoperative and postoperative groups, whereas 2 studies did not. Nine studies examined the relation between severity indices, attractiveness scores, or personality ratings and gaze patterns. Correlation was found in 7 out of the 9 studies.

Conclusions
This systematic review demonstrates the utility of eye-tracking technology as a quantifiable objective assessment and emerging research tool for evaluating outcomes in several domains of plastic and reconstructive surgery.
atomium—a Python structure parser
Authors: Ireland Sam M , Martin Andrew C R 
Published: February 2020

AbstractSummaryStructural biology relies on specific file formats to convey information about macromolecular structures. Traditionally this has been the PDB format, but increasingly newer formats, such as PDBML, mmCIF and MMTF are being used. Here we present atomium, a modern, lightweight, Python library for parsing, manipulating and saving PDB, mmCIF and MMTF file formats. In addition, we provide a web service, pdb2json, which uses atomium to give a consistent JSON representation to the entire Protein Data Bank.Availability and implementationatomium is implemented in Python and its performance is equivalent to the existing library BioPython. However, it has significant advantages in features and API design. atomium is available from atomium.bioinf.org.uk and pdb2json can be accessed at pdb2json.bioinf.org.ukSupplementary informationSupplementary data are available at Bioinformatics online.
A cautionary tale on using imputation methods for inference in matched-pairs design
Authors: Ramosaj Burim , Amro Lubna , Pauly Markus 
Published: February 2020

Abstract

Motivation
Imputation procedures in biomedical fields have turned into statistical practice, since further analyses can be conducted ignoring the former presence of missing values. In particular, non-parametric imputation schemes like the random forest have shown favorable imputation performance compared to the more traditionally used MICE procedure. However, their effect on valid statistical inference has not been analyzed so far. This article closes this gap by investigating their validity for inferring mean differences in incompletely observed pairs while opposing them to a recent approach that only works with the given observations at hand.

Results
Our findings indicate that machine-learning schemes for (multiply) imputing missing values may inflate type I error or result in comparably low power in small-to-moderate matched pairs, even after modifying the test statistics using Rubin’s multiple imputation rule. In addition to an extensive simulation study, an illustrative data example from a breast cancer gene study has been considered.

Availability and implementation
The corresponding R-code can be accessed through the authors and the gene expression data can be downloaded at www.gdac.broadinstitute.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Bayesian inference using qualitative observations of underlying continuous variables
Authors: Mitra Eshan D , Hlavacek William S 
Published: February 2020

Abstract

Motivation
Recent work has demonstrated the feasibility of using non-numerical, qualitative data to parameterize mathematical models. However, uncertainty quantification (UQ) of such parameterized models has remained challenging because of a lack of a statistical interpretation of the objective functions used in optimization.

Results
We formulated likelihood functions suitable for performing Bayesian UQ using qualitative observations of underlying continuous variables or a combination of qualitative and quantitative data. To demonstrate the resulting UQ capabilities, we analyzed a published model for immunoglobulin E (IgE) receptor signaling using synthetic qualitative and quantitative datasets. Remarkably, estimates of parameter values derived from the qualitative data were nearly as consistent with the assumed ground-truth parameter values as estimates derived from the lower throughput quantitative data. These results provide further motivation for leveraging qualitative data in biological modeling.

Availability and implementation
The likelihood functions presented here are implemented in a new release of PyBioNetFit, an open-source application for analyzing Systems Biology Markup Language- and BioNetGen Language-formatted models, available online at www.github.com/lanl/PyBNF.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Bayesian nonparametric approach for evaluating the causal effect of treatment in randomized trials with semi-competing risks
Authors: Xu Yanxun , Scharfstein Daniel , Müller Peter , Daniels Michael 
Published: February 2020

Summary
We develop a Bayesian nonparametric (BNP) approach to evaluate the causal effect of treatment in a randomized trial where a nonterminal event may be censored by a terminal event, but not vice versa (i.e., semi-competing risks). Based on the idea of principal stratification, we define a novel estimand for the causal effect of treatment on the nonterminal event. We introduce identification assumptions, indexed by a sensitivity parameter, and show how to draw inference using our BNP approach. We conduct simulation studies and illustrate our methodology using data from a brain cancer trial. The R code implementing our model and algorithm is available for download at https://github.com/YanxunXu/BaySemiCompeting.
Inflation and Output Volatility: Evidence from International Historical Data
Authors: Ćorić Bruno 
Published: February 2020

Abstract
This study adopts a historical perspective to investigate variations in output volatility within and across world economies. The analysis uses annual data for 37 OECD and non-OECD countries covering the last two centuries. We focus on the relationship between inflation and output volatility. The results of a panel analysis show a positive effect of inflation on output volatility. This finding is consistent with the view that low inflation has a stabilizing effect on output volatility over the long term.
Incidence, Risk Factors and Evaluation of Osteoporosis in Patients With Inflammatory Bowel Disease: A Danish Population-Based Inception Cohort With 10 Years of Follow-Up
Authors: Lo Bobby , Holm Jakob Præst , Vester-Andersen Marianne Kajbæk , Bendtsen Flemming , Vind Ida , Burisch Johan 
Published: February 2020

Abstract

Background
Patients with inflammatory bowel disease [IBD] including Crohn’s disease [CD] and ulcerative colitis [UC] are at risk of developing metabolic bone disease. The aims here were to investigate the screening strategy, incidence and risk factors of osteoporosis in a prospective population-based inception cohort.

Method
Between 2003 and 2004 all incident patients diagnosed with CD and UC in a well-defined Copenhagen area were included and followed until 2015. Data were compared with a control population [at a ratio of 1:20]. Regression models were performed with several covariates. The sensitivity of the Danish registries for osteoporosis was also assessed.

Results
A total of 513 patients were included [213 CD, 300 UC]. Overall, 338 (66%, CD: 164 [77%], UC: 174 [58%], p &lt; 0.001] patients received ≥ 500 mg corticosteroid within a year, resulting in 781 patient-years at risk of osteoporosis. Of those, only 83 [10.6%] patient-years were followed by a dual-energy X-ray absorptiometry scan within the same or the following 2 years.
Overall, 73 [14.2%] IBD patients (CD: 31 [14.6%], UC: 42 [14%]) and 680 [6.6%, p &lt; 0.001] controls were diagnosed with osteoporosis during follow-up. The risk of osteoporosis was increased compared to the control population (odds ratio: CD: 2.9 [95% confidence interval: 2.0–4.1], UC: 2.8 [2.1–3.9]).

Conclusion
In this population-based inception cohort, the incidence of osteoporosis was significantly higher compared to a control population. Measurement of bone mineral density is infrequent, especially in patients at high risk of developing osteoporosis. These results demonstrate the need of further awareness of the risk of osteoporosis among IBD patients, and prospective population-based studies are warranted.
The Water Channel Aquaporin 8 is a Critical Regulator of Intestinal Fluid Homeostasis in Collagenous Colitis
Authors: Escudero-Hernández Celia , Münch Andreas , Østvik Ann-Elisabet , Granlund Atle van Beelen , Koch Stefan 
Published: February 2020

AbstractBackground and AimsDiarrhoea is a common, debilitating symptom of gastrointestinal disorders. Pathomechanisms probably involve defects in trans-epithelial water transport, but the role of aquaporin [AQP] family water channels in diarrhoea-predominant diseases is unknown. We investigated the involvement of AQPs in the pathobiology of collagenous colitis [CC], which features chronic, watery diarrhoea despite overtly normal intestinal epithelial cells [IECs].MethodsWe assessed the expression of all AQP family members in mucosal samples of CC patients before and during treatment with the corticosteroid drug budesonide, steroid-refractory CC patients and healthy controls. Samples were analysed by genome-wide mRNA sequencing [RNA-seq] and quantitative real-time PCR [qPCR]. In some patients, we performed tissue microdissection followed by RNA-seq to explore the IEC-specific CC transcriptome. We determined changes in the protein levels of the lead candidates in IEC by confocal microscopy. Finally, we investigated the regulation of AQP expression by corticosteroids in model cell lines.ResultsUsing qPCR and RNA-seq, we identified loss of AQP8 expression as a hallmark of active CC, which was reverted by budesonide treatment in steroid-responsive but not refractory patients. Consistently, decreased AQP8 mRNA and protein levels were observed in IECs of patients with active CC, and steroid drugs increased AQP8 expression in model IECs. Moreover, low APQ8 expression was strongly associated with higher stool frequency in CC patients.ConclusionDown-regulation of epithelial AQP8 may impair water resorption in active CC, resulting in watery diarrhoea. Our results suggest that AQP8 is a potential drug target for the treatment of diarrhoeal disorders.
Prevalence of permanent pacemaker implantation after conventional aortic valve replacement—a propensity-matched analysis in patients with a bicuspid or tricuspid aortic valve: a benchmark for transcatheter aortic valve replacement
Authors: Haunschild Josephina , Misfeld Martin , Schroeter Thomas , Lindemann Frank , Davierwala Piroze , von Aspern Konstantin , Spampinato Ricardo A , Weiss Stefan , Borger Michael A , Etz Christian D 
Published: February 2020

Abstract

OBJECTIVES
Elective treatment of aortic valve disease by transcatheter aortic valve replacement (TAVR) is becoming increasingly popular, even in patients with low risk and intermediate risk. Even patients with a bicuspid aortic valve (BAV) are increasingly considered eligible for TAVR. Permanent pacemaker implantation (PMI) is a known—frequently understated—complication of TAVR affecting 9–15% of TAVR patients with a potentially significant impact on longevity and quality of life. BAV patients are affected by the highest PMI rates, although they are frequently younger compared to their tricuspid peers. The aim of the study is to report benchmark data—from a high-volume centre (with a competitive TAVR programme) on PMI after isolated surgical aortic valve replacement (SAVR) in patients with BAV and tricuspid aortic valve (TAV).

METHODS
We performed a retrospective single-centre analysis on 4154 patients receiving isolated SAVRs (w/o concomitant procedures), between 2000 and 2019, of whom 1108 had BAV (27%). PMI rate and early- and long-term outcomes were analysed. For better comparability of these demographically unequal cohorts, 1:1 nearest neighbour matching was performed.

RESULTS
At the time of SAVR, BAV patients were on average 10 years younger than their TAV peers (59.7 ± 12 vs 69.3 ± 9; P &lt; 0.001) and had less comorbidities; all relevant characteristics were equally balanced after statistical matching. Overall PMI rate was significantly higher in BAV patients (5.4% vs 3.8%; P = 0.03). BAV required PMI exclusively (100%) and TAV required predominately (96%) for persistent postoperative high-degree atrioventricular block. After matching, the PMI rate was similar (5.1% vs 4.4%, P = 0.5). In-hospital mortality in the matched cohort was 1% in both groups. Long-term survival was more favourable in BAV patients (94% vs 90% in TAV at 5 years; 89% vs 82% in TAV at 9 years; P = 0.013).

CONCLUSIONS
With SAVR, the overall incidence of PMI among BAV patients seems significantly higher; however, after propensity matching, no difference in PMI rates between BAV and TAV is evident. The PMI rate was remarkably lower among BAV patients after SAVR compared to the reported incidence after TAVR.
Social inequalities in medical rehabilitation outcomes—a registry-based study on 219 584 insured persons in Germany
Authors: Götz Simon , Wahrendorf Morten , Siegrist Johannes , Dragano Nico 
Published: February 2020

AbstractBackgroundGiven limited knowledge on the extent of social inequalities in longer-term work ability of people with a chronic disease, this study analyzes social inequalities of three consecutive indicators of work ability following medical rehabilitation in a large sample of insured employees.MethodsBased on data from the German statutory pension insurance, a representative 20% random sample of all employed persons undergoing medical rehabilitation between 2006 and 2008 was included in a longitudinal analysis (n=219 584 persons). Three measures of consecutive work-related outcomes (physicians’ assessment of work ability at discharge; return to work in the year thereafter; disability pension during follow-up) and socioeconomic position (SEP) (education, occupational position and income) were assessed. Adjusted relative risks (RRs) for each outcome were calculated according to SEP, applying Poisson regression analysis.ResultsThe measures of SEP were associated with all three outcomes of work ability in the fully adjusted models. Relatively strongest relationships were observed for education as SEP measure, and they were particularly pronounced for ‘low work ability’ (RR=2.38 for lower secondary education compared to tertiary education; 95% CI: 2.26–2.51). Based on average marginal effects, absolute differences of work ability by SEP indicate a socially graded pattern, with only few exceptions.ConclusionsDespite Germany’s universal access to medical and vocational rehabilitation social inequalities in longer-term work ability following chronic disease persist, thus calling for targeted programmes of prevention and occupational health promotion.
Maize (Zea mays L. Sp.) varieties significantly influence bacterial and fungal community in bulk soil, rhizosphere soil and phyllosphere
Authors: Kong Xiao , Han Zhenfei , Tai Xin , Jin Decai , Ai Sen , Zheng Xiaoxu , Bai Zhihui 
Published: February 2020

ABSTRACT
The plant–microbe interaction can affect ecosystem function, and many studies have demonstrated that plant species influence relevant microorganisms. In this study, microbial communities in bulk soil, rhizosphere soil and phyllosphere from different maize varieties were investigated using high-throughput sequencing method. Results demonstrated that cultivar Gaoneng 1 (G1) showed higher bacterial diversity in soil (both bulk and rhizosphere soils) and lower bacterial diversity in the phyllosphere, while cultivar Gaoneng 2 (G2) had lower fungal diversity in both the soil and phyllosphere compare to the other cultivars. The bacterial community structure of soils among the three varieties was significantly different; however, no significant differences were found in the soil fungal community and phyllosphere bacterial and fungal community. The soil networks from cultivar G1 and phyllosphere networks from cultivar Zhengdan (ZD) have the highest complexity in contrast to the other two cultivars. In conclusion, the bacterial community structure in bulk soil of different cultivars was significantly different, so do the co-occurrence ecological networks of phyllosphere bacterial community. This study comprehensively analyzed the microbial community among different maize cultivars and could be useful for guiding practices, such as evaluation of new plant cultivars and quality predictions of these varieties at the microbial level.
Polesworth abbey (Warwickshire) and the Marmion lord of Tamworth castle: using an Anglo-Saxon saint’s cult in the earlier twelfth century*
Authors: Tringham Nigel 
Published: February 2020

Abstract
A fifteenth-century manuscript gives an account of how a post-Conquest lord of Tamworth castle expelled nuns from nearby Polesworth (Warwickshire), later restoring them after he had been admonished in a dream by the nuns’ patron, St. Edith. The story can be tested against copies of twelfth-century charters, which show that the nuns were installed in Polesworth church anew by Robert Marmion (d. 1144), acting with his high-born wife Milisent. Political considerations were probably foremost in this process, and close ties with the royal family help to explain the convent’s association with the prestigious Continental Benedictine house at Cluny.
Spatial and temporal distribution patterns of brown shrimp (Crangon crangon) derived from commercial logbook, landings, and vessel monitoring data
Authors: Schulte K F , Siegel V , Hufnagl M , Schulze T , Temming A 
Published: February 2020

Abstract
In this study, logbook, landings, and vessel monitoring system data of German brown shrimp (Crangon crangon L.) fishers were combined to analyse spatial and temporal distribution patterns. Landings per unit effort (LPUE) were standardized to the efficiency level of a reference vessel. The standardization altered the spatial–temporal patterns of the LPUE as the vessels differed by a factor of up to 4.7. LPUE data were separated into two size classes according to sieve fractions. Small brown shrimps were characterized by LPUE values increasing early in the year in shallow waters, especially in estuaries in July. Subsequently, peak LPUE values are reached at the end of September in all depths, but with variable spatial patterns between years. LPUE data indicate a general outward migration between early summer and winter. In winter, large shrimp shows a clear increase in LPUE with depths mainly in regions adjacent to the Dutch coast and a reversed pattern close to the Danish coast. The large size class in winter—which consists mainly of mature or egg-bearing females—showed high LPUE values along two persistent diagonal bands in the German Bight. These patterns could lead to local recruitment overfishing, if fishermen are aware of such patterns.
Non-Newtonian channel flow—exact solutions
Authors: Griffiths P T 
Published: February 2020

Abstract
In this short communication, exact solutions are obtained for a range of non-Newtonian flows between stationary parallel plates. The pressure-driven flow of fluids with a variational viscosity that adheres to the Carreau governing relationship are considered. Solutions are obtained for both shear-thinning (viscosity decreasing with increasing shear-rate) and shear-thickening (viscosity increasing with increasing shear-rate) flows. A discussion is presented regarding the requirements for such analytical solutions to exist. The dependence of the flow rate on the channel half width and the governing non-Newtonian parameters is also considered.
Wiman–Valiron Discs and the Dimension of Julia Sets
Authors: Waterman James 
Published: February 2020

Abstract
We show that the Hausdorff dimension of the set of points of bounded orbit in the Julia set of a meromorphic map with a simply connected direct tract and a certain restriction on the singular values is strictly greater than one. This result is obtained by proving new results related to Wiman–Valiron theory.