bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental Physical and Perceived Quality in Hospice
Authors: Ferrante Tiziana , Villani Teresa 
Published: July 2021

Objectives: This study presents the application of post-occupancy evaluations (POEs) methodologies to facilities for palliative-hospice care, in order to directly assess the physical–spatial qualities better suited for the specific psychological needs of “fragile” users and to ensure better architectural quality in new projects and in renovation measures. Background: In international literature, there are few studies concerning the application of POEs to hospice, assessing the impact of individual environmental factors on users’ psychoemotional reactions. The set of elements that patients and their families perceive as important, defining the architectural quality of a hospice, has not been sufficiently investigated yet. Method: Therefore, a POE was performed on a sample of hospice in Italy, by preparing a self-filled questionnaire addressing patients and relatives. Indicators of perceived physical–spatial humanization, which were validated for hospital facilities (perceived hospital environment quality indicators), were used for the assessment then implemented and harmonized in relation to hospice facilities features. Results: The study revealed the indicators of architectural quality most valued by users, whose reliability was then verified, along with their average quality, by highlighting recurring shortcomings. The global quality was found to be generally high. Below-average scores were found for indicators on usability, acoustic comfort of outdoors, visual and acoustic comfort of shared indoor spaces, and artificial lighting in the recovery room. Conclusion: The study generated new knowledge on hospice and confirmed the efficacy of POEs as a tool both for purchasers and designers. Indeed, the first results of this study allow to recalibrate building programs, revisiting layouts, and elaborating appropriate technical solutions.
Reasons Why Athletes Do Not Return to Sports After Arthroscopic Bankart Repair: A Comparative Study of 208 Athletes With Minimum 2-Year Follow-up
Authors: Rossi Luciano Andrés , Tanoira Ignacio , Brandariz Rodrigo , Pasqualini Ignacio , Ranalletta Maximiliano 
Published: July 2021

Background: There is a lack of information regarding the reasons why patients do not return to sports after an arthroscopic Bankart repair and whether there is a relationship between return to sports and functional outcomes. Purpose: To evaluate the reasons why competitive athletes who underwent arthroscopic Bankart repair did not return to sports and whether there was a relationship between returning to sports and postoperative outcome scores and complications. Study Design: Cohort study; Level of evidence, 3. Methods: Of 217 competitive athletes who underwent arthroscopic Bankart repair for isolated anterior glenohumeral instability between June 2014 and December 2017, a total of 208 athletes (96%) were evaluated at minimum 2-year follow-up. Return to sports, the level of sports achieved, and the time between surgery and return to competition were assessed, and patients who did not return to sports were asked to provide the reasons for cessation. The Rowe score and the Athletic Shoulder Outcome Scoring System (ASOSS) were used to assess functional outcomes. Recurrences, reoperations, and complications were also evaluated. Results: The mean patient age was 24 years (range, 18-30 years), and the mean follow-up was 44 months (range, 24-90 months). Of the 208 athletes, 73% were able to return to sports (65% returned to their preinjury level), and 27% did not return to sports. Of those who did not return, the most frequent reasons were fear of reinjury (44%), lack of confidence in their shoulder (12%), and concern about a new rehabilitation process in case of recurrence (10%). The Rowe and ASOSS scores showed significant postoperative improvement in all patients ( P < .001), with no significant differences between the 2 study groups at the final follow-up. There were 21 recurrences (10%) and 5 complications (2.4%), and 11 patients (5.3%) underwent revision surgery, with no significant differences in these rates between the groups. Conclusion: Of patients who did not return to sports, 74% left for a reason independent of shoulder function, with the most frequent causes being fear of reinjury and a concern about new rehabilitation process. Neither outcome scores nor complications varied significantly between patients who returned and those who did not return to sports.
Outcomes of Open Versus Arthroscopic Broström Surgery for Chronic Lateral Ankle Instability: A Systematic Review and Meta-analysis of Comparative Studies
Authors: Attia Ahmed Khalil , Taha Tarek , Mahmoud Karim , Hunt Kenneth J. , Labib Sameh A. , d’Hooghe Pieter 
Published: July 2021

Background: Nearly 20% of acute ankle sprains progress to chronic lateral ankle instability that requires surgical intervention. In recent years, there has been a growing interest in arthroscopic Broström techniques as an alternative to open surgery. Purpose: To review the most up-to-date evidence comparing the outcomes of open and arthroscopic Broström procedures for chronic lateral ankle instability. Study Design: Systematic review; Level of evidence, 3. Methods: This review was performed following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. Relevant comparative studies in English up to May 2020 were identified. The primary outcomes were (1) functional scores (Karlsson Ankle Function Score and American Orthopaedic Foot & Ankle Society [AOFAS] score) and (2) the 10-point visual analog scale (VAS) score for pain. The secondary outcomes were differences in (1) postoperative anterior drawer and talar tilt, (2) surgical time and complication rate, and (3) time to return to sports and weightbearing. Results: A total of 408 patients in 8 studies met the inclusion criteria. Of these, 193 (47.3%) patients underwent open surgery, while 215 (52.7%) patients underwent arthroscopic surgery. There were significant differences between the open and arthroscopic repair groups in mean 6-month AOFAS scores (82.4 vs 92.25, respectively; mean difference [MD], 11.36; 95% CI, 0.14-2.56; I 2 = 90%; P = .03), 1-year AOFAS scores (80.05 vs 88.6; MD, –11.96; 95% CI, –21.26 to –2.76; I 2 = 82%; P = .01), 6-month VAS scores (1.7 vs 1.4; MD, –0.38; 95% CI, –0.54 to –0.21; I 2 = 78%; P < .001), and 1-year VAS scores (2.05 vs 1.45; MD, 0.31; 95% CI, 0.09-0.54; I 2 = 0%; P < .001). The mean time to weightbearing was 14.25 and 9.0 weeks in the open and arthroscopic repair groups, respectively (MD, 1.89; 95% CI, 1.24-2.54; I 2 = 99%; P < .001). There were no statistically significant differences in the remaining outcomes evaluated. Conclusion: While technically more demanding, arthroscopic Broström was superior to open Broström-Gould surgery in postoperative AOFAS scores, VAS pain scores, and time to return to weightbearing. The operative time, complication rate, talar tilt, and anterior drawer tests were excellent and statistically comparable. Long-term clinical trials are required before recommending arthroscopic Broström as the new gold standard.
Association of Jump-Landing Biomechanics With Tibiofemoral Articular Cartilage Composition 12 Months After ACL Reconstruction
Authors: Pfeiffer Steven J. , Spang Jeffrey T. , Nissman Daniel , Lalush David , Wallace Kyle , Harkey Matthew S. , Pietrosimone Laura S. , Padua Darin , Blackburn Troy , Pietrosimone Brian 
Published: July 2021

Background: Excessively high joint loading during dynamic movements may negatively influence articular cartilage health and contribute to the development of posttraumatic osteoarthritis after anterior cruciate ligament reconstruction (ACLR). Little is known regarding the link between aberrant jump-landing biomechanics and articular cartilage health after ACLR. Purpose/Hypothesis: The purpose of this study was to determine the associations between jump-landing biomechanics and tibiofemoral articular cartilage composition measured using T1ρ magnetic resonance imaging (MRI) relaxation times 12 months postoperatively. We hypothesized that individuals who demonstrate alterations in jump-landing biomechanics, commonly observed after ACLR, would have longer T1ρ MRI relaxation times (longer T1ρ relaxation times associated with less proteoglycan density). Study Design: Cross-sectional study; Level of evidence, 3. Methods: A total of 27 individuals with unilateral ACLR participated in this cross-sectional study. Jump-landing biomechanics (peak vertical ground-reaction force [vGRF], peak internal knee extension moment [KEM], peak internal knee adduction moment [KAM]) and T1ρ MRI were collected 12 months postoperatively. Mean T1ρ relaxation times for the entire weightbearing medial femoral condyle, lateral femoral condyle (global LFC), medial tibial condyle, and lateral tibial condyle (global LTC) were calculated bilaterally. Global regions of interest were further subsectioned into posterior, central, and anterior regions of interest. All T1ρ relaxation times in the ACLR limb were normalized to the uninjured contralateral limb. Linear regressions were used to determine associations between T1ρ relaxation times and biomechanics after accounting for meniscal/chondral injury. Results: Lower ACLR limb KEM was associated with longer T1ρ relaxation times for the global LTC (Δ R 2 = 0.24; P = .02), posterior LTC (Δ R 2 = 0.21; P = .03), and anterior LTC (Δ R 2 = 0.18; P = .04). Greater ACLR limb peak vGRF was associated with longer T1ρ relaxation times for the global LFC (Δ R 2 = 0.20; P = .02) and central LFC (Δ R 2 = 0.15; P = .05). Peak KAM was not associated with T1ρ outcomes. Conclusion: At 12 months postoperatively, lower peak KEM and greater peak vGRF during jump landing were related to longer T1ρ relaxation times, suggesting worse articular cartilage composition.
What Factors Influence Dental Faculty’s Willingness to Treat Pregnant Women?
Authors: Huang S.S. , Yang C. , Cohen V. , Russell S.L. 
Published: July 2021

Background: Despite evidence-based guidelines advocating for the provision of oral health care throughout pregnancy, dentists remain hesitant to provide dental treatment for pregnant women. However, little is known about attitudes toward treating pregnant women among dental school faculty, who may transmit their attitudes and treatment preferences to their students. Methods: We collected cross-sectional survey data at the New York University College of Dentistry, which produces 10% of all US dentists and is the largest US dental school, to understand faculty attitudes and knowledge regarding providing dental treatment to pregnant women. This study was part of an educational effort to improve dental care access by pregnant women and to examine what factors influence willingness to treat pregnant patients among dental faculty members. Results: We found that concerns about professional liability outweighed inadequate knowledge regarding treatment of pregnant patients in determining dental faculty’s willingness to treat pregnant women. Conclusions: Educational interventions delivered to dental faculty regarding current dental treatment guidelines for pregnant women may not be sufficient to increase faculty’s provision of dental care to women during pregnancy. Future work to design effective interventions to increase dental treatment of pregnant women among dental faculty should address liability concerns. Knowledge Transfer Statement Interventions addressing dental clinician and faculty knowledge about dental treatment for pregnant women may be insufficient to increase dental treatment among pregnant women. Instead, policy makers should consider designing, implementing, and evaluating interventions addressing malpractice and liability concerns.
Morpho-constitutional analysis of urinary stones from patients with urolithiasis in the Democratic Republic of Congo
Authors: Diangienda Pablo Kuntima Diasiama , Moningo Dieudonné Molamba , Makulo Jean-Robert Rissasy , Sumaili Ernest Kiswaya , Mafuta Eric Musalu , Mayindu Alain Ngoma , Punga-Maole Augustin M. L. , Haymann Jean-Philippe , Daudon Michel 
Published: July 2021

Abstract
Background
Urolithiasis is increasingly diagnosed worldwide. Stone analysis is an important part in the assessment of patients with urolithiasis. However, in sub-Saharan Africa, data on the composition of urinary stones are limited. This study aimed to describe the composition and sites of urinary stones and to investigate relationship between socio-demographic characteristics, clinical profile of patients, and the composition of urinary stones.

Methods
A retrospective analysis of 132 patients with urolithiasis who visited one of the seven hospitals in the Democratic Republic of Congo during eight years of study period (January 2010 to January 2018) was conducted. Stones were analyzed by infrared spectrophotometry.

Results
Most of stones analyzed (n = 82, 62.1%) originated from the upper urinary tract with a difference across gender (58.5% males vs. 41.5% females, p = 0.001). Only three stones (two from whewellite and one from anhydrous uric acid) were considered pure (2.3%), excluding the protein frame (less than 5%). Whewellite, proteins, and carbapatite were identified in 97.7%, 96.2%, and 80.3% of the stones analyzed, respectively; and in 91.7%, 89.4%, and 67.7% of the nuclei of the stones analyzed, respectively. Taking into account the proportion of each constituent in the stones analyzed, whewellite (68.9%), anhydrous uric acid (10.6%), and carbapatite (8.3%) were the main constituents in respectively 68, 9%, 10.6%, and 8.3% of the stones analyzed.

Conclusion
Whewellite, anhydrous uric acid, and carbapatite represented the most frequent main components of stones identified, suggesting that dietary hyperoxaluria could be an important factor in lithogenesis in the Democratic Republic of Congo.
SAUTE: sequence assembly using target enrichment
Authors: Souvorov Alexandre , Agarwala Richa 
Published: July 2021

Abstract
Background
Illumina is the dominant sequencing technology at this time. Short length, short insert size, some systematic biases, and low-level carryover contamination in Illumina reads continue to make assembly of repeated regions a challenging problem. Some applications also require finding multiple well supported variants for assembled regions.

Results
To facilitate assembly of repeat regions and to report multiple well supported variants when a user can provide target sequences to assist the assembly, we propose SAUTE and SAUTE_PROT assemblers. Both assemblers use de Bruijn graph on reads. Targets can be transcripts or proteins for RNA-seq reads and transcripts, proteins, or genomic regions for genomic reads. Target sequences are nucleotide and protein sequences for SAUTE and SAUTE_PROT, respectively.

Conclusions
For RNA-seq, comparisons with Trinity, rnaSPAdes, SPAligner, and SPAdes assembly of reads aligned to target proteins by DIAMOND show that SAUTE_PROT finds more coding sequences that translate to benchmark proteins. Using AMRFinderPlus calls, we find SAUTE has higher sensitivity and precision than SPAdes, plasmidSPAdes, SPAligner, and SPAdes assembly of reads aligned to target regions by HISAT2. It also has better sensitivity than SKESA but worse precision.
Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L.
Authors: Su Wei , Raza Ali , Zeng Liu , Gao Ang , Lv Yan , Ding Xiaoyu , Cheng Yong , Zou Xiling 
Published: July 2021

Abstract
Background
Lipid phosphate phosphatases (LPP) are critical for regulating the production and degradation of phosphatidic acid (PA), an essential signaling molecule under stress conditions. Thus far, the LPP family genes have not been reported in rapeseed (Brassica napus L.).

Results
In this study, a genome-wide analysis was carried out to identify LPP family genes in rapeseed that respond to different stress conditions. Eleven BnLPPs genes were identified in the rapeseed genome. Based on phylogenetic and synteny analysis, BnLPPs were classified into four groups (Group I-Group IV). Gene structure and conserved motif analysis showed that similar intron/exon and motifs patterns occur in the same group. By evaluating cis-elements in the promoters, we recognized six hormone- and seven stress-responsive elements. Further, six putative miRNAs were identified targeting three BnLPP genes. Gene ontology analysis disclosed that BnLPP genes were closely associated with phosphatase/hydrolase activity, membrane parts, phosphorus metabolic process, and dephosphorylation. The qRT-PCR based expression profiles of BnLPP genes varied in different tissues/organs. Likewise, several gene expression were significantly up-regulated under NaCl, PEG, cold, ABA, GA, IAA, and KT treatments.

Conclusions
This is the first report to describe the comprehensive genome-wide analysis of the rapeseed LPP gene family. We identified different phytohormones and abiotic stress-associated genes that could help in enlightening the plant tolerance against phytohormones and abiotic stresses. The findings unlocked new gaps for the functional verification of the BnLPP gene family during stresses, leading to rapeseed improvement.
Assessing the risk of performance and detection bias in Cochrane reviews as a joint domain is less accurate compared to two separate domains
Authors: Barcot Ognjen , Boric Matija , Dosenovic Svjetlana , Puljak Livia 
Published: July 2021

Abstract
Background
Initially, the Cochrane risk of bias (RoB) tool had a domain for “blinding of participants, personnel and outcome assessors”. In the 2011 tool, the assessment of blinding was split into two domains: blinding of participants and personnel (performance bias) and blinding of outcome assessors (detection bias). The aims of this study were twofold; first, to analyze the frequency of usage of the joint blinding domain (a single domain for performance and detection bias), and second, to assess the proportion of adequate assessments made in the joint versus single RoB domains for blinding by comparing whether authors’ RoB judgments were supported by explanatory comments in line with the Cochrane Handbook recommendations.

Methods
We extracted information about the assessment of blinding from RoB tables (judgment, comment, and whether it was specified which outcome type; e.g., objective, subjective) of 729 Cochrane reviews published in 2015-2016. In the Cochrane RoB tool, judgment (low, unclear or high risk) needs to be accompanied by a transparent comment, in which authors provide a summary justifying RoB judgment, to ensure transparency in how these judgments were reached. We reassessed RoB based on the supporting comments reported in Cochrane RoB tables, in line with instructions from the Cochrane Handbook. Then, we compared our new assessments to judgments made by Cochrane authors. We compared the frequency of adequate judgments in reviews with two separate domains for blinding versus those with a joint domain for blinding.

Results
The total number of assessments for performance bias was 6918, with 8656 for detection bias and 3169 for the joint domain. The frequency of adequate assessments was 74% for performance bias, 78% for detection bias, and 59% for the joint domain. The lowest frequency of adequate assessments was found when Cochrane authors judged low risk – 47% in performance bias, 62% in detection bias, and 31% in the joint domain. The joint domain and detection bias domain had a similar proportion of specified outcome types (17% and 18%, respectively).

Conclusions
Splitting joint RoB assessment about blinding into two domains was justified because the frequency of adequate judgments was higher in separate domains. Specification of outcome types in RoB domains should be further scrutinized.
Illness perception and health care use in individuals with irritable bowel syndrome: results from an online survey
Authors: Schwille-Kiuntke Juliane , Rüdlin Solveig Lu , Junne Florian , Enck Paul , Brenk-Franz Katja , Zipfel Stephan , Rieger Monika A. 
Published: July 2021

Abstract
Background
Individual illness perception is known to influence a range of outcome variables. However, little is known regarding illness perception in irritable bowel syndrome (IBS) and its relation to the use of the health care system. This study hypothesised a relationship between illness perception and inappropriate health care use (under-, over- and misuse).

Methods
An internet-based, cross-sectional study in participants affected by IBS symptoms was carried out (April – October 2019) using open questions as well as validated standardized instruments, e.g. the illness perception questionnaire revised (IPQ-R) and its subscales. Sub-group comparisons were done non-parametrically and effect sizes were reported. Potential predictors of (1) conventional health care utilisation and (2) utilisation of treatment approaches with lacking or weak evidence regarding effectiveness in IBS were examined with logistic regression analyses and reported as odds ratio (OR) and 95% confidence interval.

Results
Data from 513 individuals were available. More than one-third (35.7%) of participants were classified as high utilisers (> 5 doctor visits during the last year). Several indicators of inappropriate health care use were detected, such as a low proportion of state-of-the-art gynaecological evaluation of symptoms (35.0% of women) and a high proportion of individuals taking ineffective and not recommended non-steroidal antirheumatic drugs for IBS (29.4%). A majority (57.7%) used treatment approaches with lacking or weak evidence regarding the effectiveness in IBS (e.g. homeopathy). Being a high utiliser as defined above was predicted by the perceived daily life consequences of IBS (IPQ-R subscale “consequences”, OR = 1.189 [1.100–1.284], p ≤ 0.001) and age (OR = 0.980 [0.962–0.998], p = 0.027). The use of treatment approaches with lacking or weak evidence was forecasted by the perceived daily life consequences (OR = 1.155 [1.091–1.223], p ≤ 0.001) and gender (reference category male: OR = 0.537 [0.327–0.881], p = 0.014), however effect sizes were small.

Conclusions
Daily life consequences, perceived cure and personal control as aspects of individual disease perception seem to be related to individuals’ health care use. These aspects should be a standard part of the medical interview and actively explored. To face inappropriate health care use patients and professionals need to be trained. Interdisciplinary collaborative care may contribute to enhanced quality of medical supply in IBS.