bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Evaluation of Newer Remineralizing Agents on Surface Characteristics of Tooth Surface After Slenderization: An In Vitro Study
Authors: Nanwal Renu , Gupta Seema , Bhambri Eenal , Ahuja Sachin , Kothari Ridhi 
Published: November 2020

Aim: The aim of the present study was to compare the effects of remineralizing agents (nano-hydroxyapatite [n-HAP], NovaMin, calcium sucrose phosphate [CaSP], and Pro-Argin) on surface characteristics of slenderized enamel using Vickers microhardness and scanning electron microscope–energy dispersive X-ray (SEM-EDX) analysis. Materials and Method: Sixty extracted premolar teeth were divided into 6 groups: group 1—natural teeth; group 2—slenderization and polishing; group 3—n-HAP; group 4—NovaMin; group 5—CaSP; and group 6—Pro-Argin. Remineralizing agents were applied for 21 days. Specimens were evaluated using Vickers microhardness and SEM-EDX analysis. A 1-way analysis of variance (ANOVA) and post-hoc Tukey honestly significant difference (HSD) test were used for intragroup comparisons. Results: Among all remineralizing agents, CaSP showed significantly maximum surface microhardness, followed by NovaMin, n-HAP, and Pro-Argin. SEM also showed increased surface roughness for all remineralizing agents. EDX showed maximum increase in mineral content obtained with CaSP. Conclusion: All remineralizing agents significantly remineralized the stripped enamel surface. CaSP demonstrated promising results by effectively and significantly remineralizing the enamel lesions as compared to other test agents.
Siponimod: Disentangling disability and relapses in secondary progressive multiple sclerosis
Authors: Cree Bruce AC , Magnusson Baldur , Rouyrre Nicolas , Fox Robert J , Giovannoni Gavin , Vermersch Patrick , Bar-Or Amit , Gold Ralf , Piani Meier Daniela , Karlsson Göril , Tomic Davorka , Wolf Christian , Dahlke Frank , Kappos Ludwig 
Published: November 2020

Background: In multiple sclerosis, impact of treatment on disability progression can be confounded if treatment also reduces relapses. Objective: To distinguish siponimod’s direct effects on disability progression from those on relapses in the EXPAND phase 3 trial. Methods: Three estimands, one based on principal stratum and two on hypothetical scenarios (no relapses, or equal relapses in both treatment arms), were defined to determine the extent to which siponimod’s effects on 3- and 6-month confirmed disability progression were independent of on-study relapses. Results: Principal stratum analysis estimated that siponimod reduced the risk of 3- and 6-month confirmed disability progression by 14%–20% and 29%–33%, respectively, compared with placebo in non-relapsing patients. In the hypothetical scenarios, risk reductions independent of relapses were 14%–18% and 23% for 3- and 6-month confirmed disability progression, respectively. Conclusion: By controlling the confounding impact of on-study relapses on confirmed disability progression, these statistical approaches provide a methodological framework to assess treatment effects on disability progression in relapsing and non-relapsing patients. The analyses support that siponimod may be useful for treating secondary progressive multiple sclerosis in patients with or without relapses.
Community-Based Participatory Research in Action: The Patient-Centered Medical Home and Neighborhood
Authors: Williams-Livingston Arletha , Henry Akintobi Tabia , Banerjee Ananya 
Published: November 2020

Background: The Morehouse School of Medicine Patient Centered Medical Home and Neighborhood Project was developed to implement a community-based participatory research driven, integrated patient-centered medical home and neighborhood (PCMH) pilot intervention. The purpose of the PCMHN was to develop a care coordination program for underserved, high-risk patients with multiple morbidities served by the Morehouse Healthcare Comprehensive Family Health Clinic. Measures: A community needs assessment, patient surveys and provider interviews were administered. Results: Among a panel of 367 high-risk patients and potential participants, 93 participated in the intervention and 42 patients completed the intervention. The patients self-reported increased utilization of community support, increased satisfaction with health care options, and increased self-care management ability. Conclusion: The results were largely attributable to the efforts of community health workers and targeted community engagement. Lessons learned from implementation and integration of a community-based participatory approach will be used to train clinicians and small practices on how to affect change using a care coordination model for underserved, high-risk patients emphasizing CBPR.
Applied Machine Learning for Spine Surgeons: Predicting Outcome for Patients Undergoing Treatment for Lumbar Disc Herniation Using PRO Data
Authors: Pedersen Casper Friis , Andersen Mikkel Østerheden , Carreon Leah Yacat , Eiskjær Søren 
Published: November 2020

Study Design: Retrospective/prospective study. Objective: Models based on preoperative factors can predict patients’ outcome at 1-year follow-up. This study measures the performance of several machine learning (ML) models and compares the results with conventional methods. Methods: Inclusion criteria were patients who had lumbar disc herniation (LDH) surgery, identified in the Danish national registry for spine surgery. Initial training of models included 16 independent variables, including demographics and presurgical patient-reported measures. Patients were grouped by reaching minimal clinically important difference or not for EuroQol, Oswestry Disability Index, Visual Analog Scale (VAS) Leg, and VAS Back and by their ability to return to work at 1 year follow-up. Data were randomly split into training, validation, and test sets by 50%/35%/15%. Deep learning, decision trees, random forest, boosted trees, and support vector machines model were trained, and for comparison, multivariate adaptive regression splines (MARS) and logistic regression models were used. Model fit was evaluated by inspecting area under the curve curves and performance during validation. Results: Seven models were arrived at. Classification errors were within ±1% to 4% SD across validation folds. ML did not yield superior performance compared with conventional models. MARS and deep learning performed consistently well. Discrepancy was greatest among VAS Leg models. Conclusions: Five predictive ML and 2 conventional models were developed, predicting improvement for LDH patients at the 1-year follow-up. We demonstrate that it is possible to build an ensemble of models with little effort as a starting point for further model optimization and selection.
Cervical Spine Injuries in the Ice Hockey Player: Current Concepts in Epidemiology, Management and Prevention
Authors: Morrissette Cole , Park Paul J. , Lehman Ronald A. , Popkin Charles A. 
Published: November 2020

Study Design: This review article examines the biomechanics that underly hockey-related cervical spine injuries, the preventative measures to curtail them, optimal management strategies for the injured player and return to play criteria. Objective: Hockey is a sport with one of the highest rates of cervical spine injury, but by understanding the underlying pathophysiology and context in which these injuries can occur, it is possible to reduce their incidence and successfully manage the injured player. Methods: Multiple online databases including PubMed, Google Scholar, Columbia Libraries Catalog, Cochrane Library and Ovid MEDLINE were queried for original articles concerning spinal injuries in ice hockey. All relevant papers were screened and subsequently organized for discussion in our subtopics. Results: Cervical fractures in ice hockey most often occur due to an increased axial load, with a check from behind the most common precipitating event. Conclusions: Despite the recognized risk for cervical spine trauma in ice hockey, further research is still needed to optimize protocols for both mitigating injury risk and managing injured players.
Factors Associated With Patient Satisfaction After Opening-Wedge High Tibial Osteotomy
Authors: Goshima Kenichi , Sawaguchi Takeshi , Shigemoto Kenji , Iwai Shintaro , Fujita Kenji , Kataoka Tomoyuki , Taninaka Atsushi 
Published: November 2020

Background: Opening-wedge high tibial osteotomy (OWHTO) is expected to result in higher patient satisfaction compared with knee arthroplasty due to joint preservation. However, patient satisfaction rates as well as factors associated with satisfaction after OWHTO remain unclear. Purpose: To evaluate patient subjective satisfaction after OWHTO and determine factors associated with patient satisfaction after OWHTO. Study Design: Case-control study; Level of evidence, 3. Methods: This study enrolled 123 patients (123 knees) who underwent unilateral OWHTO. Clinical parameters, including range of motion (ROM), visual analog scale (VAS) score for pain, Knee injury and Osteoarthritis Outcome Score (KOOS), weightbearing line ratio (WBLR), and medial proximal tibial angle (MPTA), were assessed before surgery and at the final follow-up at a minimum of 2 years. Patient satisfaction was evaluated using a 5-point scale regarding (1) surgery, (2) pain relief, (3) knee mobility, (4) daily living function, and (5) lower extremity alignment. The mean overall satisfaction scores for the 5 questions were calculated, and the sample was divided into 2 main groups (satisfied or unsatisfied). Preoperative characteristics, physical activity level, patient expectations for surgery, ROM, and KOOS were compared between the groups. Cartilage regeneration was assessed at the time of plate removal, and WBLR and MPTA were also assessed. Factors associated with patient satisfaction were analyzed using multivariable logistic regression analysis. Results: The mean ± SD follow-up was 54.6 ± 20.6 months. The mean WBLR significantly changed from 20.7% ± 11.8% preoperatively to 66.9% ± 10.2% at the final follow-up, and all KOOS subscale scores significantly improved after surgery. Of the 123 patients, 109 (88.6%) were graded as satisfied. Factors associated with patient satisfaction were expectations met (odds ratio, 17.4; P = .026), better postoperative KOOS Pain score (odds ratio, 1.30; P = .001), and better postoperative KOOS Activities of Daily Living score (odds ratio, 1.36; P = .002). Conclusion: OWHTO is an effective treatment in terms of subjective satisfactory outcomes. Patient expectations for surgery have a significant effect on patient satisfaction. Surgeons should consider patient expectations before OWHTO and provide patient education to improve patient satisfaction.
Assessment of platelet-to-lymphocyte ratio in patients with retinal vein occlusion
Authors: Kurtul Bengi Ece , Çakmak Ayșe İdil , Elbeyli Ahmet , Özarslan Özcan Deniz , Özcan Sait Coșkun , Cankurtaran Veysel 
Published: November 2020

Purpose: To investigate platelet-to-lymphocyte ratio (PLR) in retinal vein occlusion (RVO) patients. Methods: In this study, we retrospectively reviewed data of 32 patients with RVO (RVO group) and 32 age- and sex-matched participants without RVO (control group) between January 2017 and March 2019. The PLR was determined by dividing the platelet count by the lymphocyte count. Results: Age and gender were comparable between the groups ( p = 0.204 and p = 0.800, respectively). PLR was significantly elevated in the RVO group compared with the control group (137 (113–164) vs 101 (86–129), p = 0.001)). In the receiver operator characteristics curve analysis, the optimal cut-off value of PLR for predicting RVO was 123, with 69% sensitivity and 72% specificity. Conclusion: We report that PLR are elevated in RVO, suggesting that PLR may be a useful marker for RVO.
Coinfection withPseudomonas aeruginosaandAspergillus fumigatusin cystic fibrosis
Authors: Keown Karen , Reid Alastair , Moore John E. , Taggart Clifford C. , Downey Damian G. 
Published: November 2020

ObjectivesCystic fibrosis (CF) lung disease is characterised by mucus stasis, chronic infection and inflammation, causing progressive structural lung disease and eventual respiratory failure. CF airways are inhabited by an ecologically diverse polymicrobial environment with vast potential for interspecies interactions, which may be a contributing factor to disease progression.Pseudomonas aeruginosaandAspergillus fumigatusare the most common bacterial and fungal species present in CF airways respectively and coinfection results in a worse disease phenotype.MethodsIn this review we examine existing expert knowledge of chronic co-infection withP. aeruginosaandA. fumigatusin CF patients. We summarise the mechanisms of interaction and evaluate the clinical and inflammatory impacts of this co-infection.ResultsP. aeruginosainhibitsA. fumigatusthrough multiple mechanisms: phenazine secretion, iron competition, quorum sensing and through diffusible small molecules.A. fumigatusreciprocates inhibition through gliotoxin release and phenotypic adaptations enabling evasion ofP. aeruginosainhibition. Volatile organic compounds secreted byP. aeruginosastimulateA. fumigatusgrowth, whileA. fumigatusstimulatesP. aeruginosaproduction of cytotoxic elastase.ConclusionA complex bi-directional relationship exists betweenP. aeruginosaandA. fumigatus, exhibiting both mutually antagonistic and cooperative facets. Cross-sectional data indicate a worsened disease state in coinfected patients; however, robust longitudinal studies are required to derive causality and to determine whether interspecies interaction contributes to disease progression.
Design of pulmonary rehabilitation programmes during acute exacerbations of COPD: a systematic review and network meta-analysis
Authors: Machado Ana , Matos Silva Pedro , Afreixo Vera , Caneiras Cátia , Burtin Chris , Marques Alda 
Published: November 2020

This systematic review aimed to systematise the different designs used to deliver pulmonary rehabilitation during acute exacerbations of COPD (AECOPD) and explore which ones are the most effective. PubMed, Scopus, Web of Science, EBSCO and Cochrane were searched. Randomised controlled trials comparing pulmonary rehabilitation or at least one of its components with usual care or comparing different components of pulmonary rehabilitation were included. Network meta-analysis was conducted in MetaXL 5.3 using a generalised pairwise modelling framework. Pooled effects compared each treatment to usual care.42 studies were included. Most studies were conducted in an inpatient setting (57%) and started the intervention 24–48 h after hospital admission (24%). Exercise training (71%), education and psychosocial support (57%) and breathing techniques (55%) were the most used components. Studies combining exercise with breathing techniques presented the larger effects on exercise capacity (weighted mean difference (WMD) −41.06, 95% CI −131.70–49.58) and health-related quality of life (WMD 14.64, 95% CI 8.73–20.54), and breathing techniques presented the larger effects on dyspnoea (WMD 1.90, 95% CI 0.53–3.27) and length of hospitalisation (effect size =0.15, 95% CI −0.28–0.57). A few minor adverse events were found.Pulmonary rehabilitation is a safe intervention during AECOPD. Exercise, breathing techniques, and education and psychosocial support seem to be the core components for implementing pulmonary rehabilitation during AECOPD. Studies may now focus on comparisons of optimal timings to start the intervention, total duration of the intervention, duration and frequency of sessions, and intensity for exercise prescription.
Therapeutic bronchoscopy for central airway diseases
Authors: Rosell Antoni , Stratakos Grigoris 
Published: November 2020

Over the past century rigid bronchoscopy has been established as the main therapeutic means for central airway diseases of both benign and malignant aetiology. Its use requires general anaesthesia and mechanical ventilation usually in the form of manual or high-frequency jet ventilation. Techniques applied to regain patency of the central airways include mechanical debulking, thermal ablation (laser, electrocautery and argon plasma coagulation) and cryo-surgery. Each of these techniques have their advantages and limitations and best results can be attained by combining different modalities according to the type, location and extent of the airway blockage. If needed, deployment of airway endoprostheses (stents), as either fixed-diameter silicone or self-expandable metal stents, may preserve the airways patency often at the cost of several complications. Newer generation of customised stents either three-dimensional printed or drug-eluting stents constitute a promise for improved safety and efficacy results in the near future.Treating central disease of benign or malignant aetiology, foreign body aspiration or massive bleeding in the airways requires a structured approach with combined techniques, a dedicated team of professionals and experience to treat eventual complications. Specific training and fellowships in interventional pulmonology should therefore be offered to those who wish to specialise in this field.
Evidence generation for the clinical impact of myCOPD in patients with mild, moderate and newly diagnosed COPD: a randomised controlled trial
Authors: Crooks Michael G. , Elkes Jack , Storrar William , Roy Kay , North Mal , Blythin Alison , Watson Alastair , Cornelius Victoria , Wilkinson Tom M.A. 
Published: November 2020

Self-management interventions in COPD aim to improve patients' knowledge, skills and confidence to make correct decisions, thus improving health status and outcomes. myCOPD is a web-based self-management app known to improve inhaler use and exercise capacity in individuals with more severe COPD.We explored the impact of myCOPD in patients with mild–moderate or recently diagnosed COPD through a 12-week, open-label, parallel-group, randomised controlled trial of myCOPD compared with usual care. The co-primary outcomes were between-group differences in mean COPD assessment test (CAT) score at 90 days and critical inhaler errors. Key secondary outcomes were app usage and patient activation measurement (PAM) score.Sixty patients were randomised (29 myCOPD, 31 usual care). Groups were balanced for forced expiratory volume in 1 s (FEV1% pred) but there was baseline imbalance between groups for exacerbation frequency and CAT score. There was no significant adjusted mean difference in CAT score at study completion, −1.27 (95% CI −4.47–1.92, p=0.44) lower in myCOPD. However, an increase in app use was associated with greater CAT score improvement. The odds of ≥1 critical inhaler error was lower in the myCOPD arm (adjusted OR 0.30 (95% CI 0.09–1.06, p=0.061)). The adjusted odds ratio for being in a higher PAM level at 90 days was 1.65 (95% CI 0.46–5.85) in favour of myCOPD.The small sample size and phenotypic difference between groups limited our ability to demonstrate statistically significant evidence of benefit beyond inhaler technique. However, our findings provide important insights into associations between increased app use and clinically meaningful benefit warranting further study in real world settings.
Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
Authors: Llabrés Mercè , Riera Gabriel , Rosselló Francesc , Valiente Gabriel 
Published: November 2020

Abstract
Background
The alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming software tools. However, the resulting integer linear program has a huge number of variables and constraints, rendering it of no practical use.

Results
We present a compact integer linear programming reformulation of the protein-protein interaction network alignment problem, which can be solved using state-of-the-art mathematical modeling and integer linear programming software tools, along with empirical results showing that small biological networks, such as virus-host protein-protein interaction networks, can be aligned in a reasonable amount of time on a personal computer and the resulting alignments are structurally coherent and biologically meaningful.

Conclusions
The implementation of the integer linear programming reformulation using current mathematical modeling and integer linear programming software tools provided biologically meaningful alignments of virus-host protein-protein interaction networks.
An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction
Authors: Chockalingam Sriram P. , Pannu Jodh , Hooshmand Sahar , Thankachan Sharma V. , Aluru Srinivas 
Published: November 2020

Abstract
Background
Alignment-free methods for sequence comparisons have become popular in many bioinformatics applications, specifically in the estimation of sequence similarity measures to construct phylogenetic trees. Recently, the average common substring measure, ACS, and its k-mismatch counterpart, ACSk, have been shown to produce results as effective as multiple-sequence alignment based methods for reconstruction of phylogeny trees. Since computing ACSk takes O(n logkn) time and hence impractical for large datasets, multiple heuristics that can approximate ACSk have been introduced.

Results
In this paper, we present a novel linear-time heuristic to approximate ACSk, which is faster than computing the exact ACSk while being closer to the exact ACSk values compared to previously published linear-time greedy heuristics. Using four real datasets, containing both DNA and protein sequences, we evaluate our algorithm in terms of accuracy, runtime and demonstrate its applicability for phylogeny reconstruction. Our algorithm provides better accuracy than previously published heuristic methods, while being comparable in its applications to phylogeny reconstruction.

Conclusions
Our method produces a better approximation for ACSk and is applicable for the alignment-free comparison of biological sequences at highly competitive speed. The algorithm is implemented in Rust programming language and the source code is available at https://github.com/srirampc/adyar-rs.
A generalized Robinson-Foulds distance for labeled trees
Authors: Briand Samuel , Dessimoz Christophe , El-Mabrouk Nadia , Lafond Manuel , Lobinska Gabriela 
Published: November 2020

AbstractBackgroundThe Robinson-Foulds (RF) distance is a well-established measure between phylogenetic trees. Despite a lack of biological justification, it has the advantages of being a proper metric and being computable in linear time. For phylogenetic applications involving genes, however, a crucial aspect of the trees ignored by the RF metric is the type of the branching event (e.g. speciation, duplication, transfer, etc).ResultsWe extend RF to trees with labeled internal nodes by including a nodeflipoperation, alongside edge contractions and extensions. We explore properties of this extended RF distance in the case of a binary labeling. In particular, we show that contrary to the unlabeled case, an optimal edit path may require contracting “good” edges, i.e. edges shared between the two trees.ConclusionsWe provide a 2-approximation algorithm which is shown to perform well empirically. Looking ahead, computing distances between labeled trees opens up a variety of new algorithmic directions.Implementation and simulations available athttps://github.com/DessimozLab/pylabeledrf.