bluuebunny/crossref_metadata_2025_split huggingface dataset:
Articular Cartilage Fragmentation Improves Chondrocyte Migration by Upregulating Membrane Type 1 Matrix Metalloprotease
Authors: Lei Yunliang , Peng Jiabin , Dai Zhu , Liao Ying , Liu Quanhui , Li Jian , Jiang Yonghui 
Published: October 2021

Objective This study was undertaken to elucidate the mechanism of improved chondrocyte migration after juvenile articular cartilage fragmentation. Design In vitro organ culture with rabbit cartilage fragments and cell culture with rabbit chondrocytes were performed. In part A, minced juvenile cartilage fragments (~0.5 × 0.5 × 0.5 mm) from rabbits, planted in gelatin sponge and fibrin glue, were cultured for 2, 4, or 6 weeks in vitro and compared with the cartilage chunks (~4 × 4 × 1 mm) and membrane type 1 matrix metalloprotease (MT1-MMP) inhibitor groups. Chondrocyte outgrowth was evaluated on histology and confocal laser scanning microscopy. MT1-MMP expression was compared between the cartilage fragment group and the cartilage chunks group. In part B, articular chondrocytes were harvested from juvenile rabbits, MT1-MMP was transfected into the cells, and cell migration was evaluated using the Transwell and wound healing tests. Results The histology and confocal microscopy results revealed that cell accumulation occurred at the edge of cartilage fragments, and outgrowth was better in the cartilage fragment group than those in the cartilage chunks group. Similar results were observed for MT1-MMP expression. After MT1-MMP inhibition, cells did not accumulate at the edge of the cartilage fragments, and chondrocyte outgrowth did not occur. Furthermore, overexpression of MT1-MMP enhanced the migration of articular chondrocytes. Conclusions Juvenile articular cartilage fragmentation improved chondrocyte migration by upregulating MT1-MMP.
CoMET: a randomised controlled trial of co-commencement of metformin versus placebo as an adjunctive treatment to attenuate weight gain in patients with schizophrenia newly commenced on clozapine
Authors: Siskind Dan , Russell Anthony W. , Suetani Shuichi , Flaws Dylan , Kisely Steve , Moudgil Vikas , Northwood Korinne , Robinson Gail , Scott James G. , Stedman Terry , Warren Nicola , Winckel Karl , Cosgrove Peter , Baker Andrea 
Published: October 2021

Background: There is limited evidence on interventions to minimise weight gain at clozapine commencement. We compared the effect of adjunctive metformin versus placebo at clozapine initiation. Methods: People with schizophrenia commencing on clozapine were randomised to either metformin or placebo for 24 weeks. The primary outcome was difference in the change of body weight. Secondary outcomes included comparative rates of weight gain of more than 5%, overall weight gain/loss, and differences in metabolic and psychosis outcomes. Results: The study was closed prematurely in March 2020 due to COVID-19 restrictions. Ten participants were randomised to each of the metformin and placebo groups. Eight metformin group and five placebo group participants completed the trial and were included in the analysis. The study was insufficiently powered to detect difference between the metformin and placebo groups for the primary outcome of change in weight (0.09 kg vs 2.88 kg, p = 0.231). In terms of secondary outcomes, people in the metformin group were significantly less likely to gain >5% of their body weight (12.5% vs 80%, p = 0.015) and were more likely to lose weight (37.5% vs 0% p = 0.024) compared to placebo. There was no difference between the groups in terms of adverse drug reactions (ADRs). Conclusion: While limited by the forced premature closure of the trial due to COVID19, the findings from this randomised controlled trial are promising. Clozapine and metformin co-commencement may be a promising treatment to prevent clozapine-associated weight gain, especially given the low rates of ADRs associated with metformin. This supports the consideration of use of metformin to prevent weight gain in people initiated on clozapine; however, further studies are needed to confirm this finding. Trial registration: ACTRN12617001547336
Lyme Disease Training and Knowledge Translation Resources Available to Canadian Healthcare Professionals: A Gray Literature Review
Authors: Coderre-Ball Angela M. , Sahi Sania , Anthonio Vanessa , Roberston Madison , Egan Rylan 
Published: October 2021

Introduction: Lyme Disease (LD) is the most common tick-borne disease in North America. With the number of cases increasing yearly, Canadian healthcare professionals (HCP) rely on up-to-date and evidence-informed guidelines, instruction, and resources to effectively prevent, diagnose, and treat Lyme disease (LD). This review is the first of its kind to examine gray literature and analyze the diversity of recommendations provided to Canadian HCP about the prevention, diagnosis, and treatment of Lyme disease. Methods: A gray literature review consisting of 4 search strategies was conducted to retrieve materials targeted to Canadian HCP. Searches within targeted websites, targeted Google searches, and gray literature databases, and consultation with content experts were done to look for continuing medical education (CME) events, clinical flow charts, webinars, videos, and reference documents that discussed the prevention, diagnosis, and treatment of Lyme disease. Results: A total of 115 resources were included in this study. Recommendations surrounding prevention strategies were less varied between materials, whereas diagnosis and treatment recommendations were more varied. Our findings suggest that Canadian HCP are met with varying and sometimes contradictory recommendations for diagnosing and treating LD. Conclusions: Due to the increasing incidence of LD in Canada, there is a greater need for resource consistency. Providing this consistency may help mitigate LD burden, standardize approaches to prevention, diagnosis and treatment, and improve patient outcomes.
“The Message Is You Don’t Exist”: Exploring Lived Experiences of Rural Lesbian, Gay, Bisexual, Transgender, Queer/Questioning (LGBTQ) People Utilizing Health care Services
Authors: Henriquez Nadine R. , Ahmad Nora 
Published: October 2021

Background Lesbian, gay, bisexual, transgender, queer/questioning (LGBTQ) people experience significant health inequities with well-documented negative health impacts due to their status as a sexual and gender minority population. Insensitive or discriminatory attitudes toward LGBTQ people within the health care system have negatively impacted access to health services and the overall physical and mental health and well-being of this at risk population. Few studies of LGBTQ populations in rural areas have been conducted, with even fewer in the Canadian context. Rural areas often create greater visibility for LGBTQ persons, contain fewer supports and alternatives in the face of discrimination, and are often are less accepting of LGBTQ populations due to increased stigma and social isolation. Objective The purpose of this study is to examine the lived experiences of LGBTQ people utilizing health care services in rural Manitoba. Method 12 individuals who self-identified as LGBTQ who had accessed health care services in Manitoba were recruited. Using qualitative methodology, interviews were recorded and analyzed for themes. Results Analysis revealed themes including stigma and discrimination, judgments and assumptions, gender identities, lack of knowledge, limited access/systemic barriers, rural considerations, and recommendations for changes to address the gaps in health care services and barriers to access. Conclusions This study of the LGBTQ community provides an expression of their opinions and experiences, but also provides a voice to this underserved population. The findings of this study provide a better understanding of the unique health needs and experiences of LGBTQ people in rural Manitoba, creating opportunities for meaningful change in health care delivery
A Systematic Scoping Review on Pedagogical Strategies of Interprofessional Communication for Physicians in Emergency Medicine
Authors: Ong Zhi H. , Tan Lorraine H. E. , Ghazali Haziratul Z. B. , Ong Yun T. , Koh Jeffrey W. H. , Ang Rachel Z. E. , Bok Chermaine , Chiam Min , Lee Alexia S. I. , Chin Annelissa M. C. , Zhou Jamie X. , Chan Gene W. H. , Nadarajan Gayathri D. , Krishna Lalit K. R. 
Published: October 2021

Background Interprofessional communication (IPC) is integral to interprofessional teams working in the emergency medicine (EM) setting. Yet, the coronavirus disease 2019 pandemic has laid bare gaps in IPC knowledge, skills and attitudes. These experiences underscore the need to review how IPC is taught in EM. Purpose A systematic scoping review is proposed to scrutinize accounts of IPC programs in EM. Methods Krishna's Systematic Evidence-Based Approach (SEBA) is adopted to guide this systematic scoping review. Independent searches of ninedatabases (PubMed, Embase, CINAHL, Scopus, PsycINFO, ERIC, JSTOR, Google Scholar and OpenGrey) and “negotiated consensual validation” were used to identify articles published between January 1, 2000 and December 31, 2020. Three research teams reviewed the data using concurrent content and thematic analysis and independently summarized the included articles. The findings were scrutinized using SEBA's jigsaw perspective and funneling approach to provide a more holistic picture of the data. Results In total 18,809 titles and abstracts were identified after removal of duplicates, 76 full-text articles reviewed, and 19 full-text articles were analyzed. In total, four themes and categories were identified, namely: (a) indications and outcomes, (2) curriculum and assessment methods, (3) barriers, and (4) enablers. Conclusion IPC training in EM should be longitudinal, competency- and stage-based, underlining the need for effective oversight by the host organization. It also suggests a role for portfolios and the importance of continuing support for physicians in EM as they hone their IPC skills. Highlights • IPC training in EM is competency-based and organized around stages. • IPC competencies build on prevailing knowledge and skills. • Longitudinal support and holistic oversight necessitates a central role for the host organization. • Longitudinal, robust, and adaptable assessment tools in the EM setting are necessary and may be supplemented by portfolio use.
Factors influencing knee valgus alignment in Crowe type IV hip dysplasia after total hip arthroplasty
Authors: Sun Jing-yang , Ma Hai-yang , Shen Jun-min , Du Yin-qiao , Dong Yu , Zhang Yan-chao , Zhou Yong-gang , Wang Yan 
Published: October 2021

Abstract
Background
Valgus deformity of the knee remains a complaint after total hip arthroplasty (THA) among some patients with Crowe type IV hip dysplasia. We aimed to identify the knee alignment in these patients before and after surgery, and to explore the factors contributing to postoperative knee valgus alignment.

Materials and methods
We retrospectively reviewed a series of Crowe type IV patients who received THA between February 2010 and May 2019 in our hospital. The patients’ medical data were collected from the hospital information system. On both preoperative and postoperative full limb length standing radiographs, the following parameters were measured: hip–knee–ankle angle (HKA), mechanical lateral distal femoral angle (mLDFA), medial proximal tibial angle, anatomical tibiofemoral angle, anatomical lateral distal femoral angle, femoral neck-shaft angle, pelvic obliquity, limb length, height and lateral distance of hip center, and femoral offset. Univariate and multivariate binary logistic regression were used to identify the factors influencing postoperative knee valgus alignment.

Results
A total of 64 Crowe type IV patients (87 hips) were included in the study. Overall, HKA improved from 176.54 ± 3.52° preoperatively to 179.45 ± 4.31° at the last follow-up. Those hips were subdivided into non-valgus group (≥ 177.0°, n = 65) and valgus group (< 177.0°, n = 22) according to postoperative HKA. Only postoperative mLDFA was a significant factor in the multivariate regression model.

Conclusions
The postoperative mLDFA is a major factor related to knee valgus alignment after THA, which combines the preoperative anatomy and surgical reconstruction. Other factors previously published were found to have no significance.

Level of evidence
III.
Human impact on fluvial systems in Europe with special regard to today’s river restorations
Authors: Maaß Anna-Lisa , Schüttrumpf Holger , Lehmkuhl Frank 
Published: October 2021

AbstractClimate, geology, geomorphology, soil, vegetation, geomorphology, hydrology, and human impact affect river–floodplain systems, especially their sediment load and channel morphology. Since the beginning of the Holocene, human activity is present at different scales from the catchment to the channel and has had an increasing influence on fluvial systems. Today, many river–floodplain systems are transformed in course of river restorations to “natural” hydrodynamic and morphodynamic conditions without human impacts. Information is missing for the historical or rather “natural” as well as for the present-day situation. Changes of the “natural” sediment fluxes in the last centuries result in changes of the fluvial morphology. The success of river restorations depends on substantial knowledge about historical as well as present-day fluvial morphodynamics. Therefore, it is necessary to analyze the consequences of historical impacts on fluvial morphodynamics and additionally the future implications of present-day human impacts in course of river restorations. The objective of this review is to summarize catchment impacts and river channel impacts since the beginning of the Holocene in Europe on the fluvial morphodynamics, to critically investigate their consequences on the environment, and to evaluate the possibility to return to a “natural” morphological river state.
Reference-agnostic representation and visualization of pan-genomes
Authors: Liang Qihua , Lonardi Stefano 
Published: October 2021

Abstract
Background
The pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species.

Results
Here we introduce PGV, a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering. Our experimental results demonstrate that PGV enables an intuitive, effective and interactive visualization of a pan-genome by providing a genome browser that can elucidate complex structural genomic variations.

Conclusions
The PGV software can be installed via conda or downloaded from https://github.com/ucrbioinfo/PGV. The companion PGV browser at http://pgv.cs.ucr.edu can be tested using example bed tracks available from the GitHub page.
Identifying piRNA targets on mRNAs in C. elegans using a deep multi-head attention network
Authors: Yang Tzu-Hsien , Shiue Sheng-Cian , Chen Kuan-Yu , Tseng Yan-Yuan , Wu Wei-Sheng 
Published: October 2021

Abstract
Background
Piwi-interacting RNAs (piRNAs) are the small non-coding RNAs (ncRNAs) that silence genomic transposable elements. And researchers found out that piRNA also regulates various endogenous transcripts. However, there is no systematic understanding of the piRNA binding patterns and how piRNA targets genes. While various prediction methods have been developed for other similar ncRNAs (e.g., miRNAs), piRNA holds distinctive characteristics and requires its own computational model for binding target prediction.

Results
Recently, transcriptome-wide piRNA binding events in C. elegans were probed by PRG-1 CLASH experiments. Based on the probed piRNA-messenger RNAs (mRNAs) binding pairs, in this research, we devised the first deep learning architecture based on multi-head attention to computationally identify piRNA targeting mRNA sites. In the devised deep network, the given piRNA and mRNA segment sequences are first one-hot encoded and undergo a combined operation of convolution and squeezing-extraction to unravel motif patterns. And we incorporate a novel multi-head attention sub-network to extract the hidden piRNA binding rules that can simulate the biological piRNA target recognition process. Finally, the true piRNA–mRNA binding pairs are identified by a deep fully connected sub-network. Our model obtains a supreme discriminatory power of AUC $$=$$
=
93.3% on an independent test set and successfully extracts the verified binding pattern of a synthetic piRNA. These results demonstrated that the devised model achieves high prediction performance and suggests testable potential biological piRNA binding rules.

Conclusions
In this research, we developed the first deep learning method to identify piRNA targeting sites on C. elegans mRNAs. And the developed deep learning method is demonstrated to be of high accuracy and can provide biological insights into piRNA–mRNA binding patterns. The piRNA binding target identification network can be downloaded from http://cosbi2.ee.ncku.edu.tw/data_download/piRNA_mRNA_binding.
Whole genome sequence of a non-toxigenic Corynebacterium diphtheriae strain from a hospital in southeastern China
Authors: Li Guogang , Wang Sipei , Zhao Sheng , Zhou Yangxiao , Pan Xinling 
Published: October 2021

Abstract
Background
Sporadic cases of infection with non-toxigenic Corynebacterium diphtheriae (C. diphtheriae) isolates have been reported in regions covered by the Diphtheria-Tetanus-Pertussis vaccine, but no information describing the whole genome of non-toxigenic strains collected in China is available. Therefore, in this work, the complete genome of a non-toxigenic strain of C. diphtheriae from a hospital located in southeastern China was performed.

Results
This non-toxigenic isolate belonged to the belfanti biotype and possessed a unique ST (assigned as ST799 in pubMLST). ErmX was present in the genome sequence and this isolate owned the resistance to erythromycin and clindamycin. Genes coding for virulence factors involved in adherence, iron-uptake and regulation of diphtheria toxin were also found. Two genes were involved in the interaction between pathogen and host. The phylogenetic analysis revealed that this newly isolated strain was similar to the strain NCTC10838, CMCNS703 and CHUV2995.

Conclusion
Non-toxigenic C. diphtheriae strain contained virulence factors, thus it is able to cause an infectious disease, aspect that could be clarified by performing the whole genome sequencing analysis.
Technical advance in silico and in vitro development of a new bipolar radiofrequency ablation device for renal denervation
Authors: Pérez Noel , Muffly Karl , Saddow Stephen E. 
Published: October 2021

Abstract
Background
Renal denervation with radiofrequency ablation has become an accepted treatment for drug-resistant hypertension. However, there is a continuing need to develop new catheters for high-accuracy, targeted ablation. We therefore developed a radiofrequency bipolar electrode for controlled, targeted ablation through Joule heating induction between 60 and 100 °C. The bipolar design can easily be assembled into a basket catheter for deployment inside the renal artery.

Methods
Finite element modeling was used to determine the optimum catheter design to deliver a minimum ablation zone of 4 mm (W) × 10 mm (L) × 4 mm (H) within 60 s with a 500 kHz, 60 Vp-p signal, and 3 W maximum. The in silico model was validated with in vitro experiments using a thermochromic phantom tissue prepared with polyacrylamide gel and a thermochromic ink additive that permanently changes from pink to magenta when heated over 60 °C.

Results
The in vitro ablation zone closely matched the size and shape of the simulated area. The new electrode design directs the current density towards the artery walls and tissue, reducing unwanted blood temperature increases by focusing energy on the ablation zone. In contrast, the basket catheter design does not block renal flow during renal denervation.

Conclusions
This computational model of radiofrequency ablation can be used to estimate renal artery ablation zones for highly targeted renal denervation in patients with resistant hypertension. Furthermore, this innovative catheter has short ablation times and is one of the lowest power requirements of existing designs to perform the ablation.
Prediction of all-cause mortality in coronary artery disease patients with atrial fibrillation based on machine learning models
Authors: Liu Xinyun , Jiang Jicheng , Wei Lili , Xing Wenlu , Shang Hailong , Liu Guangan , Liu Feng 
Published: October 2021

Abstract
Background
Machine learning (ML) can include more diverse and more complex variables to construct models. This study aimed to develop models based on ML methods to predict the all-cause mortality in coronary artery disease (CAD) patients with atrial fibrillation (AF).

Methods
A total of 2037 CAD patients with AF were included in this study. Three ML methods were used, including the regularization logistic regression, random forest, and support vector machines. The fivefold cross-validation was used to evaluate model performance. The performance was quantified by calculating the area under the curve (AUC) with 95% confidence intervals (CI), sensitivity, specificity, and accuracy.

Results
After univariate analysis, 24 variables with statistical differences were included into the models. The AUC of regularization logistic regression model, random forest model, and support vector machines model was 0.732 (95% CI 0.649–0.816), 0.728 (95% CI 0.642–0.813), and 0.712 (95% CI 0.630–0.794), respectively. The regularization logistic regression model presented the highest AUC value (0.732 vs 0.728 vs 0.712), specificity (0.699 vs 0.663 vs 0.668), and accuracy (0.936 vs 0.935 vs 0.935) among the three models. However, no statistical differences were observed in the receiver operating characteristic (ROC) curve of the three models (all P > 0.05).

Conclusion
Combining the performance of all aspects of the models, the regularization logistic regression model was recommended to be used in clinical practice.