bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does Having a Rotator Cuff Repair Before Total Shoulder Arthroplasty Influence Outcomes?
Authors: Erickson Brandon J. , Ling Daphne , Wong Alexandra , Dines Joshua S. , Dines David M. , Gulotta Lawrence V. 
Published: August 2020

Background: The number of rotator cuff repairs (RCRs) is increasing each year. Total shoulder arthroplasty (TSA) is a successful treatment option for patients with glenohumeral osteoarthritis with a functioning rotator cuff. Purpose/Hypothesis: The purposes of this study were to report the outcomes of TSA in patients with ipsilateral RCR and determine whether patients with a history of ipsilateral RCR who subsequently underwent TSA had differences in outcomes compared with matched controls who underwent TSA with no history of RCR. We hypothesized that patients with prior RCR will have significant improvements in clinical outcome scores, with no difference in outcomes after TSA compared with those with no prior RCR. Study Design: Cohort study; Level of evidence, 3. Methods: Patients eligible for inclusion were those with a history of prior RCR who underwent TSA at a single institution with a minimum 2-year follow-up between 2000 and 2015. Outcomes for this group, including American Shoulder and Elbow Surgeons (ASES) scores, were reported and then compared with a matched control group of patients who underwent TSA with no history of prior RCR. Controls were matched based on age, sex, and preoperative ASES score. Results: Overall, 14 patients (64% males; mean ± SD age, 65.1 ± 11.1 years) underwent prior ipsilateral RCR before TSA. ASES scores significantly improved from 42.9 to 78.5 at 2 years and to 86.6 at 5 years. When compared with 42 matched control patients (matched 1:3) who underwent TSA with no history of RCR, there was no significant difference in ASES scores at 2 years (78.5 vs 85.3; P = .19) and 5 years (86.6 vs 90.9; P = .72) between the prior RCR and no RCR groups. Conclusion: TSA in patients with a history of prior ipsilateral RCR led to significant improvements in clinical outcomes. No difference in clinical outcomes at 2 or 5 years after TSA was found between patients with and without a history of prior ipsilateral RCR.
Effect of Psychotropic Medications on Hammertoe Reconstruction Outcomes
Authors: Maidman Samuel D. , Nash Amalie E. , Fantry Amanda , Tenenbaum Shay , Daoud Yahya , Brodsky James , Bariteau Jason T. 
Published: August 2020

Background: Hammertoe deformities can seriously affect activity level and footwear. The use of prescription, mood-altering medications is very common, with some estimates as high as 25% of the population. Mood disorders, especially depression, negatively affect the results of medical and operative treatments. This study assessed the relationship of mood-altering medication use with the outcomes and complications of operative reconstruction of hammertoes. Methods: Data were prospectively collected from 116 patients who underwent hammertoe reconstruction, including demographic information, medical history, the use of mood-altering psychotropic medications (antidepressants, anxiolytics, hypnotics, and mood stabilizers), and postoperative complications. Preoperative patient-reported outcomes were measured using the visual analog scale (VAS) for pain and Short Form Health Survey (SF-36), which were repeated at 1-year follow-up. Results: A total of 36.2% of patients were taking psychotropic medications. Medication and nonmedication groups had similar pain VAS and SF-36 Physical Component Summary (PCS) scores before and after surgery. Compared with nonmedication patients, patients on psychotropic medications had significantly lower SF-36 Mental Component Summary (MCS) scores preoperatively ( P = .001) and postoperatively ( P = .006), but no significant difference in the change in MCS (ΔMCS) from preoperative to postoperative. Psychotropic medication use was associated with superficial wound infections ( P = .048), but not other complications. Conclusions: Patients taking psychotropic medications were equally likely to benefit from forefoot reconstruction as nonmedication patients. Preoperative and postoperative PCS and VAS were not significantly different between medication and nonmedication groups. Although the medication group had lower absolute MCS, they reported the same magnitude of improvement in MCS (ΔMCS) as the nonmedication group. Level of Evidence: Level II, prospective cohort study.
Autofluorescence indexes as biomarkers for antiangiogenic loading dose outcome in diabetic macular edema
Authors: Hernández Da Mota Sergio E. , Béjar Cornejo Francisco , Esquivel Velázquez Marcela , Lima Gómez Virgilio , González Saldívar Gerardo , Rodríguez Ayala Ernesto , Vélez-Montoya Raul 
Published: August 2020

Purpose: To evaluate the combination of fundus autofluorescence results with several clinical and structural variables into mathematical indexes to enhance their ability to predict visual and anatomical changes after the antivascular endothelial growth factor loading dose. Methods: Patients with diabetic macular edema were enrolled. Each patient had a comprehensive ophthalmological examination, contrast sensitivity, optical coherence tomography, and fundus autofluorescence assessment. All patients received three monthly doses of ziv-aflibercept and were followed each month for response assessment. Autofluorescence was classified according to its level into five grades. The grades were combined with other variables (best-corrected visual acuity, contrast sensitivity, central macular thickness, macular cube volume, and macular cube average thickness) into normalized indexes. Statistical assessment was done using a Spearman’s rank correlation coefficient, linear regression, and interobserver-agreement analysis. Results: There was a strong correlation between the fundus autofluorescence/baseline best-corrected visual acuity index and the fundus autofluorescence/contrast-sensitivity index at baseline with the best-corrected visual acuity after the third dose of ziv-aflibercept ( rs = −0.78, p = .000 and rs = −0.68, p = .0009 respectively). The fundus autofluorescence/baseline best-corrected visual acuity index and the fundus autofluorescence/contrast-sensitivity index, both at baseline had a mild correlation with the macular volume at 1 month of follow-up ( rs = 0.56, p = .008 and ( rs = 0.64, p = .002, respectively). Conclusion: This study suggests that it is possible to combine fundus autofluorescence results with functional and structural variables into normalized indexes that could potentially predict outcomes after antivascular endothelial growth factor loading dose in patients with diabetic macular edema.
Five decades of low intensity and low survival: adapting intensified regimens to cure pediatric Burkitt lymphoma in Africa
Authors: Ozuah Nmazuo W. , Lubega Joseph , Allen Carl E. , El-Mallawany Nader Kim 
Published: August 2020

AbstractLong-term cure of childhood Burkitt lymphoma (BL) in sub-Saharan Africa after treatment with single-agent cyclophosphamide has been documented for more than half of a century. Contemporary cure rates for the highest-risk patients with BL in high-income countries exceed 90% using intensive multiagent chemotherapy. By contrast, the majority of African children with BL still die. Data spanning 5 decades in Africa have repeatedly shown that the children most likely to achieve cure with limited cyclophosphamide regimens are those with lower-stage disease isolated to the jaw. Attempts to intensify the cyclophosphamide monotherapy backbone with the addition of vincristine, low-dose methotrexate, prednisone, doxorubicin, and/or low-dose cytarabine have not yielded significant improvement. High-dose methotrexate is a critical component in the treatment of childhood BL worldwide. Although initial efforts in Africa to incorporate high-dose methotrexate resulted in high treatment-related mortality, more recent collaborative experiences from North and West Africa, as well as Central America, demonstrate that it can be administered safely and effectively, despite limitations in supportive care resources. Recognizing the unacceptable disparity in curative outcomes for BL between the United States/Europe and equatorial Africa, there is a critical need to safely adapt contemporary treatment regimens to optimize curative outcomes amid the resource limitations in regions where BL is endemic. Here, we critically review reports of BL treatment outcomes from low- and middle-income countries, in addition to data from high-income countries that predated modern intensified regimens, to identify potential strategies to improve the therapeutic approach for children suffering from BL in sub-Saharan Africa.
Determination of the phenotypic age in residents of Mexico City: effect of accelerated ageing on lung function and structure
Authors: Buendía-Roldan Ivette , Fernández-Plata Rosario , Valdes-Bartolo Abigail , Mejia Mayra , Jaramillo Luis E. , Martínez-Briseño David , Santiago-Ruiz Armando , Tapia-Aguilar Hugo , Gómez-Zamora Brenda , Pardo Annie , Selman Moises 
Published: August 2020

IntroductionPhenotypic age better represents age-related biological dysregulation than chronological age. Recently, a multisystem-based ageing measure, which integrates chronological age and nine biomarkers, was proposed.MethodsPhenotypic age was determined in 774 residents of Mexico City over 60 years old and without respiratory problems. We arbitrarily classified as “accelerated” ageing, those showing >4 years compared with their chronological age, and “slowed” ageing, those with <4 years compared with chronological age. Demographic risk factors were analysed with structured questionnaires. Lung structure was evaluated by high-resolution computed tomography and functional competence was analysed by forced vital capacity (FVC), forced expiratory volume in 1 s (FEV1), diffusion capacity of carbon monoxide (DLCO), and the 6-minute walk test (6MWT).ResultsOverall, 13% of this cohort showed accelerated ageing, which was corroborated with four independent biomarkers of ageing, 42% had normal ageing and 46% had slowed ageing. Risk factors associated with accelerated ageing were male sex (OR 4.4, 95% CI 2.4–7.9; p<0.01), diabetes mellitus (OR 9.7, 95% CI 5.5–17.2; p<0.01), and long-term sleep duration (OR 2.9 95% CI 1.34–6.35, p<0.01). Among smokers, there was a slight but significant association with the number of pack-years. Subjects with accelerated ageing showed decreased FVC (p<0.0001), FEV1(p<0.0001),DLCO(p<0.02) and walking distance in the 6MWT (p=0.0001). Slowed-ageing subjects presented less frequently with emphysematous lesions compared with those with accelerated ageing.ConclusionsA small but significant proportion of residents of Mexico City age rapidly, which is associated with male sex, diabetes, and long-term sleep duration. They exhibit lower levels of lung function and develop emphysema more frequently.
Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach
Authors: Liguori Ludovica , Monticelli Maria , Allocca Mariateresa , Cubellis Maria Vittoria , Hay Mele Bruno 
Published: August 2020

Abstract
Background
Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science curricula, practical hands-on experiences in tight combination with wet-lab experiments are needed to motivate students.

Results
We present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea of metagenomics, a recent approach that extends biotechnology to non-culturable microbes. We presuppose that a probe for the screening of metagenomic cosmid library is needed. The students start from the chemical structure of the substrate that should be acted on by the novel enzyme and end with the sequence of the probe. To attain their goal, they discover databases such as BRENDA and programs such as BLAST and Clustal Omega.
Students’ answers to a satisfaction questionnaire show that a multistep tutorial integrated into a research wet-lab project is preferable to conventional lectures illustrating bioinformatics tools.

Conclusion
Experimental biologists can better operate basic bioinformatics if a problem-solving approach is chosen.
Clustering analysis of tumor metabolic networks
Authors: Manipur Ichcha , Granata Ilaria , Maddalena Lucia , Guarracino Mario R. 
Published: August 2020

Abstract
Background
Biological networks are representative of the diverse molecular interactions that occur within cells. Some of the commonly studied biological networks are modeled through protein-protein interactions, gene regulatory, and metabolic pathways. Among these, metabolic networks are probably the most studied, as they directly influence all physiological processes. Exploration of biochemical pathways using multigraph representation is important in understanding complex regulatory mechanisms. Feature extraction and clustering of these networks enable grouping of samples obtained from different biological specimens. Clustering techniques separate networks depending on their mutual similarity.

Results
We present a clustering analysis on tissue-specific metabolic networks for single samples from three primary tumor sites: breast, lung, and kidney cancer. The metabolic networks were obtained by integrating genome scale metabolic models with gene expression data. We performed network simplification to reduce the computational time needed for the computation of network distances. We empirically proved that networks clustering can characterize groups of patients in multiple conditions.

Conclusions
We provide a computational methodology to explore and characterize the metabolic landscape of tumors, thus providing a general methodology to integrate analytic metabolic models with gene expression data. This method represents a first attempt in clustering large scale metabolic networks. Moreover, this approach gives the possibility to get valuable information on what are the effects of different conditions on the overall metabolism.
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community
Authors: Castrignanò Tiziana , Gioiosa Silvia , Flati Tiziano , Cestari Mirko , Picardi Ernesto , Chiara Matteo , Fratelli Maddalena , Amente Stefano , Cirilli Marco , Tangaro Marco Antonio , Chillemi Giovanni , Pesole Graziano , Zambelli Federico 
Published: August 2020

Abstract
Background
The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Modern biological experiments are increasingly becoming both data and computationally intensive and the wealth of publicly available biological data is introducing bioinformatics into the “Big Data” era. For these reasons, the effective application of High Performance Computing (HPC) architectures is becoming progressively more recognized also by bioinformaticians.
Here we describe HPC resources provisioning pilot programs dedicated to bioinformaticians, run by the Italian Node of ELIXIR (ELIXIR-IT) in collaboration with CINECA, the main Italian supercomputing center.

Results
Starting from April 2016, CINECA and ELIXIR-IT launched the pilot Call “ELIXIR-IT HPC@CINECA”, offering streamlined access to HPC resources for bioinformatics. Resources are made available either through web front-ends to dedicated workflows developed at CINECA or by providing direct access to the High Performance Computing systems through a standard command-line interface tailored for bioinformatics data analysis. This allows to offer to the biomedical research community a production scale environment, continuously updated with the latest available versions of publicly available reference datasets and bioinformatic tools. Currently, 63 research projects have gained access to the HPC@CINECA program, for a total handout of ~ 8 Millions of CPU/hours and, for data storage, ~ 100 TB of permanent and ~ 300 TB of temporary space.

Conclusions
Three years after the beginning of the ELIXIR-IT HPC@CINECA program, we can appreciate its impact over the Italian bioinformatics community and draw some considerations. Several Italian researchers who applied to the program have gained access to one of the top-ranking public scientific supercomputing facilities in Europe. Those investigators had the opportunity to sensibly reduce computational turnaround times in their research projects and to process massive amounts of data, pursuing research approaches that would have been otherwise difficult or impossible to undertake. Moreover, by taking advantage of the wealth of documentation and training material provided by CINECA, participants had the opportunity to improve their skills in the usage of HPC systems and be better positioned to apply to similar EU programs of greater scale, such as PRACE. To illustrate the effective usage and impact of the resources awarded by the program - in different research applications - we report five successful use cases, which have already published their findings in peer-reviewed journals.
Postoperative outcomes of kidney transplant recipients undergoing non-transplant-related elective surgery: a systematic review and meta-analysis
Authors: Palamuthusingam Dharmenaan , Kunarajah Kuhan , Pascoe Elaine M. , Johnson David W. , Hawley Camel M. , Fahim Magid 
Published: August 2020

Abstract
Background
Reliable estimates of the absolute and relative risks of postoperative complications in kidney transplant recipients undergoing elective surgery are needed to inform clinical practice. This systematic review and meta-analysis aimed to estimate the odds of both fatal and non-fatal postoperative outcomes in kidney transplant recipients following elective surgery compared to non-transplanted patients.

Methods
Systematic searches were performed through Embase and MEDLINE databases to identify relevant studies from inception to January 2020. Risk of bias was assessed by the Newcastle Ottawa Scale and quality of evidence was summarised in accordance with GRADE methodology (grading of recommendations, assessment, development and evaluation). Random effects meta-analysis was performed to derive summary risk estimates of outcomes. Meta-regression and sensitivity analyses were performed to explore heterogeneity.

Results
Fourteen studies involving 14,427 kidney transplant patients were eligible for inclusion. Kidney transplant recipients had increased odds of postoperative mortality; cardiac surgery (OR 2.2, 95%CI 1.9–2.5), general surgery (OR 2.2, 95% CI 1.3–4.0) compared to non-transplanted patients. The magnitude of the mortality odds was increased in the presence of diabetes mellitus. Acute kidney injury was the most frequently reported non-fatal complication whereby kidney transplant recipients had increased odds compared to their non-transplanted counterparts. The odds for acute kidney injury was highest following orthopaedic surgery (OR 15.3, 95% CI 3.9–59.4). However, there was no difference in the odds of stroke and pneumonia.

Conclusion
Kidney transplant recipients are at increased odds for postoperative mortality and acute kidney injury following elective surgery. This review also highlights the urgent need for further studies to better inform perioperative risk assessment to assist in planning perioperative care.
Working conditions of healthcare workers and clients’ satisfaction with care: study protocol and baseline results of a cluster-randomised workplace intervention
Authors: Montano Diego , Kuchenbaur Marco , Geissler Heinrich , Peter Richard 
Published: August 2020

Abstract
Background
In the present investigation the study protocol and the results at baseline of a workplace intervention are reported. It is hypothesised that the reduction of the physical and psychosocial workload of healthcare workers increases 1 their self-assessed physical and mental work ability, and 2. clients’ satisfaction with care.

Methods
Two-arm, cluster-randomised trial. Outcome data on workers and clients are collected in questionnaires at baseline, and two follow-ups between 2019 and 2021. Participants of the interventions are healthcare workers of 11 healthcare providers in Germany. At baseline, the intervention arm comprised 22 clusters (n = 174 workers); the control arm, 47 clusters (n = 276). The intervention consists of interviews and workshops, in which employees propose measures aiming to reduce the physical and psychosocial load, and strengthen resources at work. The primary outcome is the workers’ physical and mental work ability. The secondary outcome is the clients’ satisfaction with care.

Results
There was no evidence of substantial differences between trial arms at baseline concerning the outcomes. The design effect estimates for physical and mental work ability were 1.29 and 1.05, respectively. At the end of the trial, effect sizes of at least 0.30 and 0.27 at the 80% power and 5% significance levels can be attained.

Conclusions
The results suggest that the implementation of the study design has been satisfactory. The intervention is expected to provide evidence of relatively small to medium-size effects of the intervention activities on the work ability of healthcare workers and the clients’ satisfaction with care.

Trial registration
Registration trial DRKS00021138 on the German Registry of Clinical Studies (DRKS), retrospectively registered on 25 March, 2020.
Historical trends in breast Cancer among women in China from age-period-cohort modeling of the 1990–2015 breast Cancer mortality data
Authors: Ding Yani , Chen Xinguang , Zhang Qingjun , Liu Qing 
Published: August 2020

Abstract
Background
Evidence on historical trends extracted embedded in recent data can advance our understanding of the epidemiology of breast cancer for Chinese women. China is a country with significant political, socioeconomic, and cultural events since the 1900s; however, no such studies are reported in the literature.

Methods
Age-specific mortality rates of breast cancer during 1990–2015 in China were analyzed using APC modeling (age-period-cohort modeling) method. Net effect from birth cohort was derived to measure cancer mortality risk during 1906–1990 when no mortality data were collected, and net effect from time period was derived to measure cancer mortality risk during 1990–2015 when data were collected. Model parameters were estimated using intrinsic estimator, a novel method to handle collinearity. The estimated effects were numerical differentiated to enhance presentations of time/age trend.

Results
Breast cancer mortality rate per 100,000 women increased from 6.83 in 1990 to 12.07 in 2015. After controlling for age and period, the risk of breast cancer mortality declined from 0.626 in 1906–10 to − 1.752 in 1991–95 (RR = 0.09). The decline consisted of 3 phases, a gradual phase during 1906–1940, a moderate phase with some fluctuations during 1941–1970, and a rapid phase with large fluctuations during 1971–1995. After controlling for age and cohort, the risk of breast cancer mortality increased from − 0.141 in 1990 to 0.258 in 2015 (RR = 1.49) with an acceleration after 2005. The time trends revealed by both the cohort effect and the period effect were in consistency with the significant political and socioeconomic events in China since the 1900s.

Conclusions
With recent mortality data in 1990–2015, we detected the risk of breast cancer mortality for Chinese women over a long period from 1906 to 2015. The risk declined more than 90% from the highest level in 1906–10 to the lowest in 1990–95, followed by an increase of 49% from 1990 to 2015. Findings of this study connected historical evidence with recent data, supporting further research to exam the relationship between development and risk of breast cancer for medical and health decision-making at the population level and prevention and treatment at the individual level.