bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Controlled Trial of the Effects of Neuromuscular Training on Physical Performance in Male and Female High School Athletes
Authors: Ling Daphne I. , Janosky Joseph , Schneider Brandon , Russomano James , Boyle Caroline , Kinderknecht James , Marx Robert G. 
Published: May 2022

Background: Neuromuscular training (NMT) has demonstrated efficacy as an intervention to decrease the risk of anterior cruciate ligament injuries and improve sports performance. The effect of this training on the mechanisms that contribute to improved physical performance has not been well defined. Hypothesis: Athletes in the NMT group will have better mechanisms of fundamental movements and agility tests that may contribute to improved sports performance. Study Design: Prospective cohort study Level of Evidence: Level 2 Methods: Eight high school teams (111 athletes, 53% male, mean age 16 years) participated, with half performing NMT. Physical performance was measured using the dorsaVi ViPerform system, a US Food and Drug Administration-cleared wireless sensor system. Agility was assessed using a timed 3-cone test. Independent sample t tests were used to compare differences between the intervention and control groups. Results: Matched pre- and postseason data were collected from 74 athletes after excluding athletes with injury and those lost to follow-up. Significant improvements were observed in the NMT group for loading/landing speed ratios during a single-leg hop test (right lower extremity = −0.19 [–0.37, 0.03], P = 0.03 and left lower extremity = −0.27 [–0.50, −0.03], P = 0.03). The control group had lower ground reaction forces compared with the NMT group ( P < 0.02), while significant improvements were found in the NMT group for initial peak acceleration ( P < 0.02) and cadence ( P = 0.01) during a straight-line acceleration/deceleration test. For the 3-cone agility test, the postseason time decreased compared with preseason in the NMT group, whereas the time for the control group increased (–0.37 s vs 0.14 s, P < 0.00). Conclusion: The results demonstrate that NMT administered by sports medicine clinicians can significantly improve some physical performance of fundamental movements in high school athletes. Clinical Relevance: Coaches should be trained to effectively deliver NMT in order to improve sports performance.
The Utility of Postoperative Bracing on Radiographic and Clinical Outcomes Following Cervical Spine Surgery: A Systematic Review
Authors: Hasan Sazid , Babrowicz Joseph , Waheed Muhammad A. , Piche Joshua David , Patel Rakesh , Aleem Ilyas 
Published: May 2022

Study Design: Systematic Review Objectives: To determine the radiographic and clinical utility of postoperative orthoses following cervical spine surgery. Methods: We performed a search of the PubMed, Cochrane Library, Medline Ovid, and SCOPUS databases from inception until November 2021. Eligible studies included outcomes of postoperative bracing vs no bracing following cervical spine surgery. The primary outcome of interest was fusion rates after cervical surgery in braced vs unbraced patients. Secondary outcomes included patient reported outcomes and complication rates. Results: A total of 3232 titles were initially screened. After inclusion criteria were applied, 7 studies (550 patients) were included, which compared results of braced vs unbraced patients after cervical spine surgery. These studies showed acceptable reliability for inclusion based on the Methodical Index for Non-Randomized studies and Critical Appraisal Skills Programme assessment tools. There were no significant differences in fusion rates or complications between braced vs unbraced patients identified in any study. Patient reported pain and quality of life measures between braced and unbraced groups varied amongst studies, without any clear overall advantages favoring either method. Conclusions: This systematic review found that external bracing, though widely used following cervical spine surgery, may not offer any advantages in patient-reported outcomes, as compared to not bracing. In regard to the effect of bracing on fusion rates, no strong consensus can be made as the methods of fusion assessment in the included studies were heterogenous and suboptimal. Future high-quality studies using recommended methods of fusion assessment are needed to adequately address this important question.
Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens
Authors: Dressler Franz F. , Schoenfeld Jana , Revyakina Olga , Vogele Daniel , Kiefer Selina , Kirfel Jutta , Gemoll Timo , Perner Sven 
Published: May 2022

AbstractObjectivesFormalin-fixed paraffin-embedded (FFPE) tissue is the standard material for diagnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction protocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservation of membrane proteins (MP) as key subgroup of functionally relevant proteins.MethodsUsing the example of urothelial carcinoma, FFPE tissue sections were subjected to various deparaffinization, protein extraction and antigen retrieval protocols and buffers as well as different extraction techniques. Performance was measured by protein concentration and western blot analysis of cellular compartment markers as well as liquid chromatography-coupled mass spectrometry (LC–MS).ResultsCommercially available extraction buffers showed reduced extraction of MPs and came at considerably increased costs. On-slide extraction did not improve PE whereas several other preanalytical steps could be simplified. Systematic variation of temperature and exposure duration demonstrated a quantitatively relevant corridor of optimal antigen retrieval.ConclusionsPreanalytical protein extraction can be optimized at various levels to improve unbiased protein extraction and to reduce time and costs.
GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure
Authors: Hadish John A. , Biggs Tyler D. , Shealy Benjamin T. , Bender M. Reed , McKnight Coleman B. , Wytko Connor , Smith Melissa C. , Feltus F. Alex , Honaas Loren , Ficklin Stephen P. 
Published: May 2022

Abstract
Background
Quantification of gene expression from RNA-seq data is a prerequisite for transcriptome analysis such as differential gene expression analysis and gene co-expression network construction. Individual RNA-seq experiments are larger and combining multiple experiments from sequence repositories can result in datasets with thousands of samples. Processing hundreds to thousands of RNA-seq data can result in challenges related to data management, access to sufficient computational resources, navigation of high-performance computing (HPC) systems, installation of required software dependencies, and reproducibility. Processing of larger and deeper RNA-seq experiments will become more common as sequencing technology matures.

Results
GEMmaker, is a nf-core compliant, Nextflow workflow, that quantifies gene expression from small to massive RNA-seq datasets. GEMmaker ensures results are highly reproducible through the use of versioned containerized software that can be executed on a single workstation, institutional compute cluster, Kubernetes platform or the cloud. GEMmaker supports popular alignment and quantification tools providing results in raw and normalized formats. GEMmaker is unique in that it can scale to process thousands of local or remote stored samples without exceeding available data storage.

Conclusions
Workflows that quantify gene expression are not new, and many already address issues of portability, reusability, and scale in terms of access to CPUs. GEMmaker provides these benefits and adds the ability to scale despite low data storage infrastructure. This allows users to process hundreds to thousands of RNA-seq samples even when data storage resources are limited. GEMmaker is freely available and fully documented with step-by-step setup and execution instructions.
Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data
Authors: Choi Jaeyong , Lee Woochan , Yoon Jung-Ki , Choi Sun Mi , Lee Chang-Hoon , Moon Hyeong-Gon , Cho Sukki , Chung Jin-Haeng , Yang Han-Kwang , Kim Jong-Il 
Published: May 2022

Abstract
Background
Although single-cell RNA sequencing of xenograft samples has been widely used, no comprehensive bioinformatics pipeline is available for human and mouse mixed single-cell analyses. Considering the numerous homologous genes across the human and mouse genomes, misalignment errors should be evaluated, and a new algorithm is required. We assessed the extents and effects of misalignment errors and exonic multi-mapping events when using human and mouse combined reference data and developed a new bioinformatics pipeline with expression-based species deconvolution to minimize errors. We also evaluated false-positive signals presumed to originate from ambient RNA of the other species and address the importance to computationally remove them.

Result
Error when using combined reference account for an average of 0.78% of total reads, but such reads were concentrated to few genes that were greatly affected. Human and mouse mixed single-cell data, analyzed using our pipeline, clustered well with unmixed data and showed higher k-nearest-neighbor batch effect test and Local Inverse Simpson’s Index scores than those derived from Cell Ranger (10 × Genomics). We also applied our pipeline to multispecies multisample single-cell library containing breast cancer xenograft tissue and successfully identified all samples using genomic array and expression. Moreover, diverse cell types in the tumor microenvironment were well captured.

Conclusion
We present our bioinformatics pipeline for mixed human and mouse single-cell data, which can also be applied to pooled libraries to obtain cost-effective single-cell data. We also address misalignment, multi-mapping error, and ambient RNA as a major consideration points when analyzing multispecies single-cell data.
tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data
Authors: Lee Jin-Ok , Chu Jiyon , Jang Gyuyeon , Lee Minho , Chung Yeun-Jun 
Published: May 2022

Abstract
Background
Recent deep sequencing technologies have proven to be valuable resources to gain insights into the expression profiles of diverse tRNAs. However, despite these technologies, the association of tRNAs with diverse diseases has not been explored in depth because analytical tools are lacking.

Results
We developed a user-friendly tool, tRNA Expression Analysis Software Utilizing R for Easy use (tReasure), to analyze differentially expressed tRNAs (DEtRNAs) from deep sequencing data of small RNAs using R packages. tReasure can quantify individual mature tRNAs, isodecoders, and isoacceptors. By adopting stringent mapping strategies, tReasure supports the precise measurement of mature tRNA read counts. The whole analysis workflow for determining DEtRNAs (uploading FASTQ files, removing adapter sequences and poor-quality reads, mapping and quantifying tRNAs, filtering out low count tRNAs, determining DEtRNAs, and visualizing statistical analysis) can be performed with the tReasure package.

Conclusions
tReasure is an open-source software available for download at https://treasure.pmrc.re.kr and will be indispensable for users who have little experience with command-line software to explore the biological implication of tRNA expression.
Comparison of an automated DNA extraction and 16S rDNA real time PCR/sequencing diagnostic method using optimized reagents with culture during a 15-month study using specimens from sterile body sites
Authors: Egli Konrad , Risch Martin , Risch Lorenz , Bodmer Thomas 
Published: May 2022

Abstract
Background
16S rDNA-PCR for the identification of a bacterial species is an established method. However, the DNA extraction reagents as well as the PCR reagents may contain residual bacterial DNA, which consequently generates false-positive PCR results. Additionally, previously used methods are frequently time-consuming. Here, we describe the results obtained with a new technology that uses DNA-free reagents for automated DNA extraction and subsequent real time PCR using sterile clinical specimens.

Results
In total, we compared 803 clinical specimens using real time PCR and culturing. The clinical specimens were mainly of orthopedic origin received at our diagnostic laboratory. In 595 (74.1%) samples, the results were concordant negative, and in 102 (12.7%) the results were concordant positive. A total of 170 (21.2%) clinical specimens were PCR-positive, of which 62 (36.5% from PCR positive, 7.7% in total) gave an additional benefit to the patient since only the PCR result was positive. Many of these 62 positive specimens were strongly positive based on crossingpoint values (54% < Cp 30), and these 62 positive clinical specimens were diagnosed as medically relevant as well. Thirty-eight (4.2%) clinical specimens were culture-positive (25 of them were only enrichment culture positive) but PCR-negative, mainly for S. epidermidis, S. aureus and C. acnes. The turnaround times for negative specimens were 4 hours (automated DNA extraction and real time PCR) and 1 working day for positive specimens (including Sanger sequencing). Melting-curve analysis of SYBR Green-PCR enables the differentiation of specific and unspecific PCR products. Using Ripseq, even mixed infections of 2 bacterial species could be resolved.

Conclusions
For endocarditis cases, the added benefit of PCR is obvious. The crucial innovations of the technology enable timely reporting of explicit reliable results for adequate treatment of patients. Clinical specimens with truly PCR-positive but culture-negative results represent an additional benefit for patients. Very few results at the detection limit still have to be critically examined.
Theoretical analysis of effects of transcranial magneto-acoustical stimulation on neuronal spike-frequency adaptation
Authors: Zhao Song , Liu Dan , Liu Minzhuang , Luo Xiaoyuan , Yuan Yi 
Published: May 2022

Abstract
Background
Transcranial magneto-acoustical stimulation (TMAS) is a noninvasive technique that has advantages in spatial resolution and penetration depth. It changes the firing properties of neurons through the current generated by focused ultrasound and a static magnetic field. Spike-frequency adaptation is an important dynamic characteristic of neural information processing.

Methods
To address the effects of TMAS on neural spike-frequency adaptation, this study employs some ultrasound and magnetic field parameters, such as magnetic flux density, ultrasonic intensity, fundamental ultrasonic frequency, modulation frequency, and duty cycle. Using these different ultrasound and magnetic field parameters, membrane potential curves, spike-frequency curves, and adapted onset spike-frequency curves are exhibited and analyzed.

Results
The results show that spike-frequency adaptation is strongly dependent on ultrasonic intensity and magnetic flux density and is rarely affected by other parameters. However, modulation frequency and duty cycle influence membrane potentials and spike frequencies to some degree.

Conclusions
This study reveals the mechanism of the effects of TMAS on neural spike-frequency adaptation and serves as theoretical guidance for TMAS experiments.
Spinal cord injury and spinal fracture in patients with ankylosing spondylitis
Authors: Tu Po-Hsun , Liu Zhuo-Hao , Yeap Mun-Chun , Liu Yu-Tse , Li Ying-Ching , Huang Yin-Cheng , Lin Tzu-Min , Chen Ching-Chang 
Published: May 2022

Abstract
Background
Spinal cord injury (SCI) and spinal fracture are major complications in patients with ankylosing spondylitis (AS) who sustain spinal trauma. The purpose of this study was to investigate the incidence, predictors, and sequelae of spinal trauma in patients with AS.

Methods
This retrospective study included patients with AS who were admitted for spinal trauma between January 1, 2006, and June 30, 2016. The study compared clinical outcomes of patients between group 1: SCI alone, group 2: spinal fracture alone (no SCI), and group 3: both SCI and spinal fracture.

Results
Of the 6285 patients with AS admitted during the retrospective study period, only 105 suffered from spinal trauma and were enrolled in the study. Case number in group 1, 2, and 3 was 11(10.48%), 45(42.85%), and 49(46.67%), respectively. Among the patients with spinal fractures, 52.1% had SCI. Bamboo spine was significantly more prevalent in the fracture group than in the nonfracture group (78.7% vs. 36.4%; P = 0.006). Patients with SCI had more instances of subluxation or dislocation (48.3% vs. 8.9%; P < 0.001) and more cases of spinal epidural hematoma (SEH; 21.7% vs. 2.2%; P = 0.003) than patients without SCI. The rate of delayed diagnosis for spinal fracture was 31.4%, with one-third of patients developing delayed SCI. Among the patients with incomplete SCI, 58.3% achieved neurological improvement after treatment (P = 0.004).

Conclusions
Patients with AS and bamboo spine at radiograph had a higher rate of spinal fracture, which may be an important factor in SCI in patients with AS. Spinal fractures involving the C3–C7 region, subluxation or dislocation, severe spinal fracture, and SEH were found to be predictive of SCI, and SCI in patients with AS resulted in higher mortality and complication rates.
The i-ACT™ in Obesity educational intervention: a pilot study on improving Canadian family physician care in obesity medicine
Authors: Wharton Sean , Macklin David , Morin Marie-Philippe , Blavignac Jessica , Menzies Stuart , Garofalo Laura , Francisco Michelle A. , Thomas Carol , Barakat Maxime 
Published: May 2022

Abstract
Background
Obesity is a chronic problem in Canada and although the Canadian Medical Association recognizes obesity as a disease, health care professionals (HCPs) are not necessarily proactively managing it as one. This study aimed to assess current obesity management knowledge and practices of Canadian family physicians (FPs) and evaluate the feasibility of an online self-directed learning platform, i-ACT™ in Obesity, in delivering learning and changing practice intentions to advance obesity management.

Methods
i-ACT™ in Obesity is an online self-directed learning program designed by Canadian obesity medicine experts to provide individualized learning curricula to participants. One hundred FPs, with an interest in weight management and managing patients with obesity, were recruited across Canada to participate in a pilot study. FP education was delivered in a stepwise manner. Each participant completed a practice profile assessment to determine knowledge gaps and educational needs. Learners then watched didactic videos across disciplines on topics assigned to their curriculum by the program algorithm based on the relative difference between indicated and desired current knowledge. FPs also completed 10 retrospective patient assessments to assess clinical management practices and planned behaviour change. Feasibility, acceptability, and satisfaction of the learning program were assessed to formulate the rationale for a more widespread deployment in the future. Survey responses and related data were analyzed using comparative measures and descriptive statistics.

Results
The program was piloted by ninety-one Canadian FPs, where 900 patients were assessed. FPs showed distinct differences between their current and desired levels of comfort in a variety of obesity-related topics. Participation was associated with an intention to use more obesity treatment interventions moving forward. The program received an overall satisfaction rating of 8.6 out of 10 and 100% of the evaluators indicated that they would recommend it to their colleagues.

Conclusion
The program was overall well received and successfully changed obesity management intentions among participating FPs, thus setting the stage for a larger more comprehensive study to examine the efficacy of i-ACT™ in Obesity in addressing knowledge gaps and advancing evidence-based, guidelines-aligned approach to obesity treatment.
Multiple events case–control study in a prospective cohort to identify systemic, cellular, and molecular biomarkers of obesity-induced accelerated aging in 30-years-olds: the ObAGE study protocol
Authors: Correa-Burrows P , Burrows R , Albala C , Court FA , Salech F , Sanhueza G , Gonzalez-Billault C 
Published: May 2022

Abstract
Background
Aging is characterized by a progressive loss of capacities linked to fundamental alterations/damage in multiple cellular and molecular pathways. It is the most significant risk factor for all non-communicable diseases (NCDs). Another contributing factor to the rise in NCDs is obesity. It has been suggested that obesity not only accelerates the onset of metabolic imbalances but also decreases lifespan and impacts cellular and molecular processes in a manner similar to aging. Obesity might accelerate the pace of aging. Guided by a lifecourse approach, we will explore how exposure to obesity in critical developmental stages disrupt homeostatic resilience mechanisms that preserve physiological integrity, inducing an early expression of aging phenotypes. Also, we will determine whether exposure to early psychosocial adversity influences vulnerability to obesity as a risk factor for accelerated aging.

Methods
Multiple events case–control study embedded in a prospective cohort of Chileans at 30-31y, 50% females, of low- to-middle socioeconomic status, who participated in nutrition research since birth. At 23y, 25% had obesity and cardiometabolic risk was high. We will use a multi-layer approach including: anthropometric assessment; DXA scan for body composition; abdominal ultrasound of the liver; stool samples collection and sequencing of the ribosomal RNA 16S gene to characterize the gut microbiome; determination of age-related pro-inflammatory cytokynes and anti-inflammatory miokynes. For the first time in Chile, we will address age-related epigenetic changes using the Horvath´s epigenetic clock. In a subset we will conduct a controlled physical challenge to characterize physical resilience (autophagy).

Discussion
ObAGE is in an excellent position to: approach aging as a process whose expression involves multiple factors from the early stages of a person's life; understand how longitudinal changes in health trajectories impact the biological mechanisms of aging; identify potential resilience mechanisms that help prevent unhealthy aging. Because SLS participants are still young, our research setting combined with advanced scientific techniques may identify individuals or groups at risk of early onset health issues. Results from ObAGE may pave the way to address the contribution of obesity to aging through lifespan from cells to systems and might be instrumental to developing interventions to improve health span in the Chilean population.

Trial registration
The proposed study does not consider any health care intervention on human participants.