bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of Concomitant Glenohumeral Stabilization After Arthroscopic Rotator Cuff Repair in Military Patients Younger Than 40 Years
Authors: Green Clare K. , Scanaliato John P. , Sandler Alexis B. , Patrick Cole M. , Dunn John C. , Parnes Nata 
Published: March 2024

Background: While concomitant rotator cuff and inferior labral tears are relatively uncommon in young civilians, military populations represent a unique opportunity to study this injury pattern. Purpose: To (1) evaluate the long-term outcomes after combined arthroscopic rotator cuff and inferior labral repair in military patients <40 years and (2) compare functional outcomes with those after isolated arthroscopic rotator cuff repair. Study Design: Cohort study; Level of evidence, 3. Methods: Military patients who underwent arthroscopic rotator cuff repair between January 2011 and December 2016 and had a minimum of 5-year follow-up data were included in this study. The patients were categorized into those who had undergone combined arthroscopic rotator cuff and inferior labral repair (RCIL cohort) and those who had isolated arthroscopic rotator cuff repair (ARCR cohort). Pre- and postoperative outcome measures—visual analog scale for pain, Single Assessment Numeric Evaluation, American Shoulder and Elbow Surgeons shoulder score, Rowe Instability Score, and range of motion—were compared between the groups. Results: A total of 50 shoulders (27 in the RCIL cohort and 23 in the ARCR cohort) were assessed. The RCIL and ARCR groups were similar in terms of age (mean, 33.19 years [range, 21-39 years] vs 35.39 years [range, 26-39 years], respectively) and sex (% male, 88.46% vs 82.61%, respectively). All patients were active-duty military at the time of surgery. The mean final follow-up was at 106.93 ± 16.66 months for the RCIL group and 105.70 ± 7.52 months for the ARCR group ( P = .75). There were no differences in preoperative outcome scores between groups. Postoperatively, both groups experienced statistically significant improvements in all outcome scores ( P < .0001 for all), and there were no significant group differences in any final postoperative outcome measures. At the final follow-up, 26 (96.30%) patients in the RCIL cohort and 20 (86.96%) in the ARCR cohort had returned to unrestricted active-duty military service ( P = .3223). Conclusion: The findings of this study suggest that concomitant glenohumeral stabilization does not portend worse outcomes after arthroscopic rotator cuff repair in military patients < 40 years. Combined repair produced statistically and clinically significant improvements in outcome scores at the long-term follow-up, indicating that simultaneous repair of combined lesions was an appropriate treatment option in this patient population.
The Top 100 Most Impactful Articles on the Achilles Tendon According to Altmetric Attention Score and Number of Citations
Authors: Bano Joseph M. , Rate William R. , Civilette Matthew D. , Wyand Trevor J. , Samuelson Eric R. , Bodendorfer Blake M. , Gould Heath P. , Hembree Walter C. 
Published: March 2024

Background: Achilles tendon injuries often generate substantial discussion in the mainstream media. The Altmetric Attention Score (AAS) measures the online dialogue pertaining to Achilles tendon research that occurs outside scientific journals, which traditional citation-based metrics fail to capture. Purpose: To characterize the top 100 most-cited Achilles tendon articles and compare them with the 100 Achilles tendon articles with the highest AAS. A secondary goal was to gain an improved understanding of the online dissemination and interpretation of Achilles tendon research through this comparison. Study Design: Cross-sectional study. Methods: The Web of Science Clarivate database was queried to isolate the 100 most-cited Achilles tendon articles, and the Altmetric database was queried to identify the Achilles tendon articles with the top 100 AAS values. Data elements were extracted for each article including study type, study topic, and geographic origin. Results: The Web of Science Clarivate database search yielded 10,890 articles published between 1970 and 2021. The 100 most-cited articles were published in 35 journals, with the American Journal of Sports Medicine being the most prevalent. The mean (±SD) number of citations was 214.5 ± 86.47. The most prevalent study type was laboratory (28.0%). The most prevalent study topic was treatment (41.0%). Of these articles, 72.0% were European. The Altmetric database search yielded 3810 articles published between 1957 and 2021. The AAS of the top 100 articles ranged from 37 to 476 with a mean of 98.17 ± 85.53. The selected articles were published in 39 journals, with the British Journal of Sports Medicine being the most prevalent. The most prevalent study type was randomized controlled trial (25.0%). The most common study topic was treatment (40.0%). Of these articles, 46.0% were European. Conclusion: Our findings suggest that, although the scientific community remains committed to high-impact journals with articles backed by high citation numbers, there is an increasing opportunity to consume Achilles tendon literature through social media.
Retroperitoneal hernia following laparoscopic living-donor nephrectomy: a case report and review of literature
Authors: Wijaya Marzuki Panji , Hendri Ahmad Zulfan 
Published: March 2024

Abstract
Background
The laparoscopic approach is the standard of care for living-donor nephrectomy. A rare postoperative complication is small bowel obstruction due to a retroperitoneal hernia. We present a case of an incidental finding of a retroperitoneal hernia in a patient with a history of laparoscopic donor nephrectomy.

Case presentation
An adult male presented with diffuse abdominal pain, vomiting, and obstipation for 12 h. He had undergone laparoscopic donor nephrectomy two months prior. Plain abdominal radiograph revealed a dilated small bowel with homogenous opacity in the left lumbar region. Due to worsening diffuse abdominal pain and a high clinical suspicion of intestinal strangulation and ischemia after conservative management, an exploratory laparotomy was performed. Intraoperatively, an incarcerated small bowel segment herniating through an 8 cm descending mesocolon defect into the retroperitoneal space was discovered, forming a closed-loop obstruction. The bowel segment was reduced, and the mesocolon defect was repaired. The patient was discharged five days postoperatively with good recovery.

Conclusion
Retroperitoneal hernia following laparoscopic living-donor nephrectomy is a rare but significant complication. Mitigation to prevent mesenteric defect creation, routine inspection, and closure of the defect can reduce the risk of hernia. Non-specific abdominal pain in patients with a history of laparoscopic donor nephrectomy prompts rapid imaging evaluation to aid in the early diagnosis of possible retroperitoneal hernia and its intervention.
Analyzing postprandial metabolomics data using multiway models: a simulation study
Authors: Li Lu , Yan Shi , Bakker Barbara M. , Hoefsloot Huub , Chawes Bo , Horner David , Rasmussen Morten A. , Smilde Age K. , Acar Evrim 
Published: March 2024

AbstractBackgroundAnalysis of time-resolved postprandial metabolomics data can improve the understanding of metabolic mechanisms, potentially revealing biomarkers for early diagnosis of metabolic diseases and advancing precision nutrition and medicine. Postprandial metabolomics measurements at several time points from multiple subjects can be arranged as asubjectsbymetabolitesbytime pointsarray. Traditional analysis methods are limited in terms of revealing subject groups, related metabolites, and temporal patterns simultaneously from such three-way data.ResultsWe introduce an unsupervised multiway analysis approach based on the CANDECOMP/PARAFAC (CP) model for improved analysis of postprandial metabolomics data guided by a simulation study. Because of the lack of ground truth in real data, we generate simulated data using a comprehensive human metabolic model. This allows us to assess the performance of CP models in terms of revealing subject groups and underlying metabolic processes. We study three analysis approaches: analysis offasting-statedata using principal component analysis,T0-correcteddata (i.e., data corrected by subtracting fasting-state data) using a CP model andfull-dynamic(i.e., full postprandial) data using CP. Through extensive simulations, we demonstrate that CP models capture meaningful and stable patterns from simulated meal challenge data, revealing underlying mechanisms and differences between diseased versus healthy groups.ConclusionsOur experiments show that it is crucial to analyze bothfasting-stateandT0-correcteddata for understanding metabolic differences among subject groups. Depending on the nature of the subject group structure, the best group separation may be achieved by CP models ofT0-correctedorfull-dynamicdata. This study introduces an improved analysis approach for postprandial metabolomics data while also shedding light on the debate about correcting baseline values in longitudinal data analysis.
Holomics - a user-friendly R shiny application for multi-omics data integration and analysis
Authors: Munk Katharina , Ilina Daria , Ziemba Lisa , Brader Günter , Molin Eva M. 
Published: March 2024

AbstractAn organism’s observable traits, or phenotype, result from intricate interactions among genes, proteins, metabolites and the environment. External factors, such as associated microorganisms, along with biotic and abiotic stressors, can significantly impact this complex biological system, influencing processes like growth, development and productivity. A comprehensive analysis of the entire biological system and its interactions is thus crucial to identify key components that support adaptation to stressors and to discover biomarkers applicable in breeding programs or disease diagnostics. Since the genomics era, several other ’omics’ disciplines have emerged, and recent advances in high-throughput technologies have facilitated the generation of additional omics datasets. While traditionally analyzed individually, the last decade has seen an increase in multi-omics data integration and analysis strategies aimed at achieving a holistic understanding of interactions across different biological layers. Despite these advances, the analysis of multi-omics data is still challenging due to their scale, complexity, high dimensionality and multimodality. To address these challenges, a number of analytical tools and strategies have been developed, including clustering and differential equations, which require advanced knowledge in bioinformatics and statistics. Therefore, this study recognizes the need for user-friendly tools by introducing Holomics, an accessible and easy-to-use R shiny application with multi-omics functions tailored for scientists with limited bioinformatics knowledge. Holomics provides a well-defined workflow, starting with the upload and pre-filtering of single-omics data, which are then further refined by single-omics analysis focusing on key features. Subsequently, these reduced datasets are subjected to multi-omics analyses to unveil correlations between 2-n datasets. This paper concludes with a real-world case study where microbiomics, transcriptomics and metabolomics data from previous studies that elucidate factors associated with improved sugar beet storability are integrated using Holomics. The results are discussed in the context of the biological background, underscoring the importance of multi-omics insights. This example not only highlights the versatility of Holomics in handling different types of omics data, but also validates its consistency by reproducing findings from preceding single-omics studies.
The first two whole mitochondrial genomes for the genus Dactylis species: assembly and comparative genomics analysis
Authors: Feng Guangyan , Jiao Yongjuan , Ma Huizhen , Bian Haoyang , Nie Gang , Huang Linkai , Xie Zheni , Ran Qifan , Fan Wenwen , He Wei , Zhang Xinquan 
Published: March 2024

Abstract
Background
Orchardgrass (Dactylis glomerata L.), a perennial forage, has the advantages of rich leaves, high yield, and good quality and is one of the most significant forage for grassland animal husbandry and ecological management in southwest China. Mitochondrial (mt) genome is one of the major genetic systems in plants. Studying the mt genome of the genus Dactylis could provide more genetic information in addition to the nuclear genome project of the genus.

Results
In this study, we sequenced and assembled two mitochondrial genomes of Dactylis species of D. glomerata (597, 281 bp) and D. aschersoniana (613, 769 bp), based on a combination of PacBio and Illumina. The gene content in the mitochondrial genome of D. aschersoniana is almost identical to the mitochondrial genome of D. glomerata, which contains 22–23 protein-coding genes (PCGs), 8 ribosomal RNAs (rRNAs) and 30 transfer RNAs (tRNAs), while D. glomerata lacks the gene encoding the Ribosomal protein (rps1) and D. aschersoniana contains one pseudo gene (atp8). Twenty-three introns were found among eight of the 30 protein-coding genes, and introns of three genes (nad 1, nad2, and nad5) were trans-spliced in Dactylis aschersoniana. Further, our mitochondrial genome characteristics investigation of the genus Dactylis included codon usage, sequences repeats, RNA editing and selective pressure. The results showed that a large number of short repetitive sequences existed in the mitochondrial genome of D. aschersoniana, the size variation of two mitochondrial genomes is due largely to the presence of a large number of short repetitive sequences. We also identified 52–53 large fragments that were transferred from the chloroplast genome to the mitochondrial genome, and found that the similarity was more than 70%. ML and BI methods used in phylogenetic analysis revealed that the evolutionary status of the genus Dactylis.

Conclusions
Thus, this study reveals the significant rearrangements in the mt genomes of Pooideae species. The sequenced Dactylis mt genome can provide more genetic information and improve our evolutionary understanding of the mt genomes of gramineous plants.
State-transition dynamics of resting-state functional magnetic resonance imaging data: model comparison and test-to-retest analysis
Authors: Islam Saiful , Khanra Pitambar , Nakuci Johan , Muldoon Sarah F. , Watanabe Takamitsu , Masuda Naoki 
Published: March 2024

AbstractElectroencephalogram (EEG) microstate analysis entails finding dynamics of quasi-stable and generally recurrent discrete states in multichannel EEG time series data and relating properties of the estimated state-transition dynamics to observables such as cognition and behavior. While microstate analysis has been widely employed to analyze EEG data, its use remains less prevalent in functional magnetic resonance imaging (fMRI) data, largely due to the slower timescale of such data. In the present study, we extend various data clustering methods used in EEG microstate analysis to resting-state fMRI data from healthy humans to extract their state-transition dynamics. We show that the quality of clustering is on par with that for various microstate analyses of EEG data. We then develop a method for examining test–retest reliability of the discrete-state transition dynamics between fMRI sessions and show that the within-participant test–retest reliability is higher than between-participant test–retest reliability for different indices of state-transition dynamics, different networks, and different data sets. This result suggests that state-transition dynamics analysis of fMRI data could discriminate between different individuals and is a promising tool for performing fingerprinting analysis of individuals.
REDCapDM: An R package with a set of data management tools for a REDCap project
Authors: Carmezim João , Satorra Pau , Peñafiel Judith , García-Lerma Esther , Pallarès Natàlia , Santos Naiara , Tebé Cristian 
Published: March 2024

AbstractBackgroundResearch Electronic Data CAPture (REDCap) is a web application for creating and managing online surveys and databases. Clinical data management is an essential process before performing any statistical analysis to ensure the quality and reliability of study information. Processing REDCap data in R can be complex and often benefits from automation. While there are several R packages available for specific tasks, none offer an expansive approach to data management.ResultsThe REDCapDM is an R package for accessing and managing REDCap data. It imports data from REDCap to R using either an API connection or the files in R format exported directly from REDCap. It has several functions for data processing and transformation, and it helps to generate and manage queries to clarify or resolve discrepancies found in the data.ConclusionThe REDCapDM package is a valuable tool for data scientists and clinical data managers who use REDCap and R. It assists in tasks such as importing, processing, and quality-checking data from their research studies.
The associations between peripheral inflammatory and lipid parameters, white matter hyperintensity, and cognitive function in patients with non-disabling ischemic cerebrovascular events
Authors: Li Binghan , Gu Zhengsheng , Wang Weisen , Du Bingying , Wu Chenghao , Li Bin , Wang Tianren , Yin Ge , Gao Xin , Chen Jingjing , Bi Xiaoying , Zhang Hailing , Sun Xu 
Published: March 2024

Abstract
Background
The global prevalence of VCI has increased steadily in recent years, but diagnostic biomarkers for VCI in patients with non-disabling ischemic cerebrovascular incidents (NICE) remain indefinite. The primary objective of this research was to investigate the relationship between peripheral serological markers, white matter damage, and cognitive function in individuals with NICE.

Methods
We collected clinical data, demographic information, and medical history from 257 patients with NICE. Using the MoCA upon admission, patients were categorized into either normal cognitive function (NCF) or VCI groups. Furthermore, they were classified as having mild white matter hyperintensity (mWMH) or severe WMH based on Fazekas scores. We then compared the levels of serological markers between the cognitive function groups and the WMH groups.

Results
Among 257 patients with NICE, 165 were male and 92 were female. Lymphocyte count (OR = 0.448, P < 0.001) and LDL-C/HDL-C (OR = 0.725, P = 0.028) were protective factors for cognitive function in patients with NICE. The sWMH group had a higher age and inflammation markers but a lower MoCA score, and lymphocyte count than the mWMH group. In the mWMH group, lymphocyte count (AUC = 0.765, P < 0.001) and LDL-C/HDL-C (AUC = 0.740, P < 0.001) had an acceptable diagnostic value for the diagnosis of VCI. In the sWMH group, no significant differences were found in serological markers between the NCF and VCI groups.

Conclusion
Lymphocyte count, LDL-C/HDL-C were independent protective factors for cognitive function in patients with NICE; they can be used as potential biological markers to distinguish VCI in patients with NICE and are applicable to subgroups of patients with mWMH.
Impact of preoperative antiviral therapy on the prognosis of hepatitis B virus-related hepatocellular carcinoma
Authors: Liang Yuxin , Zhong Deyuan , Zhang Zilong , Su Yuhao , Yan Su , Lai Chunyou , Yao Yutong , Shi Ying , Huang Xiaolun , Shang Jin 
Published: March 2024

Abstract
Background
For chronic hepatitis B virus (HBV) infection patients, increasing evidence has demonstrated the effectiveness of expanding the indications and applicable population for antiviral therapy. However, the expanded indication of antiviral therapy for hepatocellular carcinoma (HCC) remains to be further explored.

Methods
196 HBV-related HCC patients who received radical hepatectomy and nucleos(t)ide analogues (NAs) therapy at Sichuan Provincial People’s Hospital were enrolled in this study. HCC recurrence, overall survival (OS), early virological (VR) and biochemical responses (BR) of patients were compared between different NAs therapy and the use of anti-programmed cell death protein 1 (PD-1) therapy.

Results
NAs therapy at different timing of surgery was a strong independent risk factor for postoperative recurrence and overall mortality of HBV-related HCC patients. Furthermore, in HCC patients who received postoperative anti-PD-1 therapy, patients with HBV DNA < 1000 copy/mL had significantly better recurrence-free survival (RFS) and OS than those with HBV DNA ≥ 1000 copy/mL (HR: 7.783; P = 0.002; HR: 6.699; P < 0.001). However, the differences of RFS and OS rates between entecavir group and tenofovir disoproxil fumarate group were not statistically significant. Similar results were also observed in the rates of early VR, BR and combined VR and BR.

Conclusion
Timely and reasonable preoperative NAs therapy showed clinical benefit in improving the prognosis of patients with HBV-related HCC, even in the case of normal alanine aminotransferase (ALT) level and negative hepatitis e antigen (HBeAg). Furthermore, a possible synergistic effect between antiviral therapy and anti-PD-1 therapy was founded and need further verification.
Effect of health belief model-based educational intervention on prostate cancer prevention; knowledge, practices, and intentions
Authors: Khalil Marwa Ibrahim Mahfouz , Ashour Ayat , Shaala Reem Said , Allam Rasha Mahmoud , Abdelaziz Thoraya Mohamed , Mousa Enas Fouad Sayed 
Published: March 2024

Abstract
Background
Prostate cancer screening is a crucial preventive element for improving the survival rates of prostate cancer. Therefore, our research objective was to investigate the effect of health belief model-based education on prostate cancer knowledge, health beliefs, and preventive health practices among adult and older adult males.

Methods
A one-group pre-test/post-test quasi-experimental study design was carried out at the one-day outpatient clinics affiliated to General Alexandria Main University Hospital. We enrolled 110 men aged 45–75 years old in a health belief model-based educational intervention program. Various questionnaires were utilized to gather data before, immediately after, and three months following the intervention. These questionnaires included the socio-demographic questionnaire, Prostate Cancer Knowledge Questionnaire (PCKQ), Prostate Cancer Screening-Health Belief Model Scale (HBM-PCS), Prostate Cancer Preventive Practices Questionnaire (PCPPQ), and one question regarding the intention to undergo PC screening.

Results
Participants’ knowledge about prostate cancer screening improved significantly immediately after the program and this positive change was maintained at the follow-up (p = 0.000). Furthermore, participants’ perceptions and preventive practices towards prostate cancer screening had changed significantly after program completion and at follow-up (p = 0.000). After program completion, many of the participants (92.7%) expressed their intention to undergo prostate cancer screening within the coming six months (p = 0.000). The younger age group (45–49 years) showed higher scores in their perception of prostate screening (p = 0.001). Higher education and income were significantly associated with higher scores in the three scales (p = 0.000 in all scales).

Conclusion
The study findings emphasized the effectiveness of the designed health educational program based on the HBM on PC preventive behaviors, through significantly improving participants’ knowledge level, perceptions, practices, and intentions to PC screening. The program is highly recommended for prostate cancer preventive health practices among both adult and older adult males.