bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disappearing repositories: Taking an infrastructure perspective on the long-term availability of research data
Authors: Strecker Dorothea , Pampel Heinz , Schabinger Rouven , Weisweiler Nina Leonie 
Published: January 2024

Abstract
Currently, there is limited research investigating the phenomenon of research data repositories being shut down, and the impact this has on the long-term availability of data. This paper takes an infrastructure perspective on the preservation of research data by using a registry to identify 191 research data repositories that have been closed and presenting information on the shutdown process. The results show that 6.2% of research data repositories indexed in the registry were shut down. The risks resulting in repository shutdown are varied. The median age of a repository when shutting down is 12 years. Strategies to prevent data loss at the infrastructure level are pursued to varying extent. Of the repositories in the sample, 44% migrated data to another repository and 12% maintain limited access to their data collection. However, neither strategy is a permanent solution. Finally, the general lack of information on repository shutdown events as well as the effect on the findability of data and the permanence of the scholarly record are discussed.
Unreviewed science in the news: The evolution of preprint media coverage from 2014–2021
Authors: Fleerackers Alice , Shores Kenneth , Chtena Natascha , Alperin Juan Pablo 
Published: January 2024

Abstract
It has been argued that preprint coverage during the COVID-19 pandemic constituted a paradigm shift in journalism norms and practices. This study examines whether and in what ways this is the case using a sample of 11,538 preprints posted on four preprint servers—bioRxiv, medRxiv, arXiv, and SSRN—that received coverage in 94 English-language media outlets between 2014 and 2021. We compared mentions of these preprints with mentions of a comparison sample of 397,446 peer-reviewed research articles indexed in the Web of Science to identify changes in the share of media coverage that mentioned preprints before and during the pandemic. We found that preprint media coverage increased at a slow but steady rate prepandemic, then spiked dramatically. This increase applied only to COVID-19-related preprints, with minimal change in coverage of preprints on other topics. The rise in preprint coverage was most pronounced among health and medicine-focused media outlets, which barely covered preprints before the pandemic but mentioned more COVID-19 preprints than outlets focused on any other topic. These results suggest that the growth in coverage of preprints seen during the pandemic may imply only a temporary shift in journalistic norms, including a changing outlook on reporting preliminary, unvetted research.
Weaker Quadriceps Muscle Strength With a Quadriceps Tendon Graft Compared With a Patellar or Hamstring Tendon Graft at 7 Months After Anterior Cruciate Ligament Reconstruction
Authors: Holmgren David , Noory Shiba , Moström Eva , Grindem Hege , Stålman Anders , Wörner Tobias 
Published: January 2024

Background: Impaired quadriceps muscle strength after anterior cruciate ligament reconstruction (ACLR) is associated with worse clinical outcomes and a risk of reinjuries. Yet, we know little about quadriceps muscle strength in patients reconstructed with a quadriceps tendon (QT) graft, which is increasing in popularity worldwide. Purpose: To describe and compare isokinetic quadriceps strength in patients undergoing ACLR with a QT, hamstring tendon (HT), or bone–patellar tendon–bone (BPTB) autograft. Study Design: Cross-sectional study; Level of evidence, 3. Methods: We included patients with QT grafts (n = 104) and matched them to patients with HT (n = 104) and BPTB (n = 104) grafts based on age, sex, and associated meniscal surgery. Data were collected through clinical strength testing at a mean of 7 ± 1 months postoperatively. Isokinetic strength was measured at 90 deg/s, and quadriceps strength was expressed as the limb symmetry index (LSI) for peak torque, total work, torque at 30° of knee flexion, and time to peak torque. Results: Patients with QT grafts had the most impaired isokinetic quadriceps strength, with the LSI ranging between 67.5% and 75.1%, followed by those with BPTB grafts (74.4%-81.5%) and HT grafts (84.0%-89.0%). Patients with QT grafts had a significantly lower LSI for all variables compared with patients with HT grafts (mean difference: peak torque: −17.4% [95% CI, −21.7 to −13.2], P < .001; total work: −15.9% [95% CI, −20.6 to −11.1], P < .001; torque at 30° of knee flexion: −8.8% [95% CI, −14.7 to −2.9], P = .001; time to peak torque: −17.7% [95% CI, −25.8 to −9.6], P < .001). Compared with patients with BPTB grafts, patients with QT grafts had a significantly lower LSI for all variables (mean difference: peak torque: −6.9% [95% CI, −11.2 to −2.7], P < .001; total work: −7.7% [95% CI, −12.4 to −2.9], P < .001; torque at 30° of knee flexion: −6.3% [95% CI, −12.2 to −0.5], P = .03; time to peak torque: −8.8% [95% CI, −16.9 to −0.7], P = .03). None of the graft groups reached a mean LSI of >90% for peak torque (QT: 67.5% [95% CI, 64.8-70.1]; HT: 84.9% [95% CI, 82.4-87.4]; BPTB: 74.4% [95% CI, 72.0-76.9]). Conclusion: At 7 months after ACLR, patients with QT grafts had significantly worse isokinetic quadriceps strength than patients with HT and BPTB grafts. None of the 3 graft groups reached a mean LSI of >90% in quadriceps strength.
Outcomes of Arthroscopic Latarjet as a Revision Surgery After Failed Arthroscopic Bankart Repair
Authors: Calvo Emilio , Dzidzishvili Lika , Valencia María , Calvo Claudio 
Published: January 2024

Background: The role of arthroscopic Latarjet as a revision surgery after failed arthroscopic Bankart repair has yet to be established. Purpose: To compare clinical outcomes, recurrences, and complication rates of arthroscopic Latarjet as a revision procedure after failed arthroscopic Bankart repair versus arthroscopic Latarjet as a primary procedure. Design: Cohort study; Level of evidence, 3. Methods: This is a retrospective study of prospectively collected data of patients who were diagnosed with anterior shoulder instability and underwent arthroscopic Latarjet stabilization between 2009 and 2018. Patients were separated into 2 groups depending on whether Latarjet was performed after a previous instability surgery (revision) or as a primary surgery (primary). Rowe score, Western Ontario Shoulder Instability Index (WOSI), Constant-Murley Shoulder Outcome (CMSO) score, and Single Assessment Numeric Evaluation (SANE) were assessed pre- and postoperatively with a minimum 24 months of follow-up. In addition, pre- and postoperative levels of sports activity, dislocations, subluxations, and complications were assessed. Results: A total of 97 patients (n = 62 revision; n = 35 primary), with a mean age of 31.0 ± 8.8 and 29.4 ± 7.6 years old in the revision and primary Latajet group, respectively, met the inclusion criteria. The mean follow-up in the revision group was 32 months (24-53) and 35.5 months (27.7-42.2) in the primary Latarjet group. No significant differences between groups were observed in Rowe score (revision = 91.4, primary = 94.1; P = .223), CMSO score (revision = 90.7, primary = 94; P = .105), and SANE (revision = 85.8, primary = 87.3; P = .683) postoperatively. However, the postoperative difference in the WOSI score between the revision and primary Latarjet groups was nearly significant (510 ± 334 vs 403 ± 343, respectively; P = .05). Four (6.4%) postoperative dislocations were reported in the revision and 1 (2.8%) in the primary Latarjet group ( P = .14). Patients in the revision group had a lower return to the previous level of sports participation ( P = .008) and decreased external rotation with the arm by the side compared with the primary Latarjet group ( P = .000). Conclusion: Arthroscopic Latarjet as a revision surgery is a reasonable surgical option in failed Bankart repair cases. The decision to perform arthroscopic Latarjet stabilization as a revision surgery should not be influenced by the potential risk of future complications as it provides comparable clinical outcomes to the primary Latarjet procedure with a low postoperative recurrence rate. However, a decreased level of postoperative sports participation and external rotation with the arm by the side can be expected.
Hip Arthroscopic Surgery With Chondrolabral Refixation, Osteochondroplasty, and Routine Capsular Closure for Femoroacetabular Impingement Syndrome: Clinical Outcomes at a Minimum 10-Year Follow-up
Authors: Allahabadi Sachin , Chapman Reagan S. , Fenn Thomas W. , Brusalis Christopher M. , Kaplan Daniel J. , Nho Shane J. 
Published: January 2024

Background: Hip arthroscopic surgery for femoroacetabular impingement syndrome (FAIS) has proven to be an effective surgical intervention, with high rates of return to sport and work as well as favorable outcomes at short- and midterm follow-up. However, limited data exist on outcomes at long-term follow-up. Purpose: To evaluate patient-reported outcomes (PROs) at a minimum 10-year follow-up after primary hip arthroscopic surgery including labral repair, femoral osteochondroplasty, acetabular osteochondroplasty, and capsular closure for FAIS. Study Design: Case series; Level of evidence, 4. Methods: Patients who underwent primary hip arthroscopic surgery for FAIS between June 2012 and January 2013 were identified. PROs were collected preoperatively and at a minimum of 10 years postoperatively, including the Hip Outcome Score–Activities of Daily Living (HOS-ADL), Hip Outcome Score–Sports Subscale (HOS-SS), modified Harris Hip Score (mHHS), International Hip Outcome Tool–12 (iHOT-12), and visual analog scale (VAS) for pain and satisfaction. Unique minimal clinically important difference (MCID) and patient acceptable symptom state (PASS) thresholds were calculated, and their rates of achievement were analyzed. An alpha level of <.05 was used to determine statistical significance. Results: A total of 94 patients (55 female; mean age, 34.3 ± 12.4 years) were analyzed with a mean follow-up of 10.1 ± 0.3 years (range, 10.0-10.7 years). Patients demonstrated significant 10-year improvement across all PRO measures ( P < .001). MCID and PASS thresholds were calculated as follows: HOS-ADL (10.4 and 85.3, respectively), HOS-SS (14.6 and 60.2, respectively), mHHS (8.8 and 76.0, respectively), VAS pain (14.6 and 27.5, respectively), and iHOT-12 (PASS: 71.4). The majority of patients achieved the MCID and PASS for each PRO measure: HOS-ADL (73.4% and 70.9%, respectively), HOS-SS (78.5% and 77.2%, respectively), mHHS (81.0% and 70.9%, respectively), VAS pain (88.6% and 70.9%, respectively), and iHOT-12 (PASS: 73.4%). Overall, 9 patients (9.6%) underwent subsequent revision hip arthroscopic surgery at a mean 4.9 ± 3.7 years (range, 1.1-10.1 years) postoperatively, and 6 patients (6.4%) underwent conversion to total hip arthroplasty at a mean 4.1 ± 3.1 years (range, 0.9-9.3 years) postoperatively. Conclusion: Patients who underwent primary hip arthroscopic surgery for FAIS utilizing contemporary methods of labral repair, acetabular and/or femoral osteochondroplasty, and capsular closure commonly experienced sustained clinical improvement and reported high levels of satisfaction at a minimum 10-year follow-up with low rates of reoperation.
Clozapine-related tachycardia: A conundrum to identify and treat
Authors: Brennan Dermot , Lal Sweta , Hugo Frans , Waters Flavie , Shymko Gordon 
Published: January 2024

Objective This study examined the rates and persistence of clozapine-induced tachycardia and heart-rate differences in patients treated with β-blockers in the largest sample of patients with a psychotic disorder to date. Method An audit of medical files for 101 patients who attended a clozapine community clinic and analysis of monthly measurements of resting heart rates. Results 51% met the clinical criteria for tachycardia. Heart rates were stable over time. β-blockers were associated with small but significant reductions in heart rates. Conclusion The cardiovascular risks of clozapine are often overlooked. β-blockers are useful in lowering heart rates but they may be insufficient to reduce cardiac risk.
Salivary Diurnal Cortisol Predicts Post−Traumatic Stress Symptoms in Parents of Infants With Congenital Heart Disease
Authors: Lisanti Amy Jo , Dong Fanghong , Demianczyk Abigail , Vogiatzi Maria G. , Quinn Ryan , Chittams Jesse , Hoffman Rebecca , Medoff−Cooper Barbara 
Published: January 2024

Background Parents of infants born with congenital heart disease (CHD) who require open heart surgery after birth are at risk for prolonged psychological distress. Even after their infants are discharged, parents may experience anxiety, depressive, and post−traumatic stress (PTS) symptoms; yet, it is unclear which parents are at greater risk for ongoing symptoms. The purpose of this study was to explore whether measures of the biomarker cortisol in parents during their infants’ postoperative period were associated with subsequent psychological distress symptoms at three−month post discharge. Methods This was a prospective, longitudinal exploratory study of 40 parents of infants with CHD after open heart surgery using consecutive enrollment. Parents provided diurnal saliva samples for two consecutive days in the postoperative period. Six predictors were summarized and generated including waking cortisol, bedtime cortisol, cortisol awaking response, area under curve with respect to the ground (AUCg), cortisol index, and cortisol slope. Self−report outcome measures on anxiety, depressive, and PTS symptoms were collected three−months post−discharge. Linear mixed models examined the associations between each predictor and each outcome while accounting for within−dyad variance using an unstructured covariance matrix. Results Cortisol AUCg was a predictor of PTS at three−months post−discharge ( β = .34, p = .03, Cohen’s d = 2.05). No significant relationships were found with the other cortisol measures. Conclusions & Implications Findings suggest that cortisol area under curve may help to identify parents at risk for increased PTS in the months following their infants’ hospitalization for cardiac surgery, serving as a foundation for future study in this area.
Comparison of Strengths of Mandibular Angle Fractures Following Different Plate Designs: A Human Cadaver Study
Authors: Squier Brendan R. , Kongsong Wichuda , Cofield Stacey S. , Bignault Samuel , Sittitavornwong Somsak 
Published: January 2024

Study Design This institutional cross-sectional study using cadaveric mandibles aimed to measure and compare the strengths of three plating designs utilized in osteosynthesis of mandibular angle fractures. Objective There have been prior studies on angle fracture fixation though few biomechanical studies on human cadaveric specimen. This study aims to directly compare the biomechanical strength of different plating designs to the mandibular angle fracture using a human cadaveric specimen substrate. Methods After receiving an angle osteotomy and either single plate, two plate, or 3D plate fixation, the specimens underwent biomechanical testing using the Instron 5565 mechanical testing unit. The primary outcomes measured were peak load at which permanent deformation started, displacement value at peak load, and load necessary for a specific amount of displacement at 1, 3, 5, and 7 mm. Results There were 15 hemi-mandibles in each group. Based on data analysis of all the specimens, there were no significant differences in the mandibular height, ramus width, mandibular thickness, angle height, and gonial angle between the hemimandibles.. This study demonstrated a statistically significant increased strength performance of the 3D plate over the single plate fixation and the 2-plate over the single plate fixation. The results between 2-plate and 3D plate were in similar values. Conclusions In terms of biomechanical strength, the 3D plate and two plate designs outperform the single plate design to mandibular angle fractures. There are various anatomical and patient specific situations that can aid in selection between them. In the absence of the favorable angle fracture and patient, biomechanical strength to the method of fixation selection needs to be considered.
Study of changes in the aging process, microstructure, and mechanical properties of AA2024–AA1050 nanocomposites created by the accumulative roll bonding process, with the addition of 0.005 vol.% of alumina nanoparticles
Authors: Roghani Hamed , Borhani Ehsan , Ahmadi Ehsan , Jafarian Hamid Reza 
Published: January 2024

AbstractWe created AA2024–AA1050 and AA2024–AA1050/0.005 vol.% Al2O3 nanocomposites by six accumulative roll bonding (ARB) process cycles. We used AA2024 and AA1050 sheets with a thickness of 0.7 mm and plate-shaped alumina nanoparticles to create a composite. The two AA1050 and one AA2024 sheets (among the two AA1050 sheets) were ARB-ed up to six cycles with and without adding alumina nanoparticles. Also, a sample of the AA1050 without composite making was ARB-ed up to six cycles. We aged some composites after the ARB process in the furnace at 110, 150, and 190 °C. This project performed SEM, TEM, and EDS-MAP analyses, tensile strength, microhardness, and Pin-on-Disc tests to study the ARB-ed sheets. The results of the tensile tests showed that the tensile strength of AA2024–AA1050 created by the six cycles ARB process was two times more than primary AA1050. Also, the wear resistance of this composite was 74% more than six cycles ARB-ed the AA1050. Using 0.005 vol.% alumina nanoparticles in AA2024–AA1050 composite improved its wear resistance by 30%. In the following, the aging process caused an improvement in tensile strength and total elongation of AA2024–AA1050/Al2O3 nanocomposites.
Phenotype transition from wild mouflon to domestic sheep
Authors: Mereu Paolo , Pirastru Monica , Sanna Daria , Bassu Giovanni , Naitana Salvatore , Leoni Giovanni Giuseppe 
Published: January 2024

AbstractThe domestication of animals started around 12,000 years ago in the Near East region. This “endless process” is characterized by the gradual accumulation of changes that progressively marked the genetic, phenotypic and physiological differences between wild and domesticated species. The main distinctive phenotypic characteristics are not all directly attributable to the human-mediated selection of more productive traits. In the last decades, two main hypotheses have been proposed to clarify the emergence of such a set of phenotypic traits across a variety of domestic species. The first hypothesis relates the phenotype of the domesticated species to an altered thyroid hormone-based signaling, whereas the second one relates it to changes in the neural crest cells induced by selection of animals for tameness. These two hypotheses are not necessarily mutually exclusive since they may have contributed differently to the process over time and space. The adaptation model induced by domestication can be adopted to clarify some aspects (that are still controversial and debated) of the long-term evolutionary process leading from the wild Neolithic mouflon to the current domestic sheep. Indeed, sheep are among the earliest animals to have been domesticated by humans, around 12,000 years ago, and since then, they have represented a crucial resource in human history. The aim of this review is to shed light on the molecular mechanisms and the specific genomic variants that underlie the phenotypic variability between sheep and mouflon. In this regard, we carried out a critical review of the most recent studies on the molecular mechanisms that are most accredited to be responsible for coat color and phenotype, tail size and presence of horns. We also highlight that, in such a complicate context, sheep/mouflon hybrids represent a powerful and innovative model for studying the mechanism by which the phenotypic traits related to the phenotypic responses to domestication are inherited. Knowledge of these mechanisms could have a significant impact on the selection of more productive breeds. In fact, as in a journey back in time of animal domestication, the genetic traits of today’s domestic species are being progressively and deliberately shaped according to human needs, in a direction opposite to that followed during domestication.
Graph embedding on mass spectrometry- and sequencing-based biomedical data
Authors: Alvarez-Mamani Edwin , Dechant Reinhard , Beltran-Castañón César A. , Ibáñez Alfredo J. 
Published: January 2024

AbstractGraph embedding techniques are using deep learning algorithms in data analysis to solve problems of such as node classification, link prediction, community detection, and visualization. Although typically used in the context of guessing friendships in social media, several applications for graph embedding techniques in biomedical data analysis have emerged. While these approaches remain computationally demanding, several developments over the last years facilitate their application to study biomedical data and thus may help advance biological discoveries. Therefore, in this review, we discuss the principles of graph embedding techniques and explore the usefulness for understanding biological network data derived from mass spectrometry and sequencing experiments, the current workhorses of systems biology studies. In particular, we focus on recent examples for characterizing protein–protein interaction networks and predicting novel drug functions.
Prognostic value of oxidative stress-related genes in colorectal cancer and its correlation with tumor immunity
Authors: Yang Leilei , Fang Chengfeng , Zhang Ruili , Zhou Shenkang 
Published: January 2024

AbstractOxidative stress (OS) plays an essential role in chronic diseases such as colorectal cancer (CRC). In this study, we aimed to explore the relation between oxidative stress-related genes and CRC prognosis and their involvement in the immune microenvironment. Totally 101 OS-related genes were selected from the MsigDB database. Then, univariate Cox regression was used to explore the prognostic value of the selected genes correlated with the CRC patient survival in the TCGA database. A total of 9 prognostic OS-related genes in CRC were identified. Based on consensus clustering, CRC patients were then categorized into two molecular subtypes. A prognostic risk model containing 8 genes was established using Lasso regression, and CRC patients were divided into high or low-risk groups based on the median risk scores. The predictive value of the 8 genes in CRC prognosis was validated using ROC curves, which indicate that CTNNB1, STK25, RNF112, SFPQ, MMP3, and NOL3 were promising prognostic biomarkers in CRC. Furthermore, the immune cell infiltration levels in different risk groups or CRC subtypes were analyzed. We found that the high-risk or C1 subtype had immunosuppressive microenvironment, which might explain the unfavorable prognosis in the two groups of CRC patients. Additionally, functional experiments were conducted to investigate the effects of OS-related genes on CRC cell proliferation, stemness, and apoptosis. We found that CTNNB1, HSPB1, MMP3, and NOL3 were upregulated in CRC tissues and cells. Knockdown of CTNNB1, HSPB1, MMP3, and NOL3 significantly suppressed CRC cell proliferation, stemness and facilitated CRC cell apoptosis. In conclusion, we established prognostic CRC subtypes and an eight-gene risk model, which may provide novel prognostic indicators and benefit the design of individualized therapeutic strategies for CRC patients.