bluuebunny/crossref_metadata_2025_split huggingface dataset:
Purpose, Partnership, and Possibilities: The Implementation of the Dog Aging Project Biobank
Authors: Mouttham Lara , Castelhano Marta G , Akey Joshua M , Benton Brooke , Borenstein Elhanan , Castelhano Marta G , Coleman Amanda E , Creevy Kate E , Crowder Kyle , Dunbar Matthew D , Ernst Holley R , Fajt Virginia R , Fitzpatrick Annette L , Garrison Susan J , Herndon Reba S , Jaramilla Debra , Jeffery Unity , Jonlin Erica C , Kaeberlein Matt , Karlsson Elinor K , Kerr Kathleen F , Levine Jonathan M , Ma Jing , McClelland Robyn L , Prescott Jena O , Promislow Daniel EL , Ruple Audrey , Schwartz Stephen M , Shrager Sandi , Snyder-Mackler Noah , Tinkle Amanda K , Tolbert M Katherine , Urfer Silvan R , Wilfond Benjamin S 
Published: November 2022

Background: Biobanks have been supporting longitudinal prospective and retrospective studies by providing standardized services for the acquisition, transport, processing, storage, and distribution of high-quality biological material and associated data. Here, we describe how the Dog Aging Project (DAP), a large-scale longitudinal study of the domestic dog ( Canis familiaris) with translational applications for humans, developed a biobank of canine biospecimens and associated data. Design and methods: This was accomplished by working with the Cornell Veterinary Biobank, the first biobank in the world to receive accreditation to ISO 20387:2018—General Requirements for Biobanking. The biobank research team was involved in the early collection stages of the DAP, contributing to the development of appropriate workflows and processing fit-for-purpose biospecimens. In support of a dynamic strategy for real-time adjustment of processes, a pilot phase was implemented to develop, test, and optimize the biospecimen workflows, followed by an early phase of collection, processing, and banking of specimens from DAP participants. Results: During the pilot and early phases of collection, the DAP Biobank stored 164 aliquots of whole blood, 273 aliquots of peripheral blood mononuclear cells, 130 aliquots of plasma, and 70 aliquots of serum, and extracted high molecular weight genomic DNA suitable for whole-genome sequencing from 109 whole blood specimens. These specimens, along with their associated preanalytical data, have been made available for distribution to researchers. Conclusion: We discuss the challenges and opportunities encountered during the implementation of the DAP Biobank, along with novel strategies for promoting biobanking sustainability such as partnering with a DAP quality assurance manager and a DAP marketing and communication specialist and developing a pilot grant structure to fund small innovative research projects.
Association of dipeptidyl peptidase-4 inhibitor use and the risk of asthma development among type 2 diabetes patients
Authors: Li Peng-Fei , Chung Chi-Hsiang , Liu Jhih-Syuan , Lu Chieh-Hua , Su Sheng-Chiang , Kuo Feng-Chih , Ho Li-Ju , Chen Kuan-Chan , Su Yu-Te , Chu Nain-Feng , Lee Chien-Hsing , Hsieh Chang-Hsun , Hung Yi-Jen , Lin Fu-Huang , Chien Wu-Chien , Liang Yao-Jen 
Published: November 2022

Background: Numerous studies have shown that dipeptidyl peptidase-4 inhibitors (DPP-4i) may regulate immunological pathways implicated in asthma. The association between DPP-4i use and risk of asthma development is limited, however. Aim: We aimed to evaluate if DPP-4i treatment in individuals with type 2 diabetes mellitus (T2DM) is associated with a lower risk and severity of asthma. Methods: We performed a population-based retrospective cohort study using the Longitudinal National Health Insurance Research database between 2008 and 2015. After one-to-four propensity score matching from 1,914,201 patients with defined criteria, we enrolled 3001 patients who were on DPP-4i (DPP-4i group) for a diagnosis of T2DM but without a diagnosis of asthma for further analysis. Cox proportional hazards regression analysis was performed to estimate and compare the risk of developing and severity of asthma, including no acute exacerbations event (No-AE), acute exacerbations (AEs), status asthmaticus (Status), and required endotracheal intubation (ET-tube intubated), between the two groups. Results: The participants had a mean age of 66.05 ± 17.23 years and the mean follow-up time was 4.96 ± 4.39 years. The risk of asthma development was significantly lower in the DPP-4i group than in the non-DPP-4i group [adjusted hazard ratio (HR) = 0.65; 95% confidence interval (CI) = 0.29–0.83; p < 0.001], with a class effect. This trend was observed for severity of asthma as No-AE (HR = 0.55; 95% CI = 0.24–0.70; p < 0.001), AE (HR = 0.57; 95% CI = 0.26–0.73; p < 0.001), and Status (HR = 0.78; 95% CI = 0.35–0.99; p = 0.047), but not in ET-tube intubated cases (HR = 0.96; 95% CI = 0.43–1.22; p = 0.258). Conclusion: The use of DPP-4i decreased the risk and severity of asthma with a class effect among No-AE, AE, status of asthma events, but not in ET-tube intubated events. Our report suggests that DPP-4i may play a role in attenuating the impact of asthma on incidence in the future and on more severe forms of disease exacerbation in T2DM patients.
Mechanical Evaluation of Salvage Fixation Techniques for a Lateralized Fibular Tunnel in Posterolateral Corner Reconstruction of the Knee
Authors: Amirhekmat Arya , Brown Wendy E. , Athanasiou Kyriacos A. , Wang Dean 
Published: November 2022

Background: Posterolateral corner (PLC) reconstruction of the knee involves precise drilling of a single tunnel from anterolateral to posteromedial in the fibular head (FH) to ensure adequate graft fixation. Misplacement of the tunnel in a too lateral or too superior trajectory can lead to cortical breach and inadequate graft fixation. Purpose: To (1) determine the mechanical consequence of a lateralized FH tunnel in PLC reconstruction and (2) compare the mechanical strength of 3 salvage fixation techniques for a lateralized FH tunnel. Study Design: Controlled laboratory study. Methods: Sawbones models of a uniform density were utilized. FH tunnels (7-mm diameter) were drilled from anterolateral to posteromedial in positive controls (lateral cortex thickness, 7.6 ± 0.7 mm) to represent an improperly placed FH tunnel at risk of lateral cortical breach. For negative controls and salvage experimental groups, FH tunnels were drilled from anterolateral to posterolateral (lateral cortex thickness, 2.7 ± 0.9 mm). Three salvage fixation techniques were compared: suture anchor fixation, tunnel redrilling, and nitinol staple fixation. Samples (n = 5 per group) underwent uniaxial tension testing, and the ultimate tensile strength (UTS) and mode of failure were recorded. Data were analyzed using the 1-sample t test and nonparametric 1-sample Wilcoxon signed-rank test. Results: The negative control group had a 4-fold lower mean UTS relative to the positive control group (1.49 ± 0.17 vs 6.25 ± 1.98 MPa; P < .01) and exhibited failure through the lateral cortex and tunnel. Nitinol staple fixation improved the mean UTS by >16 times compared with the negative control group (24.06 ± 6.49 vs 1.49 ± 0.17 MPa; P < .01). Suture anchors and tunnel redrilling exhibited similar UTS and mode of failure to those of negative controls. Conclusion: Reinforcement of a thinned lateral FH cortex with a single nitinol staple improved graft fixation strength in a sawbones model. Clinical Relevance: A lateralized FH tunnel can be a common intraoperative pitfall during PLC reconstruction. Salvage of a thinned lateral FH cortex with a single nitinol staple may reduce the risk of cortical breach and graft failure.
Clinical evidence of interventions assessed in Friedreich ataxia: a systematic review
Authors: Jain Paridhi , Badgujar Lohit , Spoorendonk Jelle , Buesch Katharina 
Published: November 2022

Objectives: The rare inherited autosomal recessive disease Friedreich ataxia (FA) causes progressive neurodegenerative changes and disability in patients. A systematic literature review (SLR) was carried out to understand and summarize the published efficacy and safety of therapeutic interventions in this disease. Methods: Database searches were carried out in MEDLINE, Embase, and Cochrane by two independent reviewers. In addition, trial registries and conference proceedings were hand-searched. Results: Thirty-two publications were deemed eligible according to PICOS criteria. Twenty-four publications detail randomized controlled trials. The most frequently identified therapeutic intervention was idebenone ( n = 11), followed by recombinant erythropoietin ( n = 6), omaveloxolone ( n = 3), and amantadine hydrochloride ( n = 2). Other therapeutic interventions were investigated in one publication: A0001, CoQ10, creatine, deferiprone, interferon-γ-1b, the L-carnitine levorotatory form of 5-hydroxytryptophan, luvadaxistat, resveratrol, RT001, and vatiquinone (EPI-743). These studies included patients from 8 to 73 years old, and disease duration varied from 4.7 to 19 years. Disease severity as per the mean GAA1 and GAA2 allele repeat length ranged from 350 to 930 and 620 to 987 nucleotides, respectively. Most frequently reported efficacy outcomes were the International Cooperative Ataxia Rating Scale (ICARS, n = 10), the Friedreich Ataxia Rating Scale (modified FARS and FARS-neuro, n = 12), the Scale for Assessment and Rating of Ataxia (SARA, n = 7), and the Activities of Daily Living scale (ADL, n = 8). Each of these assesses the severity of disability in FA patients. In many studies, patients with FA deteriorated according to these severity scales regardless of treatment, or inconclusive results were found. Generally, these therapeutic interventions were well-tolerated and safe. Serious adverse events were atrial fibrillation ( n = 1), craniocerebral injury ( n = 1), and ventricular tachycardia ( n = 1). Conclusion: Identified literature showed a considerable unmet need for therapeutic interventions that halt or slow the deteriorating nature of FA. Novel efficacious drugs should be investigated that aim to improve symptoms or slow disease progression.
Research Progress of Refractory High Entropy Alloys: A Review
Authors: Xie Xiaochang , Li Neng , Liu Wei , Huang Shuai , He Xiaoyong , Yu Qiuying , Xiong Huaping , Wang Enhui , Hou Xinmei 
Published: November 2022

AbstractOwing to superior comprehensive performance than conventional superalloys at high temperature, refractory high entropy alloy (RHEA) is becoming a promising candidate for the next generation high-temperature material. Herein, contemporary aspects of corresponding development of RHEAs are reviewed to discuss various factors affecting the organization structure and service performance. It mainly covers alloying system and strengthening mechanism, the preparation method, plastic deformation and the related mechanism, as well as microstructure control by heat treatment. Firstly, the alloy systems and strengthening mechanism are introduced. This is followed by different preparation methods and the comparison of strengths and shortcomings based on different RHEAs. Then, hot deformation behavior and plastic deformation under different loadings are analyzed. Based on this, the influence of heat treatment on microstructures prior to and after the deformation is further summarized. Finally, some important research areas to be carried out in future are pointed out. This review will give a deep understanding of the effects of different factors on the service performance and provide scientific guide in designing RHEAs with improved performance.
Transcriptomic profiling implicates PAF1 in both active and repressive immune regulatory networks
Authors: Kenaston Matthew W. , Pham Oanh H. , Petit Marine J. , Shah Priya S. 
Published: November 2022

Abstract
Background
Sitting at the interface of gene expression and host-pathogen interaction, polymerase associated factor 1 complex (PAF1C) is a rising player in the innate immune response. The complex localizes to the nucleus and associates with chromatin to modulate RNA polymerase II (RNAPII) elongation of gene transcripts. Performing this function at both proximal and distal regulatory elements, PAF1C interacts with many host factors across such sites, along with several microbial proteins during infection. Therefore, translating the ubiquity of PAF1C into specific impacts on immune gene expression remains especially relevant.

Results
Advancing past work, we treat PAF1 knockout cells with a slate of immune stimuli to identify key trends in PAF1-dependent gene expression with broad analytical depth. From our transcriptomic data, we confirm PAF1 is an activator of traditional immune response pathways as well as other cellular pathways correlated with pathogen defense. With this model, we employ computational approaches to refine how PAF1 may contribute to both gene activation and suppression. Specifically focusing on transcriptional motifs and regulons, we predict gene regulatory elements strongly associated with PAF1, including those implicated in an immune response. Overall, our results suggest PAF1 is involved in innate immunity at several distinct axes of regulation.

Conclusions
By identifying PAF1-dependent gene expression across several pathogenic contexts, we confirm PAF1C to be a key mediator of innate immunity. Combining these transcriptomic profiles with potential regulatory networks corroborates the previously identified functions of PAF1C. With this, we foster new avenues for its study as a regulator of innate immunity, and our results will serve as a basis for targeted study of PAF1C in future validation studies.
A manually curated annotation characterises genomic features of P. falciparum lncRNAs
Authors: Hoshizaki Johanna , Adjalley Sophie H. , Thathy Vandana , Judge Kim , Berriman Matthew , Reid Adam J. , Lee Marcus C. S. 
Published: November 2022

Abstract
Background
Important regulation occurs at the level of transcription in Plasmodium falciparum and growing evidence suggests that these apicomplexan parasites have complex regulatory networks. Recent studies implicate long noncoding RNAs (lncRNAs) as transcriptional regulators in P. falciparum. However, due to limited research and the lack of necessary experimental tools, our understanding of their role in the malaria-causing parasite remains largely unelucidated. In this work, we address one of these limitations, the lack of an updated and improved lncRNA annotation in P. falciparum.

Results
We generated long-read RNA sequencing data and integrated information extracted and curated from multiple sources to manually annotate lncRNAs. We identified 1119 novel lncRNAs and validated and refined 1250 existing annotations. Utilising the collated datasets, we generated evidence-based ranking scores for each annotation and characterised the distinct genomic contexts and features of P. falciparum lncRNAs. Certain features indicated subsets with potential biological significance such as 25 lncRNAs containing multiple introns, 335 lncRNAs lacking mutations in piggyBac mutagenic studies and lncRNAs associated with specific biologic processes including two new types of lncRNAs found proximal to var genes.

Conclusions
The insights and the annotation presented in this study will serve as valuable tools for researchers seeking to understand the role of lncRNAs in parasite biology through both bioinformatics and experimental approaches.
SRGS: sparse partial least squares-based recursive gene selection for gene regulatory network inference
Authors: Guan Jinting , Wang Yang , Wang Yongjie , Zhuang Yan , Ji Guoli 
Published: November 2022

AbstractBackgroundThe identification of gene regulatory networks (GRNs) facilitates the understanding of the underlying molecular mechanism of various biological processes and complex diseases. With the availability of single-cell RNA sequencing data, it is essential to infer GRNs from single-cell expression. Although some GRN methods originally developed for bulk expression data can be applicable to single-cell data and several single-cell specific GRN algorithms were developed, recent benchmarking studies have emphasized the need of developing more accurate and robust GRN modeling methods that are compatible for single-cell expression data.ResultsWe present SRGS, SPLS (sparse partial least squares)-based recursive gene selection, to infer GRNs from bulk or single-cell expression data. SRGS recursively selects and scores the genes which may have regulations on the considered target gene based on SPLS. When dealing with gene expression data with dropouts, we randomly scramble samples, set some values in the expression matrix to zeroes, and generate multiple copies of data through multiple iterations to make SRGS more robust. We test SRGS on different kinds of expression data, including simulated bulk data, simulated single-cell data without and with dropouts, and experimental single-cell data, and also compared with the existing GRN methods, including the ones originally developed for bulk data, the ones developed specifically for single-cell data, and even the ones recommended by recent benchmarking studies.ConclusionsIt has been shown that SRGS is competitive with the existing GRN methods and effective in the gene regulatory network inference from bulk or single-cell gene expression data. SRGS is available at:https://github.com/JGuan-lab/SRGS.
Classification prediction of pancreatic cystic neoplasms based on radiomics deep learning models
Authors: Liang Wenjie , Tian Wuwei , Wang Yifan , Wang Pan , Wang Yubizhuo , Zhang Hongbin , Ruan Shijian , Shao Jiayuan , Zhang Xiuming , Huang Danjiang , Ding Yong , Bai Xueli 
Published: November 2022

Abstract
Background
Preoperative prediction of pancreatic cystic neoplasm (PCN) differentiation has significant value for the implementation of personalized diagnosis and treatment plans. This study aimed to build radiomics deep learning (DL) models using computed tomography (CT) data for the preoperative differential diagnosis of common cystic tumors of the pancreas.

Methods
Clinical and CT data of 193 patients with PCN were collected for this study. Among these patients, 99 were pathologically diagnosed with pancreatic serous cystadenoma (SCA), 55 were diagnosed with mucinous cystadenoma (MCA) and 39 were diagnosed with intraductal papillary mucinous neoplasm (IPMN). The regions of interest (ROIs) were obtained based on manual image segmentation of CT slices. The radiomics and radiomics-DL models were constructed using support vector machines (SVMs). Moreover, based on the fusion of clinical and radiological features, the best combined feature set was obtained according to the Akaike information criterion (AIC) analysis. Then the fused model was constructed using logistic regression.

Results
For the SCA differential diagnosis, the fused model performed the best and obtained an average area under the curve (AUC) of 0.916. It had a best feature set including position, polycystic features (≥6), cystic wall calcification, pancreatic duct dilatation and radiomics-DL score. For the MCA and IPMN differential diagnosis, the fused model with AUC of 0.973 had a best feature set including age, communication with the pancreatic duct and radiomics score.

Conclusions
The radiomics, radiomics-DL and fused models based on CT images have a favorable differential diagnostic performance for SCA, MCA and IPMN. These findings may be beneficial for the exploration of individualized management strategies.
Patient reported outcomes based on EQ-5D-5L questionnaires in head and neck cancer patients: a real-world study
Authors: Sprave Tanja , Gkika Eleni , Verma Vivek , Grosu Anca-Ligia , Stoian Raluca 
Published: November 2022

Abstract
Objective
Health economic comparisons of various therapies are often based on health-related quality of life (HRQOL) using EQ-5D questionnaires within the framework of clinical trials. This real-world study prospectively evaluates the patient reported outcomes (PROs)-based HRQOL of head-and-neck (H&N) cancer patients undergoing modern radiotherapy (RT) to reflect PRO trajectories.

Methods
All H&N cancer patients treated in our clinic between July 2019 and December 2020 who completed the self-reported validated EQ-5D-5L questionnaire (health state index (HI) and Visual Analog Scale (VAS)) at baseline, end of radiotherapy, and at each respective follow up (FU) were included. Descriptive analysis of clinical and sociodemographic data, the frequency and level of each dimension was conducted. To assess the significance of therapy-induced HRQOL changes within and between the group, a distribution-based approach was used.

Results
Altogether, 366 participants completed a total of 565 questionnaires. For the whole cohort, HI at baseline was 0.804 (±0.208), 0.830 (±0.162) at RT completion, 0.812 (±0.205) at the first follow-up, and 0.769 (±0.224) at the second follow-up. The respective VAS values were 62.06 (±23,94), 66.73 (±82.20), 63.30 (±22.74), and 65.48 (±23.39). Females showed significantly lower HI values compared to males, but only at baseline (p = 0.034). Significantly lower HI values were also seen in patients with definitive RT as compared to adjuvant RT at baseline (p = 0.023), the second follow-up (p = 0.047), and the third follow-up (p = 0.010). As compared to outpatients, inpatients had significantly lower HI values at RT completion (p = 0.017), the second follow-up (p = 0.007), and the third follow-up (p = 0.031). Subgroup analyses by age (< 65 vs. ≥65) and smoking status (smokers vs. non-smokers) showed no difference at any time point.

Conclusion
PROs demonstrated detectability of time- and intra−/inter-group therapy-induced HRQOL changes. A further detailed exploration of EQ-5D-5L responsiveness for H&N cancer patients is required.
Retinal arterial macroaneurysm rupture by Valsalva maneuver: a case report and literature review
Authors: Meng Yang , Xu Yishuang , Li Lu , He Lu , Yi Zuohuizi , Chen Changzheng 
Published: November 2022

Abstract
Background
Retinal artery macroaneurysms (RAMs) are focal dilations of the large retinal arteries. Most RAMs are asymptomatic, however, when hemorrhage or exudation caused by a RAM involves the macula, patients can experience marked vision loss. This article reported a rare case of a ruptured RAM due to the Valsalva maneuver in an elderly female with constipation and offered a review of the relevant literature.

Case presentation
A 78-year-old woman with several risk factors presented with multi-level retinal hemorrhages following a Valsalva maneuver during constipation. Due to the poor coagulation and heavy bleeding in this case, the blood broke through the internal limiting membrane and drained "on its own" into the vitreous cavity. First, we observed the patient and controlled for her risk factors. After the blood was completely drained into the vitreous cavity, the root cause of the bleeding was found to be a RAM rupture. After laser photocoagulation, the patient's vision recovered significantly and remained stable for a long time despite the presence of an epiretinal membrane and a lamellar macular hole.

Conclusions
This is the first reported case of a RAM rupture by Valsalva maneuver during constipation. For multi-level hemorrhages caused by RAM, measures should be taken to drain out the sub-internal limiting membrane hemorrhage and simultaneously control for risk factors. After the RAM is exposed, laser photocoagulation can be performed.