bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the quality of bibliographic data sources for measuring international research collaboration
Authors: Nguyen Ba Xuan , Luczak-Roesch Markus , Dinneen Jesse David , Larivière Vincent 
Published: September 2022

Abstract
Measuring international research collaboration (IRC) is essential to various research assessment tasks but the effect of various measurement decisions, including which data sources to use, has not been thoroughly studied. To better understand the effect of data source choice on IRC measurement, we design and implement a data quality assessment framework specifically for bibliographic data by reviewing and selecting available dimensions and designing appropriate computable metrics, and then validate the framework by applying it to four popular sources of bibliographic data: Microsoft Academic Graph, Web of Science (WoS), Dimensions, and the ACM Digital Library. Successful validation of the framework suggests it is consistent with the popular conceptual framework of information quality proposed by Wang and Strong (1996) and adequately identifies the differences in quality in the sources examined. Application of the framework reveals that WoS has the highest overall quality among the sets considered; and that the differences in quality can be explained primarily by how the data sources are organized. Our study comprises a methodological contribution that enables researchers to apply this IRC measurement tool in their studies and makes an empirical contribution by further characterizing four popular sources of bibliographic data and their impact on IRC measurement.
MicroRNA in the diagnosis of lung cancer: An overview of ten systematic reviews
Authors: Hua Jinyong , Liu Jing , Ma Mingxia , Xie Linsen , Tian Jinhui 
Published: September 2022

Objective To provide theoretical support for clinical diagnosis of lung cancer through an overview of systematic reviews (SRs) of the diagnostic value of miRNA. Methods We searched PubMed, Embase, and the Cochrane Library to collect SRs of the diagnostic value of microRNA for lung cancer until April 2021. A comprehensive database search was carried out, screened, and extracted information independently by two researchers, to compare and analyze the sensitivity and specificity of relevant literatures. The ROBIS tool was applied to assess the risk of bias of included SRs and meta-analysis. Results A total of 10 SRs were included the results of risk of bias assessment by ROBIS tool showed: 10 SRs completely matched the four questions of phase one. In phase two, nine SRs were low risk of bias in the including criteria field; one study was uncertain; nine SRs were low risk of bias, one study was uncertain in the literature search and screening field; nine SRs were low risk of bias in the data abstraction and quality assessment field, one SR was high; and 10 SRs were low risk of bias in the data synthesis field. In the phase three of comprehensive risk of bias results, 8 studies were low risk, one was high risk, and one study was uncertain. MiRNA had a pooled sensitivity of 0.77 (95% CI: 0.73–0.81) and specificity of 0.81 (95% CI: 0.79–0.84). The summarized area under the SROC curve was 0.86 (95% CI: 0.83–0.89), and combined diagnostic odds ratio was 14.68 (10.87–19.81). The sensitivity and specificity of multiple MicroRNA was 0.80 (0.73–0.85) and 0.80 (0.76–0.83); the sensitivity and specificity of single MicroRNA was 0.74 (0.69–0.79) and 0.83 (0.80–0.88). Conclusion MiRNA is a promising biomarker for the diagnosis of lung cancer in Chinese population, with advanced sensitivity and specificity. It provides a faster and less invasive assessment of lung cancer than other markers that require histopathological analysis. We should improve the reliability of the conclusion. The construction of diagnosis for lung cancer provides reliable evidence support.
Visit Intention Via Mobile App Usage in Pandemic Alleviation: Influences of Regulatory Focus and Risk
Authors: Yi Xiao (Shannon) , Kim Hwang , Luo Xiaoyan , Wan Lisa C. 
Published: September 2022

This study examines the relationship between pandemic alleviation and tourists’ intention to visit tourist and hospitality sites. It identifies that tourists’ regulatory focus affects their risk perception in visiting tourist and hospitality sites via mobile app usage during the stage of pandemic alleviation. Mixed methods that combine quantitative modeling and experiment were adopted. A total of six sets of panel data of mobile app usage in South Korea during and after the first wave of the pandemic was analyzed, supported by an experimental study to test the causal effect. Results reveal an increasing intention to engage in on-site hospitality and tourism activities in the alleviating period of a pandemic wave. This tendency is stronger for promotion-focused (vs. prevention-focused) tourists. The experimental study also confirms that risk perception mediates the relationship between pandemic alleviation and visit intention. This research provides insights for facilitating the recovery of the travel and hospitality industry. Highlights Mobile app use records reflect visit intention to tourist sites in the pandemic. Perceived risk mediates the effect of pandemic alleviation on visit intention. Promotion-focused people show higher visit intention when pandemic waves abate. A mixed-method approach was adopted to examine the aforementioned effects.
A Bayesian adaptive design for clinical trials of rare efficacy outcomes with multiple definitions
Authors: Golchi Shirin , Willard James J , Pullenayegum Eleanor , Bassani Diego G , Pell Lisa G , Thorlund Kristian , Roth Daniel E 
Published: September 2022

Introduction: Bayesian adaptive designs for clinical trials have gained popularity in the recent years due to the flexibility and efficiency that they offer. We consider the scenario where the outcome of interest comprises events with relatively low risk of occurrence and different case definitions resulting in varying control group risk assumptions. This is a scenario that occurs frequently for infectious diseases in global health research. Methods: We propose a Bayesian adaptive design that incorporates different case definitions of the outcome of interest that vary in stringency. A set of stopping rules are proposed where superiority and futility may be concluded with respect to different outcome definitions and therefore maintain a realistic probability of stopping in trials with low event rates. Through a simulation study, a variety of stopping rules and design configurations are compared. Results: The simulation results are provided in an interactive web application that allows the user to explore and compare the design operating characteristics for a variety of assumptions and design parameters with respect to different outcome definitions. The results for select simulation scenarios are provided in the article. Discussion: Bayesian adaptive designs offer the potential for maximizing the information learned from the data collected through clinical trials. The proposed design enables monitoring and utilizing multiple composite outcomes based on rare events to optimize the trial design operating characteristics.
Assessment of Anatomic Restoration and Clinical Outcomes Between Medial and Lateral Meniscal Allograft Transplantation
Authors: Jeong Ho Won , Kim Joo Sung , Nam Hee Seung , Noh Gwon Seok , Lee Yong Seuk 
Published: September 2022

Background: Proper anatomic restoration is an important consideration for meniscal allograft transplantation (MAT), even with the different anatomica characteristics between the medial meniscus and lateral meniscus. Purpose/Hypothesis: The purpose of this study was to assess the accuracy of anatomic restoration in medial and lateral MAT (MMAT and LMAT) procedures and to compare their outcomes. We hypothesized that (1) the anatomic differences between the medial and lateral menisci will mean a less accurate anatomic restoration for MMAT and (2) clinical outcomes after MMAT will be inferior compared with LMAT. Study Design: Cohort study; Level of evidence, 3. Methods: We retrospectively evaluated 20 patients who underwent MMAT using the bone plug technique and 21 patients who underwent LMAT using the keyhole technique at a single institution from July 2014 to June 2019. Demographic data, previous surgeries, and concomitant procedures were recorded, as were lower limb alignment and osteoarthritis grade on radiographs. Using preoperative and follow-up magnetic resonance imaging, the meniscal position, rotation, extrusion, and intrameniscal signal intensity were evaluated. Clinical outcomes were evaluated using the International Knee Documentation Committee and Lysholm scores. Results: The mean follow-up was 41.15 ± 18.86 and 45.43 ± 21.32 months for the MMAT and LMAT patients, respectively. Concomitant procedures were performed in 90% of MMATs and 15% of LMATs. There was no significant difference between the native and postoperative root positions after LMAT; however, for MMAT, the position of the anterior root was located significantly posteriorly ( P = .002) and medially ( P = .007) compared with preoperatively. In addition, the allograft medial meniscus was restored in a more internally rotated position ( P = .029). MMATs also exhibited significantly increased meniscal extrusion compared with LMATs (posterior horn, P < .001; midbody, P = .027; anterior horn, P = .006). However, there was no significant difference between the 2 groups at final follow-up in intrameniscal signal intensity or clinical scores. Conclusion: LMAT showed higher accuracy than MMAT in restoring meniscal position and rotation, and there was less meniscal extrusion. However, clinical scores improved after both LMAT and MMAT compared with preoperative values, and midterm clinical outcomes were similar. The small anatomical errors seen in the MMAT technique were not clinically relevant at midterm follow-up.
Comparison of Open Versus Arthroscopic Repair for Subscapularis Tendon Tears With or Without Concomitant Supraspinatus Tendon Tears
Authors: Gedikbas Mete , Ozturk Tahir , Erpala Fırat , Zengin Eyup Cagatay 
Published: September 2022

Background: The literature comparing open and arthroscopic repair of subscapularis tendon (ST) tears is insufficient. Purpose: To compare the clinical results of open versus arthroscopic repair of ST tears with or without concomitant supraspinatus tears. Study Design: Retrospective cohort study. Methods: We retrospectively evaluated 70 patients treated for isolated ST tears and ST tears with concomitant supraspinatus tendon tears at a single center between 2011 and 2019. Patients were divided into 2 groups: those who underwent open ST repairs (group O) and those with an arthroscopic ST repair (group A). Range of motion (ROM), liftoff and belly-press tests, and Constant-Murley (CM) scores were included in the pre- and postoperative functional evaluations. The minimal clinically important difference was calculated using the anchor-based method for changes in CM score. Tear size was evaluated according to the Lafosse classification. The categorical data were assessed using the Pearson chi-square, Fisher exact, and Fisher-Freeman-Halton tests. The parametric and nonparametric data were evaluated using the Student t test and Mann-Whitney U test, respectively. The dependent groups (for nonnormally distributed data) were evaluated using the Wilcoxon signed rank test. Results: Group O included 34 patients, and group A included 36 patients. The mean age was 62.9 years, and the mean follow-up period was 66.7 months. Even though group O exhibited a significantly better preoperative CM score (53.7 ± 4.6 vs 48.9 ± 6.8 [mean ± SD]; P = .001), group A had a significantly better postoperative CM score (88.7 ± 4.7 vs 84.6 ± 2.9; P < .001). Our measurements revealed a minimal clinically important difference of 11.5 points for the CM score. Group A had significantly greater postoperative ROM in abduction (153° vs 143.9°; P = .005) and forward elevation (159.1° vs 149.7°; P = .005), as well as significantly greater postoperative improvement in positive belly-press test results ( P = .028). Complications occurred in 4 patients in group O and in 1 patient in group A. Conclusion: The study findings indicated that arthroscopic ST repair was more advantageous than open repair in terms of ROM and functional outcomes.
Efficacy and safety of cilta-cel in patients with progressive multiple myeloma after exposure to other BCMA-targeting agents
Authors: Cohen Adam D. , Mateos María-Victoria , Cohen Yael C. , Rodriguez-Otero Paula , Paiva Bruno , van de Donk Niels W. C. J. , Martin Thomas , Suvannasankha Attaya , De Braganca Kevin C. , Corsale Christina , Schecter Jordan M. , Varsos Helen , Deraedt William , Wang Liwei , Vogel Martin , Roccia Tito , Xu Xiaoying , Mistry Pankaj , Zudaire Enrique , Akram Muhammad , Nesheiwat Tonia , Pacaud Lida , Avivi Irit , San-Miguel Jesus 
Published: September 2022

Abstract
B-cell maturation antigen (BCMA)–targeting therapies, including bispecific antibodies (BsAbs) and antibody-drug conjugates (ADCs), are promising treatments for multiple myeloma (MM), but disease may progress after their use. CARTITUDE-2 is a phase 2, multicohort study evaluating the safety and efficacy of cilta-cel, an anti-BCMA chimeric antigen receptor T therapy, in various myeloma patient populations. Patients in cohort C progressed despite treatment with a proteasome inhibitor, immunomodulatory drug, anti-CD38 antibody, and noncellular anti-BCMA immunotherapy. A single cilta-cel infusion was given after lymphodepletion. The primary end point was minimal residual disease (MRD) negativity at 10−5. Overall, 20 patients were treated (13 ADC exposed; 7 BsAb exposed; 1 in the ADC group also had prior BsAb exposure). Sixteen (80%) were refractory to prior anti-BCMA therapy. At a median follow-up of 11.3 months (range, 0.6-16.0), 7 of 20 (35%) patients were MRD negative (7 of 10 [70.0%] in the MRD-evaluable subset). Overall response rate (95% confidence interval [CI]) was 60.0% (36.1-80.9). Median duration of response and progression-free survival (95% CI) were 11.5 (7.9—not estimable) and 9.1 (1.5—not estimable) months, respectively. The most common adverse events were hematologic. Cytokine release syndrome occurred in 12 (60%) patients (all grade 1-2); 4 had immune effector cell-associated neurotoxicity syndrome (2 had grade 3-4); none had parkinsonism. Seven (35%) patients died (3 of progressive disease, 4 of adverse events [1 treatment related, 3 unrelated]). Cilta-cel induced favorable responses in patients with relapsed/refractory MM and prior exposure to anti-BCMA treatment who had exhausted other therapies. This trial was registered at www.clinicaltrials.gov as NCT04133636.
Effective treatment of low-risk acute GVHD with itacitinib monotherapy
Authors: Etra Aaron , Capellini Alexandra , Alousi Amin , Al Malki Monzr M. , Choe Hannah , DeFilipp Zachariah , Hogan William J. , Kitko Carrie L. , Ayuk Francis , Baez Janna , Gandhi Isha , Kasikis Stelios , Gleich Sigrun , Hexner Elizabeth , Hoepting Matthias , Kapoor Urvi , Kowalyk Steven , Kwon Deukwoo , Langston Amelia , Mielcarek Marco , Morales George , Özbek Umut , Qayed Muna , Reshef Ran , Rösler Wolf , Spyrou Nikolaos , Young Rachel , Chen Yi-Bin , Ferrara James L. M. , Levine John E. 
Published: September 2022

AbstractThe standard primary treatment for acute graft-versus-host disease (GVHD) requires prolonged, high-dose systemic corticosteroids (SCSs) that delay reconstitution of the immune system. We used validated clinical and biomarker staging criteria to identify a group of patients with low-risk (LR) GVHD that is very likely to respond to SCS. We hypothesized that itacitinib, a selective JAK1 inhibitor, would effectively treat LR GVHD without SCS. We treated 70 patients with LR GVHD in a multicenter, phase 2 trial (NCT03846479) with 28 days of itacitinib 200 mg/d (responders could receive a second 28-day cycle), and we compared their outcomes to those of 140 contemporaneous, matched control patients treated with SCSs. More patients responded to itacitinib within 7 days (81% vs 66%, P = .02), and response rates at day 28 were very high for both groups (89% vs 86%, P = .67), with few symptomatic flares (11% vs 12%, P = .88). Fewer itacitinib-treated patients developed a serious infection within 90 days (27% vs 42%, P = .04) due to fewer viral and fungal infections. Grade ≥3 cytopenias were similar between groups except for less severe leukopenia with itacitinib (16% vs 31%, P = .02). No other grade ≥3 adverse events occurred in &gt;10% of itacitinib-treated patients. There were no significant differences between groups at 1 year for nonrelapse mortality (4% vs 11%, P = .21), relapse (18% vs 21%, P = .64), chronic GVHD (28% vs 33%, P = .33), or survival (88% vs 80%, P = .11). Itacitinib monotherapy seems to be a safe and effective alternative to SCS treatment for LR GVHD and deserves further investigation.
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers
Authors: Maruyama Osamu , Li Yinuo , Narita Hiroki , Toh Hidehiro , Au Yeung Wan Kin , Sasaki Hiroyuki 
Published: September 2022

Abstract
Background
Epigenetic modifications established in mammalian gametes are largely reprogrammed during early development, however, are partly inherited by the embryo to support its development. In this study, we examine CpG island (CGI) sequences to predict whether a mouse blastocyst CGI inherits oocyte-derived DNA methylation from the maternal genome. Recurrent neural networks (RNNs), including that based on gated recurrent units (GRUs), have recently been employed for variable-length inputs in classification and regression analyses. One advantage of this strategy is the ability of RNNs to automatically learn latent features embedded in inputs by learning their model parameters. However, the available CGI dataset applied for the prediction of oocyte-derived DNA methylation inheritance are not large enough to train the neural networks.

Results
We propose a GRU-based model called CMIC (CGI Methylation Inheritance Classifier) to augment CGI sequence by converting it into variable-length k-mers, where the length k is randomly selected from the range $$k_{\min }$$

k
min

to $$k_{\max }$$

k
max

, N times, which were then used as neural network input. N was set to 1000 in the default setting. In addition, we proposed a new embedding vector generator for k-mers called splitDNA2vec. The randomness of this procedure was higher than the previous work, dna2vec.

Conclusions
We found that CMIC can predict the inheritance of oocyte-derived DNA methylation at CGIs in the maternal genome of blastocysts with a high F-measure (0.93). We also show that the F-measure can be improved by increasing the parameter N, that is, the number of sequences of variable-length k-mers derived from a single CGI sequence. This implies the effectiveness of augmenting input data by converting a DNA sequence to N sequences of variable-length k-mers. This approach can be applied to different DNA sequence classification and regression analyses, particularly those involving a small amount of data.
Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods
Authors: Yan Jindong , He Jiacheng , Li Jian’an , Ren Shuangshuang , Wang Ying , Zhou Junqin , Tan Xiaofeng 
Published: September 2022

Abstract
Background
Camellia oleifera Abel. (C. oleifera) is an important traditional woody species in China that produces edible oil. However, the current literature lacks a proper understanding of C. oleifera’s ability to adapt to different photoperiods.

Results
Our results indicate that the photoperiod can significantly impact flowering time in C. oleifera. We grew a total of nine samples under the short day condition (SD), middle day condition (MD) and long day condition (LD). Transcriptome analysis yielded 66.94 Gb of high-quality clean reads, with an average of over 6.73 Gb of reads for per sample. Following assembly, a total of 120,080 transcripts were obtained and 94,979 unigenes annotated. A total of 3475 differentially expressed genes (DEGs) were identified between the SD_MD, SD_LD, and MD_LD gene sets. Moreover, WGCNA identified ten gene modules. Genes in pink module (92 genes) were positively correlated with SD, and negatively correlated with both MD and LD. Genes in the magenta module (42 genes) were positively correlated with MD and negatively correlated with both LD and SD. Finally, genes in the yellow module (1758 genes) were positively correlated with both SD and MD, but negatively correlated with LD. KEGG enrichment analysis revealed that genes in the pink, magenta, and yellow modules were involved in flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism and circadian rhythm pathways. Additionally, eight hub genes (GI, AP2, WRKY65, SCR, SHR, PHR1, ERF106, and SCL3) were obtained through network analysis. The hub genes had high connectivity with other photoperiod-sensitive DEGs. The expression levels of hub genes were verified by qRT-PCR analysis.

Conclusion
An increase in light duration promotes earlier flowering of C. oleifera. Flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism, and circadian rhythm pathways may function in the photoperiodic flowering pathway of C. oleifera. We also identified eight hub genes that may play a role in this pathway. Ultimately, this work contributes to our understanding of the photoperiodic flowering pathway of C. oleifera and further informs molecular breeding programs on the plant’s photoperiodic sensitivity.
Subacute stent thrombosis with spontaneously resolved secondary thrombi in paroxysmal nocturnal hemoglobinuria: a case report
Authors: Kawahara Hiroshi , Watanabe Nobuhide , Endo Akihiro , Yoshitomi Hiroyuki , Tanabe Kazuaki 
Published: September 2022

Abstract
Background
Stent thrombosis (ST) is a serious complication; however, a method to prevent ST in patients with thrombophilic diseases has not been established.

Case presentation
We report a case of subacute ST in a patient with paroxysmal nocturnal hemoglobinuria (PNH) who was receiving continuous heparin treatment in addition to the usual dual antiplatelet therapy for contrast defects at the proximal site of the occluded right coronary artery and the proximal site of the left circumflex artery. Despite the resolution of thrombi in secondary lesions, subacute ST occurred. After percutaneous coronary intervention for ST, triple therapy, including oral anticoagulation for PNH-related thrombosis, was initiated. The patient subsequently underwent craniotomy hematoma removal for hemorrhagic cerebral infarction.

Conclusions
Reported cases of ST in patients with PNH are very few, and this case adds evidence with respect to antithrombotic therapy in patients with thrombotic tendencies. Both thrombosis and bleeding should be considered when administering antithrombotic therapy to patients with thrombotic diseases. If there are specific treatments for thrombophilic diseases, they should be initiated early.