bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Risk of Major Bleeding With Apixaban Administration in Patients With Acute Kidney Injury
Authors: Givens Gabrielle , Neu Daniel , Marler Jacob 
Published: October 2022

Background: Apixaban is eliminated by the kidneys and in acute kidney injury (AKI) there is potential for an increase in apixaban exposure and bleeding events. In one instance, data have shown higher than normal bleed risk in patients with AKI, unless calibrated anti-factor Xa monitoring is used, which is not widely available. Objective: To evaluate bleeding with apixaban administration to hospitalized patients with an AKI in an unmonitored real-world scenario. Methods: We conducted a retrospective study of patients admitted to a large urban academic teaching hospital from April 2015 to March 2022, who received apixaban for venous thromboembolism or nonvalvular atrial fibrillation (NVAF). The primary outcome evaluated major bleeding when apixaban was administered to patients with or without an AKI. Results: A total of 232 patients were evaluated (116 per group). Most patients (79.7%) were on apixaban for NVAF, 32.7% had chronic kidney disease, 58.2% were on a medication increasing bleed risk, and HAS-BLED score was a median of 2 in both groups. No differences were noted between groups for bleeding (AKI group 7.8% vs non-AKI 3.4%; P = 0.15), and on regression analysis, coadministration of a P2Y12 inhibitor was predictive of major bleeding (odds ratio = 5.9; 95% confidence interval = 1.4-23.6). Conclusion and Relevance: Although no differences between groups were noted, apixaban use in the AKI group resulted in a higher than normally reported incidence of apixaban-associated major bleeding, and concomitant antiplatelet use increased bleed risk as well. Cautious use of apixaban and further investigation with larger studies are warranted in this area.
Efficacy and safety comparison of Helicobacter pylori eradication between vonoprazan dual therapy versus triple therapy: a systematic review and meta-analysis
Authors: Wang Zheyu , Wang Fen 
Published: October 2022

Background: As a novel drug, vonoprazan (VPZ) has been developed as a new strategy against Helicobacter pylori ( H. pylori) infections. However, whether VPZ + amoxicillin (AMO) dual therapy has a clear advantage is still unclear. Objective: To review and meta-analyze the available literature investigating the efficacy and safety of H. pylori eradication in VPZ dual therapy. Design: A systematic review and meta-analysis were conducted. Data sources and methods: We performed a systematic search in the PubMed, Embase, EIsevier/Science Library, and Cochrane Library databases from 2015 to 2022. Meta-analyses were conducted to evaluate the actual cure rate and the incidence rate of adverse reactions in dual therapy and VPZ + AMO + clarithromycin (CLA) triple therapy; furthermore, eradication rates in CLA-resistant infections and different doses of antibiotics were evaluated in subgroup analysis. Results: Seven studies with 1490 patients were included in this meta-analysis. According to intention-to-treat analysis, the actual cure rates of VPZ dual and triple therapy were 82.8% and 84.6%, respectively [ p = 0.29, odds ratio (OR): 0.86, 95% confidence interval (CI): 0.64–1.14]. And in the per-protocol analysis, the actual cure rates of these two therapies were 84.8% and 87.0%, respectively ( p = 0.21, OR: 0.80, 95% CI: 0.57–1.13). The incidence of adverse reactions between VPZ dual and triple therapy was 26.1% versus 29.6% ( p = 0.04, OR: 0.78, 95% CI: 0.61–0.99). In subgroup analysis, the eradication rates in CLA-resistant infections were dual therapy: 85.7% for VPZ versus 71.0% for triple therapy ( p = 0.03, OR: 2.36, 95% CI: 1.10–5.05). And the actual cure rate of VPZ with high-dose antibiotics was lower than with low-dose antibiotics ( p = 0.000 in dual therapy; p = 0.011 in triple therapy). Conclusion: A combination of VPZ and a low dose of AMO should be prioritized as a treatment option for H. pylori eradication. Registration: PROSPERO registration number CRD42022346100.
Pediatric first aid, trauma knowledge, and attitude among parents and general population in Aseer region, Southern Saudi Arabia
Authors: Wani Javed Iqbal , Almushayt Nouf Omar , Abbag Wejdan Fuad , Buhran Lama Ali , Nadeem Mir 
Published: October 2022

Objectives: Around the world, accidents and injuries are the leading causes of death among children. Because mothers and family members commonly administer first aid at home and at preschools, it’s critical to learn what parents and the public think about children’s mishaps. Our objective was to assess parents’ knowledge and attitude toward pediatric first aid in the Aseer region of Saudi Arabia. Methods: A cross-sectional study was conducted in the Aseer region of Saudi Arabia to assess the parents’ level of knowledge and attitude about pediatric first aid and trauma with an electronic- and paper-based multiple-choice self-administered questionnaire covering different medical emergencies. The Arabic and English versions of the questionnaire were made from the information obtained from the first aid educational content of the Saudi Ministry of Health. Results: When the participants were asked about their knowledge of pediatric first aid, arranged in descending order from most answers, 37% (n = 135) answered it was good, 30% (n = 111) answered that it was very good, 20% (n = 74) answered that it was not enough, and 13% (n = 47) answered that it was excellent. Results of the multiple linear regression analysis showed the knowledge score to be significantly higher among participants who had higher education levels (t = 2.039, p < 0.001), who had received first aid training before (t = 2.786, p = 0.0001), those who were already healthcare providers (t = 4.336, p < 0.001), those who were from rural districts (t = 2.5, p = 0.355), and younger personnel (t = 0.821, p = 0.345) The difference was not statistically significant. Conclusion: Although this study shows that the level of first aid knowledge among personnel who care for children was low, it also shows that they are interested in obtaining proper training.
Radiographic and Clinical Outcomes After Arthroscopic Microfracture for Osteochondral Lesions of the Talus: 5-Year Results in 355 Consecutive Ankles
Authors: Fu Shaoling , Yang Kai , Li Xueqian , Chen Cheng , Mei Guohua , Su Yan , Xue Jianfeng , Zou Jian , Zhang Jieyuan , Shi Zhongmin 
Published: October 2022

Background: Arthroscopic microfracture for osteochondral lesion of the talus (OLT) has shown good functional outcomes in the short and long term. Purpose: To investigate 5-year radiographic and clinical outcomes after arthroscopic microfracture in treatment of OLT and the effectiveness of adjunct therapies including platelet-rich plasma (PRP) and hyaluronic acid (HA). Study Design: Cohort study; Level of evidence, 2. Methods: We prospectively enrolled 432 patients who underwent arthroscopic microfracture for OLT from May 1, 2011, to May 31, 2015. Magnetic resonance imaging (MRI) and weightbearing radiographs were performed annually after the initial surgery. The MOCART (magnetic resonance observation of cartilage repair tissue) score was used to evaluate the structure of the repaired cartilage on MRI, and patient-reported outcomes (American Orthopaedic Foot and Ankle Society ankle-hindfoot scale [AOFAS] and the Foot and Ankle Outcome Score) were collected annually. The primary outcome measure was 5-year AOFAS score. We recorded baseline characteristics including age, body mass index (BMI), and lesion size, and other potentially related factors including number of PRP/HA injection and change in BMI from baseline. Results: Included were 355 patients, all with minimum 5-year follow-up data. The overall reoperation rate was 9.0% (32 of 355). According to multivariable analysis, 5-year AOFAS scores were associated with number of PRP injections (correlation coefficient, 3.12 [95% CI, 2.36 to 3.89]; P < .001), BMI at baseline (correlation coefficient, -0.222 [95% CI, -0.363 to -0.082]; P = .002), and mean BMI change from baseline (correlation coefficient, -1.15 [95% CI, -1.32 to -0.98]; P < .001). When comparing number of PRP injections (0, 1-2, or ≥3), we found that patients who had serial PRP injection (≥3 with at least a 3-month interval between injections) had diminished functional and radiographic deterioration over time. Conclusion: Arthroscopic microfracture improved patient-reported and structural outcomes for patients with OLT at 5 years after surgery. Serial PRP injections and reduction in BMI from baseline were able to slow radiographic and functional deterioration. Future trials regarding the combination of microfracture and PRP in treatment of OLT should focus on the efficacy of longer term, intra-articular, serial injections of PRP instead of single injections.
Ermakovite (NH4)(As2O3)2Br, a new exhalative arsenite bromide mineral from the Fan-Yagnob coal deposit, Tajikistan
Authors: Karpenko Vladimir Yu. , Pautov Leonid A. , Siidra Oleg I. , Mirakov Mirak A. , Zaitsev Anatoly N. , Plechov Pavel Yu. , Makhmadsharif Saimudasir 
Published: October 2022

AbstractIn terrestrial rocks, Br minerals are extremely rare with only nine minerals known where Br is a dominant component. A new arsenite bromide mineral ermakovite, (NH4)(As2O3)2Br, was discovered at the tract of Kukhi-Malik, Fan-Yagnob coal deposit, ca. 75 km N of Dushanbe, Tajikistan. Ermakovite is a fumarolic mineral formed directly from gas from a natural underground coal fire. Associated minerals are sulfur, realgar, amorphous As-sulfides, salammoniac, alacránite, bonazziite and thermessaite-(NH4). In addition, there are amorphous As2S3 intergrowths associated with ermakovite. The mineral typically occurs as tabular or prismatic hexagonal crystals up to 200 μm with the following forms: c (001), m (010) and p (014). Spherulites and multi-twinned intergrowths are very common. The mineral is optically uniaxial (–), ω = 1.960 (5) and ɛ = 1.716(3) (589 nm). The measured density is 3.64(2) g/cm3. The mineral is insoluble in water, HCl, HNO3 and organic solvents. The empirical formula calculated on the basis of (As+Sb) = 4 atoms per formula unit is [(NH4)0.92Na0.01]0.93(As3.94Sb0.06)4.00O6.02(Br0.97Cl0.08I0.01)1.06. The strongest lines in the powder X-ray diffraction pattern are [d, Å (I, %) (hkl)]: 9.160 (80)(001); 4.560(90)(002); 3.228(100) (102); 2.629(80)(110); and 2.522(60)(103). Ermakovite is hexagonal, P6/mmm, a = 5.271(3), c = 9.157(6) Å, V = 220.3(3) Å3 and Z = 1. The sandwich-type structure of ermakovite is based on three types of layers: (1) a honeycomb [As2O3] arsenite layer; (2) an NH4+ layer; and (3) a Br layer. The layer stacking sequence is ⋅⋅⋅NH4–As2O3–Br–As2O3–NH4⋅⋅⋅. Ermakovite has a synthetic analogue. Infrared and Raman spectra are also reported.An overview of the processes that give rise to high concentrations of Br, leading to the formation of exotic Br minerals, is given.
Transformation of FL into DLBCL with a PMBL gene expression signature
Authors: Loveday Tristan , Duns Gerben , Rimsza Lisa M. , Rech Karen L. , Cook James R. , Robetorye Ryan S. , Rosenthal Allison C. , Ramsower Colleen A. , Yip Tameson K. , McKinney Catherine L. , Swerdlow Steven H. , Bhavsar Shweta , Steidl Christian , Gibson Sarah E. 
Published: October 2022

Abstract
We investigated the clinicopathologic features of 5 follicular lymphomas (FLs) that transformed (tFL) morphologically to diffuse large B-cell lymphomas (DLBCLs) and had a primary mediastinal large B-cell lymphoma (PMBL)–like gene expression profile (tFL-PMBLsig-pos). None of the tFL-PMBLsig-pos cases arose in the mediastinum, all cases tested had a germinal center B-cell phenotype, 20% were CD30+, 60% CD23+, 80% MAL+, 20% CD200+, and 0% CD273/PDL2+. Whole-exome sequencing detected alterations in genes associated with both FL/DLBCL (CREBBP, KMT2C, KMT2D, ARID1A, HIST1 members, and TNFRSF14) and PMBL (JAK-STAT pathway genes, B2M, and CD58). Copy number (CN) analysis detected gains/amplification of REL and STAT6 in 60%, gains of SOCS1 in 40%, and gains of chromosome 16, including IL4R, in 40% of the cases. CN gains/amplification of BCL6 and MYC and loss of TNFRSF14 and TNFAIP3 were identified in 20% of the cases. Three of 5 cases lacked a BCL2 rearrangement. Despite having some features that are less common in DLBCL (MAL and CD23 expression and JAK-STAT activation), these tFL-PMBLsig-pos cases lack the most characteristic CN alteration seen in PMBL (9p24.1 gain/amplification). This cohort expands the biologic heterogeneity of tFL, illustrating a subset with gene expression and some genetic features reminiscent of PMBL, with potential treatment implications that include the use of novel targeted therapies.
Targeting the contact system in a rabbit model of extracorporeal membrane oxygenation
Authors: Tweddell James S. , Kharnaf Mousa , Zafar Farhan , Riggs Kyle W. , Reagor James A. , Monia Brett P. , Revenko Alexey , Leino Daniel G. , Owens A. Phillip , Martin Janine K. , Gourley Benjamin , Rosenfeldt Leah , Palumbo Joseph S. 
Published: October 2022

AbstractPrevious studies suggested that contact pathway factors drive thrombosis in mechanical circulation. We used a rabbit model of veno-arterial extracorporeal circulation (VA-ECMO) to evaluate the role of factors XI and XII in ECMO-associated thrombosis and organ damage. Factors XI and XII (FXI, FXII) were depleted using established antisense oligonucleotides before placement on a blood-primed VA-ECMO circuit. Decreasing FXII or FXI to &lt; 5% of baseline activity significantly prolonged ECMO circuit lifespan, limited the development of coagulopathy, and prevented fibrinogen consumption. Histological analysis suggested that FXII depletion mitigated interstitial pulmonary edema and hemorrhage whereas heparin and FXI depletion did not. Neither FXI nor FXII depletion was associated with significant hemorrhage in other organs. In vitro analysis showed that membrane oxygenator fibers (MOFs) alone are capable of driving significant thrombin generation in a FXII- and FXI-dependent manner. MOFs also augment thrombin generation triggered by low (1 pM) or high (5 pM) tissue factor concentrations. However, only FXI elimination completely prevented the increase in thrombin generation driven by MOFs, suggesting MOFs augment thrombin-mediated FXI activation. Together, these results suggest that therapies targeting FXII or FXI limit thromboembolic complications associated with ECMO. Further studies are needed to determine the contexts wherein targeting FXI and FXII, either alone or in combination, would be most beneficial in ECMO. Moreover, studies are also needed to determine the potential mechanisms coupling FXII to end-organ damage in ECMO.
IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations
Authors: Churkin Alexander , Ponty Yann , Barash Danny 
Published: October 2022

Abstract
Background
RNA deleterious point mutation prediction was previously addressed with programs such as and . The purpose of these programs is to predict a global conformational rearrangement of the secondary structure of a functional RNA molecule, thereby disrupting its function. was designed to deal with only single point mutations in a brute force manner, while in an efficient approach to deal with multiple point mutations was developed. The approach used in is based on the stabilization of the suboptimal RNA folding prediction solutions and/or destabilization of the optimal folding prediction solution of the wild type RNA molecule. The algorithm is significantly more efficient than the brute force approach in , but in the case of long sequences and large m-point mutation sets the becomes exponential in examining all possible stabilizing and destabilizing mutations.

Results
An inherent limitation in the and programs is their ability to predict only substitution mutations, as these programs were not designed to work with deletion or insertion mutations. To address this limitation we herein develop a very fast algorithm, based on suboptimal folding solutions, to predict a predefined number of multiple point deleterious mutations as specified by the user. Depending on the user’s choice, each such set of mutations may contain combinations of deletions, insertions and substitution mutations. Additionally, we prove the hardness of predicting the most deleterious set of point mutations in structural RNAs.

Conclusions
We developed a method that extends our previous MultiRNAmute method to predict insertion and deletion mutations in addition to substitutions. The additional advantage of the new method is its efficiency to find a predefined number of deleterious mutations. Our new method may be exploited by biologists and virologists prior to site-directed mutagenesis experiments, which involve indel mutations along with substitutions. For example, our method may help to investigate the change of function in an RNA virus via mutations that disrupt important motifs in its secondary structure.
A risk factor attention-based model for cardiovascular disease prediction
Authors: Qiu Yanlong , Wang Wei , Wu Chengkun , Zhang Zhichang 
Published: October 2022

Abstract
Background
Cardiovascular disease (CVD) is a serious disease that endangers human health and is one of the main causes of death. Therefore, using the patient’s electronic medical record (EMR) to predict CVD automatically has important application value in intelligent assisted diagnosis and treatment, and is a hot issue in intelligent medical research. However, existing methods based on natural language processing can only predict CVD according to the whole or part of the context information of EMR.

Results
Given the deficiencies of the existing research on CVD prediction based on EMRs, this paper proposes a risk factor attention-based model (RFAB) to predict CVD by utilizing CVD risk factors and general EMRs text, which adopts the attention mechanism of a deep neural network to fuse the character sequence and CVD risk factors contained in EMRs text. The experimental results show that the proposed method can significantly improve the prediction performance of CVD, and the F-score reaches 0.9586, which outperforms the existing related methods.

Conclusions
RFAB focuses on the key information in EMR that leads to CVD, that is, 12 risk factors. In the stage of risk factor identification and extraction, risk factors are labeled with category information and time attribute information by BiLSTM-CRF model. In the stage of CVD prediction, the information contained in risk factors and their labels is fused with the information of character sequence in EMR to predict CVD. RFAB makes well use of the fine-grained information contained in EMR, and also provides a reliable idea for predicting CVD.
MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network
Authors: Deng Lei , Liu Dayun , Li Yizhan , Wang Runqi , Liu Junyi , Zhang Jiaxuan , Liu Hui 
Published: October 2022

Abstract
Background
Increasing evidence shows that circRNA plays an essential regulatory role in diseases through interactions with disease-related miRNAs. Identifying circRNA-disease associations is of great significance to precise diagnosis and treatment of diseases. However, the traditional biological experiment is usually time-consuming and expensive. Hence, it is necessary to develop a computational framework to infer unknown associations between circRNA and disease.

Results
In this work, we propose an efficient framework called MSPCD to infer unknown circRNA-disease associations. To obtain circRNA similarity and disease similarity accurately, MSPCD first integrates more biological information such as circRNA-miRNA associations, circRNA-gene ontology associations, then extracts circRNA and disease high-order features by the neural network. Finally, MSPCD employs DNN to predict unknown circRNA-disease associations.

Conclusions
Experiment results show that MSPCD achieves a significantly more accurate performance compared with previous state-of-the-art methods on the circFunBase dataset. The case study also demonstrates that MSPCD is a promising tool that can effectively infer unknown circRNA-disease associations.
A centenary tale: population genetic insights into the introduction history of the oriental fire-bellied toad (Bombina orientalis) in Beijing
Authors: Zhang Shan , Lin Meixi , Liu Jiawei , Chen Jiangce , Liu Dong , Zhao Jindong , Yao Meng 
Published: October 2022

AbstractBackgroundThe successful establishment of a species population following a single introduction of a few individuals to a non-native area has been limited. Nevertheless, the oriental fire-bellied toad (Bombina orientalis) population in Beijing is purportedly descended from a single introduction of about 200 individuals translocated from Yantai, Shandong Province, China, in 1927.ResultsTo resolve the introduction process and to understand the genetic consequences since that introduction approximately 90 years ago, we investigated the population’s genetic diversity and structure using 261 toads from Beijing and two native Shandong populations and inferred the species’ introduction history using simulation-based approaches. Analysis of mitochondrial DNA (mtDNA) sequences showed the two haplotypes found in Beijing nested within Yantai haplotypes, thus corroborating the historical record of the translocation source. The mtDNA and 11 nuclear microsatellite markers revealed both considerably lower genetic diversity in Beijing than in the source population and strong genetic differentiation between them. Although the current census population in Beijing may be in the range of a few thousand, the effective population size was estimated at only 20–57. Simulations also suggest that this population may have descended from 40–60 founders.ConclusionsThe Beijing population’s genetic patterns were consistent with the consequences of a severe bottleneck during introduction followed by genetic drift. The introduction trajectory constructed for thisB. orientalispopulation reveals the genetic footprints of a small population sustained in isolation for nearly a century. Our results provide an intriguing example of establishment success from limited founders and may inform ex situ conservation efforts as well as the management of biological invasions.