bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a predictive model for common bile duct stones in patients with clinical suspicion of choledocholithiasis: a single-center cohort study
Authors: Tunruttanakul Suppadech , Chareonsil Borirak , Verasmith Kotchakorn , Patumanond Jayanton , Mingmalairak Chatchai 
Published: May 2022

Abstract
BackgroundCurrent choledocholithiasis guidelines heavily focus on patients with low or no risk; they may be inappropriate for populations with high rates of choledocholithiasis. We aimed to develop a predictive scoring model for choledocholithiasis in patients with relevant clinical manifestations. MethodsDesign: A multivariable predictive model development study based on a retrospective cohort of patients with clinical suspicion of choledocholithiasis. Setting: A single 700-bed tertiary public hospital. Participants: Patients who completed three reference tests (endoscopic retrograde cholangiography, magnetic resonance cholangiopancreatography, and intraoperative cholangiography) from January 2019 to June 2021.Statistical analysis: The model was developed using logistic regression analysis. Predictor selection was conducted using a backward stepwise approach. Three risk groups were considered. Model performance was evaluated by area under the receiver-operating characteristic curve, calibration, classification measures, and decision curve analyses. Results Six hundred twenty-one patients were included; the choledocholithiasis prevalence was 59.9%. The predictors were age > 55 years, pancreatitis, cholangitis, cirrhosis, alkaline phosphatase level 125–250 or > 250 U/L, total bilirubin level > 4 mg/dL, common bile duct size > 6 mm, and common bile duct stone detection. Pancreatitis and cirrhosis each had a negative score. The sum of scores was -4.5 to 28.5. Patients were categorized into three risk groups: low-intermediate (score ≤ 5), intermediate (score 5–15), and high (score ≥ 15). Positive likelihood ratios were 0.16 and 3.47 in the low-intermediate and high risk groups, respectively.The model had an area under the receiver-operating characteristic curve of 0.80 (95% confidence interval: 0.76, 0.83) and was well-calibrated; it exhibited better statistical suitability to the high-prevalence population, compared to current guidelines. ConclusionsOur scoring model had good predictive ability for choledocholithiasis in patients with relevant clinical manifestations. Consideration of other factors is necessary for clinical application, particularly regarding the availability of expert physicians and specialized equipment.
Accelerating Minimap2 for accurate long read alignment on GPUs
Authors: SADASIVAN HARISANKAR , Maric Milos , Dawson Eric , Iyer Vishanth , Israeli Johnny , Narayanasamy Satish 
Published: May 2022

Abstract
Background

Long read sequencing technology is becoming increasingly popular for Precision Medicine applications like variant calling from Whole Genome Sequencing (WGS) and for metagenomics applications like microbial abundance estimation. Minimap2 is the state-of-the-art aligner and mapper used by the leading long read sequencing technologies, today. However, Minimap2 is very slow for long noisy reads. ∼60-70% of the run-time on a CPU comes from the highly sequential chaining step in Minimap2. On the other hand, most Point-of-Care computational workflows in long read sequencing use Graphics Processing Units (GPUs). We present minimap2-accelerated ( mm2-ax ), a heterogeneous design for sequence mapping and alignment where the compute intensive chaining step of minimap2 is sped up on the GPU and demonstrate its time and cost benefits.

Results

We extract better intra-read parallelism from chaining without loosing mapping accuracy by forward transforming Minimap2’s chaining algorithm . Further, we utilize the high memory available on modern cloud instances for better performance on the GPU by converting a sparse vector which defines the chaining workload to a dense one in order to optimize for better arithmetic intensity (more operations per byte of data fetched from high-latency global memory) on the GPU. We also optimize for better workload balancing, data locality and minimal branch divergence on the GPU. We show mm2-ax on an NVIDIA A100 GPU improves the chaining step with 12.6 - 5X speedup and 9.44 - 3.77X speedup: costup over the fastest version of Minimap2, mm2-fast , benchmarked on a single Google Cloud Platform instance of 30 SIMD cores.

Conclusions

mm2-ax is minimap2 sped-up on GPU without losing mapping accuracy. mm2-ax executable is made available at: https://doi.org/10.5281/zenodo.6374533 .
Development of a Novel Intra-Operative Evaluation Method for the Directions and Degrees of Malrotation in Supracondylar Humerus Fractures
Authors: Tang Yifu , Li Xiaoning , Guo Qiang , Huang Yuzhao , Kuang Wei , Luo Ling 
Published: May 2022

Abstract
Introduction: The malrotation of supracondylar humerus fractures (SCHF) often occurred, prolonging the reduction time during operation. An effective method should be established to achieve accurate reduction rapidly.Methods: Three dimensional (3D) printed humerus models were used to obtain the linear correlation equation between the width and projection degrees. Then, transverse fracture was performed in the peak of the humeral olecranon fossa of 3D printed models, which was examined by C-arm in the lateral 45° oblique position. Then, ten images in models and five cases in clinics with internal or external rotation within 90° were selected, as their rotation direction and degrees were evaluated by five orthopedic surgeons. Finally, the intraclass correlation coefficient (ICC) and Kappa statistic were used to analyze the accuracy of this novel method.Results: After linear regression analysis, the equation was obtained to show the correlation between the distal fracture line width and the rotation degrees. With the application of this method, the observers correctly predicted the rotation direction in 96% and correctly predicted the rotation degrees in 86% of models with a superior ICC value. Especially in the rotation range from -45° to 45°, the accuracy of rotation direction and degrees could reach to 100% and 93.3%. Also, it has an equally accuracy (24/30) in five clinical cases.Conclusions: This method provided a simple and efficient method for correcting intraoperative rotational displacement in patients with SCHF. By using this method, it can rapidly correct the malrotation displacement during operation, in order to distinctly shorten operation time, reduce bleeding volume and potential skeletal muscle injuries.
Characterization Free-living (FL) and Particle-attached (PA) bacterial communities of a canyon river reservoir on Yungui Plateau, China
Authors: Yang Yang , Chen Chen , Tao Xu 
Published: May 2022

Abstract
Bacteria play an important role in nutrient recycling and energy conversion in any aquatic ecosystem. Revealing the composition of free-living (FL) and particle-attached (PA) bacterial communities provide insights into their roles for biogeochemical processes and algal bloom dynamics. This study revealed the structure of FL and PA bacterial communities in a canyon reservoir in the Yungui-Plateau region, southern China. Firstly, we compared the difference using 3.0 µm and 5.0 µm filter for PA and FL bacterial communities (defined as PA3, FL3 and PA5, FL5), in order to choose the better sampling protocol. Secondly, we identified the differences between FL and PA in respect of their composition, diversity as well as function. Results showed that (1) dominant taxa did not change between FL3 and FL5, PA3 and PA5, but the relative abundance varied. Community composition and predicted gene functions showed significant differences between PA3 and PA5, while insignificant difference was noticed between FL3 and FL5; (2) FL was dominated by Actinobacteria and Proteobacteria, while PA was dominated by Planctomycetes and Proteobacteria; (3) there was insignificant difference on α-diversity between PA3 and PA3, but PA5 community exhibited greater dissimilarity (β-diversity) than PA3; (4) differences were detected between FL and PA community, with PA community exhibiting greater diversity and metabolic versatility than FL; (5) nitrogen metabolism related genes were abundant, implying an important role of both FL and PA in aquatic nitrogen cycling and hence in the microbial loop in this reservoir. This study provided evidence for using 5.0 µm filter to separate PA bacterial community, and also presented fundamental information on FL and PA bacterioplankton in Wujiangdu reservoir.
A Random Reversible Watermarking Schefme for Relational Data
Authors: Liu Qiang , Xian Hequn , Zhang Jiancheng , Liu Kunpeng 
Published: May 2022

Abstract
In the era of Big Data, relational data is at risk of piracy and misuse when distributed, shared and used. The use of digital watermarking technology is a reliable way to protect the copyright of relational data. In order to protect the copyright of relational data and recover the original data, many reversible watermarking schemes have been proposed in recent years, but most of them cannot extract the watermark information completely under severe attacks. To address this problem, a random-ized reversible watermarking scheme is proposed.Watermark embedding algorithm, watermark integrity checking algorithm, watermark detection algorithm and data recovery algorithm were designed. The watermark capacity is increased by embedding multiple watermarks in selected tuples, and the randomness of the watermark information distribution is increased by embedding unequal proportions of watermarks in different tuples. In extracting the watermark, the attacked bits are discarded to improve the accuracy of watermark detection. In addition, only a partition with complete watermark information is selected for watermark extraction. This not only improves the speed of watermark extraction, but also avoids the risk of key leakage from other partitions. The experimental results show that the complete watermark information can be extracted even when more than 90% of the tuples are under attack.
Increased ATP citrate lyase affects maternal diabetes-induced neural tube defects by promoting the H3K27ac modification through the Gadd45g pathway
Authors: Bai Baoling , Xiao Zonghui , Zhou Zenzhen , Wan Chunlei , Li Dan , Liu Lingyun , Sun Chunrong , Bao Yihua , Li Huili , Zhang Qin 
Published: May 2022

Abstract
Diabetes mellitus (DM) in early pregnancy increases the risk of neural tube defects (NTDs) in offspring. Enzyme-regulated histone acetylation has been reportedly linked to this pathological process. Few studies have focused on the intermediate acetyl-CoA, a substrate source of histone acetylation modification in maternal DM-induced NTDs. Here, we report that ATP citrate lyase (Acl), a metabolic enzyme of the glucose-related tricarboxylic acid cycle, has increased expression in DM-related NTDs of humans and mice, which induces acetyl-CoA accumulation and subsequently upregulates histone 3 lysine 27 acetylation (H3K27ac). Elevated H3K27ac reduces expression of genes for neural tube closure, Gadd45g and Ddit3. After inhibition of Acl, glucose-induced suppression of Gadd45g is alleviated by downregulation of H3K27ac both in vivo and in vitro, which is a possible mechanism of NTDs. Our results indicate that high glucose regulates NTD-related genes by increasing Acl and upregulating H3K27ac, which provide a novel pathological mechanism of DM-related NTDs.
Molecular Characterization of Mycobacterium tuberculosis Complex in Cattle and Humans, Maiduguri, Borno State, Nigeria: a Cross-sectional Study
Authors: Kwaghe Ayi Vandi , Ameh James Agbo , Kudi Caleb Ayuba. , Ambali Abdul-Ganiyu , Adesokan Hezekiah Kehinde , Akinseye Victor Oluwatoyin , Adelakun Olubukola Deborah , Usman Joy Gararawa , Cadmus Simeon Idowu 
Published: May 2022

Abstract
Introduction: In Nigeria, limited data exist to elucidate the inter-transmission of tuberculosis (TB) between humans and cattle. The study aimed at determining the circulating spoligotypes of Mycobacterium tuberculosis complex in cattle and humans, in Maiduguri.Methods: We conducted a cross sectional study on bovine and human tuberculosis in Maiduguri, Borno state. We calculated sample size using the method Thrusfield and Lesions suggestive of TB from 160 slaughtered cattle was obtained from Maiduguri Central Abattoir. Sputum samples from humans; 82 abattoir workers and 147 suspected TB patients from Hospitals/clinics were obtained. Lesions and sputum samples were cultured for the isolation of Mycobacterium spp. Positive cultures were subjected to deletion analysis and selected isolates were spoligotyped. Results: Fifty-two isolates were obtained from cattle. Of these, 26 (50%) belonged to M. tuberculosis complex (MTC) of which 17/26 (65.4 %) were characterized as M. bovis. In humans, seven of 12 (58.3%) MTC obtained were characterized as M. tuberculosis. Spoligotyping revealed SB0944 and SB1025 in cattle, while SIT838, SIT61 of LAM10_CAM and SIT1054, SIT46 of Haarlem (H) families were obtained from humans. Conclusions: Our findings reiterate the dominance of SB0944 and SB1025 in cattle in Nigeria. We isolated M. tuberculosis strain of the H family mainly domiciled in Europe from humans.
Diabetes treatment cost analysis in Jilin Province in 2016- 2019 using the structural change method
Authors: Zhou Zheng , Yu Jianxing , Jia Huanhuan , Feng Tianyu , Yu Xihe 
Published: May 2022

Abstract
Aim
To analyse the development trend of diabetes treatment costs in Jilin Province and its related factors from 2016–2019 and to provide a theoretical basis for the reform of the health care system in Jilin Province, the reduction of residents' disease burden and the formulation of relevant policies.
Method
Based on the SHA2011 method of health cost accounting, the data on diabetes treatment expenses in Jilin Province were collated. The change trend of diabetes treatment cost and project constitution in Jilin Province was analysed by structural analysis.
Results
The total cost of diabetes treatment increased from 2 billion 348 million yuan in 2016 to 2 billion 833 million yuan in 2019, with an average annual growth rate of 6.46%. The average outpatient expenses for diabetes in Jilin increased from 240.53 yuan to 304.61 yuan, corresponding to an average annual increase of 8.19%. The average hospitalization expenses related to diabetes in Jilin Province decreased from 7280.63 yuan to 6707.33 yuan, a decrease of 2.70%.
Conclusion
The cost of diabetes treatment in Jilin Province showed a rapid growth trend. The increase in hospitalization expenses was mainly due to the increase in the number of outpatients. The increase in outpatient expenses was mainly due to the increase in average outpatient expenses.
Predation risk of artificial ground nests in a post-mining landscape after opencast brown coal mining in the Czech Republic
Authors: Novák Jakub , Hendrychová Markéta 
Published: May 2022

Abstract
Context
Opencast mining of minerals has a considerable impact on the landscape and local ecosystems including bird communities. Suitable landscape restoration methods can replace habitats lost due to mining activities.
Objectives
Our study aimed to identify how factors such as restoration management, spatial distribution and vegetation characteristics of restored habitats can affect the risk of bird nest predation.
Methods
In 2018 and 2019 we conducted a field experiment using 726 artificial ground bird nests installed on four spoil heaps and in the surrounding landscape of North Bohemian Brown Coal Basin in the Czech Republic.
Results
Nests on the post-mining sites suffered from a significantly higher risk of predation (75.4%) than nests in the surrounding landscape (60.3%), especially on technically reclaimed sites (71.8%) compared to near-natural habitats (64.7%). A generalized linear mixed model confirmed a statistically significant impact of horizontally more heterogeneous but vertically not very diversified vegetation cover of the site on a higher risk of predation of nests installed both inside and outside post-mining sites. The risk of predation of nests adjacent to the spoil heaps decreased with increasing distance of the nest from the heap.
Conclusions
We consider spoil heaps as centres and sources of nest predation. We interpret the significant impact of the vegetation structure on risk of predation as result of post-mining rehabilitation approach. The higher risk of nest predation on post-mining sites reflected the character of technically reclaimed habitats. We recommend a greater extent of natural restoration methods in current rehabilitation policy.
Using a hybrid approach based on electrical circuit theory and the least cost method to determine possible corridors of Armenian Wild sheep (Ovis orientalis gmelini): A case study, west and northwest of Iran
Authors: Rouhi Haydar , Hasti Farzam , Almasieh Kamran , MoradKasani Mohammad 
Published: May 2022

Abstract
Maintaining linkages between remaining natural areas is increasingly important to ameliorate the negative effects of habitat loss and fragmentation on wildlife populations. Identifying environmental corridors is critical to biodiversity conservation and landscape planning. In recent decades, many methods have been developed to increase ecological linkages and establish gene binding to prevent mismanagement of protected areas. However, the multiplicity and complexity of methods can be a barrier for conservation planners. Here, we combine a limited set of several methods to provide a connection analysis framework that provides iterative, intuitive, and environmentally related connection estimates. In this study, firstly we investigated the habitat suitability of Armenian Wild sheep as a target species by ecological niche factor analysis. Then, by using the theory of electrical circuits and analysis of the least cost route of habitat communication between habitat spots was investigated. Based on flow maps, movement patterns and functional communication were identified for the target species as well as important communication areas in the study area. The results show that based on the circuit theory approach, the flow through the pixels (nodes) is equivalent to the probability of species movement. Therefore, it can be interpreted that if the target species travel between the mentioned habitats, the sections with high flow intensity will be the most probable route for their passage. Identification of important communication areas in the region is another important result of flow maps. The protection of these important areas is very important.
Fast kinetic simulator for relativistic matter
Authors: Ambrus Victor , Bazzanini Lorenzo , Gabbana Alessandro , Simeoni Daniele , succi sauro sauro , Tripiccione Raffaele 
Published: May 2022

Abstract
We present a new family of relativistic lattice kinetic schemes for the efficient simulation of relativistic flows in both strongly-interacting (fluid) and weakly-interacting (rarefied gas) regimes. The method can also deal with both massless and massive particles, thereby encompassing ultra-relativistic and mildly-relativistic regimes alike. The computational performance of the method for the simulation of relativistic flows across the aforementioned regimes is discussed in detail, along with prospects of future applications for Quark-Gluon Plasma, electron flows in graphene and systems in astrophysical contexts.
Contrast enhanced ultrasound predict hepatocellular carcinoma recurrence: a retrospective observation cohort study
Authors: Tu Haibin , Feng Siyi , Chen Lihong , Huang Yujie , Zhang Juzhen , Zhu Lingxuan , Wu Xiaoxiong 
Published: May 2022

Abstract
Background: Surgery is the main treatment for hepatocellular carcinoma (HCC), but early recurrence (ER) affects patients' prognosis. Non-invasive screening of high-risk recurrence groups is important for precise treatment to formulate personalized treatment. contrast-enhanced ultrasound (CEUS) may realize this scenarioObjectives: Construction and validation of a non-invasive prediction model for ER of HCC after surgery based on CEUS and serological biomarkers.Methods: 466 patients who underwent CEUS and curative resection between 2016.1.1 and 2019.1.1 were retrospectively recruited from one institution. The training and testing cohorts comprised 326 and 140 patients. We collected CEUS Liver Imaging Reporting and Data System (LI-RADS) grading and serological indicators. Finding risk factors for recurrence of HCC after surgery using univariate and multvariatel analysis, and the Contrast-enhanced Ultrasound Serological (CEUSS) model was constructed. Different models were compared using time-dependent area under the receiver operating characteristic curve (td-AUC) and prediction error. The CEUSS model’s performances in ER prediction were assessed.Results: Base-line data of the training and testing cohorts were equal. LI-RADS category, α-fetoprotein level, tumor maximum diameter, total bilirubin level, starting time, iso-time, and enhancement pattern were independent hazards, and their hazards ratios were 1.417, 1.309, 1.133, 1.036, 0.883, 0.985, and 0.70, respectively. The AUCs of CEUSS, BCLC, TNM, and CNLC were 0.706, 0.641, 0.647, and 0.636, respectively, in the training cohort and 0.680, 0.583, 0.607, and 0.597, respectively, in the testing cohort. The prediction errors of CEUSS, BCLC, TNM, and CNLC were 0.202, 0.205, 0.205, and 0.200, respectively, in the training cohort and 0.204, 0.221, 0.219, and 0.211, respectively, in the testing cohort.Conclusions: CEUSS model can effectively screen out high-risk recurrence population, providing an important basis for precise treatment.
Tongguan capsule for treating Myocardial Ischemia-Reperfusion Injury: Integrating Network Pharmacology and Mechanism Study
Authors: Liu Jiantao , Liu Chunping , Cen Huan , Chen Huiqi , Zhang Shihui , Yang Hailong , Liu Fang , Chen Quanfu , Wang Lei 
Published: May 2022

Abstract
Purpose
Tongguan Capsule (TGC) is widely used in the treatment of coronary atherosclerotic disease and heart failure after myocardial infarction; yet, the exact mechanism of action is still unclear. In this study, network pharmacology and experimental validation were used to examine the mechanism of TGC prescription in the treatment of myocardial ischemia-reperfusion injury (MIRI).
Methods
The components of TGC and candidate targets for MIRI therapy were searched through multiple databases. ClueGO plug-in of Cytoscape was used for enrichment analysis. The binding ability of components to the target was determined by molecular docking.Finally, MIRI model in vivo and hypoxia/reoxygenation (H/R) model in vitro were established for verification.
Results
Molecular docking results suggested that components such as kaempferol, kaempferol, luteolin, tanshinone IIA had a high affinity with autophagy-related proteins in the mTOR pathway. Further in vivo testing indicated that TGC could improve cardiac function and reduce infarct size in a MIRI mouse model. In vitro experiments also suggested that TGC inhibited H/R cell apoptosis by increasing the levels of GSK-3β, LC3, and Beclin1, and by decreasing the expression of mTOR and p62.
Conclusion
To sum up, these data indicated that TGC could protect the heart from MIRI by upregulating autophagy.