bluuebunny/crossref_metadata_2025_split huggingface dataset:
Connecting genomic islands across prokaryotic and phage genomes via protein families
Authors: Aldaihani Reem , Heath Lenwood S. 
Published: January 2023

AbstractProkaryotic genomes evolve via horizontal gene transfer (HGT), mutations, and rearrangements. A noteworthy part of the HGT process is facilitated by genomic islands (GIs). While previous computational biology research has focused on developing tools to detect GIs in prokaryotic genomes, there has been little research investigating GI patterns and biological connections across species. We have pursued the novel idea of connecting GIs across prokaryotic and phage genomes via patterns of protein families. Such patterns are sequences of protein families frequently present in the genomes of multiple species. We combined the large data set from the IslandViewer4 database with protein families from Pfam while implementing a comprehensive strategy to identify patterns making use of HMMER, BLAST, and MUSCLE. we also implemented Python programs that link the analysis into a single pipeline. Research results demonstrated that related GIs often exist in species that are evolutionarily unrelated and in multiple bacterial phyla. Analysis of the discovered patterns led to the identification of biological connections among prokaryotes and phages. These connections suggest broad HGT connections across the bacterial kingdom and its associated phages. The discovered patterns and connections could provide the basis for additional analysis on HGT breadth and the patterns in pathogenic GIs.
Molecular docking, network pharmacology and experimental verification to explore the mechanism of Wulongzhiyangwan in the treatment of pruritus
Authors: Anqi Lyu , Shijun Shan 
Published: January 2023

AbstractWulongzhiyangwan (WLZYW) is a Chinese prescription medicine for the treatment of pruritus, but its mechanism has not been clarified. The purpose of this study was to explore the mechanism of WLZYW in pruritus through network pharmacology analysis and experimental validation. The active components and corresponding targets of WLZYW were obtained from the Traditional Chinese Medicine Systematic Pharmacology (TCMSP) database. Pruritus-related targets were obtained from the GeneCards, TTD (Therapeutic Target Database), and DrugBank databases. The key compounds, core targets, main biological processes and signaling pathways related to WLZYW were identified by constructing and analyzing related networks. The binding affinity between WLZYW components and core targets was validated by AutoDock Vina software. In this study, RBL-2H3 cells were used to construct a degranulation model to simulate histamine-dependent pruritus. 10 chemical constituents, 235 targets and 3606 pruritus-related targets of WLZYW were obtained. Subsequently, 26 core targets were identified through analysis, VEGFA and AKT1 were the main candidates. A pathway enrichment analysis showed that overlapping targets were significantly enriched in the PI3K/AKT signaling pathway. A molecular docking analysis revealed tight binding of VEGF to three core compounds, kaempferol, luteolin and quercetin. Experiments showed that WZLYW inhibited mast cell degranulation, regulated VEGFa mRNA and protein expression levels by inhibiting PI3K/AKT and ERK1/2 signaling pathway activation. The mechanism of WZLYW in pruritus may be regulating VEGFa expression. Network pharmacology assays suggested that WLZYW downregulates VEGFa expression by regulating the PI3K/AKT and ERK1/2 signaling pathways in pruritis treatment.
Contact analysis and strength calculations of involute spline couplings
Authors: Li Shuting 
Published: January 2023

AbstractA finite element method (FEM) is presented to conduct loaded tooth contact analysis and strength calculations of involute spline couplings. Special FEM software has been developed. Contact, bending and shear stresses of the spline couplings are analyzed by the developed software and they are compared with results obtained by an approximation method. It is found that “Edge loads” exist at tooth tip and root contacts and also exist at two sides of the face width when the pair of teeth has different face widths. Effects of tooth profile deviations and pitch errors on tooth contacts are also investigated by the developed software respectively. It is found that tooth contact and stresses are affected by the tooth profile deviations and pitch errors greatly. Finally, reliability of the presented method and software are discussed.
Investigation of changes in ankylosing spondylitis disease activity through 2021 COVID-19 wave in Taiwan by using electronic medical record management system
Authors: Huang Pei-Ju , Chen Yun-Wen , Yen Tsai-Hung , Liu Yen-Tze , Lin Shih-Ping , Chen Hsin-Hua 
Published: January 2023

AbstractWe aim to investigate the alteration in disease activity of ankylosing spondylitis (AS) individuals before, during, and after the COVID-19 wave in Taiwan by using electronic medical-record management system (EMRMS). We identified 126 AS individuals from the single center, and gathered data of the three disease activities (Bath Ankylosing Spondylitis Disease Activity Index [BASDAI], Ankylosing Spondylitis Disease Activity Score with erythrocyte sedimentation rate [ASDAS-ESR], and Ankylosing Spondylitis Disease Activity Score with C-Reactive Protein [ASDAS-CRP]) by using EMRMS before (7 February to 1 May, 2021), during (2 May to 24 July, 2021), and after the COVID-19 wave (25 July to 16 October, 2021). We compared the disease activity measures of the three phases through a paired t test. Among the 126 individuals, CRP was significantly higher during the COVID-19 wave (0.2 (0.1, 0.5) mg/dl, p = 0.001) than before the wave (0.2 (0.1, 0.4) mg/dl), ESR (8.0 (4.0, 15.0) mm/h, p = 0.003) and ASDAS-ESR (1.4 (1.0, 1.9), p = 0.032) were significantly higher after the wave than during the wave (6.0 (3.0, 12.0) mm/h and 1.2 (0.9, 1.8) mm/h) e. ESR, CRP, ASDAS-ESR and ASDAS-CRP were all significant higher after COVID-19 wave than before. The disease activities of AS individuals in Taiwan worsened after 2021 COVID-19 wave in Taiwan.
Ischemia modified albumin can act as an independent predictor of inhospital mortality in patients with acute aortic dissection
Authors: Xiang Jun , He Ling , Pen Tailuan , Wei Shuliang 
Published: January 2023

AbstractAcute aortic dissection (AAD) is a serious disease characterized by high mortality. However, there are no accurate indicators to predict in-hospital mortality. The objective of this study was to identify the potential value of ischemia modified albumin (IMA) in prediction of in-hospital mortality of AAD patients. This was a single-center, prospective study involved 314 patients undergoing AAD, including 197 males and 117 females, aged 26–87 (57.14 ± 21.71) years old, 116 cases of TAAD and 198 cases of TBAD (37 cases of complicated, 114 cases of high risk, and 47 cases of uncomplicated), 228 cases were underwent surgery/intervention treatment (77 cases of TAAD,151 cases of TBAD) and 86 cases were underwent conservative therapy (39 cases of TAAD, 47 cases of TBAD). The basic data, on-admission IMA level, and the all-cause in-hospital mortality was recorded. IMA in the non-survivor group and TAAD group was found to be significantly higher than that in the survivor group and TBAD group (P < 0.001). Multivariate logistic regression analysis results revealed that age (OR = 1.923, 95%CI: 1.102–4.481,P = 0.020), conservative therapy (OR = 17.892, 95%CI: 7.641–24.748,P < 0.001), D-dimer level (OR = 3.517, 95%CI: 1.874–7.667,P = 0.011) and IMA level (OR = 5.406, 95%CI: 2.951–10.395,P = 0.004) served as independent risk factors for in-hospital mortality of TAAD patients. And D-dimer level (OR = 2.241, 95%CI: 1.475–5.663,P = 0.018), IMA level (OR = 3.115, 95%CI: 1.792–6.925,P = 0.009) also served as independent risk factors for in-hospital mortality of TBAD patients, whereas surgery (OR = 0.110, 95%CI: 0.075–0.269,P < 0.001) was the protective factor of in-hospital mortality of TAAD patients. After IMA prediction, the AUC, optimal cut-off value, sensitivity, and the specificity of in-hospital mortality of AAD patients were observed to be 0.801 (95%CI: 0.744–0.858), 86.55 U/mL, 79.1%, and 73.2%, respectively. In addition, it was found that AUC was 0.799 (95%CI: 0.719–0.880) in TAAD and 0.753 (95%CI: 0.641–0.866) in TBAD. Overall, it was concluded that on-admission IMA level acted as an independent prediction index for in-hospital mortality of AAD patients.
Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning
Authors: McLaughlin R. Tyler , Asthana Maansi , Di Meo Marc , Ceccarelli Michele , Jacob Howard J. , Masica David L. 
Published: January 2023

AbstractAccurately identifying somatic mutations is essential for precision oncology and crucial for calculating tumor-mutational burden (TMB), an important predictor of response to immunotherapy. For tumor-only variant calling (i.e., when the cancer biopsy but not the patient’s normal tissue sample is sequenced), accurately distinguishing somatic mutations from germline variants is a challenging problem that, when unaddressed, results in unreliable, biased, and inflated TMB estimates. Here, we apply machine learning to the task of somatic vs germline classification in tumor-only solid tumor samples using TabNet, XGBoost, and LightGBM, three machine-learning models for tabular data. We constructed a training set for supervised classification using features derived exclusively from tumor-only variant calling and drawing somatic and germline truth labels from an independent pipeline using the patient-matched normal samples. All three trained models achieved state-of-the-art performance on two holdout test datasets: a TCGA dataset including sarcoma, breast adenocarcinoma, and endometrial carcinoma samples (AUC > 94%), and a metastatic melanoma dataset (AUC > 85%). Concordance between matched-normal and tumor-only TMB improves fromR2 = 0.006 to 0.71–0.76 with the addition of a machine-learning classifier, with LightGBM performing best. Notably, these machine-learning models generalize across cancer subtypes and capture kits with a call rate of 100%. We reproduce the recent finding that tumor-only TMB estimates for Black patients are extremely inflated relative to that of white patients due to the racial biases of germline databases. We show that our approach with XGBoost and LightGBM eliminates this significant racial bias in tumor-only variant calling.
Early-life exercise primes the murine neural epigenome to facilitate gene expression and hippocampal memory consolidation
Authors: Raus Anthony M. , Fuller Tyson D. , Nelson Nellie E. , Valientes David A. , Bayat Anita , Ivy Autumn S. 
Published: January 2023

AbstractAerobic exercise is well known to promote neuroplasticity and hippocampal memory. In the developing brain, early-life exercise (ELE) can lead to persistent improvements in hippocampal function, yet molecular mechanisms underlying this phenomenon have not been fully explored. In this study, transgenic mice harboring the “NuTRAP” (Nuclear tagging and Translating Ribosome Affinity Purification) cassette in Emx1 expressing neurons (“Emx1-NuTRAP” mice) undergo ELE during adolescence. We then simultaneously isolate and sequence translating mRNA and nuclear chromatin from single hippocampal homogenates containing Emx1-expressing neurons. This approach allowed us to couple translatomic with epigenomic sequencing data to evaluate the influence of histone modifications H4K8ac and H3K27me3 on translating mRNA after ELE. A subset of ELE mice underwent a hippocampal learning task to determine the gene expression and epigenetic underpinnings of ELE’s contribution to improved hippocampal memory performance. From this experiment, we discover gene expression – histone modification relationships that may play a critical role in facilitated memory after ELE. Our data reveal candidate gene-histone modification interactions and implicate gene regulatory pathways involved in ELE’s impact on hippocampal memory.
Mangrove forests can be an effective coastal defence in the Pearl River Delta, China
Authors: De Dominicis Michela , Wolf Judith , van Hespen Rosanna , Zheng Peng , Hu Zhan 
Published: January 2023

AbstractCoastal vegetation can reduce extreme water levels during storm events, but the controlling factors and processes in complex estuary or delta systems are still unclear. This limits an effective implementation of nature-based coastal defences in delta mega-cities in low-lying coastal areas. Here we have numerically modelled how mangroves can offer coastal protection to the large coastal cities located in the Pearl River Delta (China), such as Guangzhou and Shenzhen, during strong typhoons, like Hato (2017). Water level attenuation by mangroves is effective during extreme water level conditions and differences in mangrove forests’ properties drive their coastal protection function. The local (within-wetland) attenuation of extreme water levels is more effective with wide vegetation patches and higher vegetation drag. Narrower vegetation patches can still provide non-local (upstream) water level attenuation if located in the upper estuary channels, but their design needs to avoid amplification of water levels in other delta areas.
Design and research of power system Beidou timing and positioning module based on K‐means clustering and gross error processing
Authors: Xu Yawei , Wang Wei , Yang Xiaona , Deng Ke , He Zhiyuan 
Published: January 2023

AbstractThe clock synchronisation of the power system is to realise the clock synchronisation of the whole network. The clock synchronisation network is composed of the clock synchronisation systems of power grids at all levels. Dispatching agencies, power plants, and substations have their clock synchronisation systems. By using computer technology, communication technology, and network technology, combined with the topological structure of the power grid and geographic information of the geographic information system, automatically process the key index data to ensure that the distribution network project can manage the power consumption and distribution 24 h without interruption. Considering the particularity of power, the accuracy of the receiver is strictly required, and so are the positioning, speed measurement, and time accuracy. Test indicators study a set of accurate and reliable test and evaluation methods. A gross error processing method based on the k‐means algorithm is proposed. Experiments show that gross errors can be well identified and eliminated in one‐dimensional and multidimensional data. Considering that invalid data may be hidden in the test data, to improve the identification accuracy without affecting the detection of normal gross errors, based on the proposed k‐means algorithm, the number of visible satellites is added. Because the magnitude difference between the number of visible satellites and the original three‐dimensional positioning error data is relatively large, it is normalised first. The processing data is extended from three‐dimensional to four‐dimensional. The experimental simulation shows that it can not only identify invalid data but also ensure a good effect of gross error elimination, reduce possible economic losses, bring significant direct and indirect economic benefits, and verify the feasibility and promotional value of the online monitoring platform through practice.
Radical technology innovations for high‐speed transport; ePlanes to replace rail?
Authors: Riley Paul H. , Degano Michele , Gerada Chris 
Published: January 2023

AbstractThis paper evaluates various modes of transport against the dual requirements of Net‐Zero carbon emissions and user convenience, in particular, speed of travel and cost of transportation. Results show that when operated across a whole country, battery‐powered ePlanes have the lowest energy use as measured by well‐to‐wing efficiency of other high‐speed transport systems such as the UKs HS2 and conventional diesel rail systems. This condition may not hold for extremely high passenger numbers per hour as seen in metropolitan areas with high density populations. Various proposed disruptive technologies lower cost of ownership when combined with changes in the transport paradigm that has rarely been explored in other papers.
Analysis of power quality and economic worthiness of electric motorcycle charging in a residential electrical system
Authors: Chiradeja Pathomthat , Ngaopitakkul Atthapol 
Published: January 2023

AbstractIn the urban society of Thailand, most people use motorcycles for travelling because they can meet the manoeuvrability of travelling in short distances and save energy compared to using a car. Many people are switching to electric motorcycles (EMCs), which install EMC chargers in their residential buildings. EMC chargers are power electronic devices that may produce electrical and electromagnetic interference; therefore, it is critical to evaluate the potential influence of an EMC charger on a household electrical system and other electrical equipment before installing one. Therefore, this study examined the effects of an EMC charger on residential electrical systems with and without a photovoltaic system connection as well as on individual load types in terms of power quality. The investigation revealed that EMC charging has a direct impact on the grid system's reactive power, power factor, and current harmonics. However, when the electrical load in the system has sufficient power, it is possible to reduce the reactive power and current harmonics of the grid. The cost of electricity when an EMC is connected to a residential electrical system was also analysed to determine the metre type and charging interval suitable for Thailand.
Retracted: Scientific programming using optimized machine learning techniques for software fault prediction to improve software quality
Authors: Shafiq Muhammad , Alghamedy Fatemah H. , Jamal Nasir , Kamal Tahir , Daradkeh Yousef Ibrahim , Shabaz Mohammad 
Published: January 2023

AbstractRetraction: [Muhammad Shafiq, Fatemah H. Alghamedy, Nasir Jamal, Tahir Kamal, Yousef Ibrahim Daradkeh, Mohammad Shabaz, Scientific programming using optimized machine learning techniques for software fault prediction to improve software quality, IET Software 2023 (https://doi.org/10.1049/sfw2.12091)].The above article from IET Software, published online on 6 January 2023 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the Editor‐in‐Chief, Hana Chockler, the Institution of Engineering and Technology (the IET) and John Wiley and Sons Ltd. This article was published as part of a Guest Edited special issue. Following an investigation, the IET and the journal have determined that the article was not reviewed in line with the journal’s peer review standards and there is evidence that the peer review process of the special issue underwent systematic manipulation. Accordingly, we cannot vouch for the integrity or reliability of the content. As such we have taken the decision to retract the article. The authors have been informed of the decision to retract.
UNIONS: The impact of systematic errors on weak-lensing peak counts
Authors: Ayçoberry Emma , Ajani Virginia , Guinot Axel , Kilbinger Martin , Pettorino Valeria , Farrens Samuel , Starck Jean-Luc , Gavazzi Raphaël , Hudson Michael J. 
Published: January 2023

Context. The Ultraviolet Near-Infrared Optical Northern Survey (UNIONS) is an ongoing deep photometric multiband survey of the northern sky. As part of UNIONS, the Canada-France Imaging Survey (CFIS) provides r-band data, which we use to study weak-lensing peak counts for cosmological inference.
Aims. We assess systematic effects for weak-lensing peak counts and their impact on cosmological parameters for the UNIONS survey. In particular, we present results on local calibration, metacalibration shear bias, baryonic feedback, the source galaxy redshift estimate, intrinsic alignment, and cluster member dilution.
Methods. For each uncertainty and systematic effect, we describe our mitigation scheme and the impact on cosmological parameter constraints. We obtain constraints on cosmological parameters from Monte Carlo Markov chains using CFIS data and MassiveNuS N-body simulations as a model for peak counts statistics.
Results. Depending on the calibration (local versus global, and the inclusion or not of the residual multiplicative shear bias), the mean matter density parameter, Ωm, can shift by up to −0.024 (−0.5σ). We also see that including baryonic corrections can shift Ωm by +0.027 (+0.5σ) with respect to the dark-matter-only simulations. Reducing the impact of the intrinsic alignment and cluster member dilution through signal-to-noise cuts leads to larger constraints. Finally, with a mean redshift uncertainty of Δz̄ = 0.03, we see that the shift in Ωm (+0.001, which corresponds to +0.02σ) is not significant.
Conclusions. This paper investigates, for the first time with UNIONS weak-lensing data and peak counts, the impact of systematic effects. The value of Ωm is the most impacted and can shift by up to ∼0.03, which corresponds to 0.5σ depending on the choices for each systematics. We expect constraints to become more reliable with future (larger) data catalogs, for which the current pipeline will provide a starting point. The code used to obtain the results is available on GitHub.
Correlation of Prenatal and Postnatal Diagnosis in Umbilical-Portal-Systemic Venous Shunts
Authors: Jimenez-Gomez Javier , Güizzo Javier Roberto , Betancourth Alvarenga Josue , Santiago Martínez Saioa , Gaspar Perez Mireia , Pina Perez Silvia , Beltrán Viviana Patricia , Loverdos Inés , Esteva Miró Clara , Jimenez Arribas Paula , Sanchez Vazquez Begoña , San Vicente Vela Begoña , Álvarez García Natalia , Nuñez García Bernardo 
Published: January 2023

Abstract
Introduction Umbilical-portal-systemic venous shunts (UPSVS) are rare anomalies in the development of the fetal venous system. There are several postnatal and prenatal classifications of hepatic venous anomalies but the link between them is missing. We aimed to review the prenatal to postnatal diagnosis correlation in UPSVS at our center.
Methods It is a retrospective study of patients diagnosed with UPSVS between 2019 and 2021 at our institution. Demographic, obstetric, genetic, and neonatal data were reviewed with special focus on prenatal and postnatal ultrasounds.
Results A total of seven patients were diagnosed with UPSVS at a median of 24 (20–34) weeks of gestational age. All patients were male and 62% were Caucasian. None of the patients had chromosomopathies or cardiac anomalies. One patient had renal ectopia, another one had a single umbilical artery, and a third one suffered from intrauterine growth retardation. An umbilico-systemic shunt (USS) was found in two patients and a ductus venosus-systemic shunt (DVSS) in the rest. Patients with USS were diagnosed postnatally with intrahepatic portosystemic shunts. One of the DVSS patients was transferred to another hospital and the other four had normal postnatal cardiac ultrasounds, with normal abdominal ultrasounds in two patients and lack of postnatally abdominal control in the other two. All babies were found to be doing well at a median follow-up of 1 month (0–24).
Conclusion There is a knowledge gap in the natural history of UPSVS between fetal and neonatal life. Building bridges between prenatal and postnatal research is mandatory in order to understand these rare anomalies.