bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and functional insights into the modulation of T cell costimulation by monkeypox virus protein M2
Authors: Yang Shangyu , Wang Yong , Yu Feiyang , Cheng Rao , Zhang Yiwei , Zhou Dan , Ren Xuanxiu , Deng Zengqin , Zhao Haiyan 
Published: August 2023

AbstractThe rapid spread of monkeypox in multiple countries has resulted in a global public health threat and has caused international concerns since May 2022. Poxvirus encoded M2 protein is a member of the poxvirus immune evasion family and plays roles in host immunomodulation via the regulation of innate immune response mediated by the NF-κB pathway and adaptive immune response mediated by B7 ligands. However, the interaction of monkeypox virus (MPXV) M2 with B7 ligands and structural insight into poxviral M2 function have remained elusive. Here we reveal that MPXV M2, co-existing as a hexamer and a heptamer, recognizes human B7.1 and B7.2 (hB7.1/2) with high avidities. The binding of oligomeric MPXV M2 interrupts the interactions of hB7.1/2 with CD28 and CTLA4 and subverts T cell activation mediated by B7.1/2 costimulatory signals. Cryo-EM structures of M2 in complex with hB7.1/2 show that M2 binds to the shallow concave face of hB7.1/2 and displays sterically competition with CD28 and CTLA4 for the binding to hB7.1/2. Our findings provide structural mechanisms of poxviral M2 function and immune evasion deployed by poxviruses.
A versatile, fast and unbiased method for estimation of gene-by-environment interaction effects on biobank-scale datasets
Authors: Di Scipio Matteo , Khan Mohammad , Mao Shihong , Chong Michael , Judge Conor , Pathan Nazia , Perrot Nicolas , Nelson Walter , Lali Ricky , Di Shuang , Morton Robert , Petch Jeremy , Paré Guillaume 
Published: August 2023

AbstractIdentification of gene-by-environment interactions (GxE) is crucial to understand the interplay of environmental effects on complex traits. However, current methods evaluating GxE on biobank-scale datasets have limitations. We introduce MonsterLM, a multiple linear regression method that does not rely on model specification and provides unbiased estimates of variance explained by GxE. We demonstrate robustness of MonsterLM through comprehensive genome-wide simulations using real genetic data from 325,989 individuals. We estimate GxE using waist-to-hip-ratio, smoking, and exercise as the environmental variables on 13 outcomes (N = 297,529-325,989) in the UK Biobank. GxE variance is significant for 8 environment-outcome pairs, ranging from 0.009 – 0.071. The majority of GxE variance involves SNPs without strong marginal or interaction associations. We observe modest improvements in polygenic score prediction when incorporating GxE. Our results imply a significant contribution of GxE to complex trait variance and we show MonsterLM to be well-purposed to handle this with biobank-scale data.
The sequence and de novo assembly of the genome of the Indian oil sardine, Sardinella longiceps
Authors: Sukumaran Sandhya , Sebastian Wilson , Gopalakrishnan A. , Mathew Oommen K. , Vysakh V. G. , Rohit Prathibha , Jena J. K. 
Published: August 2023

AbstractThe Indian oil sardine, Sardinella longiceps, is a widely distributed and commercially important small pelagic fish of the Northern Indian Ocean. The genome of the Indian oil sardine has been characterized using Illumina and Nanopore platforms. The assembly is 1.077 Gb (31.86 Mb Scaffold N50) in size with a repeat content of 23.24%. The BUSCO (Benchmarking Universal Single Copy Orthologues) completeness of the assembly is 93.5% when compared with Actinopterygii (ray finned fishes) data set. A total of 46316 protein coding genes were predicted. Sardinella longiceps is nutritionally rich with high levels of omega-3 polyunsaturated fatty acids (PUFA). The core genes for omega-3 PUFA biosynthesis, such as Elovl 1a and 1b,Elovl 2, Elovl 4a and 4b,Elovl 8a and 8b,and Fads 2, were observed in Sardinella longiceps. The presence of these genes may indicate the PUFA biosynthetic capability of Indian oil sardine, which needs to be confirmed functionally.
Analysis of endoplasmic reticulum stress-related gene signature for the prognosis and pattern in diffuse large B cell lymphoma
Authors: Zhang Chaofeng , Lin Qi , Li Chaoqi , Chen Zhimin , Deng Mengmeng , Weng Huixin , Zhu Xiongpeng 
Published: August 2023

AbstractDiffuse large B-cell lymphoma (DLBCL) is the most common lymphoma in adults. This study aimed to determine the prognostic significance of endoplasmic reticulum (ER) stress-related genes in DLBCL. ER stress-related genes were obtained from the molecular signatures database. Gene expression data and clinical outcomes from the gene expression omnibus and TCGA datasets were collected, and differentially expressed genes (DEGs) were screened out. Gene ontology enrichment analysis, the kyoto encyclopaedia of genes and genomes pathway analysis, and geneset enrichment analysis were used to analyse the possible biological function of ER stress-related DEGs in DLBCL. Protein–protein interaction network construction using the STRING online and hub genes were identified by cytoHubba on Cytoscape software. The significant prognosis-related genes were screened, and the differential expression was validated. The immune microenvironment assessment of significant genes were evaluated. Next, the nomogram was built using univariate and multivariate Cox regression analysis. 26 ER stress-related DEGs were screened. Functional enrichment analysis showed them to be involved in the regulation of the endoplasmic reticulum mainly. NUPR1 and TRIB3 were identified as the most significant prognostic-related genes by comparison with the GSE10846, GSE11318, and TCGA datasets. NUPR1 was correlated with a good prognosis and immune infiltration in DLBCL; on the other hand, high expression of TRIB3 significantly correlated with a poor prognosis, which was an independent prognostic factor for DLBCL. In summary, we identified NUPR1 and TRIB3 as critical ER stress-related genes in DLBCL. NUPR1 might be involved in immune infiltration in DLBCL, and TRIB3 might serve as a potential therapeutic target and prognostic factor in DLBCL.
Activation of peroxymonosulphate using a highly efficient and stable ZnFe2O4 catalyst for tetracycline degradation
Authors: Zhao Xuying , Li Wei , Gao Junyi , Li Caibin , Xiao Yansong , Liu Xue , Song Dean , Zhang Jiguang 
Published: August 2023

AbstractTetracycline (TC) is a widely used antibiotic that adversely affects ecosystems and, therefore, must be removed from the environment. Owing to their strong ability to oxidise pollutants, including antibiotics, and selectivity for these pollutants, an improved oxidation method based on sulphate radicals (SO4·−) has gained considerable interest. In this study, a novel technique for removing TC was developed by activating peroxymonosulphate (PMS) using a ZnFe2O4 catalyst. Using the co-precipitation method, a ZnFe2O4 catalyst was prepared by doping zinc into iron-based materials, which increased the redox cycle, while PMS was active and facilitated the production of free radicals. According to electron paramagnetic resonance spectroscopy results, a ZnFe2O4 catalyst may activate PMS and generate SO4·−, HO·, O2·−, and 1O2 to eliminate TC. This research offers a new method for creating highly effective heterogeneous catalysts that can activate PMS and destroy antibiotics. The study proposes the following degradation pathways: hydroxylation and ring-opening of TC based on the products identified using ultra-performance liquid chromatography-mass spectrometry. These results illustrated that the prepared ZnFe2O4 catalyst effectively removed TC and exhibited excellent catalytic performance.
High-intensity interval training versus moderate-intensity continuous training on patient quality of life in cardiovascular disease: a systematic review and meta-analysis
Authors: Yu Haohan , Zhao Xudong , Wu Xiaoxia , Yang Jing , Wang Jun , Hou Lijuan 
Published: August 2023

AbstractThis systematic review and meta-analysis aimed to compare the effects of high-intensity interval training (HIIT) and moderate-intensity continuous training (MICT) on the quality of life (QOL) and mental health (MH) of patients with cardiovascular disease (CVDs). Web of Science, Medline, Embase, Cochrane (CENTRAL), CINAHL, China National Knowledge Infrastructure, Wanfang, and China Science and Technology Journal databases were searched from their date of establishment to July, 2023. A total of 5798 articles were screened, of which 25 were included according to the eligibility criteria. The weighted mean difference (WMD) and standardized mean difference (SMD) were used to analyze data from the same and different indicator categories, respectively. The fixed-effects model (FE) or random-effects model (RE) combined data based on the between-study heterogeneity. There were no statistically significant differences regarding QOL, physical component summary (PCS), mental component summary (MCS), and MH, including depression and anxiety levels, between the HIIT and MICT groups [SMD = 0.21, 95% confidence interval (CI)  − 0.18–0.61, Z = 1.06, P = 0.290; SMD = 0.10, 95% CI  − 0.03–0.23, Z = 1.52, P = 0.128; SMD = 0.07, 95% CI  − 0.05–0.20, Z = 1.13, P = 0.25; SMD = − 0.08, 95% CI  − 0.40–0.25, Z = − 0.46, P = 0.646; WMD = 0.14. 95% CI  − 0.56–0.84, Z = 0.39, P = 0.694, respectively]. HIIT significantly improved PCS in the coronary artery disease (CAD) population subgroup relative to MICT. HIIT was also significantly superior to MICT for physical role, vitality, and social function. We conclude that HIIT and MICT have similar effects on QOL and MH in patients with CVD, while HIIT is favorable for improving patients’ self-perceived physiological functioning based on their status and social adjustment, and this effect is more significant in patients with CAD.
Molecular surveillance of Plasmodium falciparum drug-resistance markers in Vietnam using multiplex amplicon sequencing (2000–2016)
Authors: Rovira-Vallbona Eduard , Kattenberg Johanna Helena , Hong Nguyen Van , Guetens Pieter , Imamura Hideo , Monsieurs Pieter , Chiheb Driss , Erhart Annette , Phuc Bui Quang , Xa Nguyen Xuan , Rosanas-Urgell Anna 
Published: August 2023

AbstractEmergence and spread of Plasmodium falciparum resistance to artemisinin-based combination therapies (ACT) is a major challenge for Greater Mekong Subregion countries in their goal to eliminate malaria by 2030. Tools to efficiently monitor drug resistance beyond resource-demanding therapeutic efficacy studies are necessary. A custom multiplex amplicon sequencing assay based on Illumina technology was designed to target the marker of partial resistance to artemisinin (K13), five candidate modulators of artemisinin resistance, the marker of resistance to chloroquine (crt), and four neutral microsatellite loci. The assay was used to genotype 635 P. falciparum-positive blood samples collected across seven provinces of Vietnam and one of Cambodia between 2000 and 2016. Markers of resistance to artemisinin partner-drugs piperaquine (copy number of plasmepsin-2) and mefloquine (copy number of multidrug-resistance 1) were determined by qPCR. Parasite population structure was further assessed using a 101-SNP barcode. Validated mutations of artemisinin partial resistance in K13 were found in 48.1% of samples, first detection was in 2000, and by 2015 prevalence overcame > 50% in Central Highlands and Binh Phuoc province. K13-C580Y variant became predominant country-wide, quickly replacing an outbreak of K13-I543T in Central Highlands. Mutations in candidate artemisinin resistance modulator genes paralleled the trends of K13 mutants, whereas resistance to piperaquine and mefloquine remained low (≈ 10%) by 2015–2016. Genomic tools applied to malaria surveillance generate comprehensive information on dynamics of drug resistance and population structure and reflect drug efficacy profiles from in vivo studies.
Deep learning and wing interferential patterns identify Anopheles species and discriminate amongst Gambiae complex species
Authors: Cannet Arnaud , Simon-Chane Camille , Akhoundi Mohammad , Histace Aymeric , Romain Olivier , Souchaud Marc , Jacob Pierre , Sereno Darian , Mouline Karine , Barnabe Christian , Lardeux Frédéric , Boussès Philippe , Sereno Denis 
Published: August 2023

AbstractWe present a new and innovative identification method based on deep learning of the wing interferential patterns carried by mosquitoes of the Anopheles genus to classify and assign 20 Anopheles species, including 13 malaria vectors. We provide additional evidence that this approach can identify Anopheles spp. with an accuracy of up to 100% for ten out of 20 species. Although, this accuracy was moderate (> 65%) or weak (50%) for three and seven species. The accuracy of the process to discriminate cryptic or sibling species is also assessed on three species belonging to the Gambiae complex. Strikingly, An. gambiae, An. arabiensis and An. coluzzii, morphologically indistinguishable species belonging to the Gambiae complex, were distinguished with 100%, 100%, and 88% accuracy respectively. Therefore, this tool would help entomological surveys of malaria vectors and vector control implementation. In the future, we anticipate our method can be applied to other arthropod vector-borne diseases.
Characterization and comparative analysis of the Escherichia marmotae M-12 isolate from bank vole (Myodes glareolus)
Authors: Zhurilov Pavel A. , Andriyanov Pavel A. , Tutrina Anastasia I. , Razheva Irina V. , Liskova Elena A. , Gladkova Nadezda A. , Kashina Daria D. , Yashin Ivan V. , Blokhin Andrey A. 
Published: August 2023

AbstractThe Escherichia marmotae is a bacterium of the Enterobacterales order, which was first isolated from the Himalayan marmot (Marmota himalayana). Recently E. marmotae has been shown to cause severe infections in humans. Wild animals were suggested to be a natural reservoir of this bacterium. The present study describes the first case of E. marmotae isolation from an apparently healthy wild bank vole (Myodes glareolus). Phenotype, as well as genotype-based techniques, were applied to characterize E. marmotae M-12 isolate. E. marmotae M-12 had the capsule-positive phenotype, high adhesion to human erythrocytes and HEp-2 cells as well as a low invasion into HEp-2 cells. E. marmotae M-12 was avirulent in mice. The phylogenomic analyses of E. marmotae showed dispersed phylogenetic structure among isolates of different origins. Virulome analysis of M-12 isolate revealed the presence of the following factors: siderophores, heme uptake systems, capsule synthesis, curli and type I fimbriae, flagella proteins, OmpA porin, etc. Comparative virulome analysis among available E. marmotae genomes revealed the presence of capsule K1 genes mostly in pathogenic isolates and OmpA porin presence among all strains. We assume that the K1 capsule and OmpA porin play a key role in the virulence of E. marmotae. Pathogenesis of the latter might be similar to extraintestinal pathogenic E. coli.
Inhibition of insulin-degrading enzyme in human neurons promotes amyloid-β deposition
Authors: Rowland Helen A. , Moxon Samuel R. , Corbett Nicola J. , Hanson Kelsey , Fisher Kate , Kellett Katherine A.B. , Hooper Nigel M. 
Published: August 2023

Abstract
Alzheimer’s disease (AD) is characterised by the aggregation and deposition of amyloid-β (Aβ) peptides in the human brain. In age-related late-onset AD, deficient degradation and clearance, rather than enhanced production, of Aβ contributes to disease pathology. In the present study, we assessed the contribution of the two key Aβ-degrading zinc metalloproteases, insulin-degrading enzyme (IDE) and neprilysin (NEP), to Aβ degradation in human induced pluripotent stem cell (iPSC)-derived cortical neurons. Using an Aβ fluorescence polarisation assay, inhibition of IDE but not of NEP, blocked the degradation of Aβ by human neurons. When the neurons were grown in a 3D extracellular matrix to visualise Aβ deposition, inhibition of IDE but not NEP, increased the number of Aβ deposits. The resulting Aβ deposits were stained with the conformation-dependent, anti-amyloid antibodies A11 and OC that recognise Aβ aggregates in the human AD brain. Inhibition of the Aβ-forming β-secretase prevented the formation of the IDE-inhibited Aβ deposits. These data indicate that inhibition of IDE in live human neurons grown in a 3D matrix increased the deposition of Aβ derived from the proteolytic cleavage of the amyloid precursor protein. This work has implications for strategies aimed at enhancing IDE activity to promote Aβ degradation in AD.
Auditory Processing Disorder: Protocols and Controversy
Authors: Ismen Katherine , Emanuel Diana C. 
Published: August 2023

Purpose:
This study examined current auditory processing disorder (APD) protocols and audiologists' perspectives on the active debate seen in the literature regarding the status of APD as a unique disorder.

Method:
This study used a cross-sectional, nonexperimental survey design. The participants were 134 U.S. audiologists, representing diversity across experience level and work setting.

Results:
Popular APD tests from prior surveys remain popular, and a few new tests have emerged. Most audiologists use diverse strategies to identify potential comorbid disorders as part of their APD protocol, including multidisciplinary assessment and referral to other specialists. Most participants disagreed with the assertion that APD is not a unique disorder; however, many also pointed out that patients' struggles with listening need to be the primary focus of APD assessment and management, regardless of the label of the disorder. Qualitative analysis of participant comments on the controversy yielded six themes: Clinical Experience, Comorbidity, Listening Skills, Literature Support, Overdiagnosis, and More Information Needed.

Conclusion:
Most participants consider APD to be a unique disorder, citing clinical experience and the literature for support; however, many also indicated APD is complicated by comorbidity and APD may be overdiagnosed.
A virtual reality learning platform for steam generators
Authors: Mantelli Luca , Traverso Alberto , Lupinetti Katia , Giannini Franca , Monica Luigi , Anastasi Sara 
Published: August 2023

Virtual reality (VR) has proven to be an effective tool for industrial training, offering immersive and interactive learning experiences. However, it is important to accurately simulate the behavior of the equipment in order to provide realistic training activities to the users.
On these premises, the PITSTOP project aims at developing an immersive learning tool, based on the integration of dynamic models and a VR environment. Following this methodology, the first learning platform for industrial-scale steam generators was created. Adopting a mixed physics-based data-driven approach, a fast but accurate dynamic model was developed and calibrated on real data of the auxiliary steam generator of the gas turbine combined cycle plant of Tirreno Power in Vado Ligure, Italy. Accessible through an Oculus Quest VR headset, the platform allows learners to interact with a virtual steam generator and adjust control parameters to observe the effects on the system. In this way, learners can gain a better understanding of steam generation principles and practice problem solving and decision-making skills in a safe, controlled environment. The platform also provides teaching materials and an evaluation mode such that learners can assess their knowledge and estimate the correctness of their actions. This article presents an overview of the VR learning platform, with a focus on the specific features of an industrial scale application. The capabilities of the tool are demonstrated through the recreation of real operational procedures of the Tirreno Power steam generator within the VR platform.
Influence of Femoral Position and Pelvic Projection on Norberg Angle Measurements
Authors: Klever Julius , Brühschwein Andreas , Hauser Sarah , Hoffmann Anne-Sophie , Meyer-Lindenberg Andrea 
Published: August 2023

Abstract
Objective Canine hip dysplasia is a common orthopaedic disease in dogs. The Norberg angle value is a measure of hip joint laxity. The aim of this study was to quantify the degree of rotation necessary to consider the radiograph as inadequately positioned and to determine the influence of rotation on the Norberg angle.
Study Design Three sets of radiographs with different positioning and projections were acquired using 10 canine cadavers. Rotation of the pelvis was simulated by rotating the X-ray tube without changing the position of the patient.
Results In dorsoventral projections, the Norberg angle value is increased by 3.2 to 5.8%. Due to rotation along the long axis, the Norberg angle increases on one side and decreases on the contralateral side by approximately the same value. Rotation of greater than 2 degrees in a lateral direction is visually perceived by the observer as tilted. Rotation of the projection in the caudoventral to craniodorsal direction causes mild increase of the Norberg angle (≤1%), while rotation of the projection in a cranioventral to caudodorsal direction causes moderate (≤2%) decrease of the Norberg angle. Rotation of less than –10 degrees (caudoventral to craniodorsal) or greater than 10 degrees (cranioventral to caudodorsal) is visually perceived as tilted.
Conclusion Tilted images that are subjectively perceived evaluable have only little effect on the Norberg angle and are therefore probably acceptable. Dorsoventral projections can be recognized based on the proximal position of the patella and should be excluded from evaluation, as the Norberg angle value can be falsely increased.
Synthesis of AlOxNy thin films using a two-step PE-ALD process
Authors: Zeghouane Mohammed , Fernandes Paes Pinto Rocha Pedro , Boubenia Sarah , Bassani Franck , Lefevre Gauthier , Labau Sebastien , Vauche Laura , Martinez Eugénie , Veillerot Marc , Salem Bassem 
Published: August 2023

Homogeneous AlOxNy thin films with a controlled nitrogen composition, up to 7.1%, were grown on GaN substrate using plasma-enhanced atomic layer deposition. This was achieved through repeated cycles consisting of AlN thin layers deposition and subsequent in situ O2 plasma oxidation under optimized conditions. We demonstrate that the nitrogen concentration in AlOxNy films can be finely tuned from 1.5% to 7.1% by a precise control of the AlN thin film thickness from 0.25 to 0.96 nm before each oxidation step. It is shown also that higher AlN thickness, ≥1.96 nm, leads to an incomplete plasma oxidation of AlN films, resulting in the formation of AlOxNy/AlN-like structures. Several structural and physic-chemical characterizations, including focused ion beam-scanning transmission electron microscopy, Auger electron spectroscopy, XPS, and time-of-flight secondary ion mass spectrometry were performed to confirm these findings. These results highlight the importance of this approach for growing homogeneous AlOxNy thin films with controlled nitrogen doping, which can be used as dielectrics in gate stacks for high performance GaN-based transistors.