bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and ohmic contact of hydrothermally synthesized vertical ZnO and Ag/ZnO nanowires
Authors: Qu Xichun , Fu Yingchun , Duan Zhiyong , Li Mengke , Zhong Ying hui , Ma Liuhong 
Published: December 2022

Abstract
Vertically aligned ZnO nanowire arrays were synthesized by two-step hydrothermal method. ZnO seed layers were prepared on substrate by using anhydrous ethanol and zinc acetate dihydrate solution, followed by the generation of ZnO nanowire arrays by low-temperature liquid-phase hydrothermal methods. The ZnO nanowire arrays were prepared under different conditions to compare the effects of growth conditions on the morphology of ZnO nanowires, in order to explore the optimal growth conditions for ZnO nanowire arrays used in semiconductor device. The morphological changes of ZnO nanowire arrays grown under different conditions were systematically analyzed by SEM, XRD and other characterization means. The results show that the seed solution concentration, growth solution concentration, doping concentration and growth time all have certain effects on the morphology of ZnO nanowire arrays. Besides, the Ag/ZnO ohmic contact were investigated, the optimal annealing temperatures of 450 °C was obtained.
An energy method for buckling behavior analysis of functionally graded carbon nanotube-reinforced composite sandwich structures
Authors: Wang Shaoqing , Qiao Yanmei , Liu Changcun , Luo Li 
Published: December 2022

Abstract
The present work aims to investigate the buckling performance of sandwich structure of functionally graded carbon nanotube-reinforced composite (FG-CNTRC). Through first-order shear deformation theory, an analytical model for the sandwich structure of FG-CNTRC was established. The governing equation for the prediction of the buckling performance of the sandwich structure of FG-CNTRC was obtained through energy method. There was analytical solution that can satisfy both boundary conditions. The theoretical model and method were verified by literature analysis, and the influence of each parameter on the buckling performance was evaluated and performed on the basis of the corroborated model. The findings can lay a solid foundation of the design and application of the sandwich structure of FG-CNTRC.
Implications of the M-OO∙∙OO-M recombination mechanism on materials screening and the oxygen evolution reaction
Authors: Exner Kai S 
Published: December 2022

Abstract
Identification of active electrocatalysts for the oxygen evolution reaction (OER), corresponding to the bottleneck in electrolyzers to produce gaseous hydrogen as energy vector, by electronic structure calculations relies on the assumption of the mononuclear mechanism, comprising the *OH, *O, and *OOH intermediates. This mechanistic description is thermodynamically hampered by a scaling relation between the *OH and *OOH adsorbates, which may serve as an explanation why OER catalysts commonly require large overpotentials to reach sufficient current densities. Recently, an alternate OER pathway was proposed that, in contrast to the mononuclear description, consists of the formation of two adjacent *OO adsorbates, and gaseous oxygen is produced by chemical recombination of the neighboring *OO intermediates. In the present manuscript, a data-driven model based on a dedicated assessment of the elementary reaction steps is deduced, which enables evaluating the mononuclear and *OO pathways by the same set of parameters. Potential-dependent volcano plots are constructed to comprehend the energetics of the competing mechanisms. It is demonstrated that the alternate OER pathway consisting of the *OO∙∙*OO recombination step may excel the mononuclear description at overpotentials corresponding to typical OER conditions. Consequently, it is suggested that future studies, aiming at the identification of OER materials, may not omit the *OO∙∙*OO recombination mechanism when using concepts of materials screening in a heuristic fashion or multiscale modeling.
Multi-response optimization of friction stir lap welding of aluminum plates through GRA-PCA
Authors: Pandipati Suman , Potnuru Srinivasarao , Sreeramulu Dowluru 
Published: December 2022

Abstract
Friction stir welding (FSW) is a method of solid state joining in which the joint is produced below the base meta-l’s melting temperature. This research work investigates the welding properties of the aluminium alloys using the friction stir welding technique. A novel grey relational analysis (GRA)-principal component analysis (PCA) approach were used, the effect of process parameters such as tool feed rate, tool rotational speed, and tool pin profile were discussed to find the best fair weld quality. According to the full factorial design, twenty-seven experiments were designed and the quality of the experimental sample were tested for shear tensile strength, yield strength (YS), percentage elongation (PE), and weld zone hardness (HZ). The optimum process parameters of GRA-PCA results showed with the traverse speed of 70 mm min−1, a rotational speed of 1400 rpm, and a triangular tool pin profile. Analysis of variance (ANOVA) evidenced that all the three parameters were significant with the P and F value, and rotational speed was the predominant parameter with 43.56% contribution. Thus, the optimal conditions for this research showed 1.28 percent improvement in the overall weld quality.
Deep generative modeling and clustering of single cell Hi-C data
Authors: Liu Qiao , Zeng Wanwen , Zhang Wei , Wang Sicheng , Chen Hongyang , Jiang Rui , Zhou Mu , Zhang Shaoting 
Published: December 2022

Abstract
Deciphering 3D genome conformation is important for understanding gene regulation and cellular function at a spatial level. The recent advances of single cell Hi-C technologies have enabled the profiling of the 3D architecture of DNA within individual cell, which allows us to study the cell-to-cell variability of 3D chromatin organization. Computational approaches are in urgent need to comprehensively analyze the sparse and heterogeneous single cell Hi-C data. Here, we proposed scDEC-Hi-C, a new framework for single cell Hi-C analysis with deep generative neural networks. scDEC-Hi-C outperforms existing methods in terms of single cell Hi-C data clustering and imputation. Moreover, the generative power of scDEC-Hi-C could help unveil the differences of chromatin architecture across cell types. We expect that scDEC-Hi-C could shed light on deepening our understanding of the complex mechanism underlying the formation of chromatin contacts.
DeepCellEss: cell line-specific essential protein prediction with attention-based interpretable deep learning
Authors: Li Yiming , Zeng Min , Zhang Fuhao , Wu Fang-Xiang , Li Min 
Published: December 2022

AbstractMotivationProtein essentiality is usually accepted to be a conditional trait and strongly affected by cellular environments. However, existing computational methods often do not take such characteristics into account, preferring to incorporate all available data and train a general model for all cell lines. In addition, the lack of model interpretability limits further exploration and analysis of essential protein predictions.ResultsIn this study, we proposed DeepCellEss, a sequence-based interpretable deep learning framework for cell line-specific essential protein predictions. DeepCellEss utilizes a convolutional neural network and bidirectional long short-term memory to learn short- and long-range latent information from protein sequences. Further, a multi-head self-attention mechanism is used to provide residue-level model interpretability. For model construction, we collected extremely large-scale benchmark datasets across 323 cell lines. Extensive computational experiments demonstrate that DeepCellEss yields effective prediction performance for different cell lines and outperforms existing sequence-based methods as well as network-based centrality measures. Finally, we conducted some case studies to illustrate the necessity of considering specific cell lines and the superiority of DeepCellEss. We believe that DeepCellEss can serve as a useful tool for predicting essential proteins across different cell lines.Availability and implementationThe DeepCellEss web server is available at http://csuligroup.com:8000/DeepCellEss. The source code and data underlying this study can be obtained from https://github.com/CSUBioGroup/DeepCellEss.Supplementary informationSupplementary data are available at Bioinformatics online.
Variable rate of ageing within species: insights from Darwin’s frogs
Authors: Valenzuela-Sánchez Andrés , Schmidt Benedikt R , Azat Claudio , Delgado Soledad , Cunningham Andrew A , Lemaître Jean-François , Gaillard Jean-Michel , Cayuela Hugo 
Published: December 2022

AbstractActuarial senescence, the increase in adult mortality risk with increasing age, is a widespread phenomenon across the animal kingdom. Although between-species variation in the rate of increase in mortality as organisms age (i.e. ageing rate) is now well documented, the occurrence of variation in ageing rate within a given species remains much more debatable. We evaluated the level of within-species variation in ageing rate in four populations of the southern Darwin’s frog (Rhinoderma darwinii) from Chile. Our results revealed strong among-population variation in ageing rates, and these were correlated with the population-specific generation time. A higher ageing rate occurred in populations where individuals exhibited a faster pace of life. Our results, along with recent studies in evolutionarily distant amphibian species, indicate that there can be substantial within-species variation in the rate of ageing, highlighting amphibians as emerging models to study the patterns and mechanisms of intraspecific variation in ageing rate.
Idiopathic Thrombocytopaenic Purpura associated with Inflammatory Bowel Disease: a multicentre ECCO CONFER case series
Authors: Mahajna Hussein , Verstockt Bram , Bergemalm Daniel , Castiglione Fabiana , Rodríguez-Moranta Fransisco , Savarino Edoardo , Hoentjen Frank , Bessissow Talat , Pokryszka Jagoda , Cremer Anneline , Eder Piotr , Truyens Marie , Yerushalmy-Feler Anat , García María José , Kopylov Uri 
Published: December 2022

Abstract

Background
Idiopathic thrombocytopaenic purpura [ITP] is an acquired haematological disorder with an incidence of 1–6 per 100 00/year. ITP and inflammatory bowel disease [IBD] comorbidity has been reported in the literature, but insights regarding the course, outcome and optimal management are limited by its rarity. The current study aimed to evaluate the clinical presentation and outcome of ITP in patients with IBD.

Methods
This multicentre retrospective case series was performed as part of the ECCO Collaborative Network of Exceptionally Rare case reports [CONFER] project. Cases of patients with ITP and IBD were collected by participating investigators. Clinical data were recorded in a standardized collection form.

Results
This report includes 32 patients with concurrent ITP and IBD: ten were females, and the median age was 32.0 years (interquartile range [IQR] 20.5–39.5). Fourteen patients had a diagnosis of Crohn’s disease [CD] and the other 18 ulcerative colitis [UC]. The diagnosis of IBD preceded the ITP in 26 patients (median time between diagnoses was 7.0 years [IQR, 1.5–9.5]). Among those patients, 17 were in clinical remission at ITP diagnosis. Thirteen patients were treated with mesalamine, four with oral corticosteroids, one with rectal corticosteroids, two with azathioprine and five with anti-tumour necrosis factor agents. The median platelet count was 35 000/microliter [IQR, 10 000–70 000]. Eight patients had rectal bleeding, 13 had skin purpura, three had epistaxis, six had mucosal petechiae and 13 were asymptomatic. Regarding ITP treatment, 19 were treated with corticosteroids, one with anti-RhD immunoglobulin, 12 with intravenous immunoglobulins [IVIGs], four with thrombopoietin, three with rituximab and six patients eventually required splenectomy. Ten patients needed no treatment directed to the ITP. Three patients required colectomy during long-term follow-up, due to IBD or cancer but not to massive bleeding as a complication of ITP. One of eight patients who presented with rectal bleeding required splenectomy, and none required urgent colectomy. Two patients died during the follow-up, one of them due to bleeding complications located in the upper gastrointestinal tract. Median follow-up time was 6.5 years [IQR, 3–10]. With long-term follow-up, all patients had platelet counts above 50 000/microliter, and 24 were in IBD clinical remission.

Conclusion
Most ITP cases in this series occurred after the IBD diagnosis and responded well to regular ITP treatment. The course of the ITP in the IBD patients followed an expected course, including response to medical therapy and low rates of splenectomy.
Multi-modality imaging to guide the implantation of cardiac electronic devices in heart failure: is the sum greater than the individual components?
Authors: Galli Elena , Baritussio Anna , Sitges Marta , Donnellan Eoin , Jaber Wael A , Gimelli Alessia 
Published: December 2022

Abstract
Heart failure is a clinical syndrome with an increasing prevalence and incidence worldwide that impacts patients’ quality of life, morbidity, and mortality. Implantable cardioverter-defibrillator and cardiac resynchronization therapy are pillars of managing patients with HF and reduced left ventricular ejection fraction. Despite the advances in cardiac imaging, the assessment of patients needing cardiac implantable electronic devices relies essentially on the measure of left ventricular ejection fraction. However, multi-modality imaging can provide important information concerning the aetiology of heart failure, the extent and localization of myocardial scar, and the pathophysiological mechanisms of left ventricular conduction delay. This paper aims to highlight the main novelties and progress in the field of multi-modality imaging to identify patients who will benefit from cardiac resynchronization therapy and/or implantable cardioverter-defibrillator. We also want to underscore the boundaries that prevent the application of imaging-derived parameters to patients who will benefit from cardiac implantable electronic devices and orient the choice of the device. Finally, we aim at providing some reflections for future research in this field.
Maximizing lymph node dissection from fresh lung cancer specimens
Authors: Raymond Cédric , Vieira Arthur , Joubert Philippe , Ugalde Paula A 
Published: December 2022

Abstract
Evaluation of lymph nodes during lung cancer resection is essential for pathologic staging and adjuvant treatment decisions. We developed a standardized approach for grossing resected lobes and segments to better assign the N1 category to hilar and peripheral lymph nodes. Lung specimens were dissected centrifugally from the bronchial stump, and all lymph nodes at the segmental and subsegmental bifurcations were removed. When combined with mediastinal lymph node dissection, this approach will likely maximize the number of lymph nodes analysed and improve the accuracy of pathologic N descriptor classification.
Genome-wide association study to identify genomic loci associated with early vigor in bread wheat under simulated water deficit complemented with quantitative trait loci meta-analysis
Authors: Rahimi Yousef , Khahani Bahman , Jamali Ali , Alipour Hadi , Bihamta Mohammad Reza , Ingvarsson Pär K 
Published: December 2022

Abstract
A genome-wide association study (GWAS) was used to identify associated loci with early vigor under simulated water deficit and grain yield under field drought in a diverse collection of Iranian bread wheat landraces. In addition, a meta-quantitative trait loci (MQTL) analysis was used to further expand our approach by retrieving already published quantitative trait loci (QTL) from recombinant inbred lines, double haploids, back-crosses, and F2 mapping populations. In the current study, around 16%, 14%, and 16% of SNPs were in significant linkage disequilibrium (LD) in the A, B, and D genomes, respectively, and varied between 5.44% (4A) and 21.85% (6A). Three main subgroups were identified among the landraces with different degrees of admixture, and population structure was further explored through principal component analysis. Our GWAS identified 54 marker-trait associations (MTAs) that were located across the wheat genome but with the highest number found in the B sub-genome. The gene ontology (GO) analysis of MTAs revealed that around 75% were located within or closed to protein-coding genes. In the MQTL analysis, 23 MQTLs, from a total of 215 QTLs, were identified and successfully projected onto the reference map. MQT-YLD4, MQT-YLD9, MQT-YLD13, MQT-YLD17, MQT-YLD18, MQT-YLD19, and MQTL-RL1 contributed to the highest number of projected QTLs and were therefore regarded as the most reliable and stable QTLs under water deficit conditions. These MQTLs greatly facilitate the identification of putative candidate genes underlying at each MQTL interval due to the reduced confidence of intervals associated with MQTLs. These findings provide important information on the genetic basis of early vigor traits and grain yield under water deficit conditions and set the foundation for future investigations into adaptation to water deficit in bread wheat.
Is There Evidence of an Association Between Acute Health Care Utilization and Function in Older Adults Over Time? A Population-Based Cohort Study
Authors: Conneely Mairéad , Leahy Siobhán , Trépel Dominic , Robinson Katie , Boland Fiona , Moriarty Frank , Galvin Rose 
Published: December 2022

Abstract

Background and Objectives
Acute health care use varies by age, with older adults the highest users of acute health care services. Using data from The Irish Longitudinal Study on Ageing (TILDA), the aim of this study was to investigate the association between acute health care utilization (emergency department [ED] visit with or without hospitalization) at baseline and subjective and objective measures of function measured at 4-year follow-up.

Research Design and Methods
This study represents a secondary analysis of a prospective cohort study, where data from Wave 1 (baseline) and Wave 3 of TILDA were analyzed in conjunction with a public and patient involvement group of older adults. Acute health care utilization was defined as an ED visit with or without hospitalization in the previous 12 months. Function was assessed objectively using the Timed Up and Go (TUG) test and a measure of grip strength, and subjectively using self-report limitations in activities of daily living (ADL) and instrumental ADL (IADL).

Results
A total of 1 516 participants met the study inclusion criteria. Mean age was 70.9 ± 4.6 years and 48% were male. At baseline, 1 280 participants reported no acute health care use. One hundred and eighteen indicated an ED visit but no hospitalization in the previous 12 months and 118 reported both an ED visit and hospitalization. Adjusting for all covariates, compared to those with no acute health care utilization, those with an ED visit with no hospital admission had poorer TUG performance at follow-up (β = 0.67, 95% confidence interval: 0.34, 1.29, p = .039).

Discussion and Implications
This paper supports previous research that acute health care events, specifically ED usage, are associated with reduced function for older adults as assessed by TUG at follow-up. No associations were observed for grip strength, ADL, or IADL. Further research is required in this area, exploring ED visits and the possible benefits of evaluating older adults at this stage.
Barriers and facilitators to comprehensive, school-based physical activity promotion for adolescents prior to and during the COVID-19 pandemic: a qualitative study
Authors: Johnson Ashleigh M , Tandon Pooja S , Hafferty Kiana R , Senturia Kirsten , Garrett Kimberly A , Bollinger Beth J , Kroshus Emily 
Published: December 2022

Abstract
This study aimed to identify barriers and facilitators to comprehensive, school-based physical activity (PA) promotion among adolescents prior to and during the coronavirus disease of 2019 (COVID-19) pandemic, considering the perspectives of students, parents, and school staff. Data were collected from 2020 to 2021 using semi-structured individual interviews with students (n = 15), parents (n = 20), and school staff (n = 8) at a Title I middle school (i.e. high percentage of students from low-income families). Two theoretical frameworks guided analysis: the Comprehensive School Physical Activity Program framework and Bronfenbrenner’s ecological systems theory. Using an iteratively developed codebook, data were coded, thematically analyzed, and synthesized. PA barriers and facilitators were present throughout the school day, at home, and in the community. Key determinants included pandemic-induced challenges (e.g. COVID-19 exposure); neighborhood characteristics/weather (e.g. neighborhood safety); school–family communication/collaboration; implementation climate (i.e. school staff’s support for programming); time, spatial, and monetary resources (e.g. funding); staffing capacity/continuity and school champions; staffing creativity and adaptability; PA opportunities before, during, and after school; and child’s motivation/engagement. Efforts to improve school-based PA programs, irrespective of pandemic conditions, should include strategies that address factors at the community, school, family and individual levels. School–family communication/collaboration, school staff programming support, and PA opportunities throughout the day can help promote comprehensive, school-based PA.
Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis
Authors: Yue Junyang , Chen Qinyao , Wang Yingzhen , Zhang Lei , Ye Chen , Wang Xu , Cao Shuo , Lin Yunzhi , Huang Wei , Xian He , Qin Hongyan , Wang Yanli , Zhang Sijia , Wu Ying , Wang Songhu , Yue Yi , Liu Yongsheng 
Published: December 2022

Abstract
Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C. However, the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions. Here, we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv. ‘Hongyang’, named Hongyang v4.0, which is the first to achieve two de novo haploid-resolved haplotypes, HY4P and HY4A. HY4P and HY4A have a total length of 606.1 and 599.6 Mb, respectively, with almost the entire telomeres and centromeres assembled in each haplotype. In comparison with Hongyang v3.0, the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions, resulting in ~38.6–39.5 Mb extra sequences, which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A, respectively. Furthermore, our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres. Globally, centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer (Ach-CEN153) with different copy numbers among chromosomes. Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids, but also have genetic features for participation in the regulation of cell division. The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement.