bluuebunny/crossref_metadata_2025_split huggingface dataset:
CLIPreg: constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq
Authors: Kerouanton Baptiste , Schäfer Sebastian , Ho Lena , Chothani Sonia , Rackham Owen J L 
Published: June 2022

AbstractMotivationThe creation and analysis of gene regulatory networks have been the focus of bioinformatics research and underpins much of what is known about gene regulation. However, as a result of a bias in the availability of data types that are collected, the vast majority of gene regulatory network resources and tools have focused on either transcriptional regulation or protein–protein interactions. This has left other areas of regulation, for instance, translational regulation, vastly underrepresented despite them having been shown to play a critical role in both health and disease.ResultsIn order to address this, we have developed CLIPreg, a package that integrates RNA, Ribo and CLIP- sequencing data in order to construct translational regulatory networks coordinated by RNA-binding proteins and micro-RNAs. This is the first tool of its type to be created, allowing for detailed investigation into a previously unseen layer of regulation.Availability and implementationCLIPreg is available at https://github.com/SGDDNB/CLIPreg.Supplementary informationSupplementary data are available at Bioinformatics online.
scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data
Authors: Shen Siqi , Zheng Ye , Keleş Sündüz 
Published: June 2022

AbstractSummaryQuantitative tools are needed to leverage the unprecedented resolution of single-cell high-throughput chromatin conformation (scHi-C) data and integrate it with other single-cell data modalities. We present single-cell gene associating domain (scGAD) scores as a dimension reduction and exploratory analysis tool for scHi-C data. scGAD enables summarization at the gene unit while accounting for inherent gene-level genomic biases. Low-dimensional projections with scGAD capture clustering of cells based on their 3D structures. Significant chromatin interactions within and between cell types can be identified with scGAD. We further show that scGAD facilitates the integration of scHi-C data with other single-cell data modalities by enabling its projection onto reference low-dimensional embeddings. This multi-modal data integration provides an automated and refined cell-type annotation for scHi-C data.Availability and implementationscGAD is part of the BandNorm R package at https://sshen82.github.io/BandNorm/articles/scGAD-tutorial.html.Supplementary informationSupplementary data are available at Bioinformatics online.
The European Union Statistics on Income and Living Conditions after 15 Years
Authors: Wirth Heike , Pforr Klaus 
Published: June 2022

AbstractThis data brief describes the European Union Statistics on Income and Living Conditions (EU-SILC). Detailed data on income and taxes are collected, as well as information on material deprivation, labour, housing, childcare, health, access to and use of services, and education. Although primarily a social policy instrument that addresses the information needs of policymakers and is used for social monitoring at the European level, EU-SILC is also closely geared to the needs of researchers and provides an excellent database for evidence-based research on a wide variety of aspects of income, income poverty, material poverty, health, and well-being in Europe. EU-SILC is composed of national probability sample surveys and is conducted annually. The target population comprises private households. Observation units are households and all current household members. EU-SILC provides cross-sectional and longitudinal data. The data are composed of a fixed core module, and annually changing ad-hoc modules. Launched in 2003 and revised with effect from 2021, EU-SILC is currently implemented in all EU Member States and in 11 non-EU countries. During the revision process, many suggestions from the research community were incorporated.
Bacterial–viral interactions: a factor that facilitates transmission heterogeneities
Authors: Stein Richard A , Bianchini Emilia Claire 
Published: June 2022

AbstractThe transmission of infectious diseases is characterized by heterogeneities that are shaped by the host, the pathogen, and the environment. Extreme forms of these heterogeneities are called super-spreading events. Transmission heterogeneities are usually identified retrospectively, but their contribution to the dynamics of outbreaks makes the ability to predict them valuable for science, medicine, and public health. Previous studies identified several factors that facilitate super-spreading; one of them is the interaction between bacteria and viruses within a host. The heightened dispersal of bacteria colonizing the nasal cavity during an upper respiratory viral infection, and the increased shedding of HIV-1 from the urogenital tract during a sexually transmitted bacterial infection, are among the most extensively studied examples of transmission heterogeneities that result from bacterial–viral interactions. Interrogating these transmission heterogeneities, and elucidating the underlying cellular and molecular mechanisms, are part of much-needed efforts to guide public health interventions, in areas that range from predicting or controlling the population transmission of respiratory pathogens, to limiting the spread of sexually transmitted infections, and tailoring vaccination initiatives with live attenuated vaccines.
Comparative analysis of the testes from wild-type and Alkbh5-knockout mice using single-cell RNA sequencing
Authors: Hong Shihao , Shen Xiaozhong , Luo Chunhai , Sun Fei 
Published: June 2022

Abstract
The RNA demethylase ALKBH5 is regarded as the “eraser” in N6-methyladenosine modification. ALKBH5 deficiency causes male infertility in mice; however, the mechanisms that confer disruption of spermatogenesis are not completely clear. In this study, we profiled testis samples from wild-type and Alkbh5-knockout mice using single-cell RNA sequencing. We obtained single-cell RNA sequencing data of 5,596 and 6,816 testis cells from a wild-type and a knockout mouse, respectively. There were differences detected between the transcriptional profiles of the groups at various germ cell developmental stages. This ranged from the development of spermatogonia to sperm cells, in macrophages, Sertoli cells, and Leydig cells. We identified the differentially expressed genes related to spermatogenesis in germ cells and somatic cells (Sertoli cells and Leydig cells) and evaluated their functions and associated pathways, such as chromatin-related functional pathways, through gene ontology enrichment analysis. This study provides the first single-cell RNA sequencing profile of the testes of ALKBH5-deficient mice. This highlights that ALKBH5 is an important gene for germ cell development and spermatogenesis and offers new molecular mechanistic insights. These findings could provide the basis for further research into the causes and treatment of male infertility.
Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae
Authors: Meslin Camille , Mainet Pauline , Montagné Nicolas , Robin Stéphanie , Legeai Fabrice , Bretaudeau Anthony , Johnston J Spencer , Koutroumpa Fotini , Persyn Emma , Monsempès Christelle , François Marie-Christine , Jacquin-Joly Emmanuelle 
Published: June 2022

Abstract
The bitter taste, triggered via gustatory receptors, serves as an important natural defense against the ingestion of poisonous foods in animals, and the increased host breadth is usually linked to an increase in the number of gustatory receptor genes. This has been especially observed in polyphagous insect species, such as noctuid species from the Spodoptera genus. However, the dynamic and physical mechanisms leading to these gene expansions and the evolutionary pressures behind them remain elusive. Among major drivers of genome dynamics are the transposable elements but, surprisingly, their potential role in insect gustatory receptor expansion has not been considered yet. In this work, we hypothesized that transposable elements and possibly positive selection would be involved in the highly dynamic evolution of gustatory receptor in Spodoptera spp. We first sequenced de novo the full 465 Mb genome of S. littoralis, and manually annotated the main chemosensory genes, including a large repertoire of 373 gustatory receptor genes (including 19 pseudogenes). We also improved the completeness of S. frugiperda and S. litura gustatory receptor gene repertoires. Then, we annotated transposable elements and revealed that a particular category of class I retrotransposons, the SINE transposons, was significantly enriched in the vicinity of gustatory receptor gene clusters, suggesting a transposon-mediated mechanism for the formation of these clusters. Selection pressure analyses indicated that positive selection within the gustatory receptor gene family is cryptic, only 7 receptors being identified as positively selected. Altogether, our data provide a new good quality Spodoptera genome, pinpoint interesting gustatory receptor candidates for further functional studies and bring valuable genomic information on the mechanisms of gustatory receptor expansions in polyphagous insect species.
A look-ahead approach to maximizing present value of genetic gains in genomic selection
Authors: Zhang Zerui , Wang Lizhi 
Published: June 2022

Abstract
Look-ahead selection is a sophisticated yet effective algorithm for genomic selection, which optimizes not only the selection of breeding parents but also mating strategy and resource allocation by anticipating the implications of crosses in a prespecified future target generation. Simulation results using maize datasets have suggested that look-ahead selection is able to significantly accelerate genetic gain in the target generation while maintaining genetic diversity. In this paper, we propose a new algorithm to address the limitations of look-ahead selection, including the difficulty in specifying a meaningful deadline in a continuous breeding process and slow growth of genetic gain in early generations. This new algorithm uses the present value of genetic gains as the breeding objective, converting genetic gains realized in different generations to the current generation using a discount rate, similar to using the interest rate to measure the time value of cash flows incurred at different time points. By using the look-ahead techniques to anticipate the future gametes and thus present value of future genetic gains, this algorithm yields a better trade-off between short-term and long-term benefits. Results from simulation experiments showed that the new algorithm can achieve higher genetic gains in early generations and a continuously growing trajectory as opposed to the look-ahead selection algorithm, which features a slow progress in early generations and a growth spike right before the deadline.
Invariant Galton–Watson branching process for earthquake occurrence
Authors: Kovchegov Yevgeniy , Zaliapin Ilya , Ben-Zion Yehuda 
Published: June 2022

SUMMARYWe propose a theoretical modelling framework for earthquake occurrence and clustering based on a family of invariant Galton–Watson (IGW) stochastic branching processes. The IGW process is a rigorously defined approximation to imprecisely observed or incorrectly estimated earthquake clusters modelled by Galton–Watson branching processes, including the Epidemic Type Aftershock Sequence (ETAS) model. The theory of IGW processes yields explicit distributions for multiple cluster attributes, including magnitude-dependent and magnitude-independent offspring number, cluster size and cluster combinatorial depth. Analysis of the observed seismicity in southern California demonstrates that the IGW model provides a close fit to the observed earthquake clusters. The estimated IGW parameters and derived statistics are robust with respect to the catalogue lower cut-off magnitude. The proposed model facilitates analyses of multiple quantities of seismicity based on self-similar tree attributes, and may be used to assess the proximity of seismicity to criticality.
Interannual variability in size-selective winter mortality of young-of-the-year striped bass
Authors: Peres Henrique A , Robert Dominique , Mainguy Julien , Sirois Pascal 
Published: June 2022

Abstract
Early life stages of fish are characterized by high size-selective mortality rates, with selection generally acting against smaller, slow-growing individuals. Here, we investigate, for the St. Lawrence River striped bass (Morone saxatilis) population, how size of young-of-the-year juveniles (YOYs) affected survival from the pre-wintering period until the following spring, by comparing their otolith daily growth trajectory to that of one-year-old juveniles (OYOs). Otolith growth in the first 50 d after hatch was faster in post- than in pre-winter juveniles in both years, indicating that fast-growing individuals were more likely to survive to the next spring. A larger back-calculated size at age 1 in the 2016 year class compared to that observed in 2017 also suggests interannual variability in size-selective overwinter survival. Our results indicate that the design of YOY abundance surveys aimed at predicting annual recruitment strength needs to account for the effect of size-dependent mortality until the end of the first winter of life, as high abundance of relatively small YOYs in autumn may not necessarily translate into a large number of OYOs in the following spring and thus into high recruitment.
A secondary data analysis of a cluster randomized controlled trial: improved cookstoves associated with reduction in incidence of low birthweight in rural Malawi
Authors: Best Rebecca , Malava Jullita , Dube Albert , Katundu Cynthia , Kalobekamo Fredrick , Mortimer Kevin , Gordon Stephen B , Nyirenda Moffat , Crampin Amelia , McLean Estelle 
Published: June 2022

AbstractBackgroundIn northern rural Malawi, the majority of households cook using open fires and there is also a high burden of adverse birth outcomes. The use of open fires or highly polluting cookstoves is associated with low birthweight in babies. There is mixed evidence on whether implementation of cleaner burning cookstoves reduces the number of babies born with low birthweight.MethodsThis is a secondary analysis of a cluster randomized control trial in Malawi, conducted over 2014–17. Households were randomized to receive improved cookstoves or to continue current practices. For this analysis, the primary outcome was low birthweight in households under routine demographic surveillance, among births occurring within the trial time frame (N = 4010). A subset of data with stricter exposure definitions respecting the original randomized allocation was also analysed (N = 1050). A causal, forwards modelling approach was used.ResultsThe main dataset showed evidence of effect of the intervention on low birthweight [adjusted odds ratio (aOR) 0.69; 95% CI 0.48–0.99, n = 2788). The subset analysis lacked power to provide evidence of association between improved cookstoves and low birthweight in the stricter exposure definition (aOR 0.62; 95% CI 0.35–1.09, n = 932).ConclusionsThis study provides some evidence that an improved cookstove intervention in rural Malawi reduced the number of babies born with low birthweight by 30%. This direction of the effect was also seen in the subset analysis. The analysis suggests that the intervention reduced the number of infants born prematurely or with intra-uterine growth restriction, indicating that improved cookstoves could be a useful maternal health intervention.
Strategic psychology and the study of China’s whole-of-nation strategy
Authors: Chung Youngjune 
Published: June 2022

Abstract
This study explores conceptual variants underpinning the prolific threat of China’s global information operations, shedding light on the under-examined role of strategic psychology in China’s quest for global primacy. Ancient stratagems underlying the Chinese cultural identity and character are applied through a framework to provide clarifying insights into the motivations, intentions, and capacities of China’s pre- and nonkinetic actions. The aim is to identify the individual rationales and cognitive mechanisms that underlie the vast array of China’s national instruments short of war and provide an indigenous, localized perspective to fully understand China’s whole-of-nation strategy.
Automated patient self-scheduling: case study
Authors: Woodcock Elizabeth , Sen Aditi , Weiner Jonathan 
Published: June 2022

AbstractThis case study assesses the uptake, user characteristics, and outcomes of automated self-scheduling in a community-based physician group affiliated with an academic health system. We analyzed 1 995 909 appointments booked between January 1, 2019, and June 30, 2021 at more than 30 practice sites. Over the study period, uptake of self-scheduling increased from 4% to 15% of kept appointments. Younger, commercially insured patients were more likely to be users. Missed appointments were lower and cancelations were higher for self-scheduled patients. An examination of characteristics, benefits, and usage of automated self-scheduling provides insight to those organizations contemplating the implementation or expansion of similar consumer-facing digital self-scheduling platforms.
Conceptualizing clinical decision support as complex interventions: a meta-analysis of comparative effectiveness trials
Authors: Reese Thomas J , Liu Siru , Steitz Bryan , McCoy Allison , Russo Elise , Koh Brian , Ancker Jessica , Wright Adam 
Published: June 2022

Abstract

Objectives
Complex interventions with multiple components and behavior change strategies are increasingly implemented as a form of clinical decision support (CDS) using native electronic health record functionality. Objectives of this study were, therefore, to (1) identify the proportion of randomized controlled trials with CDS interventions that were complex, (2) describe common gaps in the reporting of complexity in CDS research, and (3) determine the impact of increased complexity on CDS effectiveness.

Materials and Methods
To assess CDS complexity and identify reporting gaps for characterizing CDS interventions, we used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses reporting tool for complex interventions. We evaluated the effect of increased complexity using random-effects meta-analysis.

Results
Most included studies evaluated a complex CDS intervention (76%). No studies described use of analytical frameworks or causal pathways. Two studies discussed use of theory but only one fully described the rationale and put it in context of a behavior change. A small but positive effect (standardized mean difference, 0.147; 95% CI, 0.039–0.255; P &lt; .01) in favor of increasing intervention complexity was observed.

Discussion
While most CDS studies should classify interventions as complex, opportunities persist for documenting and providing resources in a manner that would enable CDS interventions to be replicated and adapted. Unless reporting of the design, implementation, and evaluation of CDS interventions improves, only slight benefits can be expected.

Conclusion
Conceptualizing CDS as complex interventions may help convey the careful attention that is needed to ensure these interventions are contextually and theoretically informed.
Effective length of bamboo-like stiffened hollow cylindrical structures
Authors: Nishiyama Ryo , Sato Motohiro 
Published: June 2022

ABSTRACT
Hollow cylindrical structures are susceptible to local buckling because they flatten and significantly reduce their stiffness when they bend. Therefore, many previous studies aimed to improve the strength of pipelines and building structures were conducted. Our research group has focused on bamboo and has theoretically proven that stiffness anisotropy caused by bamboo's unique nodes and vascular bundles enhances the stiffness of cylindrical structures. In this study, to investigate this analytically, we carried out a finite-element analysis and succeeded in deriving a new dimensionless parameter that the stiffening effect of an anisotropic consideration. This result is applicable to a wide range of cylindrical structures, from thin-walled to thick-walled, and it is expected that bamboo-inspired bionic designs will be proposed in the future.
An alternative splicing isoform of wheat TaYRG1 resistance protein activates immunity by interacting with dynamin-related proteins
Authors: Zhang Lu , Liu Yuanming , Wang Qiaohui , Wang Chao , Lv Shikai , Wang Yanzhen , Wang Jianfeng , Wang Yajuan , Yuan Jing , Zhang Hong , Kang Zhensheng , Ji Wanquan 
Published: June 2022

Abstract
Wheat (Triticum aestivum) is a commercially important crop and its production is seriously threatened by the fungal pathogen Puccinia striiformis f. sp. tritici West (Pst). Resistance (R) genes are critical factors that facilitate plant immune responses. Here, we report a wheat R gene NB-ARC-LRR ortholog, TaYRG1, that is associated with distinct alternative splicing events in wheat infected by Pst. The native splice variant, TaYRG1.6, encodes internal-motif-deleted polypeptides with the same N- and C-termini as TaYRG1.1, resulting in gain of function. Transient expression of protein variants in Nicotiana benthamiana showed that the NB and ARC domains, and TaYRG1.6 (half LRR domain), stimulate robust elicitor-independent cell death based on a signal peptide, although the activity was negatively modulated by the CC and complete LRR domains. Furthermore, molecular genetic analyses indicated that TaYRG1.6 enhanced resistance to Pst in wheat. Moreover, we provide multiple lines of evidence that TaYRG1.6 interacts with a dynamin-related protein, TaDrp1. Proteome profiling suggested that the TaYRG1.6-TaDrp1-DNM complex in the membrane trafficking systems may trigger cell death by mobilizing lipid and kinase signaling in the endocytosis pathway. Our findings reveal a unique mechanism by which TaYRG1 activates cell death and enhances disease resistance by reconfiguring protein structure through alternative splicing.
Reading Arab American Literary Variations: An Interview with Rajia Hassib
Authors: Berrebbah Ishak 
Published: June 2022

Abstract
In this interview, Rajia Hassib provides answers to various questions related to her fiction, particularly In the Language of Miracles (2015) and A Pure Heart (2020). This interview, and the discussion that stems from it, introduce critical insights into contemporary Arab American women’s literature and thoughts about the multiple aspects that shape and characterize Arab identity in the US diaspora. The interview contributes to existing scholarship concerning the Arab American diaspora and the study of its literature.