bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Caenorhabditis elegans cullin-RING ubiquitin ligase CRL4DCAF-1 is required for proper germline nucleolus morphology and male development
Authors: Rahman Mohammad M , Balachandran Riju S , Stevenson Jonathan B , Kim Youngjo , Proenca Rui B , Hedgecock Edward M , Kipreos Edward T 
Published: July 2023

Abstract
Cullin-RING ubiquitin ligases (CRLs) are the largest class of ubiquitin ligases with diverse functions encompassing hundreds of cellular processes. Inactivation of core components of the CRL4 ubiquitin ligase produces a germ cell defect in Caenorhabditis elegans that is marked by abnormal globular morphology of the nucleolus and fewer germ cells. We identified DDB1 Cullin4 associated factor (DCAF)-1 as the CRL4 substrate receptor that ensures proper germ cell nucleolus morphology. We demonstrate that the dcaf-1 gene is the ncl-2 (abnormal nucleoli) gene, whose molecular identity was not previously known. We also observed that CRL4DCAF-1 is required for male tail development. Additionally, the inactivation of CRL4DCAF-1 results in a male-specific lethality in which a percentage of male progeny arrest as embryos or larvae. Analysis of the germ cell nucleolus defect using transmission electron microscopy revealed that dcaf-1 mutant germ cells possess significantly fewer ribosomes, suggesting a defect in ribosome biogenesis. We discovered that inactivation of the sperm-fate specification gene fog-1 (feminization of the germ line-1) or its protein-interacting partner, fog-3, rescues the dcaf-1 nucleolus morphology defect. Epitope-tagged versions of both FOG-1 and FOG-3 proteins are aberrantly present in adult dcaf-1(RNAi) animals, suggesting that DCAF-1 negatively regulates FOG-1 and FOG-3 expression. Murine CRL4DCAF-1 targets the degradation of the ribosome assembly factor periodic trptophan protein 1 (PWP1). We observed that the inactivation of Caenorhabditis elegans DCAF-1 increases the nucleolar levels of PWP1 in the germ line, intestine, and hypodermis. Reducing the level of PWP-1 rescues the dcaf-1 mutant defects of fewer germ cell numbers and abnormal nucleolus morphology, suggesting that the increase in PWP-1 levels contributes to the dcaf-1 germline defect. Our results suggest that CRL4DCAF-1 has an evolutionarily ancient role in regulating ribosome biogenesis including a conserved target in PWP1.
Inferring sparse structure in genotype–phenotype maps
Authors: Petti Samantha , Reddy Gautam , Desai Michael M 
Published: July 2023

Abstract
Correlation among multiple phenotypes across related individuals may reflect some pattern of shared genetic architecture: individual genetic loci affect multiple phenotypes (an effect known as pleiotropy), creating observable relationships between phenotypes. A natural hypothesis is that pleiotropic effects reflect a relatively small set of common “core” cellular processes: each genetic locus affects one or a few core processes, and these core processes in turn determine the observed phenotypes. Here, we propose a method to infer such structure in genotype–phenotype data. Our approach, sparse structure discovery (SSD) is based on a penalized matrix decomposition designed to identify latent structure that is low-dimensional (many fewer core processes than phenotypes and genetic loci), locus-sparse (each locus affects few core processes), and/or phenotype-sparse (each phenotype is influenced by few core processes). Our use of sparsity as a guide in the matrix decomposition is motivated by the results of a novel empirical test indicating evidence of sparse structure in several recent genotype–phenotype datasets. First, we use synthetic data to show that our SSD approach can accurately recover core processes if each genetic locus affects few core processes or if each phenotype is affected by few core processes. Next, we apply the method to three datasets spanning adaptive mutations in yeast, genotoxin robustness assay in human cell lines, and genetic loci identified from a yeast cross, and evaluate the biological plausibility of the core process identified. More generally, we propose sparsity as a guiding prior for resolving latent structure in empirical genotype–phenotype maps.
The Risks of Experiencing Severe Loneliness Across Middle and Late Adulthood
Authors: Huxhold Oliver , Henning Georg 
Published: July 2023

Abstract

Objectives
From a theoretical point of view, older adults may not necessarily face a greater risk of becoming lonely than middle-aged adults but are more likely at a disadvantage in fighting loneliness. Therefore, in this study, we differentiate between the risk of becoming lonely and the risk of remaining lonely.

Methods
A large longitudinal data set representative of the German noninstitutionalized population from 40 to 85 years of age (N = 15,408; 49% female participants) was used in the analysis. Lagged logistic regression models were estimated to investigate the effect of earlier experiences of severe loneliness on the risk of being lonely after three years across middle age and late adulthood. Individual differences in health, views on aging, and social activities were taken into account to explore their role in age differences in the risk of remaining lonely.

Results
The analysis revealed marginal age differences in the risk of becoming lonely but a marked age gradient regarding the risk of remaining lonely. Lonely older adults who were older than 75 years of age were more likely to remain lonely after three years than lonely middle-aged adults. Controlling for individual differences in health, views on aging as social loss, and social activities accounted for this age difference.

Discussion
Interventions against loneliness may prioritize older age groups because losses in capacities, shifts in motivations, and a degraded opportunity structure render it increasingly less likely that older adults leave a state of loneliness on their own accord.
Gerontology, Art, and Activism: Can the Intersection of Art, Social Research, and Community Power Lead to Lasting Change?
Authors: Campbell Sarah , Dewhurst Elaine , Chaudry Atiha , Edson Ruth , Ghafoor Rohina , Greenhalgh Marie , Lacy Suzanne , Madzunzu Tendayi 
Published: July 2023

Abstract
This paper seeks to address the question of what gerontologists and humanities scholars can learn from how their respective fields engage with critical issues of age-based intersectional disadvantage, inequality, colonialism, and exclusion. The paper considers the Uncertain Futures Project, a participatory arts-led social research study based in Manchester, United Kingdom. The project explores the inequalities of women over 50 regarding issues of work using an intersectional lens. This work has produced a complex entanglement of methodological ideas that underpin performance art, community activism, and gerontological research. The paper will consider if this model can lead to a lasting impact beyond the scope of the project and beyond the individuals involved. First, we outline the work undertaken from the conception of the project. We consider the relationship between these activities and the ongoing nature of qualitative data analysis within the complexity of academic workloads and competing priorities. We raise questions and considerations of how the elements of the work have connected, collaborated, and intertwined. We also explore the challenges within interdisciplinary and collaborative work. Finally, we address the kind of legacy and impact created by work of this nature.
Iterative approaches for regional Moho determination using on-orbit gravity gradients: a case study in Qinghai–Tibet Plateau and its near zone
Authors: Li Wei-Kai , Mu Qing-Lu , Yang Meng , Feng Wei , Zhong Min 
Published: July 2023

SUMMARY
Moho determination is an important issue in studying the Earth’s interior structure. In accordance with the isostasy-compensation hypothesis in geodesy, it is possible to recover regional or global Moho by employing gravimetric data. The nonlinear property is one of the main difficulties in solving the inverse problem of isostasy. To effectively address this issue, we propose an improved iterative inversion method that combines 3-D integration and linear regularization to achieve an approximate nonlinear solution. To estimate the contributions of different components in the gravity-gradient tensor from the Gravity field and steady-state Ocean Circulation Explorer (GOCE), other than the vertical component, we additionally develop two joint inversion scenarios that utilize diagonal horizontal components and all five non-vertical components. The validating experiments are implemented in Qinghai–Tibet Plateau and its near zone. Simulations and applications illustrate that horizontal responses of Moho undulation are also significant. Yet the off-diagonal components provide minimal contributions, adding only 0.25 km of bias to the joint inversion results. Truncation effects serve as the primary source of systematic errors, resulting in ∼1 km error in vertical inversion results and ∼2.3 km error in joint inversion results. Then, the gravimetric Moho results are compared with CRUST1.0, and they show a generally strong correlation. Differences are obvious at the northern and eastern margins of the plateau. It is maybe due to the local changes in crust–mantle density contrasts. Upwelling of asthenospheric materials and fluid flow in the middle-lower crust are the two main factors. Based on high-precision satellite gravimetry, our study could provide new insights into the tectonic structure of Qinghai–Tibet Plateau.
Consumers’ longitudinal health information needs and seeking: a scoping review
Authors: Bautista John Robert , Zhang Yan , Gwizdka Jacek , Chang Yung-Sheng 
Published: July 2023

AbstractNeeding and seeking health information often is a longitudinal everyday life information behavior that involves the use of technology. However, no reviews of consumers’ longitudinal health information needs (HIN) and health information-seeking (HIS) behavior have been conducted. We performed a scoping review to address this gap. Specifically, we surveyed the characteristics, timeline construction and research findings of studies investigating consumers’ longitudinal HIN and HIS. Initial searches were conducted in November 2019 and updated in July 2022. A total of 128 papers were identified, reviewed and analyzed using content and thematic analyses. Results showed that most papers were quantitative, conducted in the USA, related to cancer, conducted during the diagnosis and treatment phases, and followed preset time intervals. Findings concerning the development patterns of consumers’ HIN degrees and HIS effort were mixed (i.e. increasing, decreasing or being consistent over time). They seemed to be shaped by factors such as health conditions, data collection methods and the length of data collection. Consumers’ use of sources changes depending on health status and source accessibility; their medical terminologies seem to expand over time. HIS has a strong emotional dimension which may lead to adaptive or maladaptive information behaviors (e.g. information avoidance). Overall, the results revealed a lack of understanding of HIN and HIS from a longitudinal perspective, particularly along health condition progression and coping trajectories. There is also a lack of understanding of the role of technologies in the longitudinal HIS process.
The politics of methods in transitional justice knowledge production
Authors: Lühe Ulrike 
Published: July 2023

Abstract
This article is concerned with how practices of knowledge production relate to the international politics of transitional justice (TJ). It argues that quantitative scholarly studies—called for in response to the anecdotal and normative studies that prevailed in early TJ scholarship and which, it is argued, continue to shape TJ sub-fields such as the study of local justice—are themselves committed to the normative framework and the goals of TJ that they seek to provide the tools to challenge. Applying a ‘politics of methods’ lens, the article foregrounds the interpretive work of surveys and the methodological choices of large-N impact studies which circle these works back to narrowly defined ideas of what TJ ought to be. The conclusions show how these ‘politics of methods’ contribute to the decontestation of an inherently political choice and practice, and predetermine what policy and practice options are considered useful, relevant and even imaginable. As such they shape that which they claim only to examine. Contributing to both critical methodological debates in International Relations and nascent scholarship on the research–policy–practice nexus in TJ, the analysis provides an under-examined example of the co-constitutive relationship of what is considered to be detached knowledge production and politics.
Proportion of liver cancer cases and deaths attributable to potentially modifiable risk factors in China
Authors: Lin Yushi , Zheng Luyan , Fang Kailu , Zheng Yang , Wu Jie , Zheng Min 
Published: July 2023

Abstract

Background
Understanding the differences in the burden of liver cancer due to different risk factors across provinces is critical to informing and improving liver cancer prevention and control. In this study, we estimated the population attributable fractions (PAFs) of liver cancer in all 31 provinces of China in 2016.

Methods
Prevalence estimates of risk factors were derived from representative surveys. We used pooled relative risks obtained from several recent large-scale pooled analyses or high-quality meta-analyses. We calculated PAFs using multiple formulas which included exposure prevalence and relative risk data stratified by sex, age and province, and then combined and created overall PAFs by sex, risk factors and risk factor groups.

Results
Approximately 252 046 liver cancer cases {69.5% [95% confidence interval (CI) 52.6, 76.5]} and 212 704 deaths [67.7% (95% CI 50.9, 74.6)] were attributable to modifiable risk factors in China in 2016. The overall PAF for liver cancer was approximately 1.5 times higher in men than in women, with the top three risk factors in men being hepatitis B virus (HBV), smoking and alcohol drinking, whereas in women, they were HBV, excess body weight and hepatitis C virus (HCV). Among the risk factor groups, infectious agents had the highest PAF, followed by behavioural factors and metabolic factors.

Conclusions
The PAF for liver cancer caused by modifiable risk factors varies widely among provinces and socioeconomic and geographical regions in China. The use of tailored primary prevention strategies across provinces and socioeconomic and geographical regions has great potential to reduce the burden and disparities of liver cancer.
Matrix denoising with partial noise statistics: optimal singular value shrinkage of spiked F-matrices
Authors: Gavish Matan , Leeb William , Romanov Elad 
Published: July 2023

Abstract
We study the problem of estimating a large, low-rank matrix corrupted by additive noise of unknown covariance, assuming one has access to additional side information in the form of noise-only measurements. We study the Whiten-Shrink-reColour (WSC) workflow, where a ‘noise covariance whitening’ transformation is applied to the observations, followed by appropriate singular value shrinkage and a ‘noise covariance re-colouring’ transformation. We show that under the mean square error loss, a unique, asymptotically optimal shrinkage nonlinearity exists for the WSC denoising workflow, and calculate it in closed form. To this end, we calculate the asymptotic eigenvector rotation of the random spiked F-matrix ensemble, a result which may be of independent interest. With sufficiently many pure-noise measurements, our optimally tuned WSC denoising workflow outperforms, in mean square error, matrix denoising algorithms based on optimal singular value shrinkage that do not make similar use of noise-only side information; numerical experiments show that our procedure’s relative performance is particularly strong in challenging statistical settings with high dimensionality and large degree of heteroscedasticity.
Effect of Malaria Infection on Epstein-Barr Virus Persistence in Kenyan Children
Authors: Samayoa-Reyes Gabriela , Weigel Christoph , Koech Emmily , Waomba Kevin , Jackson Conner , Onditi Ian A , Sabourin Katherine R , Kenney Shannon , Baiocchi Robert A , Oakes Christopher C , Ogolla Sidney , Rochford Rosemary 
Published: July 2023

Abstract

Background
The 2 cofactors in the etiology of Burkitt lymphoma (BL) are Epstein-Barr virus (EBV) and repeated Plasmodium falciparum malaria infections. This study evaluated EBV loads in mucosal and systemic compartments of children with malaria and controls. Age was analyzed as a covariate because immunity to malaria in endemic regions is age dependent.

Methods
Children (2–10 years) with clinical malaria from Western Kenya and community controls without malaria were enrolled. Saliva and blood samples were collected, EBV viral load was assessed by quantitative polymerase chain reaction, and EpiTYPER MassARRAY was used to assess methylation of 3 different EBV genes.

Results
Regardless of the compartment, we detected EBV more frequently in malaria cases compared to controls, although the difference was not significant. When EBV was detected, there were no differences in viral load between cases and controls. However, EBV methylation was significantly lower in the malaria group compared to controls in both plasma and saliva (P &lt; .05), indicating increased EBV lytic replication. In younger children before development of immunity to malaria, there was a significant effect of malaria on EBV load in peripheral blood mononuclear cells (P = .04).

Conclusions
These data suggest that malaria can directly modulate EBV persistence in children, increasing their risk for BL.
Preliminary phylogenomic analyses reveal multiple reversions to nocturnal behavior and morphology within the primarily diurnal tribe Adesmiini (Coleoptera: Tenebrionidae)
Authors: Swichtenberg Kali L , Kamiński Marcin J , Gearner Olivia M , Lumen Ryan , Kanda Kojun , Smith Aaron D 
Published: July 2023

AbstractThe darkling beetle tribe Adesmiini (Tenebrionidae: Pimeliinae) is a prominent part of African and western Palearctic desert faunas, with most species being day-active fast-running detritivores. Taxonomic diversity within the tribe is highest in the southern Afrotropical realm (where all genera are present); only 1 genus, the species-rich Adesmia, occurs north of the Sahara. Despite notable species, such as the fog-basking beetle Onymacris unguicularis (a focal taxon in desert ecological research), Adesmiini has undergone few modern taxonomic or phylogenetic studies. Hence, generic concepts and pronounced diurnal activity, rare in the primarily nocturnal family Tenebrionidae, remain poorly explored. To investigate evolutionary relationships and diurnal origins within the tribe, we generated a genomic dataset of 529 protein-coding genes across 43 species spanning 10 of 11 Adesmiini genera. Our resulting phylogeny for the tribe rejects the monophyly of 5 currently recognized Adesmiini genera (i.e., Adesmia, Metriopus, Onymacris, Physadesmia, and Stenocara). Ancestral state reconstruction of diurnal activity using eye shape as a proxy supports the hypothesis that Adesmiini were primitively diurnal, followed by at least 4 shifts to nocturnal or crepuscular activity.
Effect of 3-nitrooxypropanol on enteric methane emissions of feedlot cattle fed with a tempered barley-based diet with canola oil
Authors: Almeida Amelia K , Cowley Frances , McMeniman Joe P , Karagiannis Alex , Walker Nicola , Tamassia Luis F M , McGrath Joseph J , Hegarty Roger S 
Published: July 2023

Abstract
A dose-response experiment was designed to examine the effect of 3-nitrooxypropanol (3-NOP) on methane (CH4) emissions, rumen function and performance of feedlot cattle fed a tempered barley-based diet with canola oil. Twenty Angus steers of initial body weight (BW) of 356 ± 14.4 kg were allocated in a randomized complete block design. Initial BW was used as the blocking criterion. Cattle were housed in individual indoor pens for 112 d, including the first 21 d of adaptation followed by a 90-d finishing period when five different 3-NOP inclusion rates were compared: 0 mg/kg dry matter (DM; control), 50 mg/kg DM, 75 mg/kg DM, 100 mg/kg DM, and 125 mg/kg DM. Daily CH4 production was measured on day 7 (last day of starter diet), day 14 (last day of the first intermediate diet), and day 21 (last day of the second intermediate diet) of the adaptation period and on days 28, 49, 70, 91, and 112 of the finisher period using open circuit respiration chambers. Rumen digesta samples were collected from each steer on the day prior to chamber measurement postfeeding, and prefeeding on the day after the chamber measurement, for determination of rumen volatile fatty acids (VFA), ammonium-N, protozoa enumeration, pH, and reduction potential. Dry matter intake (DMI) was recorded daily and BW weekly. Data were analyzed in a mixed model including period, 3-NOP dose and their interaction as fixed effects, and block as a random effect. Our results demonstrated both a linear and quadratic (decreasing rate of change) effect on CH4 production (g/d) and CH4 yield (g/kg DMI) as 3-NOP dose increased (P &lt; 0.01). The achieved mitigation for CH4 yield in our study ranged from approximately 65.5% up to 87.6% relative to control steers fed a finishing feedlot diet. Our results revealed that 3-NOP dose did not alter rumen fermentation parameters such as ammonium-N, VFA concentration nor VFA molar proportions. Although this experimental design was not focused on the effect of 3-NOP dose on feedlot performance, no negative effects of any 3-NOP dose were detected on animal production parameters. Ultimately, the knowledge on the CH4 suppression pattern of 3-NOP may facilitate sustainable pathways for the feedlot industry to lower its carbon footprint.