bluuebunny/crossref_metadata_2025_split huggingface dataset:
Function and Constraint in Enhancer Sequences with Multiple Evolutionary Origins
Authors: Fong Sarah L , Capra John A 
Published: October 2022

Abstract
Thousands of human gene regulatory enhancers are composed of sequences with multiple evolutionary origins. These evolutionarily “complex” enhancers consist of older “core” sequences and younger “derived” sequences. However, the functional relationship between the sequences of different evolutionary origins within complex enhancers is poorly understood. We evaluated the function, selective pressures, and sequence variation across core and derived components of human complex enhancers. We find that both components are older than expected from the genomic background, and complex enhancers are enriched for core and derived sequences of similar evolutionary ages. Both components show strong evidence of biochemical activity in massively parallel report assays. However, core and derived sequences have distinct transcription factor (TF)-binding preferences that are largely similar across evolutionary origins. As expected, given these signatures of function, both core and derived sequences have substantial evidence of purifying selection. Nonetheless, derived sequences exhibit weaker purifying selection than adjacent cores. Derived sequences also tolerate more common genetic variation and are enriched compared with cores for expression quantitative trait loci associated with gene expression variability in human populations. In conclusion, both core and derived sequences have strong evidence of gene regulatory function, but derived sequences have distinct constraint profiles, TF-binding preferences, and tolerance to variation compared with cores. We propose that the step-wise integration of younger derived with older core sequences has generated regulatory substrates with robust activity and the potential for functional variation. Our analyses demonstrate that synthesizing study of enhancer evolution and function can aid interpretation of regulatory sequence activity and functional variation across human populations.
Social Isolation, Loneliness, and Depressive Symptoms: A Twelve-Year Population Study of Temporal Dynamics
Authors: Luo Mengsha 
Published: October 2022

AbstractObjectivesSocial isolation and loneliness are two different aspects of social connections. Whether social isolation and loneliness precede depressive symptoms, or depressive symptoms precede feelings of loneliness and social isolation, or both, has not been fully established. This study aims to examine the possible reciprocity in the relationship between the two aspects of social connections and depressive symptoms among middle-aged and older adults.MethodThis study analyzed four waves of data (2008–2016) from the Health and Retirement Study (N = 5,393 individuals) and investigated within-person level cross-lagged associations of social isolation and loneliness with depressive symptoms using random intercept cross-lagged panel models.ResultsThis study revealed a unidirectional relationship between social isolation and depressive symptoms and a bidirectional relationship between loneliness and depressive symptoms at the within-person level. Specifically, net of trait levels and prior states, earlier state depressive symptoms predicted future state social isolation. That is, when adults feel depressed more frequently than they usually do, they are more likely to be socially disconnected than usual at a later time. In the reverse direction, earlier state social isolation did not predict future state depressive symptoms. Within-person deviation in prior expected depressive symptoms predicted deviation in expected loneliness 4 years later and vice versa. Moreover, the strength of the two cross-lagged effects did not differ.DiscussionSocial isolation and loneliness are linked to depressive symptoms differently. Though depressive symptoms might be a potential antecedent of social isolation, they might be both a potential antecedent and an outcome of loneliness.
Best genome sequencing strategies for annotation of complex immune gene families in wildlife
Authors: Peel Emma , Silver Luke , Brandies Parice , Zhu Ying , Cheng Yuanyuan , Hogg Carolyn J , Belov Katherine 
Published: October 2022

Abstract

Background
The biodiversity crisis and increasing impact of wildlife disease on animal and human health provides impetus for studying immune genes in wildlife. Despite the recent boom in genomes for wildlife species, immune genes are poorly annotated in nonmodel species owing to their high level of polymorphism and complex genomic organisation. Our research over the past decade and a half on Tasmanian devils and koalas highlights the importance of genomics and accurate immune annotations to investigate disease in wildlife. Given this, we have increasingly been asked the minimum levels of genome quality required to effectively annotate immune genes in order to study immunogenetic diversity. Here we set out to answer this question by manually annotating immune genes in 5 marsupial genomes and 1 monotreme genome to determine the impact of sequencing data type, assembly quality, and automated annotation on accurate immune annotation.

Results
Genome quality is directly linked to our ability to annotate complex immune gene families, with long reads and scaffolding technologies required to reassemble immune gene clusters and elucidate evolution, organisation, and true gene content of the immune repertoire. Draft-quality genomes generated from short reads with HiC or 10× Chromium linked reads were unable to achieve this. Despite mammalian BUSCOv5 scores of up to 94.1% amongst the 6 genomes, automated annotation pipelines incorrectly annotated up to 59% of manually annotated immune genes regardless of assembly quality or method of automated annotation.

Conclusions
Our results demonstrate that long reads and scaffolding technologies, alongside manual annotation, are required to accurately study the immune gene repertoire of wildlife species.
The Global Atlas of Bamboo and Rattan (GABR) Phase II: new resources for sustainable development
Authors: Zhao Hansheng , Hou Yinguang , Wang Jian , Sun Lei , Gan Junwei , Meng Yufei , Li Zhiqiang , Li Shanying , Fan Zeyu , Wang Yu , Fei Benhua 
Published: October 2022

Abstract
Bamboo, the fast-growing grass plant, and rattan, the spiky climbing palm, are both essential forest resources that have been closely linked with human lives, livelihoods and material culture since ancient times. To promote genetic and genomic research in bamboo and rattan, a comprehensive and coordinated international project, the Genome Atlas of Bamboo and Rattan (GABR), was launched in 2017. GABR achieved great success during Phase I (2017-2022). We will focus on investigating and protecting bamboo and rattan germplasm resources in Phase II ( 2022-2027). Here, we briefly review the achievements of Phase I and introduce the goals of Phase II.
Quantifying uncertainty of salt body shapes recovered from gravity data using trans-dimensional Markov chain Monte Carlo sampling
Authors: Wei Xiaolong , Sun Jiajia , Sen Mrinal K 
Published: October 2022

SUMMARY
Accurate delineation of salt body shapes is critical for hydrocarbon exploration. Various imaging methods based on seismic data have been developed. Due to the density contrast between salt and sedimentary rocks, gravity data have also been used as a de-risking tool to constrain the salt body shapes. However, quantifying uncertainties of the salt body shapes recovered from gravity data remains underexplored. Our goal is to understand and quantify how different constraints affect uncertainties of the salt body shapes reconstructed from gravity data. We adopt a trans-dimensional Markov chain Monte Carlo (MCMC) approach to explore the uncertainties. To address the computational challenges with MCMC sampling, we resort to two methods: sparse geometry parametrization and randomized parallel tempering. The first uses a set of simple geometries (e.g. ellipses) to approximate the complex shapes of salt bodies, greatly reducing the number of parameters to be sampled and making the MCMC approach computationally feasible. The second serves to further improve the acceptance ratio and computational efficiency. To quantify the uncertainties of the recovered salt body shapes, we design several scenarios to simulate different constraints on the top boundary of salt bodies from seismic imaging. We develop a new method to impose structural constraints on the top boundaries of salt bodies. This new method combines a set of fixed ellipses with randomly sampled ellipses through a concave hull. The results from different scenarios are compared to understand how uncertainties are reduced when stronger constraints are imposed. In addition, to make our uncertainty quantification results more relevant for practitioners, we propose to compute the salt probability models which show the spatial distribution of probabilities of salt materials at each cell. Finally, we investigate the effect of an uncertain salt density on the salt body reconstruction and the case of depth-varying densities in the sedimentary background. We apply our methods to the modified 2-D SEG-EAGE and Sigsbee salt models and quantify the uncertainties of the recovered salt body shapes in different scenarios. Our results highlight the importance of properly interpreting the uncertainty estimates in light of prior information and information content in the data.
Integrating controlled-source and ambient noise seismic measures for archaeological prospection: the Scrovegni Chapel case
Authors: Barone I , Cassiani G , Ourabah A , Boaga J , Pavoni M , Deiana R 
Published: October 2022

SUMMARY
In this paper, we present the results of an analysis of passive seismic noise recorded around the Scrovegni Chapel in Padua (Italy), using a dense 2-D network with nearly 1500 autonomous seismic nodes. Surface wave tomography using the active records allowed the imaging of several structures located at a depth of few metres, while this study focuses on the processing of about 22 hr of continuous passive records. First, the ambient noise is characterized in terms of amplitude, frequency content and azimuthal distribution, in order to ensure the applicability of the interferometric method. Second, a cross-correlation analysis is performed to retrieve virtual source gathers. Third, traveltimes are extracted from virtual source gathers using the same processing sequence applied to active gathers. Fourth, Eikonal tomography is run to retrieve isotropic phase velocity maps and azimuthal anisotropy. We compare and discuss the results obtained from the active and the passive methods, and finally propose a strategy for the integration of passive and active information. The new quasi-3-D shear wave velocity model obtained from the joint active and passive analysis is more accurate at depth, due to the addition of the passive low-frequency information.
Bovine pericardial patch repair for abdominal aortic pseudoaneurysm to preserve lumbar arteries
Authors: Nabeshima Junya , Mizuno Tomohiro , Nagaoka Eiki 
Published: October 2022

Abstract
We describe a case of aortic repair using bovine pericardium for a pseudoaneurysm of a dissecting abdominal aorta. A 71-year-old man had undergone several aortic replacement surgeries for type B aortic dissection. He developed paraparesis after thoraco-abdominal aortic surgery and recovered. After 3 years, the scheduled computed tomography scan showed a pseudoaneurysm of the dissecting abdominal aorta. Because he was at high risk of spinal cord ischaemia, aortic repair using bovine pericardium was performed, and all lumbar arteries were preserved. During the 12-month follow-up, he was asymptomatic, and computed tomography scans showed no dilation of the aorta.
Perturbations in Respiratory Syncytial Virus Activity During the SARS-CoV-2 Pandemic
Authors: Falsey Ann R , Cameron Andrew , Branche Angela R , Walsh Edward E 
Published: October 2022

Abstract
Respiratory syncytial virus (RSV) is a common cause of respiratory disease in all age groups, with young children and older adults experiencing the most severe illness. The coronavirus disease 2019 (COVID-19) pandemic resulted in striking changes in the activity of seasonal respiratory viruses, including RSV. After a period of suppression early in the pandemic, an interseasonal surge of RSV occurred in 2021. Viral activity was detected primarily in children and young adults after relaxation of public health measures, but without the usual proportional increases in infections and hospitalizations in older adults who were likely still adhering to stricter public health measures.
Bioengineered and functionalized silk proteins accelerate wound healing in rat and human dermal fibroblasts
Authors: Manoharan Chitra , Thomas Dyna Susan , Yashwant Rasalkar Sandhya , Mudagal Manjunatha Panduranga , Janadri Suresh , Roy Gourab , Kunjupillai Vijayan , Mishra Rakesh Kumar , Gopalapillai Ravikumar 
Published: October 2022

Abstract
Wound healing is an intrinsic process directed towards the restoration of damaged or lost tissue. The development of a dressing material having the ability to control the multiple aspects of the wound environment would be an ideal strategy to improve wound healing. Though natural silk proteins, fibroin, and sericin have demonstrated tissue regenerative properties, the efficacy of bioengineered silk proteins on wound healing is seldom assessed. Furthermore, silk proteins sans contaminants, having low molecular masses, and combining with other bioactive factors can hasten the wound healing process. Herein, recombinant silk proteins, fibroin and sericin, and their fusions with cecropin B were evaluated for their wound-healing effects using in vivo rat model. The recombinant silk proteins demonstrated accelerated wound closure in comparison to untreated wounds and treatment with Povidone. Among all groups, the treatment with recombinant sericin-cecropin B (RSC) showed significantly faster healing, greater than 90% wound closure by Day 12 followed by recombinant fibroin-cecropin B (RFC) (88.86%). Furthermore, histological analysis and estimation of hydroxyproline showed complete epithelialization, neovascularization, and collagenisation in groups treated with recombinant silk proteins. The wound healing activity was further verified by in vitro scratch assay using HADF cells, where the recombinant silk proteins induced cell proliferation and cell migration to the wound area. Additionally, wound healing-related gene expression showed recombinant silk proteins stimulated the upregulation of EGF and VEGF and regulated the expression of TGF-β1 and TGF-β3. Our results demonstrated the enhanced healing effects of the recombinant silk fusion proteins in facilitating complete tissue regeneration with scar-free healing. Therefore, the recombinant silks and their fusion proteins have great potential to be developed as smart bandages for wound healing.
Morphology-based Phylogenetic Analysis of Membracoidea (Hemiptera: Cicadomorpha) With Placement of Fossil Taxa and Description of a New Subfamily
Authors: Dietrich Christopher H , Dmitriev Dmitry A , Takiya Daniela M , Thomas M Jared , Webb Michael D , Zahniser James N , Zhang Yalin 
Published: October 2022

AbstractRecently discovered amber-preserved fossil Cicadellidae exhibit combinations of morphological traits not observed in the modern fauna and have the potential to shed new light on the evolution of this highly diverse family. To place the fossils explicitly within a phylogenetic context, representatives of five extinct genera from Cretaceous Myanmar amber, and one from Eocene Baltic amber were incorporated into a matrix comprising 229 discrete morphological characters and representatives of all modern subfamilies. Phylogenetic analyses yielded well resolved and largely congruent estimates that support the monophyly of most previously recognized cicadellid subfamilies and indicate that the treehoppers are derived from a lineage of Cicadellidae. Instability in the morphology-based phylogenies is mainly confined to deep internal splits that received low branch support in one or more analyses and also were not consistently resolved by recent phylogenomic analyses. Placement of fossil taxa is mostly stable across analyses. Three new Cretaceous leafhopper genera, Burmotettix gen. nov., Kachinella gen nov., and Viraktamathus gen. nov., consistently form a monophyletic group distinct from extant leafhopper subfamilies and are placed in Burmotettiginae subfam. nov. Extinct Cretaceous fossils previously placed in Ledrinae and Signoretiinae are recovered as sister to modern representatives of these groups. Eomegophthalmus Dietrich and Gonçalves from Baltic amber consistently groups with a lineage comprising treehoppers, Megophthalminae, Ulopinae, and Eurymelinae but its position is unstable. Overall, the morphology-based phylogenetic estimates agree with recent phylogenies based on molecular data alone suggesting that morphological traits recently used to diagnose subfamilies are generally informative of phylogenetic relationships within this group.
“Yes-Man” Firms: Government Campaign and Policy Positioning of Businesses in China
Authors: Naoi Megumi , Shi Weiyi , Zhu Boliang 
Published: October 2022

AbstractWe demonstrate material origin of strategic preference expression in authoritarian systems, where firms express dissent against or conform to the government's position based on what they seek to obtain from the government: politically powerful firms are more likely to dissent to negotiate policy concessions while politically weak firms are more likely to conform to the government's position to obtain side payments or to avoid punishment. We test this argument using survey experiments with firm executives in China. A treatment that signals the government's commitment to liberalize inward foreign direct investment increases the percentage of firms that report to “benefit” from the policy between 14 and 36 percentage points. Powerful firms (state- and foreign-owned) conform the least to the government and politically vulnerable firms and the recipients of government contracts conform the most. Our results suggest that political standing is a key driver of business position-taking in China.
Why Territorial Disputes Escalate: The Causes of Conquest Attempts since 1945
Authors: Altman Dan , Lee Melissa M 
Published: October 2022

AbstractAlthough attempts to conquer entire states became rare after 1945, attempts to conquer small pieces of territory persisted. Why do states so often seize—and even fight wars over—remarkably small areas? We argue that traditional explanations predicated on the material or ethnic value of disputed territories largely cannot explain the escalation of territorial disputes since 1945. Instead, actors more often seize territory to be seen seizing it. We theorize that the roots of these conquest attempts often lie in careerist incentives within militaries. Military officers seize small pieces of disputed territory in pursuit of promotions or political office, especially in states where the military wields greater political power. We test this theory with a statistical analysis of conquest attempts in territorial disputes (1965–2000) using new geospatial and conquest data along with a medium-n process analysis of all conquest attempts since 1945. Our results suggest that careerist self-aggrandizement plays an important role in contemporary territorial conflict.
Assessing the carbon footprint of digital health interventions: a scoping review
Authors: Lokmic-Tomkins Zerina , Davies Shauna , Block Lorraine J , Cochrane Lindy , Dorin Alan , von Gerich Hanna , Lozada-Perezmitre Erika , Reid Lisa , Peltonen Laura-Maria 
Published: October 2022

Abstract

Objective
Integration of environmentally sustainable digital health interventions requires robust evaluation of their carbon emission life-cycle before implementation in healthcare. This scoping review surveys the evidence on available environmental assessment frameworks, methods, and tools to evaluate the carbon footprint of digital health interventions for environmentally sustainable healthcare.

Materials and Methods
Medline (Ovid), Embase (Ovid). PsycINFO (Ovid), CINAHL, Web of Science, Scopus (which indexes IEEE Xplore, Springer Lecture Notes in Computer Science and ACM databases), Compendex, and Inspec databases were searched with no time or language constraints. The Systematic Reviews and Meta-analyses Extension for Scoping Reviews (PRISMA_SCR), Joanna Briggs Scoping Review Framework, and template for intervention description and replication (TiDiER) checklist were used to structure and report the findings.

Results
From 3299 studies screened, data was extracted from 13 full-text studies. No standardised methods or validated tools were identified to systematically determine the environmental sustainability of a digital health intervention over its full life-cycle from conception to realisation. Most studies (n = 8) adapted publicly available carbon calculators to estimate telehealth travel-related emissions. Others adapted these tools to examine the environmental impact of electronic health records (n = 2), e-prescriptions and e-referrals (n = 1), and robotic surgery (n = 1). One study explored optimising the information system electricity consumption of telemedicine. No validated systems-based approach to evaluation and validation of digital health interventions could be identified.

Conclusion
There is a need to develop standardised, validated methods and tools for healthcare environments to assist stakeholders to make informed decisions about reduction of carbon emissions from digital health interventions.
Identification of potential candidate genes and regulatory pathways related to reproductive capacity in hypothalamus and pituitarium of male ducks (Anas platyrhynchos) by differential transcriptome analysis
Authors: Zhang Zhen , Yang Yu , Huang Liming , Chen Ligen , Zhang Guixin , Gong Ping , Ye Shengqiang , Feng Yanping 
Published: October 2022

Abstract
The improvement of reproductive capacity of poultry is important for the poultry industry. The existing studies on reproductive capacity mainly focus on the testis tissue, but few reports on regulationary effect of brain neuroendocrime on reproductive capacity have been available. The hypothalamus–pituitarium–gonad (HPG) axis is an important pathway regulating spermatogenesis and sexual behavior. This study analyzed the gene expression in the hypothalamus and pituitary tissues of male ducks in high-semen-quality group (DH), low-semen-quality group (DL), and non-response group (DN) by RNA-sequencing. A total of 1980 differentially expressed genes (DEGs) were identified, and significantly less DEGs were found in pituitary gland than in hypothalamus. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DEGs were mainly enriched in nerve-related and synapse-related biological processes, mitochondrial inner membrane formation pathway, and ribosome structure pathway. Notably, the neuroactive ligand–receptor interaction pathway significantly enriched in all three comparisons (DH vs. DL, DH vs. DN, and DL vs. DN) was related to different reproductive performance such as semen quality and sexual response. Furthermore, six genes, including POMC, CPLX2, HAPLN2, EGR4, TOX3, and MSH4, were identified as candidate genes regulating reproductive capacity. Our findings provide new insights into the regulation mechanisms underlying the reproductive performance of male poultry, and offer a valuable reference for duck breeding programs aimed at promoting reproductive capacity.