bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive alien genes are maintained amid a vanishing introgression footprint in a sea squirt
Authors: Touchard Fanny , Cerqueira Frédérique , Bierne Nicolas , Viard Frédérique 
Published: April 2024

Abstract
Human transport of species across oceans disrupts natural dispersal barriers and facilitates hybridization between previously allopatric species. The recent introduction of the North Pacific sea squirt, Ciona robusta, into the native range of the North Atlantic sea squirt, Ciona intestinalis, is a good example of this outcome. Recent studies have revealed an adaptive introgression in a single chromosomal region from the introduced into the native species. Here, we monitored this adaptive introgression over time, examining both the frequency of adaptive alleles at the core and the hitchhiking footprint in the shoulders of the introgression island by studying a thousand Ciona spp. individuals collected in 22 ports of the contact zone, 14 of which were sampled 20 generations apart. For that purpose, we developed a KASP multiplex genotyping approach, which proved effective in identifying native, nonindigenous and hybrid individuals and in detecting introgressed haplotypes. We found no early generation hybrids in the entire sample, and field observations suggest a decline in the introduced species. At the core region of the introgression sweep, where the frequency of C. robusta alleles is the highest and local adaptation genes must be, we observed stable frequencies of adaptive alien alleles in both space and time. In contrast, we observed erosion of C. robusta ancestry tracts in flanking chromosomal shoulders on the edges of the core, consistent with the second phase of a local sweep and a purge of hitchhiked incompatible mutations. We hypothesize that adaptive introgression may have modified the competition relationships between the native and invasive species in human-altered environments.
Endoscopic retrograde appendicitis therapy: current and the future
Authors: Liu Dan , Zhang Jiyu , Liu Bingrong 
Published: April 2024

Abstract
This article presents an overview of endoscopic retrograde appendicitis therapy (ERAT), an innovative and minimally invasive treatment for appendicitis with an appendix-preserving manner. Since its initial application in 2009, ERAT has gained significant popularity in China, due to its rapid recovery and minimal risk of complications. The ERAT procedures comprise several steps, including appendiceal orifice access and intubation, appendiceal lumen imaging, decompression and irrigation, fecalith removal, and stenting. ERAT has been used in various forms of complicated appendicitis, such as in pregnant women and children, with continuous improvements in both technique and safety. It has the potential to become the preferred diagnostic and treatment method for appendicitis. Until 2023, over 10,000 ERAT procedures have been successfully conducted in China, and the technique has gained more attention worldwide. However, challenges remain, including training, standardization of ERAT practice, research and technology improvement, enhancing public awareness, and fostering international collaboration. In summary, ERAT can be the standard treatment for appendicitis treatment, which represents a paradigm shift in the conventional clinical practice.
Genetic susceptibility to chronic diseases leads to heart failure among Europeans: the influence of leukocyte telomere length
Authors: Wong Jason Y Y , Blechter Batel , Liu Zhonghua , Shi Jianxin , Roger Véronique L 
Published: April 2024

Abstract

Background
Genetic susceptibility to various chronic diseases has been shown to influence heart failure (HF) risk. However, the underlying biological pathways, particularly the role of leukocyte telomere length (LTL), are largely unknown. We investigated the impact of genetic susceptibility to chronic diseases and various traits on HF risk, and whether LTL mediates or modifies the pathways.

Methods
We conducted prospective cohort analyses on 404 883 European participants from the UK Biobank, including 9989 incident HF cases. Multivariable Cox regression was used to estimate associations between HF risk and 24 polygenic risk scores (PRSs) for various diseases or traits previously generated using a Bayesian approach. We assessed multiplicative interactions between the PRSs and LTL previously measured in the UK Biobank using quantitative PCR. Causal mediation analyses were conducted to estimate the proportion of the total effect of PRSs acting indirectly through LTL, an integrative marker of biological aging.

Results
We identified 9 PRSs associated with HF risk, including those for various cardiovascular diseases or traits, rheumatoid arthritis (P = 1.3E-04), and asthma (P = 1.8E-08). Additionally, longer LTL was strongly associated with decreased HF risk (P-trend = 1.7E-08). Notably, LTL strengthened the asthma-HF relationship significantly (P-interaction = 2.8E-03). However, LTL mediated only 1.13% (P &lt; 0.001) of the total effect of the asthma PRS on HF risk.

Conclusions
Our findings shed light onto the shared genetic susceptibility between HF risk, asthma, rheumatoid arthritis, and other traits. Longer LTL strengthened the genetic effect of asthma in the pathway to HF. These results support consideration of LTL and PRSs in HF risk prediction.
Usefulness of final transection of the proximal pulmonary artery in robotic left upper lobectomy
Authors: Uchida Shinsuke , Matsunaga Takeshi , Tomita Hisashi , Fukui Mariko , Hattori Aritoshi , Takamochi Kazuya , Suzuki Kenji 
Published: April 2024

Abstract

OBJECTIVES
The pulmonary artery runs around the left upper bronchus, which poses the risk of blood vessel injury when cutting in the blind spot of the bronchus. During robotic surgery, the robotic arm holds the tissue under constant tension; therefore, even if the pulmonary artery is left for final transection, it is not injured by unexpected tension. In this study, we examined the usefulness of final transection of the proximal pulmonary artery in robotic left upper lobectomy.

METHODS
This retrospective single-institution study evaluated patients who had undergone robotic lung resection. Of the 453 robotic lung resections performed at our institution between 2017 and 2022, 49 patients who had undergone left upper lobectomy were evaluated. Patients who had undergone bronchial transection followed by pulmonary artery transection were assigned to the group, bronchus prior transection (BT group, n = 38), and those who had undergone pulmonary artery transection followed by bronchial transection were assigned to the group, pulmonary artery prior transection (AT group, n = 11). Patient characteristics and perioperative outcomes were compared between the groups.

RESULTS
The groups did not differ significantly in age, sex, smoking history, tumour size, complication rates or 30-day mortality. The BT group inclined to shorter operative times and lesser blood loss. No active intraoperative bleeding occurred in the BT group. However, the AT group had 2 cases of intraoperative pulmonary artery bleeding, one of which required urgent conversion to thoracotomy.

CONCLUSIONS
Final transection of the proximal pulmonary artery is a novel and effective surgical technique for robotic left upper lobectomy.
A joint configuration method for multiple flexible resources in low carbon distribution networks based on massive scene dimensionality reduction
Authors: Zheng Zhen , Zhang Guanhua , Wang Duhong , Mou Kai , He Zhizhuo , Xing Haijun 
Published: April 2024

Abstract
Due to the extensive access of renewable sources in distribution networks, this research proposes a joint configuration method for multiple flexible resources in low carbon distribution networks based on massive scene dimensionality reduction to maximize the access capacity of renewable sources. The dimensionality reduction clustering is carried out on the wind-light-load mass high-dimensional scenes by the principal component Gaussian mixture clustering algorithm, and the typical scene set of wind-power-loads is obtained. Hereafter, a joint configuration model for multiple flexible resources of distribution network for massive scenarios is constructed, and using the second-order cone relaxation technique to convert the non-convex constraints in the model to convex processing. Last, a Portugal 54 distribution system is employed to verify the proposed method.
Scientific Advice and the COVID-19 Pandemic: Revisiting the Asian Disease Problem
Authors: Neumann Robert , Brust Oliver , Kadel Jasmin , von Hermanni Hagen , Menold Natalja 
Published: April 2024

Abstract
The coronavirus disease 2019 pandemic has underscored the importance of scientific knowledge and highlighted the challenge for politicians: They had to rely on expert advice and still had to make decisions under uncertainty due to the lack of long-term health data. This article investigates how expert judgments and expert advice affect the choices between programs that are proposed to combat the outbreak of a viral disease by means of a between-subjects design embedded in a survey. We use the classic Asian disease experiment and extend earlier applications by varying the professional background of the experts (virologists vs. social scientists) within the experimental set-up. We use data from a university wide web-survey to show the persistence of framing effects and that the disciplinary background of the expert is not related to individual decision-making under risk.
Contestation in a World of Liberal Orders
Authors: Goddard Stacie E , Krebs Ronald R , Kreuder-Sonnen Christian , Rittberger Berthold 
Published: April 2024

AbstractIt is widely acknowledged that the core institutions of the Liberal International Order (LIO) have in recent years been subject to increasingly intense contestation. There is less agreement on the sources of this contestation. This introductory paper to the special forum on “contestation in a world of liberal orders” makes two main contributions. First, the paper develops a theory of endogenous order contestation. It conceptualizes the LIO as a system of different types of suborders, which vary in the extent to which they reflect and promote liberal values and in the extent to which they are legally institutionalized. The paper explains how these different suborders generate their own types of order contestation. More liberally embedded and institutionalized suborders endogenously generate more intense and order-challenging contestation, while less liberal and less institutionalized orders are amenable to more modest and order-consistent contestation. Second, this paper identifies the specific endogenous mechanisms through which contestation shifts from order-consistent to order-challenging in especially these more liberally embedded and institutionalized suborders. It argues that not only liberal resistance to reform gives rise to order-challenging contestation, but even liberal accommodation and responsiveness can ultimately paralyze and ossify LIO institutions, which in turn lose legitimacy, frustrate would-be reformers, and drive them to order-challenging contestation. The different contributions to this special issue examine our core propositions across a range of economic, security, and social–political LIO suborders.
Jump Clustering, Information Flows, and Stock Price Efficiency
Authors: Chen Jian 
Published: April 2024

Abstract
We study the clustering behavior of stock return jumps modeled by a self/cross-exciting process embedded in a stochastic volatility model. Based on the model estimates, we propose a novel measurement of stock price efficiency characterized by the extent of jump clustering that stock returns exhibit. This measurement demonstrates the capability of capturing the speed at which stock prices assimilate new information, especially at the firm-specific level. Furthermore, we assess the predictability of self-exciting (clustered) jumps in stock returns. We employ a particle filter to sample latent states in the out-of-sample period and perform one-step-ahead probabilistic forecasting on upcoming jumps. We introduce a new statistic derived from predicted probabilities of positive and negative jumps, which has been shown to be effective in return predictions.
Addressing social needs in oncology care: another research-to-practice gap
Authors: Haines Emily , Shelton Rachel C , Foley Kristie , Beidas Rinad S , Dressler Emily V , Kittel Carol A , Chaiyachati Krisda H , Fayanju Oluwadamilola M , Birken Sarah A , Blumenthal Daniel , Rendle Katharine A 
Published: April 2024

Abstract
Social determinants of health and unmet social needs are directly related to cancer outcomes, from diagnosis to survivorship. If identified, unmet social needs can be addressed in oncology care by changing care plans in collaboration with patients’ preferences and accounting for clinical practice guidelines (eg, reducing the frequency of appointments, switching treatment modalities) and connecting patients to resources within healthcare organizations (eg, social work support, patient navigation) and with community organizations (eg, food banks, housing assistance programs). Screening for social needs is the first step to identifying those who need additional support and is increasingly recognized as a necessary component of high-quality cancer care delivery. Despite evidence about the relationship between social needs and cancer outcomes and the abundance of screening tools, the implementation of social needs screening remains a challenge, and little is known regarding the adoption, reach, and sustainability of social needs screening in routine clinical practice. We present data on the adoption and implementation of social needs screening at two large academic cancer centers and discuss three challenges associated with implementing evidence-based social needs screening in clinical practice: (1) identifying an optimal approach for administering social needs screening in oncology care, (2) adequately addressing identified unmet needs with resources and support, and (3) coordinating social needs screening between oncology and primary care.
Explaining the spatial segregation of ethnic groups in an early industrial city: the case of Vyborg
Authors: Härkönen Antti 
Published: April 2024

Abstract
An early industrial town’s spatial segregation is studied using empirical data concerning the Russian population of the town of Vyborg. Several hypotheses for explaining segregation are considered using spatial analysis. The spatial data are derived from historical maps and demographic data from various tax records. Socioeconomic segregation is studied as a possible cause of ethnic segregation. The main drivers of spatial segregation were the explicit policies of segregation enforced by both the Russian military administration and the town’s civilian administration. While the effects of segregation gradually diminished due to social diffusion, the impact of policy decisions driving segregation in the 18th and early 19th centuries was still visible in the population’s later 19th-century segregation. Yet neither the different preferences of Russians and others nor the income differences between areas explains the distribution of Russians. Segregation based on the membership of a guild was insignificant, with a few exceptions. Other factors such as discrimination, prejudice, and differences in housing market information probably contributed to segregation, but they cannot be studied with the data used.
Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing
Authors: Leduque Basile , Edera Alejandro , Vitte Clémentine , Quadrana Leandro 
Published: April 2024

Abstract
Epigenetic regulations, including chromatin accessibility, nucleosome positioning and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple chromatin features simultaneously. Here, we performed Simultaneous Accessibility and DNA Methylation Sequencing (SAM-seq) of purified plant nuclei. Thanks to the use of long-read nanopore sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibility together with endogenous cytosine methylation in plants. Analysis of naked genomic DNA revealed significant sequence preference biases of m6A-MTases, controllable through a normalisation step. By applying SAM-seq to Arabidopsis and maize nuclei we obtained fine-grained accessibility and DNA methylation landscapes genome-wide. We uncovered crosstalk between chromatin accessibility and DNA methylation within nucleosomes of genes, TEs, and centromeric repeats. SAM-seq also detects DNA footprints over cis-regulatory regions. Furthermore, using the single-molecule information provided by SAM-seq we identified extensive cellular heterogeneity at chromatin domains with antagonistic chromatin marks, suggesting that bivalency reflects cell-specific regulations. SAM-seq is a powerful approach to simultaneously study multiple epigenetic features over unique and repetitive sequences, opening new opportunities for the investigation of epigenetic mechanisms.
iM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning
Authors: Yu Haopeng , Li Fan , Yang Bibo , Qi Yiman , Guneri Dilek , Chen Wenqian , Waller Zoë A E , Li Ke , Ding Yiliang 
Published: April 2024

Abstract
DNA, beyond its canonical B-form double helix, adopts various alternative conformations, among which the i-motif, emerging in cytosine-rich sequences under acidic conditions, holds significant biological implications in transcription modulation and telomere biology. Despite recognizing the crucial role of i-motifs, predictive software for i-motif forming sequences has been limited. Addressing this gap, we introduce ‘iM-Seeker’, an innovative computational platform designed for the prediction and evaluation of i-motifs. iM-Seeker exhibits the capability to identify potential i-motifs within DNA segments or entire genomes, calculating stability scores for each predicted i-motif based on parameters such as the cytosine tracts number, loop lengths, and sequence composition. Furthermore, the webserver leverages automated machine learning (AutoML) to effortlessly fine-tune the optimal i-motif scoring model, incorporating user-supplied experimental data and customised features. As an advanced, versatile approach, ‘iM-Seeker’ promises to advance genomic research, highlighting the potential of i-motifs in cell biology and therapeutic applications. The webserver is freely available at https://im-seeker.org.
A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs
Authors: Eijlers Peter , Al-Khafaji Mohammed , Soto-Martin Eva , Fasimoye Rotimi , Stead David , Wenzel Marius , Müller Berndt , Pettitt Jonathan 
Published: April 2024

Abstract
Spliced leader trans-splicing of pre-mRNAs is a critical step in the gene expression of many eukaryotes. How the spliced leader RNA and its target transcripts are brought together to form the trans-spliceosome remains an important unanswered question. Using immunoprecipitation followed by protein analysis via mass spectrometry and RIP-Seq, we show that the nematode-specific proteins, SNA-3 and SUT-1, form a complex with a set of enigmatic non-coding RNAs, the SmY RNAs. Our work redefines the SmY snRNP and shows for the first time that it is essential for nematode viability and is involved in spliced leader trans-splicing. SNA-3 and SUT-1 are associated with the 5′ ends of most, if not all, nascent capped RNA polymerase II transcripts, and they also interact with components of the major nematode spliced leader (SL1) snRNP. We show that depletion of SNA-3 impairs the co-immunoprecipitation between one of the SL1 snRNP components, SNA-2, and several core spliceosomal proteins. We thus propose that the SmY snRNP recruits the SL1 snRNP to the 5′ ends of nascent pre-mRNAs, an instrumental step in the assembly of the trans-spliceosome.
The effects of different feeding strategies providing different levels of vitamin A on animal performance, carcass traits, and the conversion rate of subcutaneous fat color in cull-cows
Authors: Parkinson J T , Cochran H J , Kieffer J D , Relling A E , Boyles S L , Kopec R E , Garcia L G 
Published: April 2024

Abstract
Cull cows represent a significant percentage of revenue received from the U.S. beef industry; however, cull cows are heavily price discounted at time of slaughter. This experiment’s objective is to evaluate different feeding strategies and their effects on body condition score, subcutaneous fat color, and carcass yield and quality traits in cull cows. The central hypothesis is feeding a high-energy diet, with low levels of vitamin A, for 56 d will improve animal performance, carcass yield, and quality traits in addition to capturing the point (rate) of the conversion of yellow to white subcutaneous fat. In the present experiment 98 Angus crossbreed cows were utilized. Cows were fed either low vitamin A (LVA) diet consisting of whole shelled corn, soybean hulls, soybean meal, and a mineral-vitamin supplement or high vitamin A (HVA) diet, formulated using whole shelled corn, fescue hay, dry distiller grains with soluble, and a mineral-vitamin supplement for 56 d. During the 56 d feeding period, body weights and condition scores, and subcutaneous adipose samples were collected every 14 d. On day 56, cattle were slaughtered; 48 h postmortem carcass characteristics and objective color scores (subcutaneous adipose tissue) were recorded and a sample of the longissimus dorsi lumborum was collected. Subcutaneous adipose tissue samples were utilized to record subjective color scores and then ground to be analyzed for β-carotene concentration. The longissimus dorsi lumborum samples (2.54 cm slices) were removed for Warner-Bratzler shear force (WBSF) and pH testing. Data were analyzed using the MIXED procedure of SAS. Feeding cull cows LVA resulted in differences in subcutaneous carcass fat color (P = 0.01) as well as b* values (P &lt; 0.01) on day 56 compared with HVA. Subjective fat color scores were not different (P &gt; 0.10) on day 0 or 14 but were different (P ≤ 0.05) on days 28, 42, and 56. Additionally, 9-cis-β-carotene concentration on day 56 were different (P = 0.05) between treatments. A trend was noticed for all-trans-β-carotene concentration (P = 0.10) on day 56 as well. Cull cow body weights were greater (P ≤ 0.04) when fed the LVA diet starting on days 14, 28, and 42; and a trend was noticed on day 56 (P = 0.09). Overall, cows fed the LVA treatment for 56 d exhibited decreased adipose yellowness and β-carotene concentrations as well as increased live weights.