bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput mRNA-seq atlas of human placenta shows vast transcriptome remodeling from first to third trimester
Authors: Gonzalez Tania L , Wertheimer Sahar , Flowers Amy E , Wang Yizhou , Santiskulvong Chintda , Clark Ekaterina L , Jefferies Caroline A , Lawrenson Kate , Chan Jessica L , Joshi Nikhil V , Zhu Yazhen , Tseng Hsian-Rong , Karumanchi S Ananth , Williams III John , Pisarska Margareta D 
Published: January 2024

Abstract
The placenta, composed of chorionic villi, changes dramatically across gestation. Understanding differences in ongoing pregnancies are essential to identify the role of chorionic villi at specific times in gestation and develop biomarkers and prognostic indicators of maternal–fetal health. The normative mRNA profile is established using next-generation sequencing of 124 first trimester and 43 third trimester human placentas from ongoing healthy pregnancies. Stably expressed genes (SEGs) not different between trimesters and with low variability are identified. Differential expression analysis of first versus third trimester adjusted for fetal sex is performed, followed by a subanalysis with 23 matched pregnancies to control for subject variability using the same genetic and environmental background. Placenta expresses 14,979 polyadenylated genes above sequencing noise (transcripts per million &gt; 0.66), with 10.7% SEGs across gestation. Differentially expressed genes (DEGs) account for 86.7% of genes in the full cohort [false discovery rate (FDR) &lt; 0.05]. Fold changes highly correlate between the full cohort and subanalysis (Pearson = 0.98). At stricter thresholds (FDR &lt; 0.001, fold change &gt; 1.5), there remains 50.1% DEGs (3353 upregulated in first and 4155 upregulated in third trimester). This is the largest mRNA atlas of healthy human placenta across gestation, controlling for genetic and environmental factors, demonstrating substantial changes from first to third trimester in chorionic villi. Specific differences and SEGs may be used to understand the specific role of the chorionic villi throughout gestation and develop first trimester biomarkers of placental health that transpire across gestation, which can be used for future development of biomarkers for maternal–fetal health.
Bearing Witness: The Impact of Lived Experience Educators Participating in Social Work Student Supervision during Placement
Authors: Duncanson Kate , Kingston Phoebe , Tran Patricia , Blundell Barbara , Gillieatt Sue , Mahboub Lyn , Martin Robyn 
Published: January 2024

Abstract
Social work student supervision during field education is a mandated requirement where students review their activities and learning in the workplace with field educators (FEs). Inevitably service users will be discussed in supervision but will have little or no opportunity to represent their perspectives during sessions. In order to explore how service user perspectives might be integrated into supervision, this qualitative study examined the participation of two Lived Experience Educators in supervision sessions between six social work students and their FEs during final placement. Despite some initial trepidation, participants reported a significant and overwhelmingly positive impact based on more equalised power differentials, greater depth of reflection and the emergence of new ideas on increasing accountability to service users. These results have implications for the practice of supervision, with both students and staff, and for how people with lived experience expertise may contribute to improving service culture for the intended beneficiaries of social work services.
A Common Purpose? Social Work Students’ Social Justice Related Views in Finland and the island of Ireland
Authors: McFadden Paula , Bloomberg Helena , Kallio Johanna , Kroll Christian , McCartan Claire , Flanagan Niamh , Kirwin Gloria , Pentaraki Maria , Wilson Elaine 
Published: January 2024

Abstract
Exploring social work students’ views to understand how equipped they are to pursue the social justice mission of the profession should be of central academic and practical interest. There are, however, surprisingly few empirical studies focussing on social work students’ views on social justice-related issues from a comparative viewpoint. Such knowledge is thought to be of a wider international interest from a number of perspectives, including social work education and student exchange and, in a wider context, for the development of social work as a profession and for discussing the prerequisites for shared international notions of social work. This article explores the views of social work students studying in different socio-economic contexts and welfare regimes in relation to some key aspects assumed to be vital for the profession. The results based on survey data from student cohorts in Finland (N = 608) and the island of Ireland (N = 279) support the general conclusion that there are important, similar patterns of motivations and understandings amongst the students, despite substantial differences in histories, welfare state developments, current policies and social conditions in various jurisdictions. The results are of interest to educators across countries internationally and provide an important basis for future similar studies.
TRIM14 suppressed the progression of NSCLC via hexosamine biosynthesis pathway
Authors: Wei Sisi , Ai Meiling , Zhan Yuan , Yu Jieqing , Xie Tao , Hu Qinghua , Fang Yang , Huang Xuan , Li Yong 
Published: January 2024

Abstract
Tripartite Motif 14 (TRIM14) is an oncoprotein that belongs to the E3 ligase TRIM family, which is involved in the progression of various tumors except for non-small cell lung carcinoma (NSCLC). However, little is currently known regarding the function and related mechanisms of TRIM14 in NSCLC. Here, we found that the TRIM14 protein was downregulated in lung adenocarcinoma tissues compared with the adjacent tissues, which can suppress tumor cell proliferation and migration both in vitro and in vivo. Moreover, TRIM14 can directly bind to glutamine fructose-6-phosphate amidotransferase 1 (GFAT1), which in turn results in the degradation of GFAT1 and reduced O-glycosylation levels. GFAT1 is a key enzyme in the rate-limiting step of the hexosamine biosynthetic pathway (HBP). Replenishment of N-acetyl-d-glucosamine can successfully reverse the inhibitory effect of TRIM14 on the NSCLC cell growth and migration as expected. Collectively, our data revealed that TRIM14 suppressed NSCLC cell proliferation and migration through ubiquitination and degradation of GFAT1, providing a new regulatory role for TRIM14 on HBP.
Towards improving community detection in complex networks using influential nodes
Authors: Zheng Henghe , Zhao Haitao , Ahmadi Gholamreza 
Published: January 2024

AbstractComplex network analysis is inspired by empirical studies of real-world networks such as computer networks, technology networks and social networks. The analysis of community structure in complex networks is understood as an important issue by the research society. A community is a set of nodes in a network where the density of connections is high. The insight in the literature shows many approaches to identify influential nodes, but these approaches only lead to finding community centres. Meanwhile, clustering techniques are effectively used for community detection, where they can reveal group structure and hidden connections by considering topological and demographic information. This article presents an ensemble clustering algorithm based on influential nodes to improve community detection in complex networks. Considering different characteristics of the network, the proposed method seeks to discover common interests between users and their behaviours to identify the most suitable communities. First, a set of influential nodes are identified as community centres. Then, these centres are considered as cluster centres. After that, primary clusters are created based on the determined centres. Finally, the primary clusters are reclustered to form the final clusters. Here, the final clusters are considered as communities of users in the network. The simulation has been performed on real-world networks and the results confirm the effectiveness of the proposed method. Specifically, the communities identified by the proposed method are 2.1% better than the best existing state-of-the-art method in terms of modularity. Keywords: complex network; community detection; influential nodes; ensemble clustering.
Why is early-onset atrial fibrillation uncommon in patients with Duchenne muscular dystrophy? Insights from the mdx mouse
Authors: Nguyen My-Nhan , Hooper Charlotte , Stefanini Matilde , Vrellaku Besarte , Carnicer Ricardo , Wood Matthew J , Simon Jillian N , Casadei Barbara 
Published: January 2024

Abstract

Aims
A reduction in both dystrophin and neuronal nitric oxide synthase (NOS1) secondary to microRNA-31 (miR-31) up-regulation contributes to the atrial electrical remodelling that underpins human and experimental atrial fibrillation (AF). In contrast, patients with Duchenne muscular dystrophy (DMD), who lack dystrophin and NOS1 and, at least in the skeletal muscle, have raised miR-31 expression, do not have increase susceptibility to AF in the absence of left ventricular (LV) dysfunction. Here, we investigated whether dystrophin deficiency is also associated with atrial up-regulation of miR-31, loss of NOS1 protein, and increased AF susceptibility in young mdx mice.

Methods and results
Echocardiography showed normal cardiac structure and function in 12–13 weeks mdx mice, with no indication by assay of hydroxyproline that atrial fibrosis had developed. The absence of dystrophin in mdx mice was accompanied by an overall reduction in syntrophin and a lower NOS1 protein content in the skeletal muscle and in the left atrial and ventricular myocardium, with the latter occurring alongside reduced Nos1 transcript levels (exons 1–2 by quantitative polymerase chain reaction) and an increase in NOS1 polyubiquitination [assessed using tandem polyubiquitination pulldowns; P &lt; 0.05 vs. wild type (WT)]. Neither the up-regulation of miR-31 nor the substantial reduction in NOS activity observed in the skeletal muscle was present in the atrial tissue of mdx mice. At difference with the skeletal muscle, the mdx atrial myocardium showed a reduction in the constitutive NOS inhibitor, caveolin-1, coupled with an increase in NOS3 serine1177 phosphorylation, in the absence of differences in the protein content of other NOS isoforms or in the relative expression NOS1 splice variants. In line with these findings, transoesophageal atrial burst pacing revealed no difference in AF susceptibility between mdx mice and their WT littermates.

Conclusion
Dystrophin depletion is not associated with atrial miR-31 up-regulation, reduced NOS activity, or increased AF susceptibility in the mdx mouse. Compared with the skeletal muscle, the milder atrial biochemical phenotype may explain why patients with DMD do not exhibit a higher prevalence of atrial arrhythmias despite a reduction in NOS1 content.
Long-term simulated microgravity fosters carotid aging-like changes via Piezo1
Authors: Zhang Jiaxin , Wang Xinpei , Fu Zihao , Xing Changyang , Wang Zhen , Yang Hongyan , Li Jiahui , Liu Meijie , Dong Ling , Zhang Xing , Li Yongzhi , Wang Jiaping , Long Jiangang , Liu Jiankang , Wang Shengpeng , Li Jia , Gao Feng 
Published: January 2024

Abstract

Aims
Elucidating the impacts of long-term spaceflight on cardiovascular health is urgently needed in face of the rapid development of human space exploration. Recent reports including the NASA Twins Study on vascular deconditioning and aging of astronauts in spaceflight are controversial. The aims of this study were to elucidate whether long-term microgravity promotes vascular aging and the underlying mechanisms.

Methods and results
Hindlimb unloading (HU) by tail suspension was used to simulate microgravity in rats and mice. The dynamic changes of carotid stiffness in rats during 8 weeks of HU were determined. Simulated microgravity led to carotid artery aging-like changes as evidenced by increased stiffness, thickness, fibrosis, and elevated senescence biomarkers in the HU rats. Specific deletion of the mechanotransducer Piezo1 in vascular smooth muscles significantly blunted these aging-like changes in mice. Mechanistically, mechanical stretch-induced activation of Piezo1 elevated microRNA-582-5p in vascular smooth muscle cells, with resultant enhanced synthetic cell phenotype and increased collagen deposition via PTEN/PI3K/Akt signalling. Importantly, inhibition of miRNA-582-5p alleviated carotid fibrosis and stiffness not only in HU rats but also in aged rats.

Conclusions
Long-term simulated microgravity induces carotid aging-like changes via the mechanotransducer Piezo1-initiated and miRNA-mediated mechanism.
Toxigenic Clostridium perfringens Isolated from At-Risk Paediatric Inflammatory Bowel Disease Patients
Authors: Kuo James , Uzunovic Jasmina , Jacobson Amanda , Dourado Michelle , Gierke Sarah , Rajendram Manohary , Keilberg Daniela , Mar Jordan , Stekol Emily , Curry Joanna , Verstraete Sofia , Lund Jessica , Liang Yuxin , Tamburini Fiona B , Omattage Natalie S , Masureel Matthieu , Rutherford Steven T , Hackos David H , Tan Man-Wah , Byrd Allyson L , Keir Mary E , Skippington Elizabeth , Storek Kelly M 
Published: January 2024

Abstract

Background and Aims
This study aimed to identify microbial drivers of inflammatory bowel disease [IBD], by investigating mucosal-associated bacteria and their detrimental products in IBD patients.

Methods
We directly cultured bacterial communities from mucosal biopsies from paediatric gastrointestinal patients and examined for pathogenicity-associated traits. Upon identifying Clostridium perfringens as toxigenic bacteria present in mucosal biopsies, we isolated strains and further characterized toxicity and prevalence.

Results
Mucosal biopsy microbial composition differed from corresponding stool samples. C. perfringens was present in eight of nine patients’ mucosal biopsies, correlating with haemolytic activity, but was not present in all corresponding stool samples. Large IBD datasets showed higher C. perfringens prevalence in stool samples of IBD adults [18.7–27.1%] versus healthy controls [5.1%]. In vitro, C. perfringens supernatants were toxic to cell types beneath the intestinal epithelial barrier, including endothelial cells, neuroblasts, and neutrophils, while the impact on epithelial cells was less pronounced, suggesting C. perfringens may be particularly damaging when barrier integrity is compromised. Further characterization using purified toxins and genetic insertion mutants confirmed perfringolysin O [PFO] toxin was sufficient for toxicity. Toxin RNA signatures were found in the original patient biopsies by PCR, suggesting intestinal production. C. perfringens supernatants also induced activation of neuroblast and dorsal root ganglion neurons in vitro, suggesting C. perfringens in inflamed mucosal tissue may directly contribute to abdominal pain, a frequent IBD symptom.

Conclusions
Gastrointestinal carriage of certain toxigenic C. perfringens may have an important pathogenic impact on IBD patients. These findings support routine monitoring of C. perfringens and PFO toxins and potential treatment in patients.
Impact of atherosclerosis imaging-quantitative computed tomography on diagnostic certainty, downstream testing, coronary revascularization, and medical therapy: the CERTAIN study
Authors: Nurmohamed Nick S , Cole Jason H , Budoff Matthew J , Karlsberg Ronald P , Gupta Himanshu , Sullenberger Lance E , Quesada Carlos G , Rahban Habib , Woods Kevin M , Uzzilia Jeffrey R , Purga Scott L , Aquino Melissa , Hoffmann Udo , Min James K , Earls James P , Choi Andrew D 
Published: January 2024

Abstract

Aims
The incremental impact of atherosclerosis imaging-quantitative computed tomography (AI-QCT) on diagnostic certainty and downstream patient management is not yet known. The aim of this study was to compare the clinical utility of the routine implementation of AI-QCT versus conventional visual coronary CT angiography (CCTA) interpretation.

Methods and results
In this multi-centre cross-over study in 5 expert CCTA sites, 750 consecutive adult patients referred for CCTA were prospectively recruited. Blinded to the AI-QCT analysis, site physicians established patient diagnoses and plans for downstream non-invasive testing, coronary intervention, and medication management based on the conventional site assessment. Next, physicians were asked to repeat their assessments based upon AI-QCT results. The included patients had an age of 63.8 ± 12.2 years; 433 (57.7%) were male. Compared with the conventional site CCTA evaluation, AI-QCT analysis improved physician’s confidence two- to five-fold at every step of the care pathway and was associated with change in diagnosis or management in the majority of patients (428; 57.1%; P &lt; 0.001), including for measures such as Coronary Artery Disease-Reporting and Data System (CAD-RADS) (295; 39.3%; P &lt; 0.001) and plaque burden (197; 26.3%; P &lt; 0.001). After AI-QCT including ischaemia assessment, the need for downstream non-invasive and invasive testing was reduced by 37.1% (P &lt; 0.001), compared with the conventional site CCTA evaluation. Incremental to the site CCTA evaluation alone, AI-QCT resulted in statin initiation/increase an aspirin initiation in an additional 28.1% (P &lt; 0.001) and 23.0% (P &lt; 0.001) of patients, respectively.

Conclusion
The use of AI-QCT improves diagnostic certainty and may result in reduced downstream need for non-invasive testing and increased rates of preventive medical therapy.
Accuracy of diagnostic tests for acute diverticulitis that are feasible in primary care: a systematic review and meta-analysis
Authors: Vijfschagt Natasja D , de Boer Michiel R , Berger Marjolein Y , Burger Huibert , Holtman Gea A 
Published: January 2024

Abstract

Background
Recognition of acute diverticulitis is important to determine an adequate management strategy. Differentiating it from other gastrointestinal disorders is challenging as symptoms overlap. Clinical tests might assist the clinician with this diagnostic challenge. Previous reviews have focussed on prognostic questions and imaging examinations in secondary care.

Objective
To evaluate the diagnostic accuracy of clinical tests feasible in primary care for acute diverticulitis in suspected patients.

Method
We have systematically searched multiple databases for diagnostic accuracy studies of tests feasible in primary care compared to a reference standard in suspected patients. Two reviewers independently selected studies, extracted data, and assessed study quality with the QUADAS-2 tool. We have meta-analysed the results in the case of more than four studies per index test.

Results
Seventeen studies were included, all studies were performed in secondary care (median prevalence 48%). Individual signs and symptoms showed a wide range in sensitivity (range 0.00–0.98) and specificity (range 0.08–1.00). Of the four laboratory tests evaluated, CRP &gt;10 mg/l had the highest sensitivity (range 0.89–0.96) with specificity ranging from 0.28 to 0.61. Ultrasound had the highest pooled sensitivity and specificity of 0.92 (95% CI 0.86–0.96) and 0.94 (95% CI 0.88–0.97), respectively.

Conclusion
None of the studies were performed in primary care. Individual signs and symptoms alone are insufficiently informative for acute diverticulitis diagnosis. CRP showed potential for ruling out and ultrasound had a high diagnostic accuracy. More research is needed about the diagnostic accuracy of these tests in primary care.

PROSPERO registration number
CRD42021230622
Mill and Landbase Attributes Condition Response Rates to Timber Product Output Surveys in the Western United States
Authors: Affleck David L R , Gaines George C 
Published: January 2024

Abstract
Since the 1940s, the USDA Forest Service has surveyed roundwood receiving facilities to report on timber products output (TPO). The TPO program provides information on forest removals, processing capacity, and wood product markets, complementing inventory estimates of status and change. The program adopted an annual state-level probability sampling design in 2019 and this research evaluates rates of unit nonresponse (UN) in surveys of eleven western states over reference years 2019–2021. The overall response rate for this region and period was 43.7%, which appears low relative to prior western surveys. Response rates also differed significantly by state, facility type, and facility size class. Furthermore, distributions of forestland ownership and harvest levels over potential facility feedstock areas differed significantly between respondents and nonrespondents for an important class of large sawmills. Taken together, these results suggest UN is substantially degrading the precision of western TPO surveys and may be inducing appreciable bias in current estimators. At the same time, response rates were significantly higher where responses were obtained in previous years, suggesting a positive facilitation effect. The implications of these rates and patterns in UN for TPO survey design and estimation are discussed.
Study Implications: The USDA Forest Service estimates timber products output (TPO) from US forests using sample surveys of roundwood receiving facilities. In TPO samples of western states for the period 2019–2021, the average response rate was only 43.7%. The level of unit nonresponse will substantially degrade the precision of TPO estimates at state and regional levels, while the observed patterns may induce bias. Further research is needed to identify the bias and precision of current and alternative estimators and to investigate survey implementation factors or design enhancements that would allow more intensive follow-up efforts to focus on a smaller number of nonrespondents.
The unfolded protein response of the endoplasmic reticulum protects Caenorhabditis elegans against DNA damage caused by stalled replication forks
Authors: Xu Jiaming , Sabatino Brendil , Yan Junran , Ermakova Glafira , Doering Kelsie R S , Taubert Stefan 
Published: January 2024

Abstract
All animals must maintain genome and proteome integrity, especially when experiencing endogenous or exogenous stress. To cope, organisms have evolved sophisticated and conserved response systems: unfolded protein responses (UPRs) ensure proteostasis, while DNA damage responses (DDRs) maintain genome integrity. Emerging evidence suggests that UPRs and DDRs crosstalk, but this remains poorly understood. Here, we demonstrate that depletion of the DNA primases pri-1 or pri-2, which synthesize RNA primers at replication forks and whose inactivation causes DNA damage, activates the UPR of the endoplasmic reticulum (UPR-ER) in Caenorhabditis elegans, with especially strong activation in the germline. We observed activation of both the inositol-requiring-enzyme 1 (ire-1) and the protein kinase RNA-like endoplasmic reticulum kinase (pek-1) branches of the (UPR-ER). Interestingly, activation of the (UPR-ER) output gene heat shock protein 4 (hsp-4) was partially independent of its canonical activators, ire-1 and X-box binding protein (xbp-1), and instead required the third branch of the (UPR-ER), activating transcription factor 6 (atf-6), suggesting functional redundancy. We further found that primase depletion specifically induces the (UPR-ER), but not the distinct cytosolic or mitochondrial UPRs, suggesting that primase inactivation causes compartment-specific rather than global stress. Functionally, loss of ire-1 or pek-1 sensitizes animals to replication stress caused by hydroxyurea. Finally, transcriptome analysis of pri-1 embryos revealed several deregulated processes that could cause (UPR-ER) activation, including protein glycosylation, calcium signaling, and fatty acid desaturation. Together, our data show that the (UPR-ER), but not other UPRs, responds to replication fork stress and that the (UPR-ER) is required to alleviate this stress.