bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State
Authors: Smith Jason P. , Paxton Robert , Medrano Silvia , Sheffield Nathan C. , Sequeira-Lopez Maria Luisa S. , Gomez R. Ariel 
Published: July 2024

BACKGROUND:
Renin-expressing cells are myoendocrine cells crucial for the maintenance of homeostasis. Renin is regulated by cAMP, p300 (histone acetyltransferase p300)/CBP (CREB-binding protein), and Brd4 (bromodomain-containing protein 4) proteins and associated pathways. However, the specific regulatory changes that occur following inhibition of these pathways are not clear.

METHODS:
We treated As4.1 cells (tumoral cells derived from mouse juxtaglomerular cells that constitutively express renin) with 3 inhibitors that target different factors required for renin transcription: H-89-dihydrochloride, PKA (protein kinase A) inhibitor; JQ1, Brd4 bromodomain inhibitor; and A-485, p300/CBP inhibitor. We performed assay for transposase-accessible chromatin with sequencing (ATAC-seq), single-cell RNA sequencing, cleavage under targets and tagmentation (CUT&Tag), and chromatin immunoprecipitation sequencing for H3K27ac (acetylation of lysine 27 of the histone H3 protein) and p300 binding on biological replicates of treated and control As4.1 cells.

RESULTS:

In response to each inhibitor,
Ren1
expression was significantly reduced and reversible upon washout. Chromatin accessibility at the
Ren1
locus did not markedly change but was globally reduced at distal elements. Inhibition of PKA led to significant reductions in H3K27ac and p300 binding specifically within the
Ren1
super-enhancer region. Further, we identified enriched TF (transcription factor) motifs shared across each inhibitory treatment. Finally, we identified a set of 9 genes with putative roles across each of the 3 renin regulatory pathways and observed that each displayed differentially accessible chromatin, gene expression, H3K27ac, and p300 binding at their respective loci.

CONCLUSIONS:
Inhibition of renin expression in cells that constitutively synthesize and release renin is regulated by an epigenetic switch from an active to poised state associated with decreased cell-cell communication and an epithelial-mesenchymal transition. This work highlights and helps define the factors necessary for renin cells to alternate between myoendocrine and contractile phenotypes.
Causal and Chronological Relationships Predict Memory Organization for Nonlinear Narratives
Authors: Antony James , Lozano Angelo , Dhoat Pahul , Chen Janice , Bennion Kelly 
Published: July 2024

Abstract
While recounting an experience, one can employ multiple strategies to transition from one part to the next. For instance, if the event was learned out of linear order, one can recall events according to the time they were learned (temporal), similar events (semantic), events occurring nearby in time (chronological), or events produced by the current event (causal). To disentangle the importance of these factors, we had participants watch the nonlinear narrative, Memento, under different task instructions and presentation orders. For each scene of the film, we also separately computed semantic and causal networks. We then contrasted the evidence for temporal, semantic, chronological, or causal strategies during recall. Critically, there was stronger evidence for the causal and chronological strategies than semantic or temporal strategies. Moreover, the causal and chronological strategies outperformed the temporal one even when we asked participants to recall the film in the presented order, underscoring the fundamental nature of causal structure in scaffolding understanding and organizing recall. Nevertheless, time still marginally predicted recall transitions, suggesting it operates as a weak signal in the presence of more salient forms of structure. In addition, semantic and causal network properties predicted scene memorability, including a stronger role for incoming causes to an event than its outgoing effects. In summary, these findings highlight the importance of accounting for complex, causal networks in knowledge building and memory.
Impacts of Large-Scale Offshore Wind Farms on Tropical Cyclones: A Case Study of Typhoon Hato
Authors: Zhang Penghui , Deng Shaokun , Tuo Peng-Fei , Chen Shengli 
Published: July 2024

Abstract
With the rising global demand for renewable energy sources, a great number of offshore wind farms are being built worldwide, as well as in the northern South China Sea. There is, however, limited research on the impact of offshore wind farms on the atmospheric and marine environment, particularly tropical cyclones, which frequently occur in summertime in the South China Sea. In this paper, we employ the Weather Research and Forecasting (WRF) Model to investigate the impacts of large-scale offshore wind farms on tropical cyclones, using the case of Typhoon Hato, which caused severe damage in 2017. Model results reveal that maximum wind speeds in coastal areas decrease by 3–5 m s−1 and can reach a maximum of 8 m s−1. Furthermore, the wind farms change low-level moisture convergence, causing a shift in the precipitation center toward the wind farm area and causing a significant overall reduction (up to 16%) in precipitation. Model sensitivity experiments on the area and layout of the wind farm have been carried out. The results show that larger wind farm areas and denser turbine layouts cause a more substantial decrease in the wind speed over the coast and accumulated precipitation reduction, further corroborating our findings.

Significance Statement
This study holds significant implications for developing offshore wind farms in tropical cyclone-prone regions like the South China Sea. By focusing on Typhoon Hato as a case study, the research sheds light on the previously understudied relationship between large-scale offshore wind farms and tropical cyclones. The observed decrease in coastal wind speeds and altered precipitation patterns due to wind farm presence highlights the potential for mitigating cyclone-related risks in these regions. Additionally, the study’s sensitivity experiments underscore the importance of careful planning and design in optimizing wind farm layouts for maximum impact reduction. This research contributes vital insights into sustainable energy infrastructure development while minimizing environmental and meteorological risks in cyclone-prone areas.
A range of 30–62% of functioning multiciliated airway cells is sufficient to maintain ciliary airway clearance
Authors: Loges Niki T. , Marthin June Kehlet , Raidt Johanna , Olbrich Heike , Höben Inga M. , Cindric Sandra , Bracht Diana , König Julia , Rieck Cynthia , George Sebastian , Kloth Tim Luis , Wohlgemuth Kai , Pennekamp Petra , Dworniczak Bernd , Holgersen Mathias G. , Römel Jobst , Schmalstieg Christian , Aprea Isabella , Mortensen Jann , Nielsen Kim G. , Omran Heymut 
Published: July 2024

BackgroundPrimary ciliary dyskinesia is a genetic disorder caused by aberrant motile cilia function that results in defective ciliary airway clearance and subsequently leads to recurrent airway infections and bronchiectasis. We aimed to determine: how many functional multiciliated airway cells are sufficient to maintain ciliary airway clearance?MethodsTo answer this question we exploited the molecular defects of the X-linked recessive primary ciliary dyskinesia variant caused by pathogenic variants inDNAAF6(PIH1D3), characterised by immotile cilia in affected males. We carefully analysed the clinical phenotype and molecular defect (using immunofluorescence and transmission electron microscopy) and performedin vitrostudies (particle tracking in air–liquid interface cultures) andin vivostudies (radiolabelled tracer studies) to assess ciliary clearance of respiratory cells from female individuals with heterozygous and male individuals with hemizygous pathogenicDNAAF6variants.ResultsPrimary ciliary dyskinesia male individuals with hemizygous pathogenicDNAAF6variants displayed exclusively immotile cilia, absence of ciliary clearance and severe primary ciliary dyskinesia symptoms. Owing to random or skewed X-chromosome inactivation in six female carriers with heterozygous pathogenicDNAAF6variants, 54.3±10% (range 38–70%) of multiciliated cells were defective. Nevertheless,in vitroandin vivoassessment of the ciliary airway clearance was normal or slightly abnormal. Consistently, heterozygous female individuals showed no or only mild respiratory symptoms.ConclusionsOur findings indicate that having 30–62% of multiciliated respiratory cells functioning can generate either normal or slightly reduced ciliary clearance. Because heterozygous female carriers displayed either no or subtle respiratory symptoms, complete correction of 30% of cells by precision medicine could improve ciliary airway clearance in individuals with primary ciliary dyskinesia, as well as clinical symptoms.
SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies
Authors: Ouedraogo Wend Yam D. D. , Ouangraoua Aida 
Published: July 2024

Abstract
Background
SimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of the sets of transcripts produced from genes. It takes a guide gene tree as input and generates a gene sequence with its transcripts for each node of the tree, from the root to the leaves. However, the sets of transcripts simulated at different nodes of the guide gene tree lack evolutionary connections. Consequently, SimSpliceEvol is not suitable for evaluating methods for transcript phylogeny inference or gene phylogeny inference that rely on transcript conservation.

Results
Here, we introduce SimSpliceEvol2, which, compared to the first version, incorporates an explicit model of transcript evolution for simulating alternative transcripts along the branches of a guide gene tree, as well as the transcript phylogenies inferred. We offer a comprehensive software with a graphical user interface and an updated version of the web server, ensuring easy and user-friendly access to the tool.

Conclusion
SimSpliceEvol2 generates synthetic datasets that are useful for evaluating methods and tools for spliced RNA sequence analysis, such as spliced alignment methods, methods for identifying conserved transcripts, and transcript phylogeny reconstruction methods. The web server is accessible at https://simspliceevol.cobius.usherbrooke.ca, where you can also download the standalone software. Comprehensive documentation for the software is available at the same address. For developers interested in the source code, which requires the installation of all prerequisites to run, it is provided at https://github.com/UdeS-CoBIUS/SimSpliceEvol.
Identification and characterization of a new species of Taxus — Taxus qinlingensis by multiple taxonomic methods
Authors: Wu Xingtong , Wang Minqiu , Li Xinyu , Chen Yan , Liao Zhengping , Zhang Donglin , Wen Yafeng , Wang Sen 
Published: July 2024

Abstract
Background
The taxonomy of Taxus Linn. remains controversial due to its continuous phenotypic variation and unstable topology, thus adversely affecting the formulation of scientific conservation strategies for this genus. Recently, a new ecotype, known as Qinling type, is mainly distributed in the Qinling Mountains and belongs to a monophyletic group. Here, we employed multiple methods including leaf phenotype comparison (leaf shapes and microstructure), DNA barcoding identification (ITS + trnL-trnF + rbcL), and niche analysis to ascertain the taxonomic status of the Qinling type.

Results
Multiple comparisons revealed significant differences in the morphological characters (length, width, and length/width ratio) among the Qinling type and other Taxus species. Leaf anatomical analysis indicated that only the Qinling type and T. cuspidata had no papilla under the midvein or tannins in the epicuticle. Phylogenetic analysis of Taxus indicated that the Qinling type belonged to a monophyletic group. Moreover, the Qinling type had formed a relatively independent niche, it was mainly distributed around the Qinling Mountains, Ta-pa Mountains, and Taihang Mountains, situated at an elevation below 1500 m.

Conclusions
Four characters, namely leaf curvature, margin taper, papillation on midvein, and edges were put forward as primary indexes for distinguishing Taxus species. The ecotype Qingling type represented an independent evolutionary lineage and formed a unique ecological niche. Therefore, we suggested that the Qingling type should be treated as a novel species and named it Taxus qinlingensis Y. F. Wen & X. T. Wu, sp. nov.
Genome-wide analysis of the SWEET gene family in Hemerocallis citrina and functional characterization of HcSWEET4a in response to salt stress
Authors: Cao Lihong , Wang Jinyao , Wang Lixuan , Liu Huili , Wu Wenjing , Hou Feifan , Liu Yuting , Gao Yang , Cheng Xiaojing , Li Sen , Xing Guoming 
Published: July 2024

AbstractSugars will be eventually effluxed transporters (SWEETs) have been confirmed to play diverse physiological roles in plant growth, development and stress response. However, the characteristics and functions of the SWEET genes in Hemerocallis citrina remain unclear and poorly elucidated. In this study, the whole genome of Hemerocallis citrina was utilized to conduct bioinformatics analysis and a total of 19 HcSWEET genes were successfully identified. Analysis of the physicochemical properties indicated dominant differences among these HcSWEETs. A phylogenetic analysis revealed that HcSWEET proteins can be divided into 4 clades ranging from Clade I to IV, where proteins within the same clade exhibited shared conserved motifs and gene structures. Five to six exons were contained in the majority of HcSWEET genes, which were unevenly distributed across 11 chromosomes. The gene duplication analysis showed the presence of 4 gene pairs. Comparative syntenic maps revealed that the HcSWEET gene family might present more closed homology in monocotyledons than dicotyledons. Cis-acting element analysis of HcSWEET genes indicated key responsiveness to various hormones, light, and stresses. Additionally, transcriptome sequencing analysis suggested that most HcSWEET genes had a relatively higher expression in roots, and HcSWEET4a was significantly up-regulated under salt stress. Overexpression further verified the possibility that HcSWEET4a was involved in response to salt stress, which provides novel insights and facilitates in-depth studies of the functional analysis of HcSWEETs in resistance to abiotic stress.
Agile implementation of alcohol screening in primary care
Authors: Summanwar Diana , Ropert Chelan , Barton James , Hiday Rachael , Bishop Dawn , Boustani Malaz , Willis Deanna 
Published: July 2024

Abstract
Background
Despite the United States Preventive Services Task Force recommendation to screen adults for unhealthy alcohol use, the implementation of alcohol screening in primary care remains suboptimal.

Methods
A pre and post-implementation study design that used Agile implementation process to increase screening for unhealthy alcohol use in adult patients from October 2021 to June 2022 at a large primary care clinic serving minority and underprivileged adults in Indianapolis.

Results
In comparison to a baseline screening rate of 0%, the agile implementation process increased and sustained screening rates above 80% for alcohol use using the Alcohol Use Disorders Identification Test – Consumption tool (AUDIT-C).

Conclusions
Using the agile implementation process, we were able to successfully implement evidence-based recommendations to screen for unhealthy alcohol use in primary care.
Acceptability and preliminary effects of the volunteer-supported Meaningful Moments program to engage older adults with advanced dementia on a hospital-based specialized dementia care unit: a mixed methods study
Authors: Yous Marie-Lee , Coker Esther , Hunter Paulette V. , Fisher Kathryn A. , Sue Joanna L. , Nicula Maria , Kazmie Nadia , Orsini Theresa , Sussman Tamara , Thompson Genevieve , Kaasalainen Sharon 
Published: July 2024

Abstract
Background
Namaste Care offers practical skills for healthcare providers, volunteers, and families to meaningfully engage individuals with dementia in activities (e.g., music, massage, reminiscing, socialization, aromatherapy, snacks). A hospital-based specialized dementia care unit for patients with mid- to late-stage dementia offered an adapted version of the Namaste Care program, which was called Meaningful Moments. The aim of this study was to assess the acceptability and preliminary effects of this novel approach using trained volunteers for older adults with mid- to late-stage dementia.

Methods
A mixed methods multiphase design was used. Qualitative description was used to explore acceptability of the Meaningful Moments program delivered over 6 months through focus groups (e.g., charge nurses, therapeutic recreationists, nurses, social workers) and individual interviews with one volunteer and two family members. A prospective pre-post-test study design was used to evaluate the preliminary effects of the program for patients with dementia and family members. Outcomes included quality of life, neuropsychiatric symptoms, and pain for patients with dementia and family carer role stress and the quality of visits for families. Data were collected from June 2018 to April 2019. Descriptive analyses of participants’ characteristics were expressed as a mean (standard deviation [SD]) for continuous variables and count (percent) for categorical variables. Focus group and individual interview data were analyzed using thematic analysis. The generalized estimating equations (GEE) method was used to assess change in the repeated measures outcome data.

Results
A total of 15 patients received the Meaningful Moments interventions. Families, staff, and volunteers perceived that patients experienced benefits from Meaningful Moments. Staff, volunteers, and families felt fulfilled in their role of engaging patients in the Meaningful Moments program. Individualized activities provided by volunteers were perceived as necessary for the patient population. There were no statistically significant improvements in patient outcomes. There was a statistically significant decline in family carer role stress.

Conclusions
Using a one-on-one approach by volunteers, patients experienced perceived benefits such as improved mood and opportunities for social interactions. There is a need for tailored activities for older adults with advanced dementia through practical strategies that can offer benefit to patients.
Controversy between biopsy and risk in children with proteinuria: is there a paradigm war?
Authors: Yang Jingyi , Liu Xiaorong 
Published: July 2024

Abstract
Background
Proteinuria is a prevalent symptom of pediatric nephrology, while kidney biopsy remains the gold standard for kidney tissue analysis, and it is currently controversial. We report the rare case that the mutation in the AMN gene was considered to cause chronically isolated proteinuria and also suggest that renal biopsy should be chosen with caution in children with chronic isolated non-nephrotic levels of proteinuria and that genetic testing may be feasible for the early precise diagnosis.

Case presentation
A 35-month-old boy presented with excessive urine foaming for more than half a month; his proteinuria was considered non-nephrotic range and urine protein electrophoresis was suggestive of mixed proteinuria; other than that, the investigations are non-specific. Given the child’s chronic isolated proteinuria and good renal function, we chose to refine the genetic test rather than a renal biopsy; a compound heterozygous variant was found in the AMN gene of this child which was caused by a point mutation in the father, and a partial chromosomal deletion in the mother.

Conclusions
Cubilin(encoded by CUBN), amnionless(encoded by AMN), and megalin form a multiligand receptor complex; CUBN or AMN gene variants have been implicated as a hereditary cause of megaloblastic anemia, proteinuria, and neurological impairment. In the past few decades, chronic isolated proteinuria caused by CUBN gene variants is benign, non-progressive, and has normal renal function. However, the child is the first reported case of isolated proteinuria of AMN gene mutation, indicating that the earlier diagnostic genetic sequencing in an otherwise well, not nephrotic proteinuria child may be a convenient, cost-effective, and harmless option, challenging the traditional paradigm.
Tear film assessment before and after phacoemulsification in patients with age-related cataracts
Authors: Shaaban Yasmine Maher , Aziz Bassem Fayez 
Published: July 2024

Abstract
Background
The study aims to assess the tear film before and after phacoemulsification in patients with age-related cataracts.

Methods
A prospective observational study of 41 age-related cataract patients undergoing phacoemulsification procedure. Tear Film Break-Up Time (TBUT), Tear Film Meniscus Height (TMH), Meibomian glands (MG), and Lipid Layer Thickness (LLT) were assessed by a non-invasive Dry Eye Diagnostic System. All measurements were taken preoperatively, one week, one month, and three months postoperatively. The Marginal homogeneity and The Cochran Q tests were used in the statistical analysis.

Results
The value of Non-Invasive Break-Up Time (NITBUT) was statistically significantly lower at one week (7.15 ± 3.31), one month (7.61 ± 3.41), and three months (7.66 ± 3.36) postoperatively than preoperatively (10.71 ± 2.71), p < 0.001. The Non- Invasive Tear Meniscus Height (NITMH) was significantly lower at one week (0.18 ± 0.0), one month (0.20 ± 0.09), and three months (0.20 ± 0.09) postoperatively than preoperatively (0.30 ± 0.113) p < 0.001. By the first month, both (NITBUT) and (NITMH) improved significantly compared to the first post-operative week. There was no statistically significant difference between one month and three months. The (NITMH) improved to a healthy level of ≥ 0.2 mm by the first month through the third month. Both (NITBUT) and (NITMH) did not reach the baseline by the third month. The meibomian glands and the lipid layer thickness had the same preoperative grade distribution without changes.

Conclusion
Phacoemulsification surgery can cause post-operative deterioration in the tear film, which starts within a week of the procedure, followed by gradual recovery over the next weeks and months. The phacoemulsification procedure mainly affects the tear break-up time and tear meniscus height. Both the lipid layer and meibomian glands are not affected.