bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of epicardial adipose tissue on diastolic dysfunction in patients with chronic coronary syndrome and preserved left ventricular ejection fraction
Authors: Ishikawa Hirotoshi , Sugiyama Takatoshi , Otsuka Kenichiro , Yamaura Hiroki , Hojo Kana , Kono Yasushi , Ito Asahiro , Yamazaki Takanori , Shimada Kenei , Kasayuki Noriaki , Fukuda Daiju 
Published: June 2024

Abstract

Aims
This study aims to investigate the association between left ventricular diastolic dysfunction (LVDD) and epicardial adipose tissue (EAT) accumulation in patients with chronic coronary syndrome (CCS) and preserved left ventricular ejection fraction (LVEF).

Methods and results
The study included 314 patients with preserved LVEF who underwent coronary computed tomographic angiography (CCTA) and thoracic tissue Doppler echocardiography (TTDE). The EAT volume was measured using CCTA. LVDD was categorized into three groups: absent LVDD, undetermined LVDD, and LVDD. Multivariate logistic regression analysis was performed to assess the association between the clinical parameters, TTDE and CCTA findings, and LVDD. Patients (mean age: 66 ± 13 years; 52% men) were divided into LVDD present (30 patients, 9.6%), LVDD absent (219 patients, 69.7%), and LVDD undetermined (65 patients, 20.7%) groups. CCTA showed that patients with LVDD had a significantly higher coronary artery calcium (CAC) score and % plaque volume (%PV) than those without LVDD, whereas the prevalence of obstructive coronary artery disease was comparable between the groups. The EAT volume index correlated with each LVDD diagnostic component, except for tricuspid regurgitation velocity. A multivariate model showed that age [odds ratio (OR), 1.13; P &lt; 0.001] and EAT volume index (OR, 1.02; P = 0.038) were independently associated with LVDD, even after adjusting for left ventricular mass index (OR, 1.05; P = 0.005). There was no significant association between the CAC score and %PV or LVDD.

Conclusion
This study demonstrated that EAT volume index and left ventricular mass index were robust predictors of LVDD; however, there was no independent association between coronary atherosclerotic disease burden and LVDD.
Eligibility for lipid-lowering therapy when applying systemic coronary risk estimation 2 according to guidelines on apparently healthy middle-aged individuals
Authors: Yari Ali , Ueda Peter , Lundman Pia , Alfredsson Joakim , Ravn-Fischer Annica , Söderberg Stefan , Yndigegn Troels , Hagström Emil , Jernberg Tomas 
Published: June 2024

Abstract

Aims
To estimate the proportion eligible for lipid-lowering therapy (LLT) when using the systemic coronary risk estimation 2 (SCORE2) on apparently healthy individuals.

Methods and results
Individuals aged 50–64 years were randomly invited to The Swedish Cardiopulmonary Bioimage Study (n = 30 154). Participants with previous atherosclerotic cardiovascular disease (CVD), diabetes mellitus, or chronic kidney disease were excluded. The 10-year risk of CVD was estimated using the SCORE2 equation and the multicell chart. Eligibility for LLT was estimated according to the 2021 European Society of Cardiology CVD prevention guidelines. Presence of coronary atherosclerosis was determined using coronary computed tomography angiography (CCTA). Among 26 570 apparently healthy individuals, 32% had high and 4% had very high 10-year CVD risk, according to the SCORE2 equation. Among high- and very-high-risk individuals, 99% had low-density lipoprotein cholesterol levels above guideline goals making 35% of the total population eligible for LLT. Of those eligible, undergoing imaging, 38% had no signs of coronary atherosclerosis according to CCTA. Using the SCORE2 chart, 52% of the population were eligible for LLT, of which 44% had no signs of coronary atherosclerosis. In those with high or very high risk, ongoing LLT was reported in 7% and another 11% received LLT within 6 months after study participation.

Conclusion
Nearly all apparently healthy individuals with high and very high CVD risk, or 35% of the total population, were eligible for LLT according to guidelines, and a large proportion had no signs of atherosclerosis. Compared with the SCORE2 equation, the SCORE2 chart resulted in more individuals being eligible for LLT.
Multiple variants of the type VII secretion system in Gram-positive bacteria
Authors: Garrett Stephen R , Higginson Andrew B , Palmer Tracy 
Published: June 2024

Abstract
Type VII secretion systems (T7SS) are found in bacteria across the Bacillota and Actinomycetota phyla and have been well described in Staphylococcus aureus, Bacillus subtilis, and pathogenic mycobacteria. The T7SS from Actinomycetota and Bacillota share two common components, a membrane-bound EccC/EssC ATPase and EsxA, a small helical hairpin protein of the WXG100 family. However, they also have additional phylum-specific components, and as a result they are termed the T7SSa (Actinomycetota) and T7SSb (Bacillota), respectively. Here, we identify additional organizations of the T7SS across these two phyla and describe eight additional T7SS subtypes, which we have named T7SSc–T7SSj. T7SSd is found exclusively in Actinomycetota including the Olselnella and Bifodobacterium genus, whereas the other seven are found only in Bacillota. All of the novel subtypes contain the canonical ATPase (TsxC) and the WXG100-family protein (TsxA). Most of them also contain a small ubiquitin-related protein, TsxB, related to the T7SSb EsaB/YukD component. Protein kinases, phosphatases, and forkhead-associated (FHA) proteins are often encoded in the novel T7SS gene clusters. Candidate substrates of these novel T7SS subtypes include LXG-domain and RHS proteins. Predicted substrates are frequently encoded alongside genes for additional small WXG100-related proteins that we speculate serve as cosecretion partners. Collectively our findings reveal unexpected diversity in the T7SS in Gram-positive bacteria.
Comprehensive analysis of CXXX sequence space reveals that Saccharomyces cerevisiae GGTase-I mainly relies on a2X substrate determinants
Authors: Sarkar Anushka , Hildebrandt Emily R , Patel Khushi V , Mai Emily T , Shah Sumil A , Kim June H , Schmidt Walter K 
Published: June 2024

Abstract
Many proteins undergo a post-translational lipid attachment, which increases their hydrophobicity, thus strengthening their membrane association properties or aiding in protein interactions. Geranylgeranyltransferase-I (GGTase-I) is an enzyme involved in a 3-step post-translational modification (PTM) pathway that attaches a 20-carbon lipid group called geranylgeranyl at the carboxy-terminal cysteine of proteins ending in a canonical CaaL motif (C—cysteine, a—aliphatic, L—often leucine, but can be phenylalanine, isoleucine, methionine, or valine). Genetic approaches involving 2 distinct reporters were employed in this study to assess Saccharomyces cerevisiae GGTase-I specificity, for which limited data exist, toward all 8,000 CXXX combinations. Orthogonal biochemical analyses and structure-based alignments were also performed to better understand the features required for optimal target interaction. These approaches indicate that yeast GGTase-I best modifies the Cxa[L/F/I/M/V] sequence that resembles but is not an exact match for the canonical CaaL motif. We also observed that minor modification of noncanonical sequences is possible. A consistent feature associated with well-modified sequences was the presence of a nonpolar a2 residue and a hydrophobic terminal residue, which are features recognized by mammalian GGTase-I. These results thus support that mammalian and yeast GGTase-I exhibit considerable shared specificity.
Differential Responses to Aging Among the Transcriptome and Proteome of Mesenchymal Progenitor Populations
Authors: Feehan Jack , Tripodi Nicholas , Kondrikov Dmitry , Wijeratne Tissa , Gimble Jeffrey , Hill William , Apostolopoulos Vasso , Duque Gustavo 
Published: June 2024

Abstract
The biological aging of stem cells (exhaustion) is proposed to contribute to the development of a variety of age-related conditions. Despite this, little is understood about the specific mechanisms which drive this process. In this study, we assess the transcriptomic and proteomic changes in 3 different populations of mesenchymal progenitor cells from older (50–70 years) and younger (20–40 years) individuals to uncover potential mechanisms driving stem cell exhaustion in mesenchymal tissues. To do this, we harvested primary bone marrow mesenchymal stem and progenitor cells (MPCs), circulating osteoprogenitors (COP), and adipose-derived stem cells (ADSCs) from younger and older donors, with an equal number of samples from men and women. These samples underwent RNA sequencing and label-free proteomic analysis, comparing the younger samples to the older ones. There was a distinct transcriptomic phenotype in the analysis of pooled older stem cells, suggestive of suppressed proliferation and differentiation; however, these changes were not reflected in the proteome of the cells. Analyzed independently, older MPCs had a distinct phenotype in both the transcriptome and proteome consistent with altered differentiation and proliferation with a proinflammatory immune shift in older adults. COP cells showed a transcriptomic shift to proinflammatory signaling but no consistent proteomic phenotype. Similarly, ADSCs displayed transcriptomic shifts in physiologies associated with cell migration, adherence, and immune activation but no proteomic change with age. These results show that there are underlying transcriptomic changes with stem cell aging that may contribute to a decline in tissue regeneration. However, the proteome of the cells was inconsistently regulated.
Life Chances, Subjective Perceptions, and Healthy Lifestyles in Older Adults: Longitudinal Evidence From China
Authors: Wang Bin , Lu Jiehua 
Published: June 2024

Abstract

Objectives
Previous studies and theories show that healthy lifestyles are affected by life chances and subjective perceptions. However, it remains unclear how older adults change between different lifestyle profiles as they age. We proposed the healthy lifestyle duality framework and tested it among older Chinese adults using a longitudinal design.

Methods
Data were obtained from 4 Chinese Longitudinal Healthy Longevity Surveys conducted between 2008 and 2018 (N = 31,445). Latent transition analysis and hierarchical multinomial growth curve models were performed to investigate healthy lifestyle profiles and their associations with life chances and subjective perceptions over time.

Results
Four distinct healthy lifestyle profiles were identified: healthy, risky, low-standard, and mixed groups, and their changes show path dependency. Across 10 years, the proportion of the healthy group ranged from 11.16% to 16.97%. Both life chances and subjective perceptions were longitudinally associated with healthy lifestyles, with age and cohort effects observed.

Discussion
Our findings support the healthy lifestyle duality framework and reveal that life chances and subjective perceptions influence lifestyle changes over time. Public health policies and health intervention programs should adapt to the specific needs of different age groups and generations.
Physiological Profiling of Agitation in Dementia: Insights From Wearable Sensor Data
Authors: Davidoff Hannah , Van Kraaij Alex , Van den Bulcke Laura , Lutin Erika , Vandenbulcke Mathieu , Van Helleputte Nick , De Vos Maarten , Van Hoof Chris , Van Den Bossche Maarten 
Published: June 2024

Abstract

Background and Objectives
The number of people with dementia is expected to triple to 152 million in 2050, with 90% having accompanying behavioral and psychological symptoms (BPSD). Agitation is among the most critical BPSD and can lead to decreased quality of life for people with dementia and their caregivers. This study aims to explore objective quantification of agitation in people with dementia by analyzing the relationships between physiological and movement data from wearables and observational measures of agitation.

Research Design and Methods
The data presented here is from 30 people with dementia, each included for 1 week, collected following our previously published multimodal data collection protocol. This observational protocol has a cross-sectional repeated measures design, encompassing data from both wearable and fixed sensors. Generalized linear mixed models were used to quantify the relationship between data from different wearable sensor modalities and agitation, as well as motor and verbal agitation specifically.

Results
Several features from wearable data are significantly associated with agitation, at least the p &lt; .05 level (absolute β: 0.224-0.753). Additionally, different features are informative depending on the agitation type or the patient the data were collected from. Adding context with key confounding variables (time of day, movement, and temperature) allows for a clearer interpretation of feature differences when a person with dementia is agitated.

Discussion and Implications
The features shown to be significantly different, across the study population, suggest possible autonomic nervous system activation when agitated. Differences when splitting the data by agitation type point toward a need for future detection models to tailor to the primary type of agitation expressed. Finally, patient-specific differences in features indicate a need for patient- or group-level model personalization. The findings reported in this study both reinforce and add to the fundamental understanding of and can be used to drive the objective quantification of agitation.
Hecatomb: an integrated software platform for viral metagenomics
Authors: Roach Michael J , Beecroft Sarah J , Mihindukulasuriya Kathie A , Wang Leran , Paredes Anne , Cárdenas Luis Alberto Chica , Henry-Cocks Kara , Lima Lais Farias Oliveira , Dinsdale Elizabeth A , Edwards Robert A , Handley Scott A 
Published: June 2024

Abstract

Background
Modern sequencing technologies offer extraordinary opportunities for virus discovery and virome analysis. Annotation of viral sequences from metagenomic data requires a complex series of steps to ensure accurate annotation of individual reads and assembled contigs. In addition, varying study designs will require project-specific statistical analyses.

Findings
Here we introduce Hecatomb, a bioinformatic platform coordinating commonly used tasks required for virome analysis. Hecatomb means “a great sacrifice.” In this setting, Hecatomb is “sacrificing” false-positive viral annotations using extensive quality control and tiered-database searches. Hecatomb processes metagenomic data obtained from both short- and long-read sequencing technologies, providing annotations to individual sequences and assembled contigs. Results are provided in commonly used data formats useful for downstream analysis. Here we demonstrate the functionality of Hecatomb through the reanalysis of a primate enteric and a novel coral reef virome.

Conclusion
Hecatomb provides an integrated platform to manage many commonly used steps for virome characterization, including rigorous quality control, host removal, and both read- and contig-based analysis. Each step is managed using the Snakemake workflow manager with dependency management using Conda. Hecatomb outputs several tables properly formatted for immediate use within popular data analysis and visualization tools, enabling effective data interpretation for a variety of study designs. Hecatomb is hosted on GitHub (github.com/shandley/hecatomb) and is available for installation from Bioconda and PyPI.
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection
Authors: Chu Justin , Rong Jiazhen , Feng Xiaowen , Li Heng 
Published: June 2024

Abstract

Background
Due to human error, sample swapping in large cohort studies with heterogeneous data types (e.g., mix of Oxford Nanopore Technologies, Pacific Bioscience, Illumina data, etc.) remains a common issue plaguing large-scale studies. At present, all sample swapping detection methods require costly and unnecessary (e.g., if data are only used for genome assembly) alignment, positional sorting, and indexing of the data in order to compare similarly. As studies include more samples and new sequencing data types, robust quality control tools will become increasingly important.

Findings
The similarity between samples can be determined using indexed k-mer sequence variants. To increase statistical power, we use coverage information on variant sites, calculating similarity using a likelihood ratio–based test. Per sample error rate, and coverage bias (i.e., missing sites) can also be estimated with this information, which can be used to determine if a spatially indexed principal component analysis (PCA)–based prescreening method can be used, which can greatly speed up analysis by preventing exhaustive all-to-all comparisons.

Conclusions
Because this tool processes raw data, is faster than alignment, and can be used on very low-coverage data, it can save an immense degree of computational resources in standard quality control (QC) pipelines. It is robust enough to be used on different sequencing data types, important in studies that leverage the strengths of different sequencing technologies. In addition to its primary use case of sample swap detection, this method also provides information useful in QC, such as error rate and coverage bias, as well as population-level PCA ancestry analysis visualization.
The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis
Authors: Bai Mingzhou , Jiang Sanjie , Chu Shanshan , Yu Yangyang , Shan Dai , Liu Chun , Zong Liang , Liu Qun , Liu Nana , Xu Weisong , Mei Zhanlong , Jian Jianbo , Zhang Chi , Zhao Shancen , Chiu Tsan-Yu , Simonsen Henrik Toft 
Published: June 2024

Abstract

Background
Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant constituents praeruptorin (A–E), are the active constituents in the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies have attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understanding of genetic traits and thus the development of better breeding strategies.

Results
A telomere-to-telomere (T2T) genome was assembled for P. praeruptorum by combining PacBio HiFi, ONT ultra-long, and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes with genome completeness &gt;98%. Comparative genomic analysis suggested that P. praeruptorum experienced 2 whole-genome duplication events. By the transcriptomic and metabolomic analysis of the coumarin metabolic pathway, we presented coumarins’ spatial and temporal distribution and the expression patterns of critical genes for its biosynthesis. Notably, the COSY and cytochrome P450 genes showed tandem duplications on several chromosomes, which may be responsible for the high accumulation of coumarins.

Conclusions
A T2T genome for P. praeruptorum was obtained, providing molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome is an essential resource for designing engineering strategies for improving the production of these valuable compounds.
Deep-Sea Benthic Response to the Deepwater Horizon Oil Spill: Harpacticoid Families as Sentinels of Impact Through Space and Time
Authors: Baldrighi Elisa , Bang Hyun Woo , Fast Justus , Baguley Jeffrey G 
Published: June 2024

Synopsis
The Deepwater Horizon (DWH) oil spill in the northern Gulf of Mexico, occurred in 2010 at 1525 meters depth, releasing approximately 507 M liters of oil. Research cruises in 2010 and 2011 were conducted to assess the initial and subsequent effects of the oil spill on deep-sea infauna. The spatial-temporal response of the deep-sea meiofaunal harpacticoid community composition to the DWH oil spill was investigated at 34 stations ranging from &lt; 1 km to nearly 200 km from the wellhead in 2010 and 2011. The pattern of reduced harpacticoid diversity in impacted zones compared to non-impacted zones in 2010 persisted in 2011. However, an increase in Hill’s diversity index (N1) and the family richness across the two years in some of the impacted stations could suggest a first signal of a tentative recovery and an improvement of environmental conditions. The multivariate analysis of harpacticoid family composition revealed the persistence of an impact in 2011 with moderately high values of turnover diversity in the harpacticoid communities through time (37%) and space (38–39%). The consistent presence in all years and stations of long-term tolerant families (e.g., Ameiridae), the sharp decrease of fast-responding opportunistic families (e.g., Tisbidae), and the increase of more sensitive ones (e.g., Ectinosomatidae, Canthocamptidae, Cletopsyllidae, and Laophontidae) lead to the preliminary conclusion that some initial signals of recovery are evident. However, as impacts were still evident in 2011, and because recruitment and succession rates can be extremely slow in the deep sea, full community recovery had not yet occurred one year after the DWH disaster. This study confirmed that harpacticoid copepod family diversity can offer an accurate assessment of oil-spill impacts on deep-sea benthic communities over space and time as well as a better understanding of the recovery mode of the system after an oil spill event.
Proof-of-principle of a lung sealant based on functionalized polyoxazolines: experiments in an ovine acute aerostasis model
Authors: Hermans Bob P , Ten Broek Richard P G , Li Wilson W L , Roozen Edwin A , Vos Shoko , Van Der Heijden Erik H F M , Van Goor Harry , Verhagen Ad F T M 
Published: June 2024

Abstract

OBJECTIVES
More effective lung sealants are needed to prevent prolonged pulmonary air leakage (AL). Polyoxazoline-impregnated gelatin patch (N-hydroxysuccinimide ester functionalized poly(2-oxazoline)s; NHS-POx) was promising for lung sealing ex vivo. The aim of this study is to confirm sealing effectiveness in an in vivo model of lung injury.

METHODS
An acute aerostasis model was used in healthy adult female sheep, involving bilateral thoracotomy, amputation lesions (bronchioles Ø &gt; 1.5 mm), sealant application, digital chest tube for monitoring AL, spontaneous ventilation, obduction and bursting pressure measurement. Two experiments were performed: (i) 3 sheep with 2 lesions per lung (N = 4 NHS-POx double-layer, N = 4 NHS-POx single-layer, N = 4 untreated) and (ii) 3 with 1 lesion per lung (N = 3 NHS-POx single-layer, N = 3 untreated). In pooled linear regression, AL was analysed per lung (N = 7 NHS-POx, N = 5 untreated) and bursting pressure per lesion (N = 11 NHS-POx, N = 7 untreated).

RESULTS
Baseline AL was similar between groups (mean 1.38–1.47 l/min, P = 0.90). NHS-POx achieved sealing in 1 attempt in 8/11 (72.7%) and in 10/11 (90.9%) in &gt;1 attempt. Application failures were only observed on triangular lesions requiring 3 folds around the lung. No influences of methodological variation between experiments was detected in linear regression (P &gt; 0.9). AL over initial 3 h of drainage was significantly reduced for NHS-POx [median: 7 ml/min, length of interquartile range: 333 ml/min] versus untreated lesions (367 ml/min, length of interquartile range: 680 ml/min, P = 0.036). Bursting pressure was higher for NHS-POx (mean: 33, SD: 16 cmH2O) versus untreated lesions (mean: 19, SD: 15 cmH2O, P = 0.081).

CONCLUSIONS
NHS-POx was effective for reducing early AL, and a trend was seen for improvement of bursting strength of the covered defect. Results were affected by application characteristics and lesion geometry.