bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing for sexually transmitted infection: who and where? A data linkage study using population and provider data in the Rotterdam area, the Netherlands
Authors: Twisk Denise E , Meima Abraham , Richardus Jan Hendrik , Götz Hannelore M 
Published: August 2023

Abstract

Background
In the Netherlands, insight into sexually transmitted infection (STI) testing and characteristics of those tested by general practitioners (GPs) and sexual health centres (SHC) is limited. This is partly due to lacking registration of socio-demographics at GPs. We aimed to fill this gap by linking different registers.

Methods
Individual STI testing data of GPs and SHC were linked to population register data (aged ≥15 years, Rotterdam area, 2015–2019). We reported population-specific STI positivity, proportion STI tested, and GP-SHC testing rate comparison using negative binomial generalised additive models. Factors associated with STI testing were determined by the provider using logistic regression analyses with generalised estimating equations.

Results
The proportion of STI tested was 2.8% for all residents and up to 9.8% for younger and defined migrant groups. STI positivity differed greatly by subgroup and provider (3.0–35.3%). Overall, GPs performed 3 times more STI tests than the SHC. The smallest difference in GP-SHC testing rate was for 20–24-year-olds (SHC key group). Younger age, non-western migratory background, lower household income, living more urbanised, and closer to a testing site were associated with STI testing by either GP or SHC. GPs and SHC partly test different groups: GPs test women and lower-educated more often, the SHC men and middle/higher educated.

Conclusions
This study highlights GPs’ important role in STI testing. The GPs’ role in the prevention, diagnosis, and treatment of STIs needs continued support and strengthening. Inter-professional exchange and collaboration between GP and SHC is warranted to reach vulnerable groups.
A multiplexed plant–animal SNP array for selective breeding and species conservation applications
Authors: Montanari Sara , Deng Cecilia , Koot Emily , Bassil Nahla V , Zurn Jason D , Morrison-Whittle Peter , Worthington Margaret L , Aryal Rishi , Ashrafi Hamid , Pradelles Julien , Wellenreuther Maren , Chagné David 
Published: August 2023

Abstract
Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant–animal single nucleotide polymorphism array, including both closely and distantly related species, was explored. The performance of the single nucleotide polymorphism array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the single nucleotide polymorphism array as a technique to further reduce costs was evaluated. Single nucleotide polymorphism performance was generally high, and species-specific single nucleotide polymorphisms proved suitable for diverse applications. The multi-species single nucleotide polymorphism array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.
An expanded GCaMP reporter toolkit for functional imaging in Caenorhabditis elegans
Authors: Ding Jimmy , Peng Lucinda , Moon Sihoon , Lee Hyun Jee , Patel Dhaval S , Lu Hang 
Published: August 2023

Abstract
In living organisms, changes in calcium flux are integral to many different cellular functions and are especially critical for the activity of neurons and myocytes. Genetically encoded calcium indicators (GECIs) have been popular tools for reporting changes in calcium levels in vivo. In particular, GCaMPs, derived from GFP, are the most widely used GECIs and have become an invaluable toolkit for neurophysiological studies. Recently, new variants of GCaMP, which offer a greater variety of temporal dynamics and improved brightness, have been developed. However, these variants are not readily available to the Caenorhabditis elegans research community. This work reports a set of GCaMP6 and jGCaMP7 reporters optimized for C. elegans studies. Our toolkit provides reporters with improved dynamic range, varied kinetics, and targeted subcellular localizations. Besides optimized routine uses, this set of reporters is also well suited for studies requiring fast imaging speeds and low magnification or low-cost platforms.
Leveraging osteoclast genetic regulatory data to identify genes with a role in osteoarthritis
Authors: Mullin Benjamin H , Zhu Kun , Brown Suzanne J , Mullin Shelby , Dudbridge Frank , Pavlos Nathan J , Richards J Brent , Grundberg Elin , Bell Jordana T , Zeggini Eleftheria , Walsh John P , Xu Jiake , Wilson Scott G 
Published: August 2023

Abstract
There has been a growing interest in the role of the subchondral bone and its resident osteoclasts in the progression of osteoarthritis (OA). A recent genome-wide association study (GWAS) identified 100 independent association signals for OA traits. Most of these signals are led by noncoding variants, suggesting that genetic regulatory effects may drive many of the associations. We have generated a unique human osteoclast-like cell-specific expression quantitative trait locus (eQTL) resource for studying the genetics of bone disease. Considering the potential role of osteoclasts in the pathogenesis of OA, we performed an integrative analysis of this dataset with the recently published OA GWAS results. Summary data-based Mendelian randomization (SMR) and colocalization analyses identified 38 genes with a potential role in OA, including some that have been implicated in Mendelian diseases with joint/skeletal abnormalities, such as BICRA, EIF6, CHST3, and FBN2. Several OA GWAS signals demonstrated colocalization with more than one eQTL peak, including at 19q13.32 (hip OA with BCAM, PRKD2, and BICRA eQTL). We also identified a number of eQTL signals colocalizing with more than one OA trait, including FAM53A, GCAT, HMGN1, MGAT4A, RRP7BP, and TRIOBP. An SMR analysis identified 3 loci with evidence of pleiotropic effects on OA-risk and gene expression: LINC01481, CPNE1, and EIF6. Both CPNE1 and EIF6 are located at 20q11.22, a locus harboring 2 other strong OA candidate genes, GDF5 and UQCC1, suggesting the presence of an OA-risk gene cluster. In summary, we have used our osteoclast-specific eQTL dataset to identify genes potentially involved with the pathogenesis of OA.
Association of Kidney Function With Dementia and Structural Brain Differences: A Large Population-Based Cohort Study
Authors: Wang Shuqi , Wang Jiao , Guo Jie , Dove Abigail , Xu Hong , Qi Xiuying , Xu Weili 
Published: August 2023

Abstract

Background
The association between kidney function and dementia risk and the mechanisms underlying this relationship remain unclear.

Methods
Within the UK Biobank, 191 970 dementia-free participants aged ≥60 (mean age: 64.1 ± 2.9 years) were followed for 16 years to detect incident dementia. Serum creatinine and Cystatin C were measured at baseline to calculate estimated glomerular filtration rate (eGFR, mL/min/1.73 m2). Kidney function was categorized as normal (eGFR ≥ 90), mildly impaired (60 ≤ eGFR &lt; 90), or moderately to severely impaired (eGFR &lt; 60). Dementia was assessed based on self-reported medical history and medical records. During the follow-up, a subsample of 12 637 participants underwent brain MRI scans. Volumes of total brain, gray matter, white matter, hippocampus, and white matter hyperintensities were assessed.

Results
Over the follow-up, 5 327 (2.8%) participants developed dementia. Compared to normal kidney function, there was an increased risk of dementia with moderate to severely impaired kidney function (hazard ratio = 1.53, 95% confidence interval [CI]: 1.32–1.76) but not mildly impaired kidney function. In Laplace regression, dementia onset among people with moderate to severely impaired kidney function occurred 1.53 (95% CI: 0.98–2.08) years earlier than those with normal kidney function. Moderate to severely impaired kidney function was related to significantly lower gray matter volume (β = −0.11, 95% CI: −0.19 to −0.03), but not to other brain magnetic resonance imaging measures.

Conclusions
Impaired kidney function is associated with about 50% increased risk of dementia and anticipates dementia onset by more than 1.5 years. Brain neurodegeneration may underlie the kidney function–dementia association.
Validation of the Pittsburgh Performance Fatigability Index in the Study of Muscle, Mobility and Aging
Authors: Qiao Yujia (Susanna) , Harezlak Jaroslaw , Cawthon Peggy M , Cummings Steven R , Forman Daniel E , Goodpaster Bret H , Hawkins Marquis , Moored Kyle D , Nicklas Barbara J , Toledo Frederico G S , Toto Pamela E , Santanasto Adam J , Strotmeyer Elsa S , Newman Anne B , Glynn Nancy W 
Published: August 2023

Abstract

Background
The Pittsburgh Performance Fatigability Index (PPFI) quantifies the percent decline in cadence using accelerometry during standardized walking tasks. Although PPFI has shown strong correlations with physical performance, the developmental sample was relatively homogenous and small, necessitating further validation.

Methods
Participants from the Study of Muscle, Mobility and Aging (N = 805, age = 76.4 ± 5.0 years, 58% women, 85% White) wore an ActiGraph GT9X on the nondominant wrist during usual-paced 400 m walk. Tri-axial accelerations were analyzed to compute PPFI (higher score = greater fatigability). To evaluate construct and discriminant validity, Spearman correlations (rs) between PPFI and gait speed, Short Physical Performance Battery (SPPB), chair stand speed, leg peak power, VO2peak, perceived fatigability, and mood were examined. Sex-specific PPFI cut-points that optimally discriminated gait speed using classification and regression tree were then generated. Their discriminate power in relation to aforementioned physical performance were further evaluated.

Results
Median PPFI score was 1.4% (25th–75th percentile range: 0%–21.7%), higher among women than men (p &lt; .001). PPFI score was moderate-to-strongly correlated with gait speed (rs = −0.75), SPPB score (rs = −0.38), chair stand speed (rs = −0.36), leg peak power (rs = −0.34) and VO2peak (rs = −0.40), and less strongly with perceived fatigability (rs = 0.28–0.29), all p &lt; .001. PPFI score was not correlated with mood (|rs| &lt; 0.08). Sex-specific PPFI cut-points (no performance fatigability: PPFI = 0%; mild performance fatigability: 0% &lt; PPFI &lt; 3.5% [women], 0% &lt; PPFI &lt; 5.4% [men]; moderate-to-severe performance fatigability: PPFI ≥ 3.5% [women], PPFI ≥ 5.4% [men]) discriminated physical performance (all p &lt; .001), adjusted for demographics and smoking status.

Conclusion
Our work underscores the utility of PPFI as a valid measure to quantify performance fatigability in future longitudinal epidemiologic studies and clinical/pharmaceutical trials.
Scanned information exposure and support for tobacco regulations among US youth and young adult tobacco product users and non-users
Authors: Kim Kwanho 
Published: August 2023

AbstractThe influences of information exposure on youth and young adults’ (YYA) support for smoking/vaping regulations have been understudied. This study examines (i) the relationships between routine exposure to (i.e. scanning) anti-smoking/pro-vaping information and YYA support for anti-smoking/vaping regulations and (ii) whether these relationships differ across YYA users and non-users of tobacco products. We analyzed the data from a nationally representative two-wave rolling cross-sectional survey of YYA in the United States, collected from 2014 to 2017 (baseline n = 10 642; follow-up n = 4001). Less than 5% of the participants ever scanned pro-smoking and anti-vaping information. Scanning anti-smoking information had significant positive relationships with support for all anti-smoking policies cross-sectionally, and this pattern was longitudinally significant in two anti-smoking policy contexts. Scanning pro-vaping information had significant negative associations with support for anti-vaping policies cross-sectionally, but not longitudinally. The lagged positive relationships between scanning anti-smoking information and support for anti-smoking regulations were stronger among YYA smokers than among YYA non-smokers, whereas evidence from adult data suggested the opposite pattern. The findings suggest that scanning information can affect YYA support for tobacco regulations. Future efforts are required to investigate mechanisms underlying the influences of scanned information on YYA support for tobacco regulations.
The transcription factor CsS40 negatively regulates TCS1 expression and caffeine biosynthesis in connection to leaf senescence in Camellia sinensis
Authors: Yao Xinzhuan , Chen Hufang , Ai Antao , Wang Fen , Lian Shanshan , Tang Hu , Jiang Yihe , Jiao Yujie , He Yumei , Li Tong , Lu Litang 
Published: August 2023

Abstract
Caffeine is considered as one of the most important bioactive components in the popular plant beverages tea, cacao, and coffee, but as a wide-spread plant secondary metabolite its biosynthetic regulation at transcription level remains largely unclear. Here, we report a novel transcription factor Camellia sinensis Senescnece 40 (CsS40) as a caffeine biosynthesis regulator, which was discovered during screening a yeast expression library constructed from tea leaf cDNAs for activation of tea caffeine synthase (TCS1) promoter. Besides multiple hits of the non-self-activation CsS40 clones that bound to and activated TCS1 promoter in yeast-one-hybrid assays, a split-luciferase complementation assay demonstrated that CsS40 acts as a transcription factor to activate the CsTCS1 gene and EMSA assay also demonstrated that CsS40 bound to the TCS1 gene promoter. Consistently, immunofluorescence data indicated that CsS40-GFP fusion was localized in the nuclei of tobacco epidermal cells. The expression pattern of CsS40 in ‘Fuding Dabai’ developing leaves was opposite to that of TCS1; and knockdown and overexpression of CsS40 in tea leaf calli significantly increased and decreased TCS1 expression levels, respectively. The expression levels of CsS40 were also negatively correlated to caffeine accumulation in developing leaves and transgenic calli of ‘Fuding Dabai’. Furthermore, overexpression of CsS40 reduced the accumulation of xanthine and hypoxanthine in tobacco plants, meanwhile, increased their susceptibility to aging. CsS40 expression in tea leaves was also induced by senescence-promoting hormones and environmental factors. Taken together, we showed that a novel senescence-related factor CsS40 negatively regulates TCS1 and represses caffeine accumulation in tea cultivar ‘Fuding Dabai’. The study provides new insights into caffeine biosynthesis regulation by a plant-specific senescence regulator in tea plants in connection to leaf senescence and hormone signaling.
Spatio-temporal species distribution models reveal dynamic indicators for ecosystem-based fisheries management
Authors: Badger J J , Large S I , Thorson J T 
Published: August 2023

Abstract
Many economic sectors rely on marine ecosystem services, and holistic management is necessary to evaluate trade-offs between sectors and facilitate sustainable use. Integrated ecosystem assessments (IEA) integrate system components so that managers can evaluate pathways to achieve desired goals. Indicators are a central element of IEAs and capture the status and trend of individual components and should be sensitive to changes in the system; however, most indicators are aggregated over space and time as annual values, potentially leading to incomplete or inaccurate inferences about system change. Here, we demonstrate the utility of spatially and temporally explicit ecological indicators by fitting multivariate spatio-temporal models to survey data from the northeast US Shelf Ecosystem, encompassing three distinct ecoregions: Georges Bank, Gulf of Maine, and mid-Atlantic Bight. We evaluate three case studies to explore how these models can help assess ecosystem performance relative to management objectives, such as to: (1) identify dominant modes of variation in zooplankton communities; (2) quantify components of system stability; and (3) assess the density-dependent condition of groundfish over time. Collectively, these three examples demonstrate multiple interesting processes, but particularly highlight the rapid zooplankton changes and associated changes in benthivore condition and stability in the Gulf of Maine. Attributing changes in ecosystem indicators to localized processes is difficult using conventional “regionally aggregated” indicators, so this example highlights the benefits of spatio-temporal methods for integrated ecosystem analysis in this and other regions.
A Dual-Process Model of Xunzi’s Philosophy of Music
Authors: Kim Hannah H 
Published: August 2023

Abstract
Music, alongside ritual, plays an important role in Confucian moral education. Among all the Confucians, Xunzi gives music the most radical ability to transform people, and this is striking given his pessimistic view of human nature. Though he set the standard for Chinese aesthetics for millennia, there is no systematic account that brings together Xunzi’s various commitments: that only music from virtuous previous dynasties are morally conducive, that music can bring about lasting character change, that even those uninterested in moral cultivation can benefit from music, and that the junzi (“gentleman”) and the xiaoren (“petty man”) derive joy in different ways while listening to music. In this article, I explain why currently existing accounts cannot capture all the commitments, and I turn to analytic aesthetics to provide a new Dual-Process Model of Xunzi’s philosophy of music. Jenefer Robinson’s discussions of “the Jazzercise effect” and emotional misattribution will be key in the new account.
Serratia endocarditis: antimicrobial management strategies and clinical outcomes
Authors: Shah Sunish , McCrary Madeline , Schranz Asher J , Clarke Lloyd , Davis Matthew W , Marx Ashley , Slain Douglas , Stoner Bobbi Jo , Topal Jeffrey , Shields Ryan K 
Published: August 2023

Abstract

Objectives
The incidence of Serratia endocarditis is increasing, yet optimal treatment has not been defined. Our objective was to investigate the outcomes of patients with Serratia endocarditis by treatment strategy.

Methods
We reviewed adult patients with definitive Serratia endocarditis at two independent health systems between July 2001 and April 2023. Combination therapy was defined as receipt of ≥2 in vitro active agents for ≥72 h.

Results
Seventy-five patients were included; 64% (48/75) were male and 85% (64/75) were people who inject drugs. Compared with monotherapy, receipt of combination therapy was associated with lower rates of microbiological failure (0% versus 15%, P = 0.026) and 90 day all-cause mortality (11% versus 31%, P = 0.049). Antimicrobial discontinuation due to an adverse event was more common among patients receiving combination therapy compared with monotherapy (36% versus 8%, P = 0.058).

Conclusions
In the largest series of Serratia endocarditis to date, combination antibiotic treatment was associated with improved outcomes. However, larger, prospective studies are warranted.
A model of evaluative opinion to encourage greater transparency and justification of interpretation in postmortem forensic toxicology
Authors: Maskell Peter D , Elliott Simon , Desharnais Brigitte , Findell Martin , Jackson Graham 
Published: August 2023

Abstract
Over the past decades, the calls to improve the robustness of interpretation in forensic science have increased in magnitude. Forensic toxicology has seen limited progress in this regard. In this work, we propose a transparent interpretive pathway for use in postmortem forensic toxicology cases. This process allows the selection of the interpretive methodology based on the amount of previous information that is available for the drug(s) in question. One approach is an assessment of various pharmacological and circumstantial considerations resulting in a toxicological significance score (TSS), which is particularly useful in situations where limited information about a drug is available. When there is a robust amount of case data available, then a probabilistic approach, through the evaluation of likelihood ratios by the forensic toxicologist and of prior probabilities by the fact finder, is utilized. This methodology provides a transparent means of making an interpretive decision on the role of a drug in the cause of death. This will allow the field of forensic toxicology to take a step forward in using best practice in evaluative reporting, a tool already used by many other forensic science disciplines.
Parameter interpretations of wave dispersion and attenuation in rock physics based on deep neural network
Authors: Wang Bochen , Liu Jiawei , Guo Zhenwei 
Published: August 2023

Abstract
Acoustic wave features, including velocity dispersion and attenuation, induced by fluid flow in porous media have attracted significant attention in reservoir exploration. To enhance the quantitative understanding of these features, various wave propagation mechanisms have been developed. It has been discovered that wave dispersion and attenuation are associated with multiple reservoir parameters, each with different sensitivity. It is difficult to distinguish the effects of individual physical parameters on acoustic features by traditional wave equations. Considering the ability of deep neural networks (DNNs) in establishing the relationships between two datasets, a fully connected DNN has been employed as a surrogate rock physics model, and the Shapley additive explanations model (SHAP) based on this DNN has been introduced to evaluate the contributions of different parameters. In this study, the classic White model is used to generate datasets for training the DNN. Datasets include seven parameters (bulk modulus, shear modulus, and density of the solid matrix, frequency, porosity, fluid saturation, and permeability), along with velocity dispersion and attenuation. By embedding SHAP into the trained DNN, the presented ShaRock algorithm allows for a clear quantification of the contributions of various reservoir parameters to acoustic features. Furthermore, we analyze the underlying interactions between two parameters by using their combined quantified contributions to the features. The application of this proposed algorithm, which is based on wave propagation mechanisms, demonstrates its potential in providing valuable insights for parameter inversions in hydrocarbon exploration.