bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the Presence of Recent Adaptation in the Human Genome With Mixture Density Regression
Authors: Salazar-Tortosa Diego F , Huang Yi-Fei , Enard David 
Published: September 2023

Abstract
How much genome differences between species reflect neutral or adaptive evolution is a central question in evolutionary genomics. In humans and other mammals, the presence of adaptive versus neutral genomic evolution has proven particularly difficult to quantify. The difficulty notably stems from the highly heterogeneous organization of mammalian genomes at multiple levels (functional sequence density, recombination, etc.) which complicates the interpretation and distinction of adaptive versus neutral evolution signals. In this study, we introduce mixture density regressions (MDRs) for the study of the determinants of recent adaptation in the human genome. MDRs provide a flexible regression model based on multiple Gaussian distributions. We use MDRs to model the association between recent selection signals and multiple genomic factors likely to affect the occurrence/detection of positive selection, if the latter was present in the first place to generate these associations. We find that an MDR model with two Gaussian distributions provides an excellent fit to the genome-wide distribution of a common sweep summary statistic (integrated haplotype score), with one of the two distributions likely enriched in positive selection. We further find several factors associated with signals of recent adaptation, including the recombination rate, the density of regulatory elements in immune cells, GC content, gene expression in immune cells, the density of mammal-wide conserved elements, and the distance to the nearest virus-interacting gene. These results support the presence of strong positive selection in recent human evolution and highlight MDRs as a powerful tool to make sense of signals of recent genomic adaptation.
Fluoxetine Promotes Longevity via Reactive Oxygen Species in Caenorhabditis elegans
Authors: Zhou Can , Zhou Yiming , Liang Yu , Chen Lijuan , Liu Li , Wei Fang , Li Guolin 
Published: September 2023

Abstract
Although several antidepressants have been identified as potential geroprotectors, the effect and mechanism of fluoxetine, a representative selective serotonin reuptake inhibitor, on longevity have not been fully elucidated. Here, we found that fluoxetine promoted longevity in Caenorhabditis elegans with a concomitant extension of a healthy life span as indicated by increasing mobility, reducing fertility and lipofuscin accumulation, and enhanced resistance to different abiotic stresses. Fluoxetine increased the level of reactive oxygen species (ROS), and antioxidant N-acetylcysteine abolished ROS elevation and the pro-longevity effect of fluoxetine. Additionally, fluoxetine extended life span through the daf-2-sod-3 pathway in daf-16-dependent and -independent manners, and fluoxetine-induced life-span extension was abolished in C. elegans sod-3, daf-2, and daf-16 mutants. In conclusion, these findings suggest that fluoxetine can promote health and longevity in C. elegans via the interaction of ROS and insulin signaling.
Establishment of Baseline Urinary Antimicrobial Peptide Levels by Age: A Prospective Observational Study
Authors: Caterino Jeffrey M , Stephens Julie A , Wexler Randell , Camargo Carlos A , Hunold Katherine M , Wei Lai , Hains David , Southerland Lauren T , Bischof Jason J , Schwaderer Andrew 
Published: September 2023

Abstract

Background
Antimicrobial peptides (AMPs) are key effectors of urinary tract innate immunity. Identifying differences in urinary AMP levels between younger and older adults is important in understanding older adults’ susceptibility and response to urinary tract infections (UTI) and AMP use as diagnostic biomarkers. We hypothesized that uninfected older adults have higher urinary human neutrophil peptides 1-3 (HNP 1-3), human alpha-defensin-5 (HD-5), and human beta-defensin-2 (hBD-2), but lower urinary cathelicidin (LL-37) than younger adults.

Methods
We conducted a cross-sectional study of patients aged ≥18 years completing a family medicine clinic nonacute visit. Enzyme-linked immunosorbent assays were performed for AMPs. We identified associations between age and AMPs using unadjusted and multivariable linear regression models.

Results
Of the 308 subjects, 144 (46.8%) were ≥65 years of age. Comparing age ≥65 versus &lt; 65 years, there were no significant differences in HNP 1-3 (p = .371), HD5 (p = .834), or LL-37 (p = .348) levels. Values for hBD-2 were lower in older adults versus younger (p &lt; .001). In multivariable analyses, older males and females had significantly lower hBD-2 levels (p &lt; .001 and p = .004). Models also showed urine leukocyte esterase was associated with increased levels of HNP 1-3 and HD5; hematuria with increased hBD-2; and urine cultures with contamination with increased HNP 1-3 and hBD-2.

Conclusions
Baseline urinary HNP 1-3, HD-5, and LL-37 did not vary with age. Older adults had lower baseline hBD-2. This finding has implications for the potential use of urinary AMPs as diagnostic markers and will facilitate further investigation into the role of innate immunity in UTI susceptibility in older adults.
The Effectiveness of Home-Based Exergames Training on Cognition and Balance in Older Adults: A Comparative Quasi-Randomized Study of Two Exergame Interventions
Authors: Begde Ahmet , Alqurafi Alaa , Pain Matthew T G , Blenkinsop Glen , Wilcockson Thomas D W , Hogervorst Eef 
Published: September 2023

Abstract

Background and Objectives
The effectiveness of exergames on fall risk and related physical and cognitive function in older adults is still unclear, with conflicting findings. The discrepancy in these results could be due to the different components and task-specific demands of individual exergame interventions. This open-label quasi-randomized study aimed to compare the efficacy of 2 different home-based dual-task exergame treatments on cognition, mobility, and balance in older people.

Research Design and Methods
Fifty older adults (65–85 years of age) were allocated to one of two 8-week exergame interventions: Cognitive-Intensive Exergame Training (CIT) or Physical-Intensive Exergame Training (PIT). Cognitive functions, balance, and mobility were assessed at baseline and after 8 weeks. Group × time interaction was measured by repeated-measure ANOVA, and both intention-to-treat (ITT) and per-protocol (PP) analyses were performed to assess the effectiveness of exergame interventions.

Results
ITT analyses showed that improvement in visual processing speed and visuospatial working memory was greater in the CIT group, with a medium effect size (p = .04; η2 = 0.09 and p = .01; η2 = 0.12). The improvement in verbal memory and attention was significant within both groups (p &lt; .05), but this improvement was not different between the groups (p &gt; .05). A significant improvement in balance was also observed in the PIT group, with a medium effect size (p = .04; η2 = 0.09). Although mobility improved significantly in both groups (p &lt; .01), there was no significant difference between groups (p = .08). These results were largely supported by the PP analysis.

Discussion and Implications
Dual-task exergame training can improve mobility and cognition in older adults. However, the different cognitive and physical demands of these interventions may have varying impacts on fall risk and related physical or cognitive functions. Therefore, a training program that includes both cognitive and physical domains with appropriate intensity is essential for the development of tailored exergame interventions to reduce fall risk in older adults.
A daisy chain method to quickly determine lithosphere, asthenosphere and mantle properties from the loading history of an area
Authors: Cathles Lawrence M , Fjeldskaar Willy , Amantov Aleksey 
Published: September 2023

SUMMARY
The lithosphere and asthenosphere are fundamental to plate tectonics and many other earth processes. Vertical motions can be measured quickly and accurately by the satellite Global Positioning System, GPS and other methods. This paper describes a new analytic method for inferring the elastic and viscous properties of the lithosphere and upper mantle from the uplift rate and history of an area that has been subjected to past surface load changes. The viscous response time of the centre of loading is determined from the dimensions of the load, a loading history comprised of linear segments, an estimate of the flexural rigidity of the lithosphere and a single constraint such as the current central uplift rate. The response time is then interpreted in terms of the elastic properties of the lithosphere, and the elastic and viscous depth profiles of the underlying mantle. The method is described mathematically and then illustrated through analysis of the isostatic adjustment observed in nine areas affected by Little Ice Age glaciation. The method replicates published conclusions, extracts insights from an extensive literature, provides new ways to separate the impacts of the lithosphere and asthenosphere on uplift rates and emergence, and indicates the widespread geographic distribution of a thin asthenosphere.
Spherical-wave elastic inversion in transversely isotropic media with a vertical symmetry axis
Authors: Cheng Guangsen , He Chuanlin , Liang Zhanyuan , Yin Xingyao , Zhang Xiaoyu , Zheng Yi 
Published: September 2023

SUMMARY
Although subsurface media are usually assumed to be isotropic, anisotropy is ubiquitous in crustal rocks and leads to the variation of seismic response with direction. Transversely isotropic media with a vertical symmetry axis (VTI media) are widely found in the real world, such as in textured shale reservoirs. Plane-wave reflection coefficients (PRCs) in VTI media have been widely exploited in amplitude variation with offset (AVO) inversion to estimate the elastic and anisotropy parameters of subsurface media. However, the PRCs in VTI media meet some fundamental problems, especially at near-critical or post-critical incidence angles where the spherical-wave effect is significant. To consider the wave front curvature, a complex spherical-wave reflection coefficient (SRC) in VTI media is derived. To better understand the spherical-wave seismic response in VTI media, we investigate the dependence of the complex SRC on frequency, reflector depth and Thomsen anisotropy parameters ($\varepsilon $ and $\delta $). Based on a complex convolution model, a spherical-wave AVO inversion approach in VTI media is proposed to estimate the vertical (symmetry-axis) compressional and shear wave velocities (P and S waves), density and Thomsen anisotropy parameters from observed seismic data with different incidence angle and frequency components. Synthetic data with Gaussian random noise are used to verify the robustness of the spherical-wave AVO inversion approach in VTI media. Field data examples show that the proposed approach can produce reasonable inversion results that match well with the well-logging data.
Earnings, job satisfaction, and turnover of nurse practitioners across employment settings
Authors: Hnath Joseph G P , Rambur Betty , Grabowski David C 
Published: September 2023

Abstract
Nurse practitioners (NPs) are an important part of the health care workforce. However, little information is available on NP earnings, job satisfaction, or turnover. National survey data from 2018 offer a pre–COVID-19 baseline for ongoing NP workforce monitoring. We found evidence that NPs earned approximately $92 500 annually, ranging from $82 800 in long-term care to $95 600 in hospital settings. Wages increased with tenure in the workforce and varied considerably by geography. Approximately 1 in 5 NPs switched jobs annually, with some net in-flow to ambulatory settings. Both NPs who left their position or considered leaving reported better pay and benefits, burnout, management role, stressful work environment, career advancement, and inadequate staffing as the primary explanations. These findings were augmented by analysis of 2012–2022 Bureau of Labor Statistics data that illustrated substantial growth in the NP workforce. Improving NP job satisfaction has the direct benefit of supporting a critical and growing segment of the health workforce; it has the additional benefit of reducing job turnover and the associated costs, potentially increasing earnings for NPs. Policies that improve working conditions for NPs in different employment settings will not just increase immediate job satisfaction but also ideally strengthen the longer-term labor market to improve patient outcomes.
A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis inChaenomeles speciosa
Authors: He Shaofang , Weng Duanyang , Zhang Yipeng , Kong Qiusheng , Wang Keyue , Jing Naliang , Li Fengfeng , Ge Yuebin , Xiong Hui , Wu Lei , Xie De-Yu , Feng Shengqiu , Yu Xiaqing , Wang Xuekui , Shu Shaohua , Mei Zhinan 
Published: September 2023

AbstractChaenomeles speciosa (2n = 34), a medicinal and edible plant in the Rosaceae, is commonly used in traditional Chinese medicine. To date, the lack of genomic sequence and genetic studies has impeded efforts to improve its medicinal value. Herein, we report the use of an integrative approach involving PacBio HiFi (third-generation) sequencing and Hi-C scaffolding to assemble a high-quality telomere-to-telomere genome of C. speciosa. The genome comprised 650.4 Mb with a contig N50 of 35.5 Mb. Of these, 632.3 Mb were anchored to 17 pseudo-chromosomes, in which 12, 4, and 1 pseudo-chromosomes were represented by a single contig, two contigs, and four contigs, respectively. Eleven pseudo-chromosomes had telomere repeats at both ends, and four had telomere repeats at a single end. Repetitive sequences accounted for 49.5% of the genome, while a total of 45 515 protein-coding genes have been annotated. The genome size of C. speciosa was relatively similar to that of Malus domestica. Expanded or contracted gene families were identified and investigated for their association with different plant metabolisms or biological processes. In particular, functional annotation characterized gene families that were associated with the biosynthetic pathway of oleanolic and ursolic acids, two abundant pentacyclic triterpenoids in the fruits of C. speciosa. Taken together, this telomere-to-telomere and chromosome-level genome of C. speciosa not only provides a valuable resource to enhance understanding of the biosynthesis of medicinal compounds in tissues, but also promotes understanding of the evolution of the Rosaceae.
The boundary between digital goods and E-services in cross-border E-commerce and implication for non-discrimination under the WTO system
Authors: Tanodomdej Papawadee 
Published: September 2023

Abstract
One of the biggest challenges of implementing value-added tax (VAT) collection on cross-border digital goods and services is the compliance with World Trade Organization (WTO) obligations. The lack of a clear distinction between goods and services in the WTO agreements and divergent classifications adopted by states have led to fragmented and inconsistent VAT collection, potentially creating trade barriers in international e-commerce. This article analyses various approaches to classify goods and services including technological neutrality and tradability. It also uses the modernization of Thailand’s VAT system as a case study to demonstrate the complexity of categorizing digital goods and services for VAT enforcement in international e-commerce. It finds that technological neutrality and tradability are key criteria to separate digital goods from e-services for the proper implementation of WTO obligations. The article concludes with remarks on the correlation between categorizing digital goods and services in VAT collection and protectionism in cross-border e-commerce.
Thin Polytopes: Lattice Polytopes With Vanishing Local h*-Polynomial
Authors: Borger Christopher , Kretschmer Andreas , Nill Benjamin 
Published: September 2023

Abstract
In this paper, we study the novel notion of thin polytopes: lattice polytopes whose local $h^{*}$-polynomials vanish. The local $h^{*}$-polynomial is an important invariant in modern Ehrhart theory. Its definition goes back to Stanley with fundamental results achieved by Karu, Borisov, and Mavlyutov; Schepers; and Katz and Stapledon. The study of thin simplices was originally proposed by Gelfand, Kapranov, and Zelevinsky, where in this case the local $h^{*}$-polynomial simply equals its so-called box polynomial. Our main results are the complete classification of thin polytopes up to dimension 3 and the characterization of thinness for Gorenstein polytopes. The paper also includes an introduction to the local $h^{*}$-polynomial with a survey of previous results.
Phloem anatomy restricts root system architecture development: theoretical clues from in silico experiments
Authors: Zhou Xiao-Ran , Schnepf Andrea , Vanderborght Jan , Leitner Daniel , Vereecken Harry , Lobet Guillaume 
Published: September 2023

Abstract
Plant growth and development involve the integration of numerous processes, influenced by both endogenous and exogenous factors. At any given time during a plant’s life cycle, the plant architecture is a readout of this continuous integration. However, untangling the individual factors and processes involved in the plant development and quantifying their influence on the plant developmental process is experimentally challenging. Here we used a combination of computational plant models (CPlantBox and PiafMunch) to help understand experimental findings about how local phloem anatomical features influence the root system architecture. Our hypothesis was that strong local phloem resistance would restrict local carbon flow and locally modify root growth patterns. To test this hypothesis, we simulated the mutual interplay between the root system architecture development and the carbohydrate distribution to provide a plausible mechanistic explanation for several experimental results. Our in silico experiments highlighted the strong influence of local phloem hydraulics on the root growth rates, growth duration and final length. The model result showed that a higher phloem resistivity leads to shorter roots due to the reduced flow of carbon within the root system. This effect was due to local properties of individual roots, and not linked to any of the pleiotropic effects at the root system level. Our results open a door to a better representation of growth processes in a plant computational model.
Artificial neural network approaches to identify maternal and infant risk and asset factors using Peridata.Net: a WI-MIOS study
Authors: Holt Jeana M , Talsma AkkeNeel , Johnson Teresa S , Ehlinger Timothy 
Published: September 2023

Abstract

Objective
To analyze PeriData.Net, a clinical registry with linked maternal–infant hospital data of Milwaukee County residents, to demonstrate a predictive analytic approach to perinatal infant risk assessment.

Materials and Methods
Using unsupervised learning, we identified infant birth clusters with similar multivariate health indicator patterns, measured using perinatal variables from 2008 to 2019 from n = 43 969 clinical registry records in Milwaukee County, WI, followed by supervised learning risk-propagation modeling to identify key maternal factors. To understand the relationship between socioeconomic status (SES) and birth outcome cluster assignment, we recoded zip codes in Peridata.Net according to SES level.

Results
Three self-organizing map clusters describe infant birth outcome patterns that are similar in the multivariate space. Birth outcome clusters showed higher hazard birth outcome patterns in cluster 3 than clusters 1 and 2. Cluster 3 was associated with lower Apgar scores at 1 and 5 min after birth, shorter infant length, and premature birth. Prediction profiles of birth clusters indicate the most sensitivity to pregnancy weight loss and prenatal visits. Majority of infants assigned to cluster 3 were in the 2 lowest SES levels.

Discussion
Using an extensive perinatal clinical registry, we found that the strongest predictive performance, when considering cluster membership using supervised learning, was achieved by incorporating social and behavioral risk factors. There were inequalities in infant birth outcomes based on SES.

Conclusion
Identifying infant risk hazard profiles can contribute to knowledge discovery and guide future research directions. Additionally, presenting the results to community members can build consensus for community-identified health and risk indicator prioritization for intervention development.
Pork quality traits and associated muscle metabolic changes in pigs under chronic prenatal and postnatal heat stress
Authors: Lebret Bénédicte , Serviento Aira Maye , Renaudeau David 
Published: September 2023

Abstract
Chronic heat stress (HS) is a major concern affecting pig growth performance and metabolism, with potential consequences on carcass and meat quality traits. The objective of this study was to assess the influence of prenatal (PE) and growing (GE) thermal environments, and their combination, on muscle metabolism, carcass characteristics, and pork quality. From 6 to 109 d of gestation, 12 sows (1 per block) were kept under thermoneutral (TN) conditions (cyclic 18 to 24 °C; PTN) and 12 sows under chronic HS (cyclic 28 to 34 °C; PHS). Two female offspring per sow were selected based on body weight at weaning, for a total of 48 female pigs (12 blocks of 2 sisters from each PE), and one sister was placed in each GE. Gilts were housed from 82 to 140 d of age under cyclic GTN (18 to 24 °C; n = 24) or GHS (28 to 34 °C; n = 24) environments. Data were analyzed using a mixed model including PE, GE, and PE × GE interaction as main effects, and sire, sow within PE, pen within PE × GE, and slaughter day (for plasma, muscle, and meat traits) as random effects. No significant PE × GE interaction was found on any trait under study (P ≥ 0.05). Prenatal HS did not affect growth performance and carcass traits (P ≥ 0.05). Compared with GTN, GHS pigs had lower average daily feed intake, average daily gain, and hot carcass weight (P &lt; 0.01), but similar carcass lean meat content (P ≥ 0.05). Prenatal HS had scarce effects on pork quality, with only higher a* and C* values (P &lt; 0.05) in the Gluteus superficialis. Growing HS led to a higher pH 24 h (P &lt; 0.05) in the Longissimus thoracis et lumborum (LTL) and ham muscles, and higher meat quality index in the ham muscles. In contrast, quality traits of the Semispinalis capitis (SC) were not affected by either PE or GE (P &gt; 0.05). Except a tendency for a higher citrate synthase activity in the SC (P = 0.065), PHS did not affect muscle metabolism. Growing HS induced muscle-specific metabolic responses, with reduced glycolytic potential (P &lt; 0.01) and metabolic enzyme activities (P &lt; 0.05) in the glycolytic LTL, but not in the oxidative SC (P &gt; 0.05). Plasma glucose content at slaughter was lower in the GHS compared with GTN pigs (P = 0.002), indicating an altered energy metabolism in pigs under GHS. Altogether, growing HS altered growth without affecting carcass traits, but improved technological quality of loin and ham. Prenatal HS, alone or combined with GHS, had limited or even no effect on carcass and pork quality.