bluuebunny/crossref_metadata_2025_split huggingface dataset:
hespdiv: an R package for spatially constrained, hierarchical and contiguous regionalization in palaeobiogeography
Authors: Daumantas Liudas , Spiridonov Andrej 
Published: June 2024

AbstractThe objective determination of boundaries of bioregions is a nontrivial problem. Here we present a new method family, HespDiv, and an algorithm for its implementation in a new R package: hespdiv. The hespdiv algorithm performs iterative hierarchical nonlinear spatial subdivisions of taxic data into topologically contiguous geographic regions. Bioregions obtained in this way can be viewed as realistic and causally important entities belonging to eco‐genealogical Bretskyan hierarchy. The possibilities of the hespdiv algorithm are successfully demonstrated on the Miocene mammal data from the contiguous United States, where a hierarchical set of bioregions was determined. The algorithm works in a decision‐tree‐like manner by generating multiple split‐lines, that each subdivide a study area and data into two parts per iteration per region. The performance of each split‐line is measured using a combination of data generalization and comparison functions that can be custom made or selected from pre‐set subdivision methods. In each iteration, the best split‐line is used to produce a subdivision, until no more adequate split‐lines are found. The process results in a hierarchy of subdivisions of distribution of taxonomic occurrences in space. Benefits of hespdiv include the delineation of spatially contiguous clusters, flexibility, and unique representations of spatial hierarchy tree. The package is shown to be effective in determining significant contiguous spatial structures of biota, so called geobiomes, in sufficiently sampled time intervals and regions. The flexibility and ease to use of the approach allows its application to the whole range of palaeo‐variables and environmental proxies.
Genome‐wide expression quantitative trait locus analysis reveals silk‐preferential gene regulatory network in maize
Authors: Wang Xiaoli , Lu Jiawen , Han Mingfang , Wang Zheyuan , Zhang Hongwei , Liu Yunjun , Zhou Peng , Fu Junjie , Xie Yuxin 
Published: June 2024

AbstractSilk of maize (Zea mays L.) contains diverse metabolites with complicated structures and functions, making it a great challenge to explore the mechanisms of metabolic regulation. Genome‐wide identification of silk‐preferential genes and investigation of their expression regulation provide an opportunity to reveal the regulatory networks of metabolism. Here, we applied the expression quantitative trait locus (eQTL) mapping on a maize natural population to explore the regulation of gene expression in unpollinated silk of maize. We obtained 3,985 silk‐preferential genes that were specifically or preferentially expressed in silk using our population. Silk‐preferential genes showed more obvious expression variations compared with broadly expressed genes that were ubiquitously expressed in most tissues. We found that trans‐eQTL regulation played a more important role for silk‐preferential genes compared to the broadly expressed genes. The relationship between 38 transcription factors and 85 target genes, including silk‐preferential genes, were detected. Finally, we constructed a transcriptional regulatory network around the silk‐preferential gene Bx10, which was proposed to be associated with response to abiotic stress and biotic stress. Taken together, this study deepened our understanding of transcriptome variation in maize silk and the expression regulation of silk‐preferential genes, enhancing the investigation of regulatory networks on metabolic pathways.
Leaf morphology related genes revealed by integrating Pan‐transcriptome, GWAS and eQTL analyses in a Liriodendron population
Authors: Wu Hainan , Liu Xiao , Zong Yaxian , Yang Lichun , Wang Jing , Tong Chunfa , Li Huogen 
Published: June 2024

AbstractLeaf plays an indispensable role in plant development and growth. Although many known genes related to leaf morphology development have been identified, elucidating the complex genetic basis of leaf morphological traits remains a challenge. Liriodendron plants are common ornamental trees due to their unique leaf shapes, while the molecular mechanism underlying Liriodendron leaf morphogenesis has remained unknown. Herein, we firstly constructed a population‐level pan‐transcriptome of Liriodendron from 81 accessions to explore the expression presence or absence variations (ePAVs), global expression differences at the population level, as well as differentially expressed genes (DEGs) between the Liriodendron chinense and Liriodendron tulipifera accessions. Subsequently, we integrated a genome‐wide association study (GWAS), expression quantitative trait loci (eQTL), and transcriptome‐wide association study (TWAS) to identify candidate genes related to leaf morphology. Through GWAS analysis, we identified 18 and 17 significant allelic loci in the leaf size and leaf shape modules, respectively. In addition, we discerned 16 candidate genes in relation to leaf morphological traits via TWAS. Further, integrating the co‐localization results of GWAS and eQTL, we determined two regulatory hotspot regions, hot88 and hot758, related to leaf size and leaf shape, respectively. Finally, co‐expression analysis, eQTL, and linkage mapping together demonstrated that Lchi_4g10795 regulate their own expression levels through cis‐eQTL to affect the expression of downstream genes and cooperatively participate in the development of Liriodendron leaf morphology. These findings will improve our understanding of the molecular regulatory mechanism of Liriodendron leaf morphogenesis and will also accelerate molecular breeding of Liriodendron.
Land ownership and nutrition in Nepal
Authors: Tiwari Manda 
Published: June 2024

AbstractThis paper provides empirical evidence on the relationship between women's land ownership and nutritional outcomes in Nepal. Using three waves of the Nepal Demographic and Health Survey and employing a bounding technique by Oster, I estimate bounded treatment effects of land ownership. The results show that women's land ownership is associated with a reduction in the incidence of childhood underweight and stunting and an increase in women's body mass index. Additionally, I find the selection on unobservable characteristics has to be larger than the selection on observable characteristics to drive these estimates to zero, suggesting that land ownership credibly improves nutritional outcomes. Furthermore, heterogeneous results show that the negative association between land ownership and childhood nutritional status is more prominent in male children and children from the Brahmin caste. Similarly, the negative relationship between land ownership and underweight in women is more pronounced in women employed in agriculture and rural areas. While I argue that landownership improves nutrition, these estimates are sensitive to the assumptions made.
Evaluation of the correlation of serological and intradermal allergen testing with clinical history in 29 dogs with atopic dermatitis
Authors: Chong Eric , Austel Michaela , Banovic Frane 
Published: June 2024

AbstractBackgroundLimited information exists about the correlation between clinical history and positive serum (SAT) and intradermal allergen test (IDAT) results in atopic dogs.ObjectivesTo evaluate the correlation between clinical history and SAT/IDAT results in atopic dogs.AnimalsTwenty‐nine client‐owned dogs with nonseasonal atopic dermatitis with or without seasonal exacerbation were enrolled.Materials and MethodsIDAT, SAT (immunoglobulin (Ig)M antibody capture enzyme‐linked immunosorbent assay [MacELISA] with bromelain CCD inhibitor) and clinical information collected in a questionnaire regarding seasonal variations in pruritus affecting the dogs were performed on the same day. Two independent investigators (Inv A and Inv B) recorded IDAT results.ResultsThe kappa coefficients agreement for positive IDAT scores between Inv A and B was substantial. The agreement between IDAT and SAT results at different ELISA absorbance units (EAU) cut‐offs (>79 and ≥300) was slight and fair for both investigators, respectively. A higher agreement was observed between IDAT and SAT (≥300 EAU) than between IDAT and SAT (>79 EAU) with the exception of mite and flea allergens. There was a statistically significant association between clinical history and positive IDAT results for seasonal allergens (Inv A and Inv B, p = 0.016). There was no significance between positive SAT results and clinical history. Five (IDAT) and 12 of 13 (SAT) atopic dogs without clinical seasonal exacerbation showed positive results for seasonal allergens.Conclusions and Clinical RelevanceThe agreement between IDAT and SAT ≥300 EAU results was fair and the agreement between IDAT and SAT >79 EAU results was slight for all allergens. Only positive IDAT results significantly correlated with clinical history.
A new antshrike (Aves: Thamnophilidae) endemic to the Caatinga and the role of climate oscillations and drainage shift in shaping cryptic diversity of Neotropical seasonal dry forests
Authors: Cerqueira Pablo , Gonçalves Gabriela R. , Quaresma Tânia F. , Silva Marcelo , Pichorim Mauro , Aleixo Alexandre 
Published: June 2024

AbstractThe Caatinga is the largest patch of Seasonal Dry Tropical Forest in the Neotropics, located in northeastern Brazil and characterized mainly by deciduous vegetation and extreme rainfall seasonality. It has historically been treated as a biologically impoverished domain, but recent studies uncovered new diversification patterns and several new taxa of frogs, mammals, insects, and fishes. Here we employed a dense sampling regime to evaluate whether the São Francisco River (SFR) would have promoted genetic diversification and fixed phenotypic differences and how Quaternary climatic oscillations shaped distribution and population sizes in a Caatinga endemic species, the Silvery‐cheeked Antshrike (Sakesphoroides cristatus). We adopted an integrative approach using multilocus genetic, plumage, vocal data, and ecological niche modelling (ENM) to characterize evolutionary units and niche suitability in past scenarios. We recovered strong genetic structure across the SFR that was congruent with plumage and vocal variation, revealing a yet undescribed species named herein as Sakesphoroides niedeguidonae, sp. nov. (urn:lsid:zoobank.org:act:2B9FC637‐008A‐4E9A‐B92B‐69ED7FE23823s). The splitting time estimated between the newly described species and S. cristatus is consistent with the establishment of the modern course of SFR, with a more recent course shift apparently promoting the secondary contact between the two species in the Raso da Catarina region. After their split, both species experienced increases in population sizes and range sizes at similar times during the Last Glacial Maximum. We expect other Caatinga avian endemic lineages to show similar patterns of genetic differentiation across the SFR that were enhanced by Quaternary climatic oscillations.
Kinetostatics Modeling and Analysis of a Spherical Parallel Continuum Manipulator
Authors: Duan Xuyang , Yan Wei , Yan Tianyi , Chen Genliang , Wang Hao 
Published: June 2024

Abstract
In this paper, a spherical parallel continuum manipulator (SPCM) which is the flexible version of the 3-RRR“Agile Eye” mechanism is proposed and analyzed. The SPCM consists of three parallel flexible limbs, each limb is formed by compliant truncated cone elements, and the moving platform connects each limb with a passive revolute joint. Three servo motors are used to control the manipulator actively, and the spherical motion is realized by the coupled large deflections of the flexible links. An equivalent compliance analysis method of the element is developed based on finite element analysis and principal axis decomposition. By combining all three limbs, the kinetostatics model of the whole manipulator is derived, and a gradient iteration algorithm is developed to solve the forward and inverse kinetostatics. Finally, a prototype of the manipulator is constructed using 3D-printing technology, and the accuracy for element equivalence and end-effector characteristics is validated by experiments. The results show that the derived kinetostatics model can accurately describe the force–deflection behavior of the SPCM.
Modeling Abduction Mechanism of Soft Actuator With Elastica for Robotic Hands
Authors: Lin Sheng-Guan , Chang Jen-Yuan (James) 
Published: June 2024

Abstract
Soft actuators, composed of pliable materials, are increasingly adopted in industrial grippers owing to their inherent flexibility, elasticity, and safety attributes, making them well-suited for anthropomorphic robotic applications. A significant gap in existing literature is the detailed exploration of hand abduction movements. Addressing this gap, the present study makes three principal contributions. First, it introduces the abduction soft-actuator (ASA), an innovative design tailored specifically for robotic hand abduction. Second, it establishes an analytical framework using the large deformation virtual beam (LDVB) theory for soft elastica, which enables a detailed analysis of the intrinsic physical properties of the actuator's internal membrane. Third, this study highlights the ASA's versatility, showcasing its ability to integrate membranes and springs seamlessly, thereby broadening its utility across diverse design paradigms. Empirical results underscore the ASA's capability to predict operational angles with varying spring stiffnesses, enhancing the precision of spring selection for a range of applications. This ASA exhibits an abduction angle ranging from 14.17 deg to 27.78 deg as the spring stiffness K varies from 200 N/m to 1600 N/m, with a root mean square error associated with these measurements ranging from 0.3321 deg to 1.2651 deg. Unlike traditional soft actuators that typically utilize a single material, the ASA demonstrates modularity, facilitating easy adjustments of springs to meet varied requirements. Contrasting with the typical case-by-case analytical approaches, the ASA significantly extends its applicability. Validation experiments using inflated silicone membranes corroborate the LDVB theoretical framework, suggesting that these empirically based estimations are conducive to analytical prediction. Collectively, this methodological advancement not only bridges the current technological divide but also enhances the understanding of soft actuator mechanics across a wide range of applications.
Use of computer-assisted self-interview in detection of and referral for depression among adolescents living with HIV at an urban HIV treatment clinic in Uganda: a quasi-experimental study
Authors: Alinaitwe Racheal , Elyanu Peter James , Kanywa Jacqueline Balungi , Akena Dickens 
Published: June 2024

BackgroundDepression is common among adolescents living with HIV (ALHIV) and impacts their quality of life. However, it is not routinely detected and treated due to a lack of screening tools, coupled with large numbers of clients in the HIV clinics and limited staff. Enabling adolescents to do a self-assessment for depression on a tablet computer could possibly improve the detection of depression in this population. We set out to assess the detection and referral of depression among ALHIV in care in Uganda.MethodsThis was a quasi-experimental study design with a historical control at Baylor College of Medicine of Children’s Foundation. We conducted a retrospective chart review of 425 adolescents covering a 3-month period and documented the proportion screened for depression and referred to the clinic counsellors. From July to September 2022, eligible adolescents aged 10–19 years who had assented and consented self-assessed for depression using a Patient Health Questionnaire-Adolescent on a tablet computer-assisted self-interview (CASI). Adolescents who screened positive had a prompt on the tablet computers referring them to the counsellor for mental healthcare. We compared the proportions of participants screened for depression and referred to counsellors from clinic chart review and on the CASI using paired t-tests.ResultsOut of 425 medical records reviewed, 54% (231/425) were females and the median age was 15 years. Of the participants who self-assessed on the CASI, 52% (222/425) were males and the median age of all participants was 16 years. Self-assessment on the CASI increased the rate of detection of depression from 0% to 23.3%. Of those referred on the CASI, 15% accessed care at the referral point.ConclusionThe use of CASI improves the rate of detection of depression among ALHIV; however, there is a need to address the barriers to effective referral for mental health services.
MaterniCode: New Bioinformatic Pipeline to Detect Fetal Aneuploidies and Rearrangements Using Next‐Generation Sequencing
Authors: Gabrielli Federico , Papa Filomena Tiziana , Di Pietro Fabio , Paytuví-Gallart Andreu , Julian Daniel , Sanseverino Walter , Alfonsi Cinzia 
Published: June 2024

Objective: The present study is aimed at introducing and evaluating MaterniCode, a state‐of‐the‐art bioinformatic pipeline for noninvasive prenatal testing (NIPT) that leverages the Ion Torrent semiconductor sequencing platform. The initiative strives to revolutionize prenatal diagnostics by offering a rapid and cost‐effective method without sacrificing accuracy.Methods: Two distinct bioinformatic strategies were employed for fetal sex determination, one of which achieved 100% accuracy. We analyzed 1225 maternal blood samples for fetal aneuploidies, benchmarking against the industry standard Illumina VeriSeq™ NIPT Solution v2. The capability of MaterniCode to detect and characterize complex chromosomal anomalies was also assessed.Results: MaterniCode achieved near‐perfect accuracy in fetal sex determination through chromosome Y (chrY )–specific gene analysis, whereas the alternative method, employing the ratio of high‐quality mapped reads on chrY relative to all reads, delivered 100% accuracy. For fetal aneuploidy detection, both the integrated WisecondorX and NIPTeR algorithms demonstrated a 100% sensitivity and specificity rate, consistent with Illumina VeriSeq™ NIPT Solution v2. The pipeline also successfully identified and precisely mapped significant chromosomal abnormalities, exemplified by a 2.4 Mb deletion on chromosome 13 and a 3 Mb duplication on chromosome 2.Conclusion: MaterniCode has proven to be an innovative and highly efficient tool in the domain of NIPT, demonstrating excellent sensitivity and specificity. Its robust capability to effectively detect a wide range of complex chromosomal aberrations, including rare and subtle variations, positions it as a promising and valuable addition to prenatal diagnostic technologies. This enhancement to diagnostic precision significantly aids clinicians in making informed decisions during pregnancy management.
Zinc-alpha-2-glycoprotein Secreted by Triple-Negative Breast Cancer Promotes Peritumoral Fibrosis
Authors: Verma Surbhi , Giagnocavo Stephanie D. , Curtin Meghan C. , Arumugam Menusha , Osburn-Staker Sandra M. , Wang Guoying , Atkinson Aaron , Nix David A. , Lum David H. , Cox James E. , Hilgendorf Keren I. 
Published: June 2024

Abstract

Obesity is a modifiable predisposition factor for postmenopausal breast cancer. This suggests a localized, reciprocal interaction between breast cancer cells and the surrounding mammary white adipose tissue. To investigate how breast cancer cells alter the composition and function of adipose tissue, we screened the secretomes of 10 human breast cancer cell lines for the ability to modulate the differentiation of adipocyte stem and progenitor cells. The screen identified an adipogenic modulator, zinc-alpha-2-glycoprotein (ZAG/AZGP1) that is secreted by triple-negative breast cancer (TNBC) cells. TNBC-secreted ZAG inhibits adipogenesis and instead induces the expression of fibrotic genes. Accordingly, depletion of ZAG in TNBC cells attenuates fibrosis in white adipose tissue and inhibits tumor growth. Further, high expression of ZAG is linked to poor prognosis in patients with TNBC but not in patients with other clinical subtypes of breast cancer. Our findings suggest a role of TNBC-secreted ZAG in promoting the transdifferentiation of adipocyte stem and progenitor cells into cancer-associated fibroblasts to support tumorigenesis.

Significance:
Functional screening of breast cancer secretomes revealed that triple-negative breast cancer promotes fibrosis in the adipose tissue microenvironment by secreting zinc-alpha-2-glycoprotein and promoting the transdifferentiation of adipocyte stem cells into myofibroblasts.
Machine Learning Detects Symptomatic Plaques in Patients With Carotid Atherosclerosis on CT Angiography
Authors: Pisu Francesco , Williamson Brady J. , Nardi Valentina , Paraskevas Kosmas I. , Puig Josep , Vagal Achala , de Rubeis Gianluca , Porcu Michele , Cau Riccardo , Benson John C. , Balestrieri Antonella , Lanzino Giuseppe , Suri Jasjit S. , Mahammedi Abdelkader , Saba Luca 
Published: June 2024

BACKGROUND:
This study aimed to develop and validate a computed tomography angiography based machine learning model that uses plaque composition data and degree of carotid stenosis to detect symptomatic carotid plaques in patients with carotid atherosclerosis.

METHODS:
The machine learning based model was trained using degree of stenosis and the volumes of 13 computed tomography angiography derived intracarotid plaque subcomponents (eg, lipid, intraplaque hemorrhage, calcium) to identify plaques associated with cerebrovascular events. The model was internally validated through repeated 10-fold cross-validation and tested on a dedicated testing cohort according to discrimination and calibration.

RESULTS:

This retrospective, single-center study evaluated computed tomography angiography scans of 268 patients with both symptomatic and asymptomatic carotid atherosclerosis (163 for the derivation set and 106 for the testing set) performed between March 2013 and October 2019. The area-under-receiver-operating characteristics curve by machine learning on the testing cohort (0.89) was significantly higher than the areas under the curve of traditional logit analysis based on the degree of stenosis (0.51,
P
<0.001), presence of intraplaque hemorrhage (0.69,
P
<0.001), and plaque composition (0.78,
P
<0.001), respectively. Comparable performance was obtained on internal validation. The identified plaque components and associated cutoff values that were significantly associated with a higher likelihood of symptomatic status after adjustment were the ratio of intraplaque hemorrhage to lipid volume (≥50%, 38.5 [10.1–205.1]; odds ratio, 95% CI) and percentage of intraplaque hemorrhage volume (≥10%, 18.5 [5.7–69.4]; odds ratio, 95% CI).

CONCLUSIONS:
This study presented an interpretable machine learning model that accurately identifies symptomatic carotid plaques using computed tomography angiography derived plaque composition features, aiding clinical decision-making.