bluuebunny/crossref_metadata_2025_split huggingface dataset:
Six Principles for Embracing Gender and Sexual Diversity in Postsecondary Biology Classrooms
Authors: Zemenick Ash T , Turney Shaun , Webster Alex J , Jones Sarah C , Weber Marjorie G 
Published: February 2022

Abstract
Sexual and gender minorities face considerable inequities in society, including in science. In biology, course content provides opportunities to challenge harmful preconceptions about what is “natural” while avoiding the notion that anything found in nature is inherently good (the appeal-to-nature fallacy). We provide six principles for instructors to teach sex- and gender-related topics in postsecondary biology in a more inclusive and accurate manner: highlighting biological diversity early, presenting the social and historical context of science, using inclusive language, teaching the iterative process of science, presenting students with a diversity of role models, and developing a classroom culture of respect and inclusion. To illustrate these six principles, we review the many definitions of sex and demonstrate applying the principles to three example topics: sexual reproduction, sex determination or differentiation, and sexual selection. These principles provide a tangible starting place to create more scientifically accurate, engaging, and inclusive classrooms.
Emerging Adults’ Intentions to Participate in Radical Protest Actions: The Role of the Parents in the Midst of Extra-Familial Influences and the Offspring’s Political Characteristics
Authors: Chui Wing Hong , Khiatani Paul Vinod , Ip Ping Lam 
Published: February 2022

Abstract
This study explored the influence of parental socialisation, relative to that from crucial dispositions of the offspring and other socialisation agents, on the offspring’s intentions to engage in radical protest actions in Hong Kong, a city that has been experiencing periodical socio-political upheavals and generational rifts over politics. A sample of 666 university students, aged eighteen to twenty-five years, from eight universities in Hong Kong completed the survey. Employing hierarchical regression analysis, the results revealed that participation in ritual protests among fathers positively associated with radicalism intentions. With the introduction of a broader group of socialisation agents, however, its effect on the dependent variable became statistically non-significant. Rather, peer influence and media consumption positively associated with radicalism intentions, whilst family discussions about politics negatively associated with such intentions. After including the respondents’ political characteristics in the final model, which accounted for the greatest variance in the dependent variable, no variables reflecting influences from the household remained statistically significant. Apart from peer influence and media consumption, the respondents’ past histories of activism and radicalism and his/her political sympathies over the self-determination stance positively associated with radicalism intentions. In the light of the findings, implications for future studies and social work practice are discussed.
Phylogenetic relationships of Aquilaria and Gyrinops (Thymelaeaceae) revisited: evidence from complete plastid genomes
Authors: Lee Shiou Yih , Turjaman Maman , Chaveerach Arunrat , Subasinghe Smcup , Fan Qiang , Liao Wenbo 
Published: February 2022

Abstract
The agarwood-producing genera, Aquilaria and Gyrinops, have been treated as sister genera in Thymelaeaceae (Aquilarieae, Malvales). However, there are differing opinions about their taxonomic positions. Using new evidence from complete plastid genome (plastome) sequences of 12 Aquilaria spp. and seven Gyrinops spp., corresponding to more than half the total number of species recognized in each genus, we reconstructed a phylogenetic tree of Aquilarieae. Members of both genera shared similar sequence variations at the plastome level. The phylogenetic relationships of the two genera were completely resolved using the complete plastome sequences. Gyrinops was paraphyletic to Aquilaria, i.e. Aquilaria nested in Gyrinops. Overlapping clustering patterns were observed from topology-clustering analysis using the complete plastome and the protein-coding gene sequences, which further reinforced the paraphyletic link. The maximum-likelihood-based RelTime analysis suggested that Aquilarieae and Daphneae diverged c. 44 Mya during the Eocene, followed by a rapid divergence event in Aquilarieae, with the split between G. vidalii and G. walla c. 1.24 Mya during the Pleistocene. Our new phylogenetic estimation demonstrates the relationship between the two genera, which will aid in future taxonomic revisions involving members of Aquilarieae.
Combinatory lung tumor inhibition by myo-inositol and iloprost/rapamycin: association with immunomodulation
Authors: Kassie Fekadu , Bagherpoor Alireza Jian , Kovacs Katalin , Seelig Davis 
Published: February 2022

Abstract
Although both preclinical and clinical studies have suggested that myo-inositol (MI) may be a safe and effective lung cancer chemopreventive agent, its efficacy is moderate. To test whether the chemopreventive agents iloprost (IL) or rapamycin enhance the lung tumor inhibitory effects of MI, A/J mice were treated with the tobacco smoke carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and, beginning one week after the end of NNK treatment, given MI, IL, rapamycin, MI + IL or MI + rapamycin for 17 weeks. Analyses of the number and size of tumors on the surface of the lung have indicated that MI, IL, rapamycin, MI + IL and MI + rapamycin reduced the multiplicity of NNK-induced lung tumors by 41, 34, 46, 79 and 67%, respectively, and larger tumors (lung tumors with a diameter of 1–2 or &gt;2 mm) were absent in the MI + IL and MI + rapamycin groups. These results clearly indicated that MI + IL and MI + rapamycin are more effective than MI alone in inhibiting the formation and growth of lung tumors. Assessment of the immunomodulatory effects of the drugs showed that whereas MI + rapamycin and MI + IL increased the infiltration of lung tumors by CD4+ and CD8+ T cells, MI + rapamycin reduced the expression of the immune checkpoint protein programmed-death ligand-1 (PD-L1). Moreover, all treatments, except IL, increased apoptosis, whereas cell proliferation was markedly suppressed in all treated groups. In summary, these results suggest that IL and rapamycin could enhance the efficacy of MI in lung cancer chemoprevention trials.
Identification of subjective cognitive decline due to Alzheimer’s disease using multimodal MRI combining with machine learning
Authors: Lin Hua , Jiang Jiehui , Li Zhuoyuan , Sheng Can , Du Wenying , Li Xiayu , Han Ying 
Published: February 2022

Abstract
Subjective cognitive decline (SCD) is a preclinical asymptomatic stage of Alzheimer’s disease (AD). Accurate diagnosis of SCD represents the greatest challenge for current clinical practice. The multimodal magnetic resonance imaging (MRI) features of 7 brain networks and 90 regions of interests from Chinese and ANDI cohorts were calculated. Machine learning (ML) methods based on support vector machine (SVM) were used to classify SCD plus and normal control. To assure the robustness of ML model, above analyses were repeated in amyloid β (Aβ) and apolipoprotein E (APOE) ɛ4 subgroups. We found that the accuracy of the proposed multimodal SVM method achieved 79.49% and 83.13%, respectively, in Chinese and ANDI cohorts for the diagnosis of the SCD plus individuals. Furthermore, adding Aβ pathology and ApoE ɛ4 genotype information can further improve the accuracy to 85.36% and 82.52%. More importantly, the classification model exhibited the robustness in the crossracial cohorts and different subgroups, which outperforms any single and 2 modalities. The study indicates that multimodal MRI imaging combining with ML classification method yields excellent and powerful performances at categorizing SCD due to AD, suggesting potential for clinical utility.
Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth, and microbial communities
Authors: Qi Yueling , Ossowicki Adam , Yergeau Étienne , Vigani Gianpiero , Geissen Violette , Garbeva Paolina 
Published: February 2022

Abstract
Plastic mulch film residues have been accumulating in agricultural soils for decades, but so far, little is known about its consequences on soil microbial communities and functions. Here, we tested the effects of plastic residues of low-density polyethylene and biodegradable mulch films on soil suppressiveness and microbial community composition. We investigated how plastic residues in a Fusarium culmorum suppressive soil affect the level of disease suppressiveness, plant biomass, nutrient status, and microbial communities in rhizosphere using a controlled pot experiment. The addition of 1% plastic residues to the suppressive soil did not affect the level of suppression and the disease symptoms index. However, we did find that plant biomasses decreased, and that plant nutrient status changed in the presence of plastic residues. No significant changes in bacterial and fungal rhizosphere communities were observed. Nonetheless, bacterial and fungal communities closely attached to the plastisphere were very different from the rhizosphere communities with overrepresentation of potential plant pathogens. The plastisphere revealed a high abundance of specific bacterial phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) and fungal genera (Rhizoctonia and Arthrobotrys). Our work revealed new insights and raises emerging questions for further studies on the impact of microplastics on the agroecosystems.
Noncanonical necrosis in 2 different cell types in a Caenorhabditis elegans NAD+ salvage pathway mutant
Authors: Reza Rifath N , Serra Nicholas D , Detwiler Ariana C , Hanna-Rose Wendy , Crook Matt 
Published: February 2022

Abstract
Necrosis was once described as a chaotic unregulated response to cellular insult. We now know that necrosis is controlled by multiple pathways in response to many different cellular conditions. In our pnc-1 NAD+ salvage deficient Caenorhabditis elegans model excess nicotinamide induces excitotoxic death in uterine-vulval uv1 cells and OLQ mechanosensory neurons. We sought to characterize necrosis in our pnc-1 model in the context of well-characterized necrosis, apoptosis, and autophagy pathways in C. elegans. We confirmed that calpain and aspartic proteases were required for uv1 necrosis, but changes in intracellular calcium levels and autophagy were not, suggesting that uv1 necrosis occurs by a pathway that diverges from mec-4d-induced touch cell necrosis downstream of effector aspartic proteases. OLQ necrosis does not require changes in intracellular calcium, the function of calpain or aspartic proteases, or autophagy. Instead, OLQ survival requires the function of calreticulin and calnexin, pro-apoptotic ced-4 (Apaf1), and genes involved in both autophagy and axon guidance. In addition, the partially OLQ-dependent gentle nose touch response decreased significantly in pnc-1 animals on poor quality food, further suggesting that uv1 and OLQ necrosis differ downstream of their common trigger. Together these results show that, although phenotypically very similar, uv1, OLQ, and touch cell necrosis are very different at the molecular level.
A numerical framework for genetic hitchhiking in populations of variable size
Authors: Friedlander Eric , Steinrücken Matthias 
Published: February 2022

AbstractNatural selection on beneficial or deleterious alleles results in an increase or decrease, respectively, of their frequency within the population. Due to chromosomal linkage, the dynamics of the selected site affect the genetic variation at nearby neutral loci in a process commonly referred to as genetic hitchhiking. Changes in population size, however, can yield patterns in genomic data that mimic the effects of selection. Accurately modeling these dynamics is thus crucial to understanding how selection and past population size changes impact observed patterns of genetic variation. Here, we model the evolution of haplotype frequencies with the Wright–Fisher diffusion to study the impact of selection on linked neutral variation. Explicit solutions are not known for the dynamics of this diffusion when selection and recombination act simultaneously. Thus, we present a method for numerically evaluating the Wright–Fisher diffusion dynamics of 2 linked loci separated by a certain recombination distance when selection is acting. We can account for arbitrary population size histories explicitly using this approach. A key step in the method is to express the moments of the associated transition density, or sampling probabilities, as solutions to ordinary differential equations. Numerically solving these differential equations relies on a novel accurate and numerically efficient technique to estimate higher order moments from lower order moments. We demonstrate how this numerical framework can be used to quantify the reduction and recovery of genetic diversity around a selected locus over time and elucidate distortions in the site-frequency-spectra of neutral variation linked to loci under selection in various demographic settings. The method can be readily extended to more general modes of selection and applied in likelihood frameworks to detect loci under selection and infer the strength of the selective pressure.
Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis
Authors: Healey Hope M , Bassham Susan , Cresko William A 
Published: February 2022

AbstractSingle-cell RNA sequencing is a powerful technique that continues to expand across various biological applications. However, incomplete 3′-UTR annotations can impede single-cell analysis resulting in genes that are partially or completely uncounted. Performing single-cell RNA sequencing with incomplete 3′-UTR annotations can hinder the identification of cell identities and gene expression patterns and lead to erroneous biological inferences. We demonstrate that performing single-cell isoform sequencing in tandem with single-cell RNA sequencing can rapidly improve 3′-UTR annotations. Using threespine stickleback fish (Gasterosteus aculeatus), we show that gene models resulting from a minimal embryonic single-cell isoform sequencing dataset retained 26.1% greater single-cell RNA sequencing reads than gene models from Ensembl alone. Furthermore, pooling our single-cell sequencing isoforms with a previously published adult bulk Iso-Seq dataset from stickleback, and merging the annotation with the Ensembl gene models, resulted in a marginal improvement (+0.8%) over the single-cell isoform sequencing only dataset. In addition, isoforms identified by single-cell isoform sequencing included thousands of new splicing variants. The improved gene models obtained using single-cell isoform sequencing led to successful identification of cell types and increased the reads identified of many genes in our single-cell RNA sequencing stickleback dataset. Our work illuminates single-cell isoform sequencing as a cost-effective and efficient mechanism to rapidly annotate genomes for single-cell RNA sequencing.
The utility of a closed breeding colony of Peromyscus leucopus for dissecting complex traits
Authors: Long Phillip N , Cook Vanessa J , Majumder Arundhati , Barbour Alan G , Long Anthony D 
Published: February 2022

Abstract
Deermice of the genus Peromyscus are well suited for addressing several questions of biologist interest, including the genetic bases of longevity, behavior, physiology, adaptation, and their ability to serve as disease vectors. Here, we explore a diversity outbred approach for dissecting complex traits in Peromyscus leucopus, a nontraditional genetic model system. We take advantage of a closed colony of deer-mice founded from 38 individuals and subsequently maintained for ∼40–60 generations. From 405 low-pass short-read sequenced deermice we accurate impute genotypes at 16 million single nucleotide polymorphisms. Conditional on observed genotypes simulations were conducted in which three different sized quantitative trait loci contribute to a complex trait under three different genetic models. Using a stringent significance threshold power was modest, largely a function of the percent variation attributable to the simulated quantitative trait loci, with the underlying genetic model having only a subtle impact. We additionally simulated 2,000 pseudo-individuals, whose genotypes were consistent with those observed in the genotyped cohort and carried out additional power simulations. In experiments employing more than 1,000 mice power is high to detect quantitative trait loci contributing greater than 2.5% to a complex trait, with a localization ability of ∼100 kb. We finally carried out a Genome-Wide Association Study on two demonstration traits, bleeding time and body weight, and uncovered one significant region. Our work suggests that complex traits can be dissected in founders-unknown P. leucopus colony mice and similar colonies in other systems using easily obtained genotypes from low-pass sequencing.
Genetically predicted sex hormone levels and health outcomes: phenome-wide Mendelian randomization investigation
Authors: Yuan Shuai , Wang Lijuan , Sun Jing , Yu Lili , Zhou Xuan , Yang Jie , Zhu Yimin , Gill Dipender , Burgess Stephen , Denny Joshua C , Larsson Susanna C , Theodoratou Evropi , Li Xue 
Published: February 2022

AbstractBackgroundSex hormone-binding globulin (SHBG), testosterone and oestradiol have been associated with many diseases in observational studies; however, the causality of associations remains unestablished.MethodsA phenome-wide Mendelian randomization (MR) association study was performed to explore disease outcomes associated with genetically proxied circulating SHBG, testosterone and oestradiol levels by using updated genetic instruments in 339 197 unrelated White British individuals (54% female) in the UK Biobank. Two-sample MR analyses with data from large genetic studies were conducted to replicate identified associations in phenome-wide MR analyses. Multivariable MR analyses were performed to investigate mediation effects of hormone-related biomarkers in observed associations with diseases.ResultsPhenome-wide MR analyses examined associations of genetically predicted SHBG, testosterone and oestradiol levels with 1211 disease outcomes, and identified 28 and 13 distinct phenotypes associated with genetically predicted SHBG and testosterone, respectively; 22 out of 28 associations for SHBG and 10 out of 13 associations for testosterone were replicated in two-sample MR analyses. Higher genetically predicted SHBG levels were associated with a reduced risk of hypertension, type 2 diabetes, diabetic complications, coronary atherosclerotic outcomes, gout and benign and malignant neoplasm of uterus, but an increased risk of varicose veins and fracture (mainly in females). Higher genetically predicted testosterone levels were associated with a lower risk of type 2 diabetes, coronary atherosclerotic outcomes, gout and coeliac disease mainly in males, but an increased risk of cholelithiasis in females.ConclusionsThese findings suggest that sex hormones may causally affect risk of several health outcomes.
A Shrewd Inspection of Vertebral Regionalization in Large Shrews (Soricidae: Crocidurinae)
Authors: Smith Stephanie M , Angielczyk Kenneth D 
Published: February 2022

SynopsisThe regionalization of the mammalian spinal column is an important evolutionary, developmental, and functional hallmark of the clade. Vertebral column regions are usually defined using transitions in external bone morphology, such as the presence of transverse foraminae or rib facets, or measurements of vertebral shape. Yet the internal structure of vertebrae, specifically the trabecular (spongy) bone, plays an important role in vertebral function, and is subject to the same variety of selective, functional, and developmental influences as external bone morphology. Here, we investigated regionalization of external and trabecular bone morphology in the vertebral column of a group of shrews (family Soricidae). The primary goals of this study were to: (1) determine if vertebral trabecular bone morphology is regionalized in large shrews, and if so, in what configuration relative to external morphology; (2) assess correlations between trabecular bone regionalization and functional or developmental influences; and (3) determine if external and trabecular bone regionalization patterns provide clues about the function of the highly modified spinal column of the hero shrew Scutisorex. Trabecular bone is regionalized along the soricid vertebral column, but the configuration of trabecular bone regions does not match that of the external vertebral morphology, and is less consistent across individuals and species. The cervical region has the most distinct and consistent trabecular bone morphology, with dense trabeculae indicative of the ability to withstand forces in a variety of directions. Scutisorex exhibits an additional external morphology region compared to unmodified shrews, but this region does not correspond to a change in trabecular architecture. Although trabecular bone architecture is regionalized along the soricid vertebral column, and this regionalization is potentially related to bone functional adaptation, there are likely aspects of vertebral functional regionalization that are not detectable using trabecular bone morphology. For example, the external morphology of the Scutisorex lumbar spine shows signs of an extra functional region that is not apparent in trabecular bone analyses. It is possible that body size and locomotor mode affect the degree to which function is manifest in trabecular bone, and broader study across mammalian size and ecology is warranted to understand the relationship between trabecular bone morphology and other measures of vertebral function such as intervertebral range of motion.
Outpatient parenteral antimicrobial therapy (OPAT) in the UK: findings from the BSAC National Outcomes Registry (2015–19)
Authors: Gilchrist Mark , Barr David , Drummond Felicity , Muir Alison , Williams John , Scriven James , Snape Susan , Hemsley Carolyn , Durojaiye Chris O , Patel Sanjay , Andrew Seaton R. 
Published: February 2022

Abstract

Background
Reporting of outpatient parenteral antimicrobial therapy (OPAT) outcomes with national benchmarking is key to informing service development and supporting quality improvement.

Objectives
To analyse and report on data collected by the BSAC OPAT National Outcomes Registry from 2015 to 2019.

Methods
Quarterly data to 2020 was extracted from the BSAC National Outcomes Registry and analysed.

Results
57 organizations submitted data on 27 841 patient episodes and 442 280 OPAT treatment days. A diverse range of infections and antimicrobials were reported with a mean OPAT treatment duration of 16.7 days (adults) and 7.7 days (paediatrics). In adults, the top five conditions treated were skin and soft tissue (27.6%), bronchiectasis (11.4%), urinary tract infections (7.6%), and diabetic foot infections (5.5%). Ceftriaxone followed by teicoplanin, ertapenem and piperacillin/tazobactam were the most-used antimicrobials. A median of 1.4 vascular-device-related complications were observed per 1000 OPAT treatment days (range 0.11 to 10.4) with device infections in 0.3 per 1000 OPAT days (range 0.1 to 1.7). Other adverse events (rash, blood dyscrasias, antibiotic-associated diarrhoea) were observed in a median of 1.9 per 1000 OPAT days. OPAT infection outcome (cured/improved) was 92.4% and OPAT outcome (success/partial success) was 90.7%.

Conclusions
This report demonstrates the safety, breadth, and complexity of modern UK OPAT practice. Future analyses of OPAT data should focus on infection- and service-specific quality indicators. OPAT registries remain central to planning and assessing safe, effective, and efficient delivery of patient-centred care and should be an important focus for UK and global OPAT practice.