bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic analysis of daf-18/PTEN missense mutants for starvation resistance and developmental regulation during Caenorhabditis elegans L1 arrest
Authors: Chen Jingxian , Tang Linda Y , Powell Maya E , Jordan James M , Baugh L Ryan 
Published: April 2022

Abstract
Mutations in the well-known tumor suppressor PTEN are observed in many cancers. PTEN is a dual-specificity phosphatase that harbors lipid and protein-phosphatase activities. The Caenorhabditis elegans PTEN ortholog is daf-18, which has pleiotropic effects on dauer formation, aging, starvation resistance, and development. Function of 3 daf-18 point-mutants, G174E, D137A, and C169S, had previously been investigated using high-copy transgenes in a daf-18 null background. These alleles were generated based on their mammalian counterparts and were treated as though they specifically disrupt lipid or protein-phosphatase activity, or both, respectively. Here, we investigated these alleles using genome editing of endogenous daf-18. We assayed 3 traits relevant to L1 starvation resistance, and we show that each point mutant is essentially as starvation-sensitive as a daf-18 null mutant. Furthermore, we show that G174E and D137A do not complement each other, suggesting overlapping effects on lipid and protein-phosphatase activity. We also show that each allele has strong effects on nucleocytoplasmic localization of DAF-16/FoxO and dauer formation, both of which are regulated by PI3K signaling, similar to a daf-18 null allele. In addition, each allele also disrupts M-cell quiescence during L1 starvation, though D137A has a weaker effect than the other alleles, including the null. Our results confirm that daf-18/PTEN is important for promoting starvation resistance and developmental arrest and that it is a potent regulator of PI3K signaling, and they highlight challenges of using genetic analysis to link specific DAF-18/PTEN enzymatic activities to particular phenotypes.
Subgenome dominance and its evolutionary implications in crop domestication and breeding
Authors: Wang Zheng , Yang Jinghua , Cheng Feng , Li Peirong , Xin Xiaoyun , Wang Weihong , Yu Yangjun , Zhang Deshuang , Zhao Xiuyun , Yu Shuancang , Zhang Fenglan , Dong Yang , Su Tongbing 
Published: April 2022

Abstract
Polyploidization or whole-genome duplication (WGD) is a well-known speciation and adaptation mechanism in angiosperms, while subgenome dominance is a crucial phenomenon in allopolyploids, established following polyploidization. The dominant subgenomes contribute more to genome evolution and homoeolog expression bias, both of which confer advantages for short-term phenotypic adaptation and long-term domestication. In this review, we firstly summarize the probable mechanistic basis for subgenome dominance, including the effects of genetic [transposon, genetic incompatibility, and homoeologous exchange (HE)], epigenetic (DNA methylation and histone modification), and developmental and environmental factors on this evolutionary process. We then move to Brassica rapa, a typical allopolyploid with subgenome dominance. Polyploidization provides the B. rapa genome not only with the genomic plasticity for adapting to changeable environments, but also an abundant genetic basis for morphological variation, making it a representative species for subgenome dominance studies. According to the ‘two-step theory’, B. rapa experienced genome fractionation twice during WGD, in which most of the genes responding to the environmental cues and phytohormones were over-retained, enhancing subgenome dominance and consequent adaption. More than this, the pangenome of 18 B. rapa accessions with different morphotypes recently constructed provides further evidence to reveal the impacts of polyploidization and subgenome dominance on intraspecific diversification in B. rapa. Above and beyond the fundamental understanding of WGD and subgenome dominance in B. rapa and other plants, however, it remains elusive why subgenome dominance has tissue- and spatiotemporal-specific features and could shuffle between homoeologous regions of different subgenomes by environments in allopolyploids. We lastly propose acceleration of the combined application of resynthesized allopolyploids, omics technology, and genome editing tools to deepen mechanistic investigations of subgenome dominance, both genetic and epigenetic, in a variety of species and environments. We believe that the implications of genomic and genetic basis of a variety of ecologically, evolutionarily, and agriculturally interesting traits coupled with subgenome dominance will be uncovered and aid in making new discoveries and crop breeding.
Circulating Hormones and Dominance Status Predict Female Behavior during Courtship in a Lekking Species
Authors: Earl Alexis D , Kimmitt Abigail A , Yorzinski Jessica L 
Published: April 2022

AbstractFemale competitive behaviors during courtship can have substantial fitness consequences, yet we know little about the physiological and social mechanisms underlying these behaviors—particularly for females of polygynous lek mating species. We explored the hormonal and social drivers of female intersexual and intrasexual behavior during courtship by males in a captive population of Indian peafowl. We investigated whether (1) female non-stress induced circulating estradiol (E2) and corticosterone (CORT) levels or (2) female dominance status in a dyad predicts female solicitation behavior. We also tested whether female circulating E2 and CORT predict dominant females’ aggressive behaviors toward subordinate females in the courtship context. Our findings demonstrate that females with higher levels of circulating E2 as well as higher levels of circulating CORT solicit more courtships from males. Dominant females also solicit more courtships from males than subordinate females. Female intrasexual aggressive behaviors during courtship, however, were not associated with circulating levels of E2 or CORT. Overall, we conclude that circulating steroid hormones in conjunction with social dominance might play a role in mediating female behaviors associated with competition for mates. Experimental manipulation and measures of hormonal flexibility throughout the breeding season in relation to competitive and sexual behaviors will be necessary to further examine the link between hormonal mechanisms and female behavior in polygynous lekking systems.
Discards of cod (Gadus morhua) in the Norwegian coastal fisheries: improving past and future estimates
Authors: Berg Hilde Sofie Fantoft , Clegg Thomas L , Blom Geir , Kolding Jeppe , Ono Kotaro , Nedreaas Kjell 
Published: April 2022

Abstract
Discarding can be an unknown source of biases and uncertainties in stock assessments. Discarding patterns and quantities vary so a routine methodology for estimating discards is important to give a better picture of total catches, and potentially mortality, in fisheries. Using data from the Norwegian Reference Fleet between 2012 and 2018, this study presents a revised methodology for estimating discards of cod (Gadus morhua) in the Norwegian coastal gillnet fisheries, which accounts for variations in discarding between vessels and uncertainties in the conversion of numbers to weight discarded. The estimated average discard rate of cod (weight of cod discarded as percentage of total weight caught) is 0.55% (95% confidence interval: 0.45–0.70%), although discard rates in southern areas were an order of magnitude higher than in northern areas. We also present an exploratory analysis of the drivers behind discarding using a random forest regression model. Spatial variations and fishing intensity were identified as the most important drivers of discarding. Results from this study suggest ways in which self-sampled data can be used to estimate discards in Norwegian coastal fisheries, and where the accuracy of future estimates can be improved when a higher resolution data collection programme is established.
Machine Learning Quantifies Accelerated White-Matter Aging in Persons With HIV
Authors: Petersen Kalen J , Strain Jeremy , Cooley Sarah , Vaida Florin , Ances Beau M 
Published: April 2022

AbstractBackgroundPersons with HIV (PWH) undergo white matter changes, which can be quantified using the brain-age gap (BAG), the difference between chronological age and neuroimaging-based brain-predicted age. Accumulation of microstructural damage may be accelerated in PWH, especially with detectable viral load (VL).MethodsIn total, 290 PWH (85% with undetectable VL) and 165 HIV-negative controls participated in neuroimaging and cognitive testing. BAG was measured using a Gaussian process regression model trained to predict age from diffusion magnetic resonance imaging in publicly available normative controls. To test for accelerated aging, BAG was modeled as an age × VL interaction. The relationship between BAG and global neuropsychological performance was examined. Other potential predictors of pathological aging were investigated in an exploratory analysis.ResultsAge and detectable VL had a significant interactive effect: PWH with detectable VL accumulated +1.5 years BAG/decade versus HIV-negative controls (P = .018). PWH with undetectable VL accumulated +0.86 years BAG/decade, although this did not reach statistical significance (P = .052). BAG was associated with poorer global cognition only in PWH with detectable VL (P &lt; .001). Exploratory analysis identified Framingham cardiovascular risk as an additional predictor of pathological aging (P = .027).ConclusionsAging with detectable HIV and cardiovascular disease may lead to white matter pathology and contribute to cognitive impairment.
Osamu Tezuka’sBuddha, Canonical Authority, and Remix Theory in the Study of Religion
Authors: Walker Seth M 
Published: April 2022

AbstractContemporary narrative repositories of religious traditions are often the ambiguous product of dialogic oral transmissions that occurred over many years, undergoing variation based on audience, context, or ideological purpose. Through an application of remix theory, both official and unauthorized narrative developments among the sacred stories of religious traditions can be understood as sampling processes in which select elements are sourced from archival spaces of narrative data in the creation of unique versions for the contexts in which they emerge. This is specifically demonstrated through Osamu Tezuka’s Buddha manga series, but the questions it raises and the conceptual challenges it presents for doctrinal notions of authority and authenticity are also relevant outside the immediate context of Buddhism for the canonical traditions within other religious systems. Thus, this article demonstrates how remix theory can be utilized to better challenge the ways such concepts are understood and taken for granted in religious traditions.
Targeted protein degradation and drug discovery
Authors: Naito Mikihiko 
Published: April 2022

Abstract
Targeted protein degradation attracts attention as a novel modality for drug discovery, as well as for basic research. Various types of degrader molecules have been developed so far, which include proteolysis-targeting chimaeras (PROTACs) and specific and nongenetic IAP-dependent protein erasers (SNIPERs), E3 modulators, hydrophobic tagging molecules, IAP antagonists and deubiquitylase inhibitors. PROTACs and SNIPERs are chimeric degrader molecules consisting of a target ligand linked to another ligand that binds to an E3 ubiquitin ligase. In the cells, they recruit an E3 ligase to the target protein, thereby inducing ubiquitylation and proteasomal degradation of the target protein. Because of their modular structure, novel PROTACs and SNIPERs targeting proteins of your interest can be rationally developed by substituting target ligands. In this article, various compounds capable of inducing protein degradation were overviewed, including SNIPER compounds developed in our laboratory.
Effects of Elevated Temperatures on the Growth and Development of Adult Anopheles gambiae (s.l.) (Diptera: Culicidae) Mosquitoes
Authors: Agyekum Thomas P , Arko-Mensah John , Botwe Paul K , Hogarh Jonathan N , Issah Ibrahim , Dwomoh Duah , Billah Maxwell K , Dadzie Samuel K , Robins Thomas G , Fobil Julius N 
Published: April 2022

Abstract
Higher temperatures expected in a future warmer climate could adversely affect the growth and development of mosquitoes. This study investigated the effects of elevated temperatures on longevity, gonotrophic cycle length, biting rate, fecundity, and body size of Anopheles gambiae (s.l.) (Diptera: Culicidae) mosquitoes. Anopheles gambiae (s.l.) eggs obtained from laboratory established colonies were reared under eight temperature regimes (25, 28, 30, 32, 34, 36, 38, and 40°C), and 80 ± 10% RH. All adults were allowed to feed on a 10% sugar solution soaked in cotton wool; however, some mosquitoes were provided blood meal using guinea pig. Longevity was estimated for both blood-fed and non-blood-fed mosquitoes and analyzed using the Kaplan–Meier survival analysis. One-way ANOVA was used to test the effect of temperature on gonotrophic cycle length, biting rate, and fecundity. Adult measurement data were log-transformed and analyzed using ordinary least square regression with robust standard errors. Increasing temperature significantly decreased the longevity of both blood-fed (Log-rank test; X2(4) = 904.15, P &lt; 0.001) and non-blood-fed (Log-rank test; X2(4) = 1163.60, P &lt; 0.001) mosquitoes. In addition, the fecundity of mosquitoes decreased significantly (ANOVA; F(2,57) = 3.46, P = 0.038) with an increase in temperature. Body size (β = 0.14, 95% CI, 0.16, 0.12, P &lt; 0.001) and proboscis length (β = 0.13, 95% CI, 0.17, 0.09, P &lt; 0.001) significantly decreased with increasing temperature from 25 to 34°C. Increased temperatures expected in a future warmer climate could cause some unexpected effects on mosquitoes by directly influencing population dynamics and malaria transmission.
Nonparametric Differentially Private Confidence Intervals for the Median
Authors: Drechsler Jörg , Globus-Harris Ira , Mcmillan Audra , Sarathy Jayshree , Smith Adam 
Published: April 2022

Abstract
Differential privacy is a restriction on data processing algorithms that provides strong confidentiality guarantees for individual records in the data. However, research on proper statistical inference, that is, research on properly quantifying the uncertainty of the (noisy) sample estimate regarding the true value in the population, is currently still limited. This article proposes and evaluates several strategies to compute valid differentially private confidence intervals for the median. Instead of computing a differentially private point estimate and deriving its uncertainty, we directly estimate the interval bounds and discuss why this approach is superior if ensuring privacy is important. We also illustrate that addressing both sources of uncertainty—the error from sampling and the error from protecting the output—simultaneously should be preferred over simpler approaches that incorporate the uncertainty in a sequential fashion. We evaluate the performance of the different algorithms under various parameter settings in extensive simulation studies and demonstrate how the findings could be applied in practical settings using data from the 1940 Decennial Census.
Low Complexity Regions in Mammalian Proteins are Associated with Low Protein Abundance and High Transcript Abundance
Authors: Dickson Zachery W. , Golding G. Brian 
Published: April 2022

Abstract
Low Complexity Regions (LCRs) are present in a surprisingly large number of eukaryotic proteins. These highly repetitive and compositionally biased sequences are often structurally disordered, bind promiscuously, and evolve rapidly. Frequently studied in terms of evolutionary dynamics, little is known about how LCRs affect the expression of the proteins which contain them. It would be expected that rapidly evolving LCRs are unlikely to be tolerated in strongly conserved, highly abundant proteins, leading to lower overall abundance in proteins which contain LCRs. To test this hypothesis and examine the associations of protein abundance and transcript abundance with the presence of LCRs, we have integrated high-throughput data from across mammals. We have found that LCRs are indeed associated with reduced protein abundance, but are also associated with elevated transcript abundance. These associations are qualitatively consistent across 12 human tissues and nine mammalian species. The differential impacts of LCRs on abundance at the protein and transcript level are not explained by differences in either protein degradation rates or the inefficiency of translation for LCR containing proteins. We suggest that rapidly evolving LCRs are a source of selective pressure on the regulatory mechanisms which maintain steady-state protein abundance levels.
Associations between Music Therapy, Pain and Heart Rate for Children Receiving Palliative Care
Authors: Delaney Angela M , Herbert Anthony R , Bradford Natalie , Bernard Anne 
Published: April 2022

AbstractMusic therapy (MT) is a widely used non-pharmacological intervention in pediatric health care, an integral part of pediatric palliative care (PPC). Yet, there is a lack of evidence of efficacy, and best practices are not well established. The nature and extent of physiologic impacts of MT in PPC have not previously been reported. This study explores how MT contributes to psycho-physiological changes in children receiving palliative care. We used a convergent mixed-methods feasibility study with a pre–post design. MT sessions were delivered to children (0–18 years), who were registered with a statewide Pediatric Palliative Care Service. Pre–post measures of pain and heart rate were collected using validated and objective measures and analyzed using mixed-model analysis. Analysis of 36 MT sessions demonstrated a statistically significant reduction in pain scores and heart rate after MT sessions. Post measures of pain measured with Face, Legs, Activity, Cry, Consolability scale (FLACC scale) scores were −1.57 (95% confidence interval [CI] −2.31 to −0.83) and by Likert pain scale −2.03 (95% CI −2.79 to −1.27). Heart rate reduced by a mean of −7.6 beats per minute (95% CI −10.74 to −3.37). Five parents participated in semi-structured interviews. Following thematic analysis, two major themes emerged: (1) MT has a positive impact on physiological symptoms and (2) MT enhances the opportunity to experience joy. Results demonstrate the feasibility of study components and may inform future research design for a larger study. This research contributes to the limited evidence about non-pharmacological interventions enhancing the quality of life for children receiving PPC.
vRhyme enables binning of viral genomes from metagenomes
Authors: Kieft Kristopher , Adams Alyssa , Salamzade Rauf , Kalan Lindsay , Anantharaman Karthik 
Published: April 2022

Abstract
Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs supervised machine learning to identify nucleotide feature similarities, which are compiled into iterations of weighted networks and refined bins. To refine bins, vRhyme utilizes unique features of viral genomes, namely a protein redundancy scoring mechanism based on the observation that viruses seldom encode redundant genes. Using simulated viromes, we displayed superior performance of vRhyme compared to available binning tools in constructing more complete and uncontaminated vMAGs. When applied to 10,601 viral scaffolds from human skin, vRhyme advanced our understanding of resident viruses, highlighted by identification of a Herelleviridae vMAG comprised of 22 scaffolds, and another vMAG encoding a nitrate reductase metabolic gene, representing near-complete genomes post-binning. vRhyme will enable a convention of binning uncultivated viral genomes and has the potential to transform metagenome-based viral ecology.
Rare central nervous system tumors in adults: a population-based study of ependymomas, pilocytic astrocytomas, medulloblastomas, and intracranial germ cell tumors
Authors: Ho Vincent K Y , Gijtenbeek Anja (J) M M , Wagemakers Michiel , Taal Walter , van Linde Myra E , Swaak-Kragten Annemarie T , Kurt Erkan , van der Weide Hiske L , Wesseling Pieter , de Vos Filip Y , Bromberg Jacoline E C 
Published: April 2022

Abstract

Background
Ependymomas, pilocytic astrocytomas, medulloblastomas, and intracranial germ cell tumors occur relative frequently in children, but are rare central nervous system (CNS) tumors in adults. In this population-based survey, we established incidence, treatment, and survival patterns for these tumors diagnosed in adult patients (≥18 years) over a 30-year period (1989–2018).

Methods
Data on 1384 ependymomas, 454 pilocytic astrocytomas, 205 medulloblastomas, and 112 intracranial germ cell tumors were obtained from the Netherlands Cancer Registry (NCR) on the basis of a histopathological diagnosis. For each tumor type, age-standardized incidence rates and estimated annual percentage change were calculated. Trends in incidence and main treatment modalities were reported per 5-year periods. Overall survival was calculated using the Kaplan–Meier method, and relative survival rates were estimated using the Pohar-Perme estimator.

Results
Incidence and survival rates remained generally stable for pilocytic astrocytomas, medulloblastomas, and germ cell tumors. Increasing incidence was observed for spinal ependymomas, mostly for myxopapillary ependymomas, and survival improved over time for grade II ependymomas (P &lt; .01). Treatment patterns varied over time with shifting roles for surgery in ependymomas and for chemotherapy and radiation in medulloblastomas and germinomas.

Conclusions
The study provides baseline information for highly needed national and international standard treatment protocols, and thus for further improving patient outcomes in these rare CNS tumors.