bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Neurospora rca-1 Gene Complements an Aspergillus flbD Sporulation Mutant but Has No Identifiable Role in Neurospora Sporulation
Authors: Shen Wei-Chiang , Wieser Jenny , Adams Thomas H , Ebbole Daniel J 
Published: February 2021

Abstract
The Aspergillus nidulans flbD gene encodes a protein with a Myb-like DNA-binding domain that is proposed to act in concert with other developmental regulators to control initiation of conidiophore development. We have identified a Neurospora crassa gene called rca-1 (regulator of conidiation in Aspergillus) based on its sequence similarity to flbD. We found that N. crassa rca-1 can complement the conidiation defect of an A. nidulans flbD mutant and that induced expression of rca-1 caused conidiation in submerged A. nidulans cultures just as was previously observed for overexpression of flbD. Thus, the N. crassa gene appears to be a functional homologue of A. nidulans flbD and this is the first demonstration of functional complementation of an A. nidulans sporulation defect using a gene from an evolutionarily distant fungus. However, deletion of the rca-1 gene in N. crassa had no major effect on growth rate, macroconidiation, microconidiation, or ascospore formation. The only phenotype displayed by the rca-1 mutant was straight or counterclockwise hyphal growth rather than the clockwise spiral growth observed for wild type. Thus, if rca-1 is involved in N. crassa development, its role is subtle or redundant.
Marker-Assisted Selection Efficiency in Populations of Finite Size
Authors: Moreau Laurence , Charcosset Alain , Hospital Frédéric , Gallais André 
Published: February 2021

Abstract
The efficiency of marker-assisted selection (MAS) based on an index incorporating both phenotypic and molecular information is evaluated with an analytical approach that takes into account the size of the experiment. We consider the case of a population derived from a cross between two homozygous lines, which is commonly used in plant breeding, and we study the relative efficiency of MAS compared with selection based only on phenotype in the first cycle of selection. It is shown that the selection of the markers included in the index leads to an overestimation of the effects associated with these markers. Taking this bias into account, we study the influence of several parameters, including experiment size and heritability, on MAS efficiency. Even if MAS appears to be most interesting for low heritabilities, we point out the existence of an optimal heritability (~0.2) below which the low power of quantitative trait loci detection and the bias caused by the selection of markers reduce the efficiency. In this situation, increasing the power of detection by using a higher probability of type I error can improve MAS efficiency. This approach, validated by simulations, gives results that are generally consistent with those previously obtained by simulations using a more sophisticated biological model than ours. Thus, though developed from a simple genetic model, our approach may be a useful tool to optimize the experimental means for more complex genetic situations.
Cell Cycle Arrest in cdc20 Mutants of Saccharomyces cerevisiae Is Independent of Ndc10p and Kinetochore Function but Requires a Subset of Spindle Checkpoint Genes
Authors: Tavormina Penny A , Burke Daniel J 
Published: February 2021

Abstract
The spindle checkpoint ensures accurate chromosome segregation by inhibiting anaphase onset in response to altered microtubule function and impaired kinetochore function. In this study, we report that the ability of the anti-microtubule drug nocodazole to inhibit cell cycle progression in Saccharomyces cerevisiae depends on the function of the kinetochore protein encoded by NDC10. We examined the role of the spindle checkpoint in the arrest in cdc20 mutants that arrest prior to anaphase with an aberrant spindle. The arrest in cdc20 defective cells is dependent on the BUB2 checkpoint and independent of the BUB1, BUB3, and MAD spindle checkpoint genes. We show that the lesion recognized by Bub2p is not excess microtubules, and the cdc20 arrest is independent of kinetochore function. We show that Cdc20p is not required for cyclin proteolysis at two points in the cell cycle, suggesting that CDC20 is distinct from genes encoding integral proteins of the anaphase promoting complex.
Approximate Analysis of QTL-Environment Interaction with No Limits on the Number of Environments
Authors: Korol Abraham B , Ronin Yefim I , Nevo Eviatar 
Published: February 2021

Abstract
An approach is presented here for quantitative trait loci (QTL) mapping analysis that allows for QTL × environment (E) interaction across multiple environments, without necessarily increasing the number of parameters. The main distinction of the proposed model is in the chosen way of approximation of the dependence of putative QTL effects on environmental states. We hypothesize that environmental dependence of a putative QTL effect can be represented as a function of environmental mean value of the trait. Such a description can be applied to take into account the effects of any cosegregating QTLs from other genomic regions that also may vary across environments. The conducted Monte-Carlo simulations and the example of barley multiple environments experiment demonstrate a high potential of the proposed approach for analyzing QTL × E interaction, although the results are only approximated by definition. However, this drawback is compensated by the possibility to utilize information from a potentially unlimited number of environments with a remarkable reduction in the number of parameters, as compared to previously proposed mapping models with QTL × E interactions.
The Homeobox Gene cut Interacts Genetically With the Homeotic Genes proboscipedia and Antennapedia
Authors: Johnston Laura A , Ostrow Bruce D , Jasoni Christine , Blochlinger Karen 
Published: February 2021

Abstract
The cut locus (ct) codes for a homeodomain protein (Cut) and controls the identity of a subset of cells in the peripheral nervous system in Drosophila. During a screen to identify ct-interacting genes, we observed that flies containing a hypomorphic ct mutation and a heterozygous deletion of the Antennapedia complex exhibit a transformation of mouthparts into leg and antennal structures similar to that seen in homozygous proboscipedia (pb) mutants. The same phenotype is produced with all heterozygous pb alleles tested and is fully penetrant in two different ct mutant backgrounds. We show that this phenotype is accompanied by pronounced changes in the expression patterns of both ct and pb in labial discs. Furthermore, a significant proportion of ct mutant flies that are heterozygous for certain Antennapedia (Antp) alleles have thoracic defects that mimic loss-of-function Antp phenotypes, and ectopic expression of Cut in antennal discs results in ectopic Antp expression and a dominant Antp-like phenotype. Our results implicate ct in the regulation of expression and/or function of two homeotic genes and document a new role of ct in the control of segmental identity.
Multigene Family of Ribosomal DNA in Drosophila melanogaster Reveals Contrasting Patterns of Homogenization for IGS and ITS Spacer Regions: A Possible Mechanism to Resolve This Paradox
Authors: Polanco Carlos , González Ana I , de la Fuente Álvaro , Dover Gabriel A 
Published: February 2021

AbstractThe multigene family of rDNA in Drosophila reveals high levels of within-species homogeneity and between-species diversity. This pattern of mutation distribution is known as concerted evolution and is considered to be due to a variety of genomic mechanisms of turnover (e.g., unequal crossing over and gene conversion) that underpin the process of molecular drive. The dynamics of spread of mutant repeats through a gene family, and ultimately through a sexual population, depends on the differences in rates of turnover within and between chromosomes. Our extensive molecular analysis of the intergenic spacer (IGS) and internal transcribed spacer (ITS) spacer regions within repetitive rDNA units, drawn from the same individuals in 10 natural populations of Drosophila melanogaster collected along a latitudinal cline on the east coast of Australia, indicates a relatively fast rate of X-Y and X-X interchromosomal exchanges of IGS length variants in agreement with a multilineage model of homogenization. In contrast, an X chromosome-restricted 24-bp deletion in the ITS spacers is indicative of the absence of X-Y chromosome exchanges for this region that is part of the same repetitive rDNA units. Hence, a single lineage model of homogenization, coupled to drift and/or selection, seems to be responsible for ITS concerted evolution. A single-stranded exchange mechanism is proposed to resolve this paradox, based on the role of the IGS region in meiotic pairing between X and Y chromosomes in D. melanogaster.
Bias in two-sample Mendelian randomization when using heritable covariable-adjusted summary associations
Authors: Hartwig Fernando Pires , Tilling Kate , Davey Smith George , Lawlor Deborah A , Borges Maria Carolina 
Published: February 2021

Abstract

Background
Two-sample Mendelian randomization (MR) allows the use of freely accessible summary association results from genome-wide association studies (GWAS) to estimate causal effects of modifiable exposures on outcomes. Some GWAS adjust for heritable covariables in an attempt to estimate direct effects of genetic variants on the trait of interest. One, both or neither of the exposure GWAS and outcome GWAS may have been adjusted for covariables.

Methods
We performed a simulation study comprising different scenarios that could motivate covariable adjustment in a GWAS and analysed real data to assess the influence of using covariable-adjusted summary association results in two-sample MR.

Results
In the absence of residual confounding between exposure and covariable, between exposure and outcome, and between covariable and outcome, using covariable-adjusted summary associations for two-sample MR eliminated bias due to horizontal pleiotropy. However, covariable adjustment led to bias in the presence of residual confounding (especially between the covariable and the outcome), even in the absence of horizontal pleiotropy (when the genetic variants would be valid instruments without covariable adjustment). In an analysis using real data from the Genetic Investigation of ANthropometric Traits (GIANT) consortium and UK Biobank, the causal effect estimate of waist circumference on blood pressure changed direction upon adjustment of waist circumference for body mass index.

Conclusions
Our findings indicate that using covariable-adjusted summary associations in MR should generally be avoided. When that is not possible, careful consideration of the causal relationships underlying the data (including potentially unmeasured confounders) is required to direct sensitivity analyses and interpret results with appropriate caution.
Feix–Kaledin Metric on the Total Spaces of Cotangent Bundles to Kähler Quotients
Authors: Abasheva Anna 
Published: February 2021

Abstract
In this paper, we study the geometry of the total space $Y$ of a cotangent bundle to a Kähler manifold $N$ where $N$ is obtained as a Kähler reduction from $\mathbb{C}^n$. Using the hyperkähler reduction, we construct a hyperkähler metric on $Y$ and prove that it coincides with the canonical Feix–Kaledin metric. This metric is in general non-complete. We show that the metric completion $\widetilde Y$ of the space $Y$ is equipped with a structure of a stratified hyperkähler space (in the sense of [ 31]). We give a necessary condition for the Feix–Kaledin metric to be complete using an observation of R. Bielawski. Pick a complex structure $J$ on $\widetilde Y$ induced from the quaternions. Suppose that $J\ne \pm I$ where $I$ is the complex structure whose restriction to $Y = T^{*}N$ is induced by the complex structure on $N$. We prove that the space $\widetilde{Y}_J$ admits an algebraic structure and is an affine variety.
Potential roles of G-quadruplex structures in RNA granules for physiological and pathological phase separation
Authors: Asamitsu Sefan , Shioda Norifumi 
Published: February 2021

Abstract
Cellular liquid–liquid phase separation is a physiologically inevitable phenomenon in molecularly crowded environments inside cells and serves to compartmentalize biomolecules to facilitate several functions, forming cytoplasmic and nuclear RNA granules. Abnormalities in the phase separation process in RNA granules are implicated in the onset of several neurodegenerative diseases; the initial liquid-like phase-separated droplets containing pathogenic proteins are prone to aberrantly mature into solid-like droplets. RNAs are involved in the maturation of physiological and pathological RNA granules and are essential for governing the fate of phase-transition processes. Notably, RNA G-quadruplex (G4RNA), which is the secondary structure of nucleic acids that are formed in guanine-rich sequences, appears to be an advantageous scaffold for RNA-derived phase separation because of its multivalent interactions with RNAs and RNA-binding proteins. Here, we summarize the properties of RNA granules in physiological and pathological phase separation and discuss the potential roles of G4RNA in granules.
Estimation of the Postmortem Interval Through the Use of Development Time of Two South American Species of Forensic Importance of the Genus Lucilia (Diptera: Calliphoridae)
Authors: Acosta Ximena , González-Reyes Andrea X , Corronca José A , Centeno Néstor D 
Published: February 2021

Abstract
Obtaining the specific development time of each species of forensic interest is crucial for the estimation of an accurate and reliable Minimum Postmortem Interval (PMImin). In Argentina, Lucilia ochricornis (Wiedemann) and Lucilia purpurascens (Walker) (Diptera: Calliphoridae) were masked under the name Lucilia cluvia (Walker) for a long time still in forensic expertise. For this reason, the objective of this work is to deepen the study of the development time of these species and utilize this relevant information in the generation of different associated methods that can be used in forensics to estimate the PMI. Immature stages of L. ochricornis and L. purpurascens were reared in a brood chamber according to the following temperature treatments: 13.4, 15.1, 22.3, and 23.6°C. The development time of each stage/state of these flies was recorded as well as the resulting accumulated degree-hours (ADH), to build isomorphen diagrams and thermal summation models for each species. The development time and ADH were different between both species and their development stages. On the other hand, the methods provided for estimating PMImin provide the forensic entomologist more tools to reach accurate and reliable estimates.
High Frequency of Recurrent Falls Among Prefrail and Frail Women With and Without HIV
Authors: Sharma Anjali , Hoover Donald R. , Shi Qiuhu , Gustafson Deborah R. , Plankey Michael , Tien Phyllis C , Weber Kathleen M. , Vance David E. , Floris-Moore Michelle , Bolivar Hector H. , Golub Elizabeth T. , Holstad Marcia M. , Yin Michael T. 
Published: February 2021

Background:
Frailty may occur at younger ages among HIV+ populations. We evaluated associations of the frailty status with self-reported single and recurrent falls in the Women's Interagency HIV Study (WIHS).

Methods:
The frailty status was defined using the Fried Frailty Phenotype (FFP) among 897 HIV+ and 392 HIV− women; median age 53 years. Women were classified as robust (FFP 0), prefrail (FFP 1–2), and frail (FFP 3–5). Stepwise logistic regression models adjusting for the HIV status and study site were fit to evaluate associations of the FFP with self-reported single (1 vs. 0) and recurrent falls (≥2 vs. 0) over the prior 12 months.

Results:
HIV+ women were less likely to be frail (9% vs. 14% vs. P = 0.009), but frequency of falls did not differ by the HIV status. In multivariate analyses, recurrent falls were more common among prefrail [adjusted odds ratio (AOR) 2.23, 95% confidence interval (CI): 1.40 to 3.57, P = 0.0008] and frail (AOR 3.61, 95% CI: 1.90 to 6.89, P < 0.0001) than robust women. Among HIV+ women, single (AOR 2.88, 95% CI: 1.16 to 7.20, P = 0.023) and recurrent falls (AOR 3.50, 95% CI: 1.24 to 9.88, P = 0.018) were more common among those who were frail; recurrent, but not single falls, were more common among prefrail than robust HIV+ women (AOR 2.00, 95% CI: 1.03 to 3.91, P = 0.042).

Conclusions:
HIV+ women were less likely to be frail. Compared with robust women, prefrail and frail women with and without HIV were more likely to experience single or recurrent falls within a 12-month period. Additional studies are needed to develop interventions that decrease development of frailty and reduce risk of recurrent falls among HIV+ women.
AeroForm Tissue Expander
Authors: Huang Hao , Bogue Jarrod T. , Otterburn David M. 
Published: February 2021

Background
Device-based reconstruction, the most common approach to breast reconstruction, typically occurs in 2 stages to allow for the breast envelope to be expanded serially before exchanging for a permanent implant. The AeroForm tissue expander is a carbon dioxide–based expansion system that allows for patient-initiated filling, and compared with the traditional saline expander, it has been shown to decrease the median time to full expansion and implant exchange. Furthermore, multiple changes have been incorporated into the newer V2.5 iteration resulting in reductions in device-related malfunctions, including overinflation.

Case Presentation
A 57-year-old woman who had a diagnosis of stage 1 ductal carcinoma in situ (T1c = 1.3 cm, ER/PR-negative, HER2-positive) underwent bilateral nipple-sparing mastectomy with sentinel lymph node biopsy and V2.5 AeroForm expander reconstruction. The procedure and subsequent postoperative follow-up visits were unremarkable without complications. However, once she entered an magnetic resonance imaging examination room for evaluation of an incidentally found meningioma, the carbon dioxide reservoir valve in both expanders was suddenly activated, releasing filling gas and maximally inflating the device to its 800-mL capacity. She elected to retain the expanders, and they were exchanged for permanent silicone implants 1 month later.

Conclusions
Although the V2.5 AeroForm expander is associated with a much lower rate of overinflation than its predecessor, our case suggests that autoexpansion remains of concern and likely occurs via a different mechanism when the device is subjected to clinical strength magnetic field. Clinicians should not order magnetic resonance imaging scans for women with AeroForm expanders due to the risk of unintended expansion.
A genetically-informed study disentangling the relationships between tobacco smoking, cannabis use, alcohol consumption, substance use disorders and respiratory infections, including COVID-19
Authors: Rosoff Daniel B. , Yoo Joyce , Lohoff Falk W. 
Published: February 2021

ABSTRACTBackgroundObservational studies suggest smoking, cannabis use, alcohol consumption, cannabis use, and substance use disorders (SUDs) may play a role in the susceptibility for respiratory infections and disease, including coronavirus 2019 (COVID-2019). However, causal inference is challenging due to comorbid substance use.MethodsUsing genome-wide association study data of European ancestry (data from >1.7 million individuals), we performed single-variable and multivariable Mendelian randomization to evaluate relationships between smoking, cannabis use, alcohol consumption, SUDs, and respiratory infections.ResultsGenetically predicted lifetime smoking was found to be associated with increased risk for hospitalized COVID-19 (odds ratio (OR)=4.039, 95% CI 2.335-6.985,P-value=5.93×10−7) and very severe hospitalized COVID-19 (OR=3.091, 95% CI, 1.883-5.092,P-value=8.40×10−6). Genetically predicted lifetime smoking was also associated with increased risk pneumoniae (OR=1.589, 95% CI, 1.214-2.078,P-value=7.33×10−4), lower respiratory infections (OR=2.303, 95% CI, 1.713-3.097,P-value=3.40×10−8), and several others. Genetically predicted cannabis use disorder (CUD) was associated with increased bronchitis risk (OR=1.078, 95% CI, 1.020-1.128,P-value=0.007).ConclusionsWe provide strong genetic evidence showing smoking increases the risk for respiratory infections and diseases even after accounting for other substance use and abuse. Additionally, we provide find CUD may increase the risk for bronchitis, which taken together, may guide future research SUDs and respiratory outcomes.
The effect of TTM-based nutrition education on decisional balance, self-efficacy and processes of change for fat intake
Authors: Gordali Maedeh , Bazhan Marjan , Ghaffari Mohtasham , Omidvar Nasrin , Rashidkhani Bahram 
Published: February 2021

PurposeThe purpose of this study is to determine how transtheoretical model (TTM) constructions change through nutrition education for fat intake modification among overweight and obese women living in Shazand city, Iran.Design/methodology/approachA semi-experimental design with intervention and control groups (50 women in each group) was performed. TTM constructions for dietary fat intake were measured through a questionnaire in four phases: before the intervention, immediately, one month and six months after the intervention. Participants in two groups were classified into inactive and active subgroups, based on their determined stage of change. Then in the intervention group, each subgroup received a separate education program of five or eight sessions for the active and inactive subgroups, respectively.FindingsThe intervention resulted in significant progress in participants' stage of change compared to the control group (p = 0.002). Also, it resulted in an increase in the self-efficacy and decisional balance scores in both of the intervention subgroups, with these effects being more pronounced in the inactive subgroup, and these significant differences, compared to the control group, remained in the third and fourth phases. The intervention also positively impacted the behavioral processes, but this effect was not so long-lasting and decreased after six months.Originality/valueThe results indicated the intervention effectiveness and the necessity of planning educational interventions to change fat consumption behavior. This study provides further insight into effective and sustainable nutrition education strategies based on behavioral change stages rather than traditional approaches. These methods should be used to design group interventions to change individuals' health behavior in future works.