bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel Independent Losses of G-Type Lysozyme Genes in Hairless Aquatic Mammals
Authors: Zhang Xiaoqing , Chi Hai , Li Gang , Irwin David M , Zhang Shuyi , Rossiter Stephen J , Liu Yang 
Published: August 2021

Abstract
Lysozyme enzymes provide classic examples of molecular adaptation and parallel evolution, however, nearly all insights to date come from chicken-type (c-type) lysozymes. Goose-type (g-type) lysozymes occur in diverse vertebrates, with multiple independent duplications reported. Most mammals possess two g-type lysozyme genes (Lyg1 and Lyg2), the result of an early duplication, although some lineages are known to have subsequently lost one copy. Here we examine g-type lysozyme evolution across &gt;250 mammals and reveal widespread losses of either Lyg1 or Lyg2 in several divergent taxa across the mammal tree of life. At the same time, we report strong evidence of extensive losses of both gene copies in cetaceans and sirenians, with an additional putative case of parallel loss in the tarsier. To validate these findings, we inspected published short-read data and confirmed the presence of loss of function mutations. Despite these losses, comparisons of selection pressures between intact g- and c-type lysozyme genes showed stronger purifying selection in the former, indicative of conserved function. Although the reasons for the evolutionary loss of g-type lysozymes in fully aquatic mammals are not known, we suggest that this is likely to at least partially relate to their hairlessness. Indeed, although Lyg1 does not show tissue-specific expression, recent studies have linked Lyg2 expression to anagen hair follicle development and hair loss. Such a role for g-type lysozyme would explain why the Lyg2 gene became obsolete when these taxa lost their body hair.
Homologous Recombinational Repair of Double-Strand Breaks in Yeast Is Enhanced by MAT Heterozygosity Through yKU-Dependent and -Independent Mechanisms
Authors: Clikeman Jennifer A. , Khalsa Guru Jot , Barton Sandra L. , Nickoloff Jac A. 
Published: August 2021

Abstract
DNA double-strand breaks (DSBs) are repaired by homologous recombination (HR) and nonhomologous end-joining (NHEJ). NHEJ in yeast chromosomes has been observed only when HR is blocked, as in rad52 mutants or in the absence of a homologous repair template. We detected yKu70p-dependent imprecise NHEJ at a frequency of ∼0.1% in HR-competent Rad+ haploid cells. Interestingly, yku70 mutation increased DSB-induced HR between direct repeats by 1.3-fold in a haploid strain and by 1.5-fold in a MAT homozygous (a/a) diploid, but yku70 had no effect on HR in a MAT heterozygous (a/α) diploid. yku70 might increase HR because it eliminates the competing precise NHEJ (religation) pathway and/or because yKu70p interferes directly or indirectly with HR. Despite the yku70-dependent increase in a/a cells, HR remained 2-fold lower than in a/α cells. Cell survival was also lower in a/a cells and correlated with the reduction in HR. These results indicate that MAT heterozygosity enhances DSB-induced HR by yKu-dependent and -independent mechanisms, with the latter mechanism promoting cell survival. Surprisingly, yku70 strains survived a DSB slightly better than wild type. We propose that this reflects enhanced HR, not by elimination of precise NHEJ since this pathway produces viable products, but by elimination of yKu-dependent interference of HR.
The correlation of substitution effects across populations and generations in the presence of nonadditive functional gene action
Authors: Legarra Andres , Garcia-Baccino Carolina A. , Wientjes Yvonne C. J. , Vitezica Zulma G. 
Published: August 2021

AbstractAllele substitution effects at quantitative trait loci (QTL) are part of the basis of quantitative genetics theory and applications such as association analysis and genomic prediction. In the presence of nonadditive functional gene action, substitution effects are not constant across populations. We develop an original approach to model the difference in substitution effects across populations as a first order Taylor series expansion from a “focal” population. This expansion involves the difference in allele frequencies and second-order statistical effects (additive by additive and dominance). The change in allele frequencies is a function of relationships (or genetic distances) across populations. As a result, it is possible to estimate the correlation of substitution effects across two populations using three elements: magnitudes of additive, dominance, and additive by additive variances; relationships (Nei’s minimum distances or Fst indexes); and assumed heterozygosities. Similarly, the theory applies as well to distinct generations in a population, in which case the distance across generations is a function of increase of inbreeding. Simulation results confirmed our derivations. Slight biases were observed, depending on the nonadditive mechanism and the reference allele. Our derivations are useful to understand and forecast the possibility of prediction across populations and the similarity of GWAS effects.
The quantitative genetics of the prevalence of infectious diseases: hidden genetic variation due to indirect genetic effects dominates heritable variation and response to selection
Authors: Bijma Piter , Hulst Andries D , de Jong Mart C M 
Published: August 2021

AbstractInfectious diseases have profound effects on life, both in nature and agriculture. However, a quantitative genetic theory of the host population for the endemic prevalence of infectious diseases is almost entirely lacking. While several studies have demonstrated the relevance of transmission of infections for heritable variation and response to selection, current quantitative genetics ignores transmission. Thus, we lack concepts of breeding value and heritable variation for endemic prevalence, and poorly understand response of endemic prevalence to selection. Here, we integrate quantitative genetics and epidemiology, and propose a quantitative genetic theory for the basic reproduction number R0 and for the endemic prevalence of an infection. We first identify the genetic factors that determine the prevalence. Subsequently, we investigate the population-level consequences of individual genetic variation, for both R0 and the endemic prevalence. Next, we present expressions for the breeding value and heritable variation, for endemic prevalence and individual binary disease status, and show that these depend strongly on the prevalence. Results show that heritable variation for endemic prevalence is substantially greater than currently believed, and increases strongly when prevalence decreases, while heritability of disease status approaches zero. As a consequence, response of the endemic prevalence to selection for lower disease status accelerates considerably when prevalence decreases, in contrast to classical predictions. Finally, we show that most heritable variation for the endemic prevalence is hidden in indirect genetic effects, suggesting a key role for kin-group selection in the evolutionary history of current populations and for genetic improvement in animals and plants.
Early-Life Stress Induces Prodromal Features of Parkinsonism in Ageing Rats
Authors: Ren Chao , Wang Fen , He Kai-Jie , Zhang Yu-Ting , Li Ling-Xi , Zhang Jin-Bao , Chen Jing , Mao Cheng-Jie , Liu Chun-Feng 
Published: August 2021

Abstract
Early-life stress (ELS) can cause long-term effects on human health, ranging from adolescence to adulthood, and even to gerontic. Although clinical retrospective data suggest that ELS may be related to senile neurodegenerative diseases such as Parkinson’s disease (PD), there are few prospective investigations to explore its real contribution to PD. Here, we investigated the behavioral, histochemical, neuromorphological, and transcriptional changes induced by maternal separation (MS), an ELS model. Without neurotoxin, MS rats showed behavioral alterations in olfaction, locomotion, and gait characters after depression compared with control rats. Based on neuroimaging and histochemistry, although we found that the dopaminergic system in the striatum was impaired after MS, the decrease of striatal dopamine level was ~33%. Consistently, tyrosine hydroxylase immunostaining positive neurons of MS rats in the substantia nigra showed deficit by about 20% in cell counting. Furthermore, using transcriptome sequencing, we discovered many differentially expressed genes (DEGs) of MS rats in the striatum significantly enriched in the pathway of dopaminergic synapse, and the biological process of locomotion and neuromuscular process controlling balance. Encouragingly, some representative DEGs relating to PD were singled out. These results suggest that ELS-depression rats potentially mimic some key features of prodromal stage of PD during natural senescence. In conclusion, our findings provide some novel insights into the future pathogenesis and therapeutic studies for PD related to depression.
Canagliflozin Increases Intestinal Adenoma Burden in Female ApcMin/+ Mice
Authors: Korfhage Justin , Skinner Mary E , Basu Jookta , Greenson Joel K , Miller Richard A , Lombard David B 
Published: August 2021

Abstract
The diabetes drug canagliflozin extends life span in male mice. Since malignant neoplasms are the major cause of death in most mouse strains, this observation suggests that canagliflozin might exert anti-neoplastic effects in male mice. Here, we treated a mouse neoplasia model, the adenoma-prone ApcMin/+ strain, with canagliflozin, to test the effects of this drug on intestinal tumor burden. Surprisingly, canagliflozin increased the total area of intestine involved by adenomas, an effect most marked in the distal intestine and in female mice. Immunohistochemical analysis suggested that canagliflozin may not influence adenoma growth via direct SGLT1/2 inhibition in neoplastic cells. Our results are most consistent with a model where canagliflozin aggravates adenoma development by altering the anatomic distribution of intestinal glucose absorption, as evidenced by increases in postprandial GLP-1 levels driven by delayed glucose absorption. We hypothesize that canagliflozin exacerbates adenomatosis in the ApcMin/+ model via complex, cell-non-autonomous mechanisms, and that sex differences in GLP-1 responses may in part underlie sexually dimorphic effects of this drug on life span.
Trans-Ethnic Meta-Analysis of Interactions Between Genetics and Early-Life Socioeconomic Context on Memory Performance and Decline in Older Americans
Authors: Faul Jessica D , Kho Minjung , Zhao Wei , Rumfelt Kalee E , Yu Miao , Mitchell Colter , Smith Jennifer A 
Published: August 2021

AbstractBackgroundLater-life cognitive function is influenced by genetics as well as early- and later-life socioeconomic context. However, few studies have examined the interaction between genetics and early childhood factors.MethodsUsing gene-based tests (interaction sequence kernel association test [iSKAT]/iSKAT optimal unified test), we examined whether common and/or rare exonic variants in 39 gene regions previously associated with cognitive performance, dementia, and related traits had an interaction with childhood socioeconomic context (parental education and financial strain) on memory performance or decline in European ancestry (EA, N = 10 468) and African ancestry (AA, N = 2 252) participants from the Health and Retirement Study.ResultsOf the 39 genes, 22 in EA and 19 in AA had nominally significant interactions with at least one childhood socioeconomic measure on memory performance and/or decline; however, all but one (father’s education by solute carrier family 24 member 4 [SLC24A4] in AA) were not significant after multiple testing correction (false discovery rate [FDR] &lt; .05). In trans-ethnic meta-analysis, 2 genes interacted with childhood socioeconomic context (FDR &lt; .05): mother’s education by membrane-spanning 4-domains A4A (MS4A4A) on memory performance, and father’s education by SLC24A4 on memory decline. Both interactions remained significant (p &lt; .05) after adjusting for respondent’s own educational attainment, apolipoprotein-ε4 allele (APOE ε4) status, lifestyle factors, body mass index, and comorbidities. For both interactions in EA and AA, the genetic effect was stronger in participants with low parental education.ConclusionsExamination of common and rare variants in genes discovered through genome-wide association studies shows that childhood context may interact with key gene regions to jointly impact later-life memory function and decline. Genetic effects may be more salient for those with lower childhood socioeconomic status.
Do Perceptions of Cognitive Changes Matter in Self-Management Behaviors Among Persons With Mild Cognitive Impairment?
Authors: Kim Hyejin , Sereika Susan M , Albert Steven M , Bender Catherine M , Lingler Jennifer H 
Published: August 2021

Abstract

Background and Objectives
This secondary analysis examined (a) the association between illness perceptions (perceived understanding and cause of mild cognitive impairment [MCI]) and self-management behaviors for cognitive health, and (b) whether sociodemographic and clinical factors moderate such relationships among persons with MCI.

Research Design and Methods
We conducted a cross-sectional study of 85 participants using baseline data from the Return of Amyloid Imaging Scan Results Study. The coherence and causality subscales of the Revised Illness Perceptions Questionnaires were used. Self-management behaviors (dietary changes, physical activity, mental activities, dietary supplements) were assessed using the Risk Evaluation and Education for ALzheimer’s disease health behavior measure. Sociodemographic and clinical information was extracted from patients’ medical records. We performed hierarchical linear regression and binary logistic regression.

Results
We found no main effects for illness perceptions and self-management of cognitive health. Interaction effects were detected, including (a) coherence and age on the total number of self-management behaviors (b = 0.01, p = .04) and on physical activity (p = .04, odds ratio [OR] = 1.02, 95% confidence interval [CI] = 1.00–1.03), (b) causality and age on dietary supplements (p = .03, OR = 1.31, 95% CI = 1.02–1.67), and (c) causality and education on mental activities (p = .02, OR = 0.44, 95% CI = 0.22–0.88).

Discussion and Implications
Findings suggest that age and education moderate the relationship between illness perceptions and self-management behaviors. Health care professionals should consider subjective perceptions about MCI in light of sociodemographic and clinical factors when discussing cognitive health self-management.
Once after a full moon: acute type A aortic dissection and lunar phases
Authors: Bjursten Henrik , Oudin Åström Daniel , Nozohoor Shahab , Ahmad Khalil , Tang Mariann , Bjurbom Markus , Hansson Emma C , Jeppsson Anders , Joost Holdflod Møller Christian , Jormalainen Miko , Juvonen Tatu , Mennander Ari , Olsen Peter S , Olsson Christian , Ahlsson Anders , Oudin Anna , Pan Emily , Raivio Peter , Wickbom Anders , Sjögren Johan , Geirsson Arnar , Gudbjartsson Tomas , Zindovic Igor 
Published: August 2021

Abstract

OBJECTIVES
Acute type A aortic dissection (ATAAD) is a rare but severe condition, routinely treated with emergent cardiac surgery. Many surgeons have the notion that patients with ATAAD tend to come in clusters, but no studies have examined these observations. This investigation was undertaken to study the potential association between the lunar cycle and the incidence of ATAAD.

METHODS
We collected information on 2995 patients who underwent ATAAD surgery at centres from the Nordic Consortium for Acute Type A Aortic Dissection collaboration. We cross-referenced the time of surgery with lunar phase using a case-crossover design with 2 different definitions of full moon (&gt;99% illumination and the 7-day full moon period).

RESULTS
The period when the moon was illuminated the most (99% definition) did not show any significant increase in incidence for ATAAD surgery. However, when the full moon period was compared with all other moon phases, it yielded a relative risk of 1.08 [95% confidence interval (CI) 1.00–1.17, P = 0.057] and, compared to waxing moon, only the relative risk was 1.11 (95% CI 1.01–1.23, P = 0.027). The peak incidence came 4–6 days after the moon was fully illuminated.

CONCLUSIONS
This study found an overrepresentation of surgery for ATAAD during the full moon phase. The explanation for this is not known, but we speculate that sleep deprivation during full moon leads to a temporary increase in blood pressure, which in turn could trigger rupture of the aortic wall. While this finding is interesting, it needs to be corroborated and the clinical implications are debateable.
On the resolution requirements for accurately representing interactions between plant canopy structure and function in three-dimensional leaf-resolving models
Authors: Bailey Brian N , Kent Eric R 
Published: August 2021

Abstract
While functional–structural plant models (FSPMs) have been proposed as a tool for better analysing and predicting interactions between plant structure and function, it is still unclear as to what spatial resolution is required to adequately resolve such interactions. Shadows cast by neighbouring leaves in a plant canopy create extremely large spatial gradients in absorbed radiation at the sub-leaf scale, which are usually not fully resolved in ‘leaf-resolving’ plant models. This failure to resolve sharp radiative gradients can propagate to other dependent biophysical models, and result in dramatic overprediction of whole-plant and -canopy fluxes with errors significantly higher than that of a statistical ‘big leaf’ or turbid medium model. Under-resolving radiative gradients creates a diffusive effect in the probability distribution of absorbed radiation, and smears out the effect of canopy structure, effectively undermining the original goal of a leaf-resolving model. Errors in whole-canopy fluxes of photosynthesis increased approximately linearly with increasing LAI, projected area fraction G, and decreased logarithmically as the fraction of incoming diffuse radiation was increased. When only one discrete element per leaf was used, errors in whole-canopy net CO2 flux could be in excess of 100 %. Errors due to sub-leaf resolution decreased exponentially as the number of elements per leaf was increased. These results prompt closer consideration of the impact of sub-leaf resolution on model errors, which is likely to prompt an increase in resolution relative to current common practice.
Detailed reconstruction of trees from terrestrial laser scans for remote sensing and radiative transfer modelling applications
Authors: Janoutová Růžena , Homolová Lucie , Novotný Jan , Navrátilová Barbora , Pikl Miroslav , Malenovský Zbyněk 
Published: August 2021

AbstractThis study presents a method for three-dimensional (3D) reconstruction of forest tree species that are, for instance, required for simulations of 3D canopies in radiative transfer modelling. We selected three forest species of different architecture: Norway spruce (Picea abies) and European beech (Fagus sylvatica), representatives of European production forests, and white peppermint (Eucalyptus pulchella), a common forest species of Tasmania. Each species has a specific crown structure and foliage distribution. Our algorithm for 3D model construction of a single tree is based on terrestrial laser scanning (TLS) and ancillary field measurements of leaf angle distribution, percentage of current-year and older leaves, and other parameters that could not be derived from TLS data. The algorithm comprises four main steps: (i) segmentation of a TLS tree point cloud separating wooden parts from foliage, (ii) reconstruction of wooden parts (trunks and branches) from TLS data, (iii) biologically genuine distribution of foliage within the tree crown and (iv) separation of foliage into two age categories (for spruce trees only). The reconstructed 3D models of the tree species were used to build virtual forest scenes in the Discrete Anisotropic Radiative Transfer model and to simulate canopy optical signals, specifically: angularly anisotropic top-of-canopy reflectance (for retrieval of leaf biochemical compounds from nadir canopy reflectance signatures captured in airborne imaging spectroscopy data) and solar-induced chlorophyll fluorescence signal (for experimentally unfeasible sensitivity analyses).
Using evolutionary functional–structural plant modelling to understand the effect of climate change on plant communities
Authors: de Vries Jorad 
Published: August 2021

AbstractThe ‘holy grail’ of trait-based ecology is to predict the fitness of a species in a particular environment based on its functional traits, which has become all the more relevant in the light of global change. However, current ecological models are ill-equipped for this job: they rely on statistical methods and current observations rather than the mechanisms that determine how functional traits interact with the environment to determine plant fitness, meaning that they are unable to predict ecological responses to novel conditions. Here, I advocate the use of a 3D mechanistic modelling approach called functional–structural plant (FSP) modelling in combination with evolutionary modelling to explore climate change responses in natural plant communities. Gaining a mechanistic understanding of how trait–environment interactions drive natural selection in novel environments requires consideration of individual plants with multidimensional phenotypes in dynamic environments that include abiotic gradients and biotic interactions, and their combined effect on the different vital rates that determine plant fitness. Evolutionary FSP modelling explicitly simulates the trait–environment interactions that drive eco-evolutionary dynamics from individual to community scales and allows for efficient navigation of the large, complex and dynamic fitness landscapes that emerge from considering multidimensional plants in multidimensional environments. Using evolutionary FSP modelling as a tool to study climate change responses of plant communities can further our understanding of the mechanistic basis of these responses, and in particular, the role of local adaptation, phenotypic plasticity and gene flow.