bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sex differences in the strength of selection under facultative sex
Authors: Haaland Thomas R. , Ebert Dieter , Kokko Hanna 
Published: October 2021

AbstractFacultative sex, the ability to reproduce both sexually and asexually, is widespread across the tree of life. In anisogamous species, the frequency of sex modulates selection on traits with sex-specific expression. Current theory on conditional gene expression posits that the strength of selection on loci only expressed by a subset of individuals, and/or in a subset of environments, is proportional to the frequency of expressers in the population. We show here that this assumption does not hold when the subsets in question are males or females (because of the Fisher condition) and is most important in facultatively sexual populations. In this case, the proportion of sexually produced offspring is not determined by male frequency (sex ratio), but on relative female investment in sexual versus asexual reproduction. This breaks the link between the frequency of expressers and selection for loci with sex-specific expression. However, certain conditions can re-establish this link, for example male traits that predict mating success better under strong male-male competition, and sex ratio affecting the relative fecundity of sexual versus asexual females. Our work highlights the importance of the Fisher condition for understanding the efficiency of selection and has implications for differences in the genetic load among sexes.
Survey evaluation of dog owners’ feeding habits in a household setting and comparison of FDA hygiene protocols on dog bowl bacterial contamination as evaluated by total aerobic cell counts
Authors: Luisana Emily , Saker Korinn , Jaykus Lee-Ann , Getty Caitlyn 
Published: October 2021

AbstractIn-home pet food handling and food dish hygiene practices can have adverse health impacts for both humans and pets. Safe food and dish handling guidelines are not easily evidenced for pet owners. The study was designed to investigate dog owners’ feeding habits and evaluate the impact of the Food and Drug Association (FDA) hygiene protocols on dog food dish contamination. Procedures and surveys were approved by NCSU-IACUC and -IRB. Pet feeding and food dish hygiene data were collected from 417 dog owner surveys and 68 food dish swabs. Total aerobic cell counts (TAC) were performed on 68 dishes and randomly assigned into Group A (FDA pet food handling and dish hygiene guidelines), Group B (FDA pet and human food handling and dish hygiene guidelines), or Group C (no guidelines). Hygiene protocols were instituted in-home for 1 week, followed by a second TAC and follow-up survey. Survey from dog owners-households indicated: 4.7% were aware of FDA pet food handling and dish hygiene guidelines; 36% have individuals ≤ 13 years old and/or immunocompromised; 43% store dog food 0-5 feet from human food; 34% wash their hands after feeding; and 33% prepare their dog food on human food preparation surfaces. The hygiene protocols followed by Groups A and B resulted in significant decreases in food dish TAC (P<0.001; 1.40; p=0.026; 0.604, respectively), as compared to Group C (p=0.373). Hot water (>160F) washing decreased TAC (p=0.005) over cold/lukewarm water. In the follow-up survey, 8% of Group A and B respondents reported likely to adhere to protocols long-term. This study suggests a need for pet food handling and dish hygiene guideline education to minimize bacterial contamination of dishes, especially in high-risk households.
Pupillometry and electroencephalography in the digit span task
Authors: Pavlov Yuri G. , Kasanov Dauren , Kosachenko Alexandra I. , Kotyusov Alexander I. , Busch Niko A. 
Published: October 2021

AbstractThis dataset consists of raw 64-channel EEG, cardiovascular (electrocardiography and photoplethysmography), and pupillometry data from 86 human participants recorded during 4 minutes of eyes-closed resting and during performance of a classic working memory task – digit span task with serial recall. The participants either memorized or just listened to sequences of 5, 9, or 13 digits presented auditorily every 2 seconds. The dataset can be used for (1) developing algorithms for cognitive load discrimination and detection of cognitive overload; (2) studying neural (event-related potentials and brain oscillations) and peripheral (electrocardiography, photoplethysmography, and pupillometry) physiological signals during encoding and maintenance of each sequentially presented memory item; (3) correlating cognitive load and individual differences in working memory to neural and peripheral physiology, and studying the relationship between the physiological signals; (4) integration of the physiological findings with the vast knowledge coming from behavioral studies of verbal working memory in simple span paradigms. The data are shared in Brain Imaging Data Structure (BIDS) format and freely available on OpenNeuro (https://openneuro.org/datasets/ds003838).
Individual-based modelling of shelled pteropods
Authors: Hofmann Elizondo Urs , Vogt Meike 
Published: October 2021

AbstractShelled pteropods are cosmopolitan, free-swimming organisms of biogeochemical and commercial importance. They are widely used as sentinel species for the overall response of marine ecosystems to environmental stressors associated with climate change and changes in ocean chemistry. However, currently we are unable to project the effects of climate change on shelled pteropods at the population level, due to the missing spatio-temporal characterization of the response of pteropods to environmental stressors, and the limited information on the pteropod life history and life cycle. In this study, we implement a shelled pteropod Individual-Based Model (IBM), i.e. we simulate a pteropod population as a set of discrete individuals over several generations, life stages (eggs, larvae, juveniles and adults) and as a function of temperature, food availability and aragonite saturation state. The model is able to provide an abundance signal that is consistent with the abundance signal measured in the temperate region. In addition, the modeled life stage progression matches the reported size spectrum across the year, with two major spawning periods in spring and fall, and maturation in March and September. Furthermore, our IBM correctly predicts the abundance maxima of younger, smaller and potentially more susceptible life stages in spring and winter. Thus, our model provides a tool for advancing our understanding of the response of pteropod populations to future environmental changes.
The amount range of membrane cholesterol required for robust cell adhesion and proliferation in serum-free condition
Authors: Takii Shino , Wu Jun , Okamura Daiji 
Published: October 2021

AbstractSerum-containing medium is widely used to support cell attachment, stable growth and serial passaging of various cancer cell lines. However, the presence of cholesterols and lipids in serum greatly hinders the analysis of the effects of cholesterol depletion on cells in culture. In this study, we develop a defined serum-free culture condition accessible to a variety of different types of adherent cancer cells. We tested different factors that are considered essential for cell culture and various extracellular matrix for plate coating, and found cells cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) basal media supplemented with Albumin (BSA) and insulin-transferrin-selenium-ethanolamine (ITS-X) on fibronectin-precoated well (called as “DA-X condition”) showed comparable proliferation and survival to those in a serum-containing medium. Interestingly, we observed that DA-X condition could be adapted to a wide variety of adherent cancer cell lines, which enabled the analysis of how cholesterol depletion affected cancer cells in culture. Mechanistically, we found the beneficial effects of the DA-X condition in part can be attributed to the appropriate level of membrane cholesterol, and fibronectin-mediated signaling plays an important role in the suppression of cholesterol production.
Formulation of Dry Powders of Vaccines Containing MF59 or AddaVax by Thin-Film Freeze-Drying
Authors: AboulFotouh Khaled , Uno Naoko , Xu Haiyue , Moon Chaeho , Sahakijpijarn Sawittree , Christensen Dale J. , Davenport Gregory J. , Cano Chris , Ross Ted M , Williams Robert O. , Cui Zhengrong 
Published: October 2021

AbstractOil-in-water (O/W) nanoemulsion-based vaccine adjuvants such as MF59® are often used in seasonal and pandemic influenza vaccines. However, vaccines containing nanoemulsions require cold chain for storage and are sensitive to accidental freezing. We explored the feasibility of developing dry powders of vaccines adjuvanted with MF59 or AddaVax™, a preclinical grade nanoemulsion that has the same composition and droplet size as MF59, by thin-film freeze-drying (TFFD). AddaVax alone was successfully converted from a liquid to dry powders by TFFD using trehalose as a stabilizing agent while maintaining the droplet size distribution of the AddaVax when reconstituted, whereas subjecting the same AddaVax composition to conventional shelf freeze-drying led to significant aggregation or fusion. TFFD was then applied to convert liquid AddaVax-adjuvanted vaccines containing either model antigens such as ovalbumin and lysozyme, mono-, bi-, and tri-valent recombinant hemagglutinin (rHA) protein-based H1 and/or H3 (universal) influenza vaccine candidates, as well as the MF59-containing Fluad® Quadrivalent influenza vaccine to dry powders. Antigens, stabilizing agents, and buffer showed different effects on the physical properties of the vaccines (e.g., mean particle size and particle size distribution) after subjected to TFFD, but the integrity and hemagglutination activity of the rHA antigens did not significantly change and the immunogenicity of reconstituted influenza vaccine candidates was preserved when evaluated in BALB/c mice. The vaccine dry powder was not sensititve to repeated freezing-and-thawing, in contrast to its liquid counterpart. It is concluded that TFFD can be applied to convert vaccines containing MF59 or an nanoemulsion with the same composition and droplet size as MF59 from liquid to dry powders while maintaining the immunogencity of the vaccines, and it may be used to prepare dry powders of multivalent universal influenza vaccines.
Influences of rare copy number variation on human complex traits
Authors: Hujoel Margaux L.A. , Sherman Maxwell A. , Barton Alison R. , Mukamel Ronen E. , Sankaran Vijay G. , Loh Po-Ru 
Published: October 2021

AbstractThe human genome contains hundreds of thousands of regions exhibiting copy number variation (CNV). However, the phenotypic effects of most such polymorphisms are unknown because only larger CNVs (spanning tens of kilobases) have been ascertainable from the SNP-array data generated by large biobanks. We developed a new computational approach that leverages abundant haplotype-sharing in biobank cohorts to more sensitively detect CNVs co-inherited within extended SNP haplotypes. Applied to UK Biobank, this approach achieved 6-fold increased CNV detection sensitivity compared to previous analyses, accounting for approximately half of all rare gene inactivation events produced by genomic structural variation. This extensive CNV call set enabled the most comprehensive analysis to date of associations between CNVs and 56 quantitative traits, identifying 269 independent associations (P < 5 × 10−8) – involving 97 loci – that rigorous statistical fine-mapping analyses indicated were likely to be causally driven by CNVs. Putative target genes were identifiable for nearly half of the loci, enabling new insights into dosage-sensitivity of these genes and implicating several novel gene-trait relationships. CNVs at several loci created extended allelic series including deletions or duplications of distal enhancers that associated with much stronger phenotypic effects than SNPs within these regulatory elements. These results demonstrate the ability of haplotype-informed analysis to empower structural variant detection and provide insights into the genetic basis of human complex traits.
The human frontal operculum is involved in visuomotor performance monitoring
Authors: Quirmbach Felix , Limanowski Jakub 
Published: October 2021

AbstractFor adaptive goal-directed action, the brain needs to monitor action performance and detect errors. The corresponding information may be conveyed via different sensory modalities; for instance, visual and proprioceptive body position cues may inform about current manual action performance. Thereby, contextual factors such as the current task set may also determine the relative importance of each sensory modality for action guidance. Here, we analysed human behavioral, fMRI, and MEG data from two VR-based hand-target phase matching studies to identify the neuronal correlates of performance monitoring and error processing under instructed visual or proprioceptive task sets. Our main result was a general, modality-independent response of the bilateral FO to poor phase matching accuracy, as evident from increased BOLD signal and increased gamma power. Furthermore, functional connectivity of the bilateral FO to the right PPC increased under a visual vs proprioceptive task set. These findings suggest that the bilateral FO generally monitors manual action performance; and, moreover, that when visual action feedback is used to guide action, the FO may signal an increased need for control to visuomotor regions in the right PPC following errors.
The Mettl3 epitranscriptomic writer amplifies p53 stress responses
Authors: Raj Nitin , Wang Mengxiong , Seoane Jose A. , Moonie Nancie A. , Demeter Janos , Kaiser Alyssa M. , Boutelle Anthony M. , Mulligan Abigail S. , Moffatt Clare , Curtis Christina , Chang Howard Y. , Jackson Peter. K. , Attardi Laura D. 
Published: October 2021

SUMMARYThe p53 transcription factor, encoded by the most frequently mutated gene in human cancer, plays a critical role in tissue homeostasis in response to stress signals. The mechanisms through which p53 promotes downstream tumor suppressive gene expression programs remain, however, only superficially understood. Here, we used tandem affinity purification and mass spectrometry to reveal new components of the p53 response. This approach uncovered Mettl3, a component of the m6A RNA methyltransferase complex (MTC), as a p53-interacting protein. Analysis of Mettl3- deficient cells revealed that Mettl3 promotes p53 protein stabilization and target gene expression in response to DNA damage. Mettl3 acts in part by competing with the p53 negative regulator, Mdm2, for binding to the p53 transactivation domains to promote methyltransferase-independent stabilization of p53. In addition, Mettl3 relies on its catalytic activity to augment p53 responses, with p53 recruiting Mettl3 to p53 target genes to co-transcriptionally direct m6A modification of p53 pathway transcripts to enhance their expression. Mettl3 also promotes p53 activity downstream of oncogenic signals in vivo, in both allograft and autochthonous lung adenocarcinoma models, suggesting cooperative action of p53 and Mettl3 in tumor suppression. Accordingly, we found in diverse human cancers that mutations in MTC components perturb expression of p53 target genes and that MTC mutations are mutually exclusive with TP53 mutations, suggesting that the MTC enhances the p53 transcriptional program in human cancer. Together, these studies reveal a fundamental role for Mettl3 in amplifying p53 signaling through protein stabilization and epitranscriptome regulation.
Non-motile subpopulations of Pseudomonas aeruginosa repress flagellar motility in motile cells through a type IV pili- and Pel-dependent mechanism
Authors: Lewis Kimberley A. , Vermilyea Danielle M. , Webster Shanice S. , Geiger Christopher J. , de Anda Jaime , Wong Gerard C. L. , O’Toole George A. , Hogan Deborah A. 
Published: October 2021

AbstractThe downregulation of Pseudomonas aeruginosa flagellar motility is a key event in biofilm formation, host-colonization, and the formation of microbial communities, but the external factors that repress motility are not well understood. Here, we report that under swarming conditions, swarming motility can be repressed by cells that are non-motile due to the absence of a flagellum or flagellar rotation. Non-swarming cells, due to mutations that prevent either flagellum biosynthesis or rotation, present at 5% of the total population suppressed swarming of wild-type cells under the conditions tested in this study. Non-swarming cells required functional type IV pili and the ability to produce Pel exopolysaccharide to suppress swarming by the flagellated wild type. In contrast, flagellated cells required only type IV pili, but not Pel production, in order for swarming to be repressed by non-flagellated cells. We hypothesize that interactions between motile and non-motile cells may enhance the formation of sessile communities including those involving multiple genotypes, phenotypically-diverse cells, and perhaps other species.ImportanceOur study shows that, under the conditions tested, a small population of non-swarming cells can impact the motility behavior of the larger population. The interactions that lead to the suppression of swarming motility require type IV pili and a secreted polysaccharide, two factors with known roles in biofilm formation. These data suggest that interactions between motile and non-motile cells may enhance the transition to sessile growth in populations and promote interactions between cells with different genotypes.
Physical activity and posture profile of a South African cohort of middle-aged men and women as determined by integrated hip and thigh accelerometry
Authors: Micklesfield Lisa K. , Westgate Kate , Smith Antonia , Kufe Clement , Mendham Amy E. , Lindsay Tim , Wijndaele Katrien , Goedecke Julia H. , Brage Soren 
Published: October 2021

AbstractBackgroundPhysical activity and sedentary behaviour are central to public health recommendations and highlight the need for precise measurement. Descriptive studies of objectively measured physical activity behaviours in African populations are rare. We aimed to develop a method of combining the signals from hip and thigh accelerometers to quantify physical behaviours and describe these by socio-demographic factors in a population of middle-aged men and women from urban South Africa.MethodsPhysical behaviours were quantified by integrating the signals from two triaxial accelerometers worn simultaneously during free-living, in a subsample of participants from the Middle-aged Soweto Cohort (MASC) (n=794; mean (SD) age: 53.7 (6.3) years). Acceleration time-series from the two accelerometers were combined and movement-related acceleration derived using Euclidean Norm Minus One (ENMO, in milli-g). This was summarised as total movement volume (mean ENMO) and time spent in non-movement (<28mg), light intensity physical activity (LPA, 28-85 mg) and moderate-vigorous intensity physical activity (MVPA, >85 mg); thigh pitch angle and a sleep diary were used to further divide non-movement time (min/day) spent into sleep, awake sitting/lying, and standing. Socio-demographic factors were self-reported, and weight and height were measured.ResultsMean (SD) wear time for combined thigh-hip accelerometry was 128 (48) hours. Movement volume was 15.0 (6.5) mg for men (n=437; 53.6 (6.2) years) and 12.2 (3.4) mg for women (n=357; 53 (5.8) years). Men spent more time in MVPA and sitting/lying, while women spent more time standing. Age was inversely associated with movement volume, MVPA and LPA in men and women. When compared to their normal weight counterparts, men who were overweight or obese spent less average daily time in MVPA, while women who were overweight or obese spent less time in LPA and more time sitting/lying. Socio-economic status was inversely associated with volume, MVPA and time spent sleeping, and positively associated with time spent sitting/lying, in both men and women.ConclusionsIntegrating signals from hip and thigh accelerometers enables characterisation of physical behaviours that can be applied in an African population. Age, female sex, BMI and socio-economic status are inversely associated with physical activity and directly associated with sedentary behaviour.
An improved sparrow search algorithm based on levy flight and opposition-based learning
Authors: Chen Danni , Zhao JianDong , Huang Peng , Deng Xiongna , Lu Tingting 
Published: October 2021

Purpose
Sparrow search algorithm (SSA) is a novel global optimization method, but it is easy to fall into local optimization, which leads to its poor search accuracy and stability. The purpose of this study is to propose an improved SSA algorithm, called levy flight and opposition-based learning (LOSSA), based on LOSSA strategy. The LOSSA shows better search accuracy, faster convergence speed and stronger stability.

Design/methodology/approach
To further enhance the optimization performance of the algorithm, The Levy flight operation is introduced into the producers search process of the original SSA to enhance the ability of the algorithm to jump out of the local optimum. The opposition-based learning strategy generates better solutions for SSA, which is beneficial to accelerate the convergence speed of the algorithm. On the one hand, the performance of the LOSSA is evaluated by a set of numerical experiments based on classical benchmark functions. On the other hand, the hyper-parameter optimization problem of the Support Vector Machine (SVM) is also used to test the ability of LOSSA to solve practical problems.

Findings
First of all, the effectiveness of the two improved methods is verified by Wilcoxon signed rank test. Second, the statistical results of the numerical experiment show the significant improvement of the LOSSA compared with the original algorithm and other natural heuristic algorithms. Finally, the feasibility and effectiveness of the LOSSA in solving the hyper-parameter optimization problem of machine learning algorithms are demonstrated.

Originality/value
An improved SSA based on LOSSA is proposed in this paper. The experimental results show that the overall performance of the LOSSA is satisfactory. Compared with the SSA and other natural heuristic algorithms, the LOSSA shows better search accuracy, faster convergence speed and stronger stability. Moreover, the LOSSA also showed great optimization performance in the hyper-parameter optimization of the SVM model.