Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary stasis of a heritable morphological trait in a wild fish population despite apparent directional selection

Abstract Comparing observed versus theoretically expected evolutionary responses is important for our understanding of the evolutionary process, and for assessing how species may cope with anthropogenic change. Here, we document directional selection for larger female size in Atlantic salmon, using pedigree‐derived estimates of lifetime reproductive success as a fitness measure. We show the trait is heritable and, thus, capable of responding to selection. The Breeder's Equation, which predicts microevolution as the product of phenotypic selection and heritability, predicted evolution of larger size. This was at odds, however, with the observed lack of either phenotypic or genetic temporal trends in body size, a so‐called “paradox of stasis. ” To investigate this paradox, we estimated the additive genetic covariance between trait and fitness, which provides a prediction of evolutionary change according to Robertson's secondary theorem of selection (STS) that is unbiased by missing variables. The STS prediction was consistent with the observed stasis. Decomposition of phenotypic selection gradients into genetic and environmental components revealed a potential upward bias, implying unmeasured factors that covary with trait and fitness. These results showcase the power of pedigreed, wild population studies—which have largely been limited to birds and mammals—to study evolutionary processes on contemporary timescales.
Program Boosting or Crowd-Sourcing for Correctness

A great deal of effort has been spent on both trying to specify software requirements and on ensuring that software actually matches these requirements. A wide range of techniques that includes theorem proving, model checking, type-based analysis, static analysis, runtime monitoring, and the like have been proposed. However, in many areas adoption of these techniques remains spotty. In fact, obtaining a specification or a precise notion of correctness is in many cases quite elusive. In this paper we investigate an approach we call program boosting, which involves crowd-sourcing imperfect solutions to a difficult programming problem from developers and then blending these programs together in a way that improves their correctness. We show how interesting and highly non-trivial tasks such as writing regular exepressions for URLs or email addresses can be effectively crowd-sourced. We demonstrate that carefully blending the crowd-sourced results together consistently produces a boost, yielding results that are better than any of the starting programs. Our experiments on 465 programs show consistent boosts in accuracy and demonstrate that program boosting can be performed at a relatively modest monetary cost.
Maintenance productivity factors-a case study

A project is described where maintenance productivity savings of 70% have been made, at the same time, accompanied by service-level improvements. The author describes the changes made and suggests what the underlying productivity factors may be. The organization was changed into three teams initially to separate the support and maintenance activities with a single service desk. A metrics program was implemented using a problem management system to log incoming queries and problems. A program of preventive maintenance was established. Full management control was established with procedures for the maintenance processes and interfaces, including, for example, testing, quality control, configuration management and version control, release management and problem management. <<ETX>>
Identifying parameters of host cell vulnerability during Salmonella infection by quantitative image analysis and modeling

Salmonella target and enter epithelial cells at permissive entry sites: some cells are more likely to be infected than others. However the parameters that lead to host cell heterogeneity are not known. Here, we quantitatively characterized host cell “vulnerability” towards Salmonella infection based on imaged parameters. We performed successive infections of the same host cell population followed by automated high-throuput microscopy and observed that infected cells have higher probability of being re-infected. Establishing a predictive model we identified two combined origins of host cell vulnerability: the pathogen-induced cellular vulnerability emerging from Salmonella uptake and persisting at later stage of the infection, and the host cell-inherent vulnerability. We linked the host cell inherent vulnerability with its morphological attributes such as the local cell crowding, and with host cell cholesterol content. This showed that the probability of Salmonella infection success can be forecast from morphological or molecular host cell parameters.
Diversity of fall armyworm, Spodoptera frugiperda and their gut bacterial community in Kenya

The invasive fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is a polyphagous pest that causes widespread damage particularly to maize and sorghum in Africa. The microbiome associated with S. frugiperda could play a role in their success and adaptability. However, these bacterial communities remain poorly studied, especially for S. frugiperda in Africa. We investigated the composition, abundance and diversity of microbiomes associated with larval and adult specimens of S. frugiperda collected from four maize growing regions in Kenya through high throughput sequencing of bacterial 16S rRNA gene. We identified Proteobacteria and Firmicutes as the most dominant phyla and lesser proportions of Bacteroidetes and Actinobacteria. We also observed differences in bacterial microbiome diversity between larvae and adults that are a likely indication that some prominent larval bacterial groups are lost during metamorphosis. Several bacterial groups were found in both adults and larvae suggesting that they are transmitted across developmental stages. Reads corresponding to several known entomopathogenic bacterial clades as well as the non-bacterial entomopathogen, Metarhizium rileyi (Farl.) Kepler, Rehner & Humber (2014), were observed. Mitochondrial DNA haplotyping of the S. frugiperda population in Kenya indicated the presence of both ‘Rice’ and ‘Corn’ strains, with a higher prevalence of the ‘Rice’ strain. Insights into the microbiota may ultimately provide alternative avenues for controlling of this pest.
A Systematic Review of Thirty-One Assessment Tests to Evaluate Mobility in Older Adults

Assessments of gait, balance, and transfer in elderly people play a valuable role in maintaining healthy aging and preventing a decline in mobility. Several evaluation tools have been proposed; however, clinicians should select the most accurate ones wisely, based on numerous criteria. This systematic review aims to identify all applicable elderly mobility assessment tests and show their measurement properties with as much detail as possible. Initially, a broad search was performed. Articles were screened based on their titles and abstracts, and only studies published in English were considered. Based on our inclusion and exclusion criteria, 31 assessment tests evaluating the mobility of healthy elderly people were found. Then, further searches were completed to identify the measurement properties of each test. These characteristics include the origin and year of establishment, several practicality factors, and validity. The analysis of our outcomes illustrates the similarities and differences between the identified tests.
Phenome-wide search for pleiotropic loci highlights key genes and molecular pathways for human complex traits

Over recent decades, genome-wide association studies (GWAS) have dramatically changed the understanding of human genetics. A recent genetic data release by UK Biobank has allowed many researchers worldwide to have comprehensive look into the genetic architecture of thousands of human phenotypes. In this study, we developed a novel statistical framework to assess phenome-wide significance and genetic pleiotropy across the human phenome based on GWAS summary statistics. We demonstrate widespread sharing of genetic architecture components between distinct groups of traits. Apart from known multiple associations inside the MHC locus, we discover high degree of pleiotropy for genes involved in immune system function, apoptosis, hemostasis cascades, as well as lipid and xenobiotic metabolism. We find several notable examples of novel pleiotropic loci (e.g., the MIR2113 microRNA broadly associated with cognition), and provide several possible mechanisms for these association signals. Our results allow for a functional phenome-wide look into the shared components of genetic architecture of human complex traits, and highlight crucial genes and pathways for their development.
'SUPERCRYPT' ASIC technology facilitates a new device family for data encryption

SUPERCRYPT, a new hardware implementation of the DES Data Encryption Standard by means of a semi-custom cell-based ASIC technology is described. An encryption speed of 100 Mbits/s has been achieved on silicon applying 1 micron design rules, whereas a scaled 0.8 micron version will be operating faster than 140 Mbit/s. The semi-custom design methodology is briefly outlined and practical experiences are reported. Typical device parameters and applications are summarised. <<ETX>>
Effect of Efficient Microorganisms on Bioproductive Indicators of Pre-fattening Pigs

ORCID: https://orcid.org/0000-0001-5265-045X RESUMEN Antecedentes: En la actualidad, una alternativa para aumentar el rendimiento productivo en los animales es el empleo de aditivos. El objetivo del trabajo fue evaluar el efecto de la inclusión de microorganismos eficientes (EM) sobre los indicadores bioproductivos de la preceba porcina. Métodos: Fueron utilizados 80 animales del genotipo Yorkshire/Landrace x CC21 con promedio de edad y peso de 38 días y 7,8 kg, respectivamente, en un diseño completamente aleatorio con cuatro grupos de 20 animales cada uno: un grupo control; tratamiento 1 (inclusión de 60 mL de EM/5 kg de pienso); tratamiento 2 (igual al anterior más 1 mL de EM/5 L de agua) y tratamiento 3 (administración de 1 mL de EM/5 L de agua). Se evaluó peso inicial, peso final, incremento de peso, ganancia media diaria, conversión alimentaria, mortalidad, morbilidad y viabilidad; estos indicadores se midieron durante 49 días. Los resultados se compararon mediante un análisis de covarianza utilizando el PI como covariable y las comparaciones entre medias se realizaron con pruebas de comparaciones múltiples. Resultados: Los valores de peso final, incremento de peso, ganancia media diaria y conversión alimentaria revelaron diferencias significativas (P ≤ 0,05) entre los tratamientos y el control; exceptuando la ganancia media diaria del tercer tratamiento. La mortalidad, morbilidad y viabilidad se mostraron significativamente diferentes respecto a los tres grupos tratados y el control. Conclusiones: Se obtuvieron los mejores resultados en el primer tratamiento concluyéndose que el uso de microorganismos eficientes en preceba porcinas mejora los indicadores bioproductivos.
Are We on the Same Page? Exploring National, State, and Local Educational-response Themes for Extension Master Gardener Coordinators and Volunteers

Extension provides outreach to the general public and works to disseminate the latest information and research generated by land grant university (LGU) scientists. The Extension Master Gardener (EMG) volunteer program is one of the most widely recognized programs of extension, created to educate people about research-based consumer horticulture (CH) and gardening practices through a network of trained volunteers. Ideally, EMG program initiatives should address local issues and needs and align with the priorities of extension’s federal stakeholder, U.S. Department of Agriculture National Institute for Food and Agriculture (USDA NIFA). Before 2015, there were no national standards for EMG volunteer programs, and at this time, there is no official work plan or prioritization of educational programming. A quantitative national study of EMG state and local coordinators and volunteers was conducted in Fall 2016 to assess the importance of six educational-response themes (ERTs) (i.e., the strategy for EMG volunteer outreach) for program management (state and local coordinators) and program participants (EMG volunteers). The study compared theme importance between program management and participants, and, in turn, allowed a comparison with previously published historical data. Response to individual inquiry is consistently the most important ERT for EMG programs, regardless of the responder position within the program (management or volunteer). Results revealed that state and local coordinators (program management) score ERTs similarly. EMG volunteers score the importance of ERTs similarly to each other, as well, although some differences are apparent between urban, suburban, and rural programs. Although there are slight differences in the importance of response themes between program management and EMG volunteers, it appears that the EMG volunteer program has an effective organizational structure with an upper and middle management generally aligned at every level. It is plausible that the variability in importance of response themes could be attributed to nuances in local issues and needs. Historical comparison indicates that the importance of ERTs has changed over time, suggesting that themes cycle and change. Although the EMG program does not have a national plan for programming, this assessment of EMG volunteer program ERTs provides a perspective on program direction and a useful starting point for discussion. It is a timely conversation, as EMG programs are increasingly expected to be more accountable and show community impact, and these assessments serve as an important baseline for a national program poised for growth and development.
Heterozygosity at neutral and immune loci is not associated with neonatal mortality due to microbial infection in Antarctic fur seals

Abstract Numerous studies have reported correlations between the heterozygosity of genetic markers and fitness. These heterozygosity–fitness correlations (HFCs) play a central role in evolutionary and conservation biology, yet their mechanistic basis remains open to debate. For example, fitness associations have been widely reported at both neutral and functional loci, yet few studies have directly compared the two, making it difficult to gauge the relative contributions of genome‐wide inbreeding and specific functional genes to fitness. Here, we compared the effects of neutral and immune gene heterozygosity on death from bacterial infection in Antarctic fur seal (Arctocephalus gazella) pups. We specifically developed a panel of 13 microsatellites from expressed immune genes and genotyped these together with 48 neutral loci in 234 individuals, comprising 39 pups that were classified at necropsy as having most likely died of bacterial infection together with a five times larger matched sample of healthy surviving pups. Identity disequilibrium quantified from the neutral markers was positive and significant, indicative of variance in inbreeding within the study population. However, multilocus heterozygosity did not differ significantly between healthy and infected pups at either class of marker, and little evidence was found for fitness associations at individual loci. These results support a previous study of Antarctic fur seals that found no effects of heterozygosity at nine neutral microsatellites on neonatal survival and thereby help to refine our understanding of how HFCs vary across the life cycle. Given that nonsignificant HFCs are underreported in the literature, we also hope that our study will contribute toward a more balanced understanding of the wider importance of this phenomenon.
Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Pseudomonas virus vB_PaeM_PA5oct is a compelling model phage to investigate phage-bacteria interactions and is a potent candidate for phage therapy. Combining hybrid genome sequencing, RNA-Seq, and mass spectrometry of virion-associated proteins allowed us to accurately assemble and annotate PA5oct’s 286,783 bp genome. It encodes 461 coding regions, of which 93 were identified as virion-associated proteins using ESI-MS/MS. RNA-seq revealed twelve tRNA genes, four ncRNA regions, and a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. Although PA5oct is not organized into strictly contiguous regions of temporal transcription, defined genomic regions are expressed in early, middle, and late phases of infection. Interestingly, we observed distinct regions showing limited transcription activity throughout the infection cycle. The infection of Pseudomonas aeruginosa by PA5oct triggers the upregulation of bacterial operons related to NAD biosynthesis, Psl exopolysaccharide, and periplasmic nitrate reductase production and downregulates Type IV pili gene products, suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position this isolate amongst other phages using a protein-sharing network. This study expands our understanding of the molecular diversity of jumbo viruses and opens new questions towards cellular regulation and phage-encoded hijacking mechanisms.
FEELnc: A tool for Long non-coding RNAs annotation and its application to the dog transcriptome

Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. Among the plethora of reconstructed transcripts, one of the main bottlenecks consists in correctly identifying the different classes of RNAs, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program which accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames. Benchmarking versus five state-of-art tools shows that FEELnc achieves similar or better classification performance on GENCODE and NONCODE datasets. The program also provides several specific modules that enable to fine-tune classification accuracy, to formalize the annotation of lncRNA classes and to annotate lncRNAs even in the absence of training set of noncoding RNAs. We used FEELnc on a real dataset comprising 20 new canine RNA-seq samples produced in the frame of the European LUPA consortium to expand the canine genome annotation and classified 10,374 novel lncRNAs and 58,640 new mRNA transcripts. FEELnc represents a standardized protocol for identifying and annotating lncRNAs and is freely accessible at https://github.com/tderrien/FEELnc.
Vascular Stem/Progenitor Cell Migration and Differentiation in Atherosclerosis.

SIGNIFICANCE Atherosclerosis is a major cause for the death of human beings, and it takes place in large- and middle-sized arteries. The pathogenesis of the disease has been widely investigated, and new findings on vascular stem/progenitor cells could have an impact on vascular regeneration. Recent Advances: Recent studies have shown that abundant stem/progenitor cells present in the vessel wall are mainly responsible for cell accumulation in the intima during vascular remodeling. It has been demonstrated that the mobilization and recruitment of tissue-resident stem/progenitor cells give rise to endothelial and smooth muscle cells (SMCs) that participate in vascular repair and remodeling such as neointimal hyperplasia and arteriosclerosis. Interestingly, cell lineage tracing studies indicate that a large proportion of SMCs in neointimal lesions is derived from adventitial stem/progenitor cells. CRITICAL ISSUES The influence of stem/progenitor cell behavior on the development of atherosclerosis is crucial. An understanding of the regulatory mechanisms that control stem/progenitor cell migration and differentiation is essential for stem/progenitor cell therapy for vascular diseases and regenerative medicine. FUTURE DIRECTIONS Identification of the detailed process driving the migration and differentiation of vascular stem/progenitor cells during the development of atherosclerosis, discovery of the environmental cues, and signaling pathways that control cell fate within the vasculature will facilitate the development of new preventive and therapeutic strategies to combat atherosclerosis. Antioxid. Redox Signal. 00, 000-000.
Secure Coding Standards

Secure coding standards define rules and recommendations to guide the development of secure software systems. Establishing secure coding standards provides a basis for secure system development as well as a common set of criteria that can be used to measure and evaluate software development efforts and software development tools and processes. This paper describes plans by the CERT/Coordination Center at the Software Engineering Institute at Carnegie Mellon University to establish, through a coordinated community effort, a set of secure coding standards for commonly used programming languages.
Analyzing pathogenic MEK variants in zebrafish

Somatic gain-of-function (GOF) mutations in components of the Ras/extracellular signal-regulated kinase (ERK) signaling pathway have been known for some time to cause cancer. Only recently have germline GOF mutations in the same components of the Ras/ERK pathway been shown to cause a common class of developmental disorders, known as RASopathies. Advances in genome sequencing have led to the identification of hundreds of such pathogenic mutations, but so far, the effects of a small subset of these mutations have been investigated using animal models. In Chapter 1, we review the animal models of RASopathies and find that they recapitulate many of the developmental abnormalities found in humans. However, it is not known whether individual mutations translate into different patient-specific phenotypic severity and causative abnormal Ras/ERK signaling dynamics. In the rest of this thesis, we focus on mutations in MEK1, an ERK kinase. In Chapter 2, we report that the aspect ratio of the yolk shape of early zebrafish embryos can be used as a metric to efficiently rank these mutations. Furthermore, the ranking is conserved in other zebrafish-specific and Drosophila-specific assays and is predictive of drug dose needed to reverse the aspect ratio abnormality. These assays can be used to test the strengths of existing and newly found mutations in MEK1 and other pathway components, providing the first step in the development of rational guidelines for patient-specific diagnostics and treatment of RASopathies. In Chapter 3, using spatially-resolved immunofluorescence experiments on embryos mosaic for the GOF MEK1 variants, we find that the MEK1 variants cause both higher and lower levels of Ras/ERK signaling in different parts of the embryo. We also find that some GOF MEK1 variants only have activity in the presence of upstream Ras signaling in zebrafish. Our results suggest that quantitative assays for certain Ras/ERK-dependent developmental processes in the early zebrafish can yield insights into how pathogenic MEK1 mutations work. In Chapter 4, we discuss conclusions and future directions, including the importance iii of analyzing how these mutations affect the Michaelis-Menten parameters of MEK1 and to generate zebrafish lines heterozygous for RASopathy mutations to analyze the severity of adult phenotypes.