Miracle-dz/UniFAR-FTUs huggingface dataset:
Seabird diversity and biomass enhance cross-ecosystem nutrient subsidies

Mobile consumers are key vectors of cross-ecosystem nutrients, yet have experienced population declines which threaten their ability to fill this role. Despite their importance and vulnerability, there is little information on how consumer biodiversity, in addition to biomass, influences the magnitude of nutrient subsidies. Here, we show that both biomass and diversity of seabirds enhanced the provisioning of nutrients across tropical islands and coral reefs, but their relative influence varied across systems. Seabird biomass was particularly important for terrestrial and near-shore subsidies and enhancing fish biomass, while seabird diversity was associated with nutrient subsidies further offshore. The positive effects of diversity were likely driven by high functional complementarity among seabird species in traits related to nutrient storage and provisioning. However, introduced rats and non-native vegetation reduced seabird biomass and diversity, with rats having a stronger effect on biomass and vegetation having a stronger effect on diversity. Accordingly, the restoration of cross-ecosystem nutrient flows provided by seabirds will likely be most successful when both stressors are removed, thus protecting both high biomass and diversity. Recognizing the importance of mobile consumer diversity and biomass, and their underlying drivers, is a necessary step to conserving these species and the ecosystem functions they provide.
Causes and Consequences of Interindividual Response Variability: A Call to Apply a More Rigorous Research Design in Acute Exercise-Cognition Studies

The different responses of humans to an apparently equivalent stimulus are called interindividual response variability. This phenomenon has gained more and more attention in research in recent years. The research field of exercise-cognition has also taken up this topic, as shown by a growing number of studies published in the past decade. In this perspective article, we aim to prompt the progress of this research field by (i) discussing the causes and consequences of interindividual variability, (ii) critically examining published studies that have investigated interindividual variability of neurocognitive outcome parameters in response to acute physical exercises, and (iii) providing recommendations for future studies, based on our critical examination. The provided recommendations, which advocate for a more rigorous study design, are intended to help researchers in the field to design studies allowing them to draw robust conclusions. This, in turn, is very likely to foster the development of this research field and the practical application of the findings.
Action mechanisms, biodiversity, and omics approaches in biocontrol and plant growth-promoting Pseudomonas: an updated review

ABSTRACT Pseudomonas spp. are phylogenetically diverse bacteria with a broad range of metabolic and ecological functions. Pseudomonas spp. beneficially interact with plants by colonising the rhizosphere and various plant compartments. Pseudomonas spp. promote plant growth by facilitating nutrient absorption, modulating phytohormone levels, and providing direct and indirect phytopathogen biocontrol via induced systemic resistance. The recent publication of genomes for numerous plant-associated Pseudomonas have elucidated their growth-stimulating characteristics. The present review surveyed the mechanisms and genetic variability of pseudomonads investigated by omics approaches. These studies furnish clues about the evolution and taxonomic relationships of pseudomonads with the ability to stimulate plant growth, protect and defend the host plant against pathogens. Clarification of pseudomonads and their attributes that are beneficial to crops could help improve crop nutrition and protection in sustainable agricultural production.
Specialty Crop Consumer Preferences for Product Characteristics and Marketing Channels

Abstract Little research has studied consumer preferences for product characteristics and marketing channels in combination. We survey 938 specialty crop consumers in Missouri to inform preferences for 21 specialty crop products, six attributes (local, organic, GMO-free, pesticide-free, appearance, price), and four marketing channels (direct-from-farm, farmers market, warehouse club, grocery store). We observe that local and pesticide-free attributes are significantly more important than organic and GMO-free attributes to Missouri specialty crop consumers. Consumers who prefer local and pesticide-free characteristics are more likely to buy food from direct marketing channels price-oriented consumers are more likely to buy food at the grocery store.
The Effect of Job Experience on the Maintenance Proficiency of Army Automotive Mechanics

The proficiency of 70 Army automotive mechanics in performing two repair tasks was examined under controlled test conditions. The tasks were installation of a generator and a starter on a tank engine. The subjects were assigned to one of 10 job-experience (JE) categories based on the number of times they had performed the repair tasks. The 10 experience categories ranged from no previous experience to nine or more times. Six dimensions of maintenance proficiency were measured: quality checks, adherence to procedures, repair time, information use, tool selection, and tool use. Overall, proficiency improved markedly for mechanics in the 0 to 5 JE range, peaked between 5 and 6 JE, and declined somewhat for mechanics with more than 6 JE. The job-experience/proficiency function was similar for both repair tasks and all six dimensions of proficiency. The results indicate that job experience could be a valid predictor of maintenance proficiency and training needs if based on an analysis of a larger sample of representative maintenance tasks and validated with a larger subject population.
4D‐Var Inversion of European NH3 Emissions Using CrIS NH3 Measurements and GEOS‐Chem Adjoint With Bi‐Directional and Uni‐Directional Flux Schemes

We conduct the first 4D‐Var inversion of NH3 accounting for NH3 bi‐directional flux, using CrIS satellite NH3 observations over Europe in 2016. We find posterior NH3 emissions peak more in springtime than prior emissions at continental to national scales, and annually they are generally smaller than the prior emissions over central Europe, but larger over most of the rest of Europe. Annual posterior anthropogenic NH3 emissions for 25 European Union members (EU25) are 25% higher than the prior emissions and very close (<2% difference) to other inventories. Our posterior annual anthropogenic emissions for EU25, the UK, the Netherlands, and Switzerland are generally 10%–20% smaller than when treating NH3 fluxes as uni‐directional emissions, while the monthly regional difference can be up to 34% (Switzerland in July). Compared to monthly mean in‐situ observations, our posterior NH3 emissions from both schemes generally improve the magnitude and seasonality of simulated surface NH3 and bulk NHx wet deposition throughout most of Europe, whereas evaluation against hourly measurements at a background site shows the bi‐directional scheme better captures observed diurnal variability of surface NH3. This contrast highlights the need for accurately simulating diurnal variability of NH3 in assimilation of sun‐synchronous observations and also the potential value of future geostationary satellite observations. Overall, our top‐down ammonia emissions can help to examine the effectiveness of air pollution control policies to facilitate future air pollution management, as well as helping us understand the uncertainty in top‐down NH3 emissions estimates associated with treatment of NH3 surface exchange.
Priorisierung von Quelltextduplikaten in Testcode durch die Kombination von Clone-Detection und testspezifischer Coverage

Zusammenfassung Durch Clone-Detection aufgedeckte Codeduplikate in Testcode sind schwieriger zu bewerten als solche in Produktivcode und in der Praxis werden sie häufig ignoriert. In der Folge bleiben redundante Codeabschnitte in Testcode erhalten. Diese führen zu Wartungsproblemen und es besteht die Gefahr ungewollt inkonsistenter Änderungen. In diesem Artikel wird hinterfragt, ob die Kombination von Ergebnissen einer Clone-Detection mit testspezifischer Code Coverage helfen kann, Klonfunde in Testcode automatisch zu bewerten. Tests, die zwar von der Clone-Detection als redundant erkannt werden, aber stark unterschiedliche Teile im Code ausführen, werden von Entwicklern aufgrund der so anzunehmenden semantischen Entfernung möglicherweise weniger oft refaktoriert. Entsprechend sollten Klone von Tests mit einer hohen Ausführungsüberdeckung als wichtiger eingestuft werden. Durch die erhöhte Treffsicherheit soll die CloneDetection von Entwicklern als nützlicheres Werkzeug anerkannt werden. Es wurden Codeduplikate im Testcode von neun Open-Source-Projekten untersucht und die Ergebnisse von Entwicklern evaluiert. Dabei zeigte sich eine moderat positive Korrelation zwischen automatischer Bewertung und Entwicklerstimmen.
Allele‐specific knockouts reveal a role for apontic‐like in the evolutionary loss of larval melanin pigmentation in the domesticated silkworm, Bombyx mori

The domesticated silkworm, Bombyx mori, and its wild progenitor, B. mandarina, are extensively studied as a model case of the evolutionary process of domestication. A conspicuous difference between these species is the dramatic reduction in melanin pigmentation in both larval and adult B. mori. Here we evaluate the efficiency of CRISPR/Cas9‐targeted knockouts of pigment‐related genes as a tool to understand their potential contributions to domestication‐associated melanin pigmentation loss in B. mori. To demonstrate the efficacy of targeted knockouts in B. mandarina, we generated a homozygous CRISPR/Cas9‐targeted knockout of yellow‐y. In yellow‐y knockout mutants, black body colour became lighter throughout the larval, pupal and adult stages, confirming a role for this gene in melanin pigment formation. Further, we performed allele‐specific CRISPR/Cas9‐targeted knockouts of the pigment‐related transcription factor, apontic‐like (apt‐like) in B. mori × B. mandarina F1 hybrid individuals which exhibit B. mandarina‐like larval pigmentation. Knockout of the B. mandarina allele of apt‐like in F1 embryos results in white patches on the dorsal integument of larvae, whereas corresponding knockouts of the B. mori allele consistently exhibit normal F1 larval pigmentation. These results demonstrate a contribution of apt‐like to the evolution of reduced melanin pigmentation in B. mori. Together, our results demonstrate the feasibility of CRISPR/Cas9‐targeted knockouts as a tool for understanding the genetic basis of traits associated with B. mori domestication.
A detailed landscape of genomic alterations in malignant peripheral nerve sheath tumor cell lines challenges the current MPNST diagnosis

Background Malignant peripheral nerve sheath tumors (MPNSTs) are soft tissue sarcomas that arise from the peripheral nervous system. Half of the tumors develop in the context of the genetic disease Neurofibromatosis type 1 (NF1) and the rest are sporadic sarcomas. MPNSTs have a dismal prognosis due to their aggressiveness and tendency to metastasize, and new treatment options are needed. The diagnosis of MPNSTs can be challenging, especially outside of the NF1 context since specific histological criteria have not been completely established. Genomic analysis may both facilitate differential diagnoses and suggest precision medicine strategies. Methods We generated a complete genomic resource of a set of widely used human NF1-related and sporadic MPNST cell lines by applying ploidy analysis, whole genome and whole exome sequencing and SNP-array analysis, complemented by methylome-based classification and immunofluorescence of cell identity markers (SOX9, SOX10, S100B). Results NF1 MPNST cell lines faithfully recapitulated the genomic copy number profile of primary MPNSTs. Structural variants were key players in the complete inactivation of most recurrently altered tumor suppressor genes (TSGs) (NF1, CDKN2A, SUZ12/EED), while small variants played a minor role in the NF1 context, both concerning TSG inactivation and due to the absence of gain-of-function mutations. In clear contrast, the sporadic cell lines (STS-26T, HS-Sch-2, HS-PSS) did not recapitulate the copy number profile of primary MPNSTs. They carried different TSG inactivation and exhibited gain-of-function mutations by predicted kinase activation or generation of fusion genes. Mutational frequencies and signatures emerged as promising informative tools for aiding in MPNST differential diagnosis. Due to the multiple genomic differences exhibited, we complemented their characterization using a methylome-based classifier. All NF1-related cell lines were assigned within the MPNST group, while sporadic cell lines clustered either with melanomas or with an uncertain MPNST-like sarcoma group. The staining of cell identity markers reinforced the idea of a potential misdiagnose of the MPNSTs used to derive the sporadic cell lines analyzed. Conclusions Deep genomic analysis, together with methylome-based sarcoma classification and cell identity marker analysis, challenged the MPNST identity of sporadic cell lines. Results presented here open an opportunity to revise MPNST differential diagnosis and classification.
Phasing of de novo mutations using a scaled‐up multiple amplicon long‐read sequencing approach

De novo mutations (DNMs) play an important role in severe genetic disorders that reduce fitness. To better understand their role in disease, it is important to determine the parent‐of‐origin and timing of mutational events that give rise to these mutations, especially in sex‐specific developmental disorders such as male infertility. However, currently available short‐read sequencing approaches are not ideally suited for phasing, as this requires long continuous DNA strands that span both the DNM and one or more informative single‐nucleotide polymorphisms. To overcome these challenges, we optimized and implemented a multiplexed long‐read sequencing approach using Oxford Nanopore technologies MinION platform. We focused on improving target amplification, integrating long‐read sequenced data with high‐quality short‐read sequence data, and developing an anchored phasing computational method. This approach handled the inherent phasing challenges of long‐range target amplification and the normal accumulation of sequencing error associated with long‐read sequencing. In total, 77 of 109 DNMs (71%) were successfully phased and parent‐of‐origin identified. The majority of phased DNMs were prezygotic (90%), the accuracy of which is highlighted by an average mutant allele frequency of 49.6% and standard error of 0.84%. This study demonstrates the benefits of employing an integrated short‐read and long‐read sequencing approach for large‐scale DNM phasing.
The funny current If is essential for the fight-or-flight response in cardiac pacemaker cells

The sympathetic nervous system fight-or-flight response is characterized by a rapid increase in heart rate, which is mediated by an increase in the spontaneous action potential (AP) firing rate of pacemaker cells in the sinoatrial node. Sympathetic neurons stimulate sinoatrial myocytes (SAMs) by activating β adrenergic receptors (βARs) and increasing cAMP. The funny current (If) is among the cAMP-sensitive currents in SAMs. If is critical for pacemaker activity, however, its role in the fight-or-flight response remains controversial. In this study, we used AP waveform analysis, machine learning, and dynamic clamp experiments in acutely-isolated SAMs from mice to quantitatively define the AP waveform changes and role of If in the fight-or-flight response. We found that while βAR stimulation significantly altered nearly all AP waveform parameters, the increase in AP firing rate was only correlated with changes in a subset of parameters (diastolic duration, late AP duration, and diastolic depolarization rate). Dynamic clamp injection of the βAR-sensitive component of If showed that it accounts for approximately 41% of the fight-or-flight increase in AP firing rate and 60% of the decrease in the interval between APs. Thus, If is an essential contributor to the fight-or-flight increase in heart rate.
Identification of viral dose and administration time in simulated phage therapy occurrences

The rise in multidrug-resistant bacteria has sprung a renewed interest in applying phages as antibacterial, a procedure Western practitioners eventually abandoned due to several downfalls, including poor understanding of the dynamics between phages and bacteria. A successful phage therapy needs to account for the loss of infective virions and the multiplication of the hosts. The parameters critical inoculation size (VF) and failure threshold time (TF) have been introduced to assure that the viral dose (vϕ) and administration time (tϕ) would lead to an effective treatment. The problem with the definition of VF and TF is that they are non-linear equations with two unknowns; thus, their solution is cumbersome and not unique. The current study used machine learning in the form of a decision tree algorithm to determine ranges for the viral dose and administration times required to achieve an effective phage therapy. Within these ranges, a Pareto optimal solution of a multi-criterial optimization problem (MCOP) provides values leading to effective treatment. The algorithm was tested on a series of microbial consortia that described allochthonous invasions (the outgrowing of a species at high cell density by another species initially present at low concentration) to inhibit the growth of the invading species. The present study also introduced the concept of ‘mediated phage therapy’, where targeting a booster bacteria might decrease the virulence of a pathogen immune to phagial infection. The results demonstrated that the MCOP could provide pairs of vϕ and tϕ that could effectively wipe out the bacterial target from the considered micro-environment. In summary, the present work introduced a novel method for investigating the phage/bacteria interaction that could help increase the effectiveness of phage therapy. Author summary Phage therapy is a treatment that can help fight infections with bacteria resistant to antibiotics. However, several phage therapy application have failed, possibly because phages were administered at the wrong time or in insufficient amounts. The present study implemented a machine learning protocol to correctly calculate the administration time and viral load to obtain effective phage therapy. Four simulated microbial consortia, including one case where the pathogen was not directly a phage’s host, were employed to prove the procedure’s concept. The results demonstrated that the procedure is suitable to help the microbiologists to instantiate an effective phage therapy and clear infections.
Mosaic patterns of selection in genomic regions associated with diverse human traits

Natural selection shapes the genetic architecture of many human traits. However, the prevalence of different modes of selection on genomic regions associated with variation in traits remains poorly understood. To address this, we developed an efficient computational framework to calculate enrichment of different evolutionary measures among regions associated with complex traits. We applied the framework to summary statistics from >900 genome-wide association studies (GWASs) and 11 evolutionary measures of sequence constraint, population differentiation, and allele age while accounting for linkage disequilibrium, allele frequency, and other potential confounders. We demonstrate that this framework yields consistent results across GWASs with variable sample sizes, numbers of trait-associated SNPs, and analytical approaches. The resulting evolutionary atlas maps diverse signatures of selection on genomic regions associated with complex human traits on an unprecedented scale. We detected positive enrichment for sequence conservation among trait-associated regions for the majority of traits (>77% of 290 high power GWASs), which was most dominant in reproductive traits. Many traits also exhibited substantial enrichment for population differentiation and recent positive selection, especially among hair, skin, and pigmentation traits. In contrast, we detected widespread negative enrichment for balancing selection (51% GWASs) and no evidence of enrichment for selection signals in regions associated with late-onset Alzheimer’s disease. These results support a pervasive role for negative selection on regions of the human genome that contribute to variation in complex traits, but also demonstrate where diverse modes of selection have shaped trait-associated loci. This atlas of signatures of different modes of natural selection across the diversity of available GWASs will enable exploration of the relationship between the genetic architecture and selection in the human genome.
Incorporating uniparental markers and demographic information in kinship analysis

Knowledge of kinship relations between members of wild populations is of great importance in ecological and conservation genetic studies. The bi-parentally inherited autosomal markers has been the Golden Standard in kinship analysis. However, analysis of kin relationship can be challenging in wild populations. The uni-parentally inherited markers and population demographic information can be helpful for identifying false-positive in kinship analysis. Here we showed how incorporating uniparental genetic and demographic information can improve the correct classification rate of kinship analyses by reanalyzing data of a recent study published in Science Advances. The application of next generation high-throughput sequencing to address fundamental ecological questions is of immense benefit to the field of molecular ecology, which could also generate uniparentally inherited organelle genomes together with nuclear data. We strongly recommended that uniparental genetic markers and demographic information be seriously considered in kinship analyses of wild populations.