Miracle-dz/UniFAR-FTUs huggingface dataset:
Mosaic changes to the global transcriptome in response to inhibiting ribosome formation versus inhibition of ribosome function

Cell fate is susceptible to several internal and external stresses. Stress resulting from mutations in genes for ribosomal proteins and assembly factors leads to many congenital diseases, collectively called ribosomopathies. Even though such mutations all depress the cell’s protein synthesis capacity, they are manifested in many different phenotypes. This prompted us to use Saccharomyces cerevisiae to explore whether reducing the protein synthesis capacity by different mechanisms result in the same or different changes to the global transcriptome. We have compared the transcriptome after abolishing the assembly of new ribosomes and inhibiting the translocation of ribosomes on the mRNA. Our results show that these alternate obstructions generate different mosaics of expression for several classes of genes, including genes for ribosomal proteins, mitotic cell cycle, cell wall synthesis, and protein transport.
Magnetic inhibition of the recollimation instability in relativistic jets

In this paper, we describe the results of three-dimensional relativistic magnetohydrodynamic simulations aimed at probing the role of regular magnetic field on the development of the instability that accompanies recollimation of relativistic jets. In particular, we studied the recollimation driven by the reconfinement of jets from active galactic nuclei (AGN) by the thermal pressure of galactic coronas. We find that a relatively weak azimuthal magnetic field can completely suppress the recollimation instability in such jets, with the critical magnetization parameter σcr < 0.01. We argue that the recollimation instability is a variant of the centrifugal instability (CFI) and show that our results are consistent with the predictions based on the study of magnetic CFI in rotating fluids. The results are discussed in the context of AGN jets in general and the nature of the Fanaroff–Riley morphological division of extragalactic radio sources in particular.
Examining the Effects of Cultural Value Orientations, Emotional Intelligence, and Motivational Orientations: How do LMX Mediation and Gender-Based Moderation Make a Difference?

We examined the role of leader–member exchange (LMX) as a mediator between individual differences and outcomes across three separate studies with 838 participants. Gender-based moderation was used with the LMX mediation effect. Our results suggest that gender makes a dramatic difference. Specifically, we found that LMX mediation lowered the tendency of counterproductive work behaviors (CWBs) for men. In addition, we found that LMX mediated the effect extrinsic motivation has on extrinsic job satisfaction for women. We trace these differences to a tendency for women to express a more democratic and participative leadership style, which implies a different criterion for leader performance in some situations. We also present suggestions for how the findings of our studies can be extended via organizational practice and future research.
A Theory of Instrument-Specific Absolute Pitch

While absolute pitch (AP)—the ability to name musical pitches globally and without reference—is rare in expert musicians, anecdotal evidence suggests that some musicians may better identify pitches played on their primary instrument than pitches played on other instruments. We call this phenomenon “instrument-specific absolute pitch” (ISAP). In this paper we present a theory of ISAP. Specifically, we offer the hypothesis that some expert musicians without global AP may be able to more accurately identify pitches played on their primary instrument(s), and we propose timbral cues and articulatory motor imagery as two underlying mechanisms. Depending on whether informative timbral cues arise from performer- or instrument-specific idiosyncrasies or from timbre-facilitated tonotopic representations, we predict that performance may be enhanced for notes played by oneself, notes played on one’s own personal instrument, and/or notes played on any exemplar of one’s own instrument type. Sounds of one’s primary instrument may moreover activate kinesthetic memory and motor imagery, aiding pitch identification. In order to demonstrate how our theory can be tested, we report the methodology and analysis of two exemplary experiments conducted on two case-study participants who are professional oboists. The aim of the first experiment was to determine whether the oboists demonstrated ISAP ability, while the purpose of the second experiment was to provide a preliminary investigation of the underlying mechanisms. The results of the first experiment revealed that only one of the two oboists showed an advantage for identifying oboe tones over piano tones. For this oboist demonstrating ISAP, the second experiment demonstrated that pitch-naming accuracy decreased and variance around the correct pitch value increased as an effect of transposition and motor interference, but not of instrument or performer. These preliminary data suggest that some musicians possess ISAP while others do not. Timbral cues and motor imagery may both play roles in the acquisition of this ability. Based on our case study findings, we provide methodological considerations and recommendations for future empirical testing of our theory of ISAP.
Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae

Abstract During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.
Phenotypic and Genotypic Investigation of Two Representative Strains of Microbacterium Species Isolated From Micro-Filtered Milk: Growth Capacity and Spoilage-Potential Assessment

The microbiota that spoil long-life micro-filtered milk generally includes species of the genus Microbacterium. The metabolic properties of this of microorganisms that could potentially modify the quality of micro-filtered milk are still unexplored when compared to better-known microorganisms, such as the spore-forming Bacillus and Paenibacillus spp. , and Gram-negative contaminants, such as species of the genera Pseudomonas and Acinetobacter. In this preliminary study, two strains of Microbacterium (M. lacticum 18H and Microbacterium sp. 2C) isolated from micro-filtered milk were characterized in depth, both phenotypically and genotypically, to better understand their role in long-term milk spoilage. The study highlights the ability of these strains to produce high cell numbers and low acidification in micro-filtered milk under storage and shelf-life conditions. Phenotypic analyses of the two Microbacterium sp. isolates revealed that both strains have low proteolytic and lipolytic activity. In addition, they have the ability to form biofilms. This study aims to be a preliminary investigation of milk-adapted strains of the Microbacterium genus, which are able to grow to high cellular levels and perform slight but not negligible acidification that could pose a potential risk to the final quality of micro-filtered milk. Furthermore, M. lacticum 18H and Microbacterium sp. 2C were genotypically characterized in relation to the characteristics of interest in the milk environment. Some protein-encoding genes involved in lactose metabolism were found in the genomes, such as β-galactosidase, lactose permease, and L-lactate dehydrogenase. The phenotypically verified proteolytic ability was supported in the genomes by several genes that encode for proteases, peptidases, and peptide transferases.
Macroevolutionary Analyses Provide New Evidences of Phasmid Wings Evolution as a Reversible Process

The concept that complex ancestral traits can never be re-acquired after their loss has grown popular since its initial formulation and it’s often referred to as Dollo’s law. Nonetheless, several macroevolutionary evidences - along with molecular ones - suggest instances where complex phenotypes could have been lost throughout a clade evolutionary history and subsequently reverted to their former state in derived lineages. One of the first and most notable rejection of Dollo’s law is represented by wing evolution in phasmids: this polyneopteran order of insects - which comprises stick and leaf insects - has played a central role in initiating a long-standing debate on the topic. In this study, a novel and comprehensive time-tree - including over 300 Phasmatodea species - is used as a framework for investigating wing’s evolutionary patterns in the clade. Despite accounting for several possible biases and sources of uncertainty, macroevolutionary analyses consistently support a dynamic and reversible evolution of wings, with multiple transitions to ancestral states taking place after their loss. Our findings suggest that wings and flight are decoupled from Phasmatodea diversification dynamics and that brachyptery is an unstable state, unless when co-opted for non-aerodynamic adaptations. We also explored how different assumptions of wings’ reversals probability could impact their inference: we found that until reversals are assumed to be over 30 times more unlikely than losses, they are consistently retrieved despite uncertainty in tree and model parameters. Our findings demonstrate that wings evolution can be a reversible and dynamic process in phasmids and contribute to shape our understanding of how complex phenotypes evolve.
Effect of renal function on neutrophil decreases following eribulin administration

Eribulin therapy has recently attracted attention from various viewpoints, including quality of life, and is considered a standard therapy for inoperable or recurrent breast cancer. Although a reduction in renal function reportedly decreases total eribulin clearance, its association with dose‐limiting toxicity and the reduction of neutrophils remain unclear.
Explaining black-box text classifiers for disease-treatment information extraction

Deep neural networks and other intricate Artificial Intelligence (AI) models have reached high levels of accuracy on many biomedical natural language processing tasks. However, their applicability in real-world use cases may be limited due to their vague inner working and decision logic. A post-hoc explanation method can approximate the behavior of a black-box AI model by extracting relationships between feature values and outcomes. In this paper, we introduce a post-hoc explanation method that utilizes confident itemsets to approximate the behavior of black-box classifiers for medical information extraction. Incorporating medical concepts and semantics into the explanation process, our explanator finds semantic relations between inputs and outputs in different parts of the decision space of a black-box classifier. The experimental results show that our explanation method can outperform perturbation and decision set based explanators in terms of fidelity and interpretability of explanations produced for predictions on a disease-treatment information extraction task.
Ascorbate Oxidase Induces Systemic Resistance in Sugar Beet Against Cyst Nematode Heterodera schachtii

Ascorbate oxidase (AO) is an enzyme involved in catalyzing the oxidation of apoplastic ascorbic acid (AA) to dehydroascorbic acid (DHA). In this research, the potential of AO spraying to induce systemic resistance was demonstrated in the interaction between sugar beet root and cyst nematode Heterodera schachtii and the mechanism was elucidated. Plant bioassays showed that roots of AO-sprayed plants were infested by a significantly lower number of females and cysts when compared with mock-sprayed control plants. Hormone measurements showed an elevated level of jasmonic acid (JA) salicylic acid (SA) and ethylene (ET) in the roots of AO-sprayed plants, with a dynamic temporal pattern of activation. Experiments with chemical inhibitors showed that AO-induced systemic resistance is partially dependent on the JA, ET and SA pathways. Biochemical analyses revealed a primed accumulation of hydrogen peroxide (H2O2), and phenylalanine ammonia lyase (PAL) activity in the roots of AO-sprayed plants upon infection by cyst nematodes. In conclusion, our data shows that AO works as an effective systemic defense priming agent in sugar beet against cyst nematode infection, through activation of multiple basal plant defense pathways.
Aryl hydrocarbon receptor ligand production by the gut microbiota is decreased in celiac disease leading to intestinal inflammation

Impaired AhR ligand production by the gut microbiota decreases AhR pathway activation, promoting inflammation in celiac disease. The advantage of a high-tryptophan diet Although 40% of the worldwide population express celiac disease susceptibility genes, only 1% will develop the disorder, suggesting a role for environmental factors, including the gut microbiota. Lamas et al. show that celiac disease is associated with an impaired capacity of the gut microbiota to metabolize tryptophan into aryl hydrocarbon receptor (AhR) ligands in patients with celiac disease. Gluten-induced immunopathology in mice expressing a celiac disease susceptibility gene was ameliorated after AhR pathway activation by a high-tryptophan diet, or by treatment with a pharmacological AhR agonist or bacteria producing AhR ligands. AhR pathway modulation by the gut microbiota may have potential as a therapeutic strategy for treating celiac disease. Metabolism of tryptophan by the gut microbiota into derivatives that activate the aryl hydrocarbon receptor (AhR) contributes to intestinal homeostasis. Many chronic inflammatory conditions, including celiac disease involving a loss of tolerance to dietary gluten, are influenced by cues from the gut microbiota. We investigated whether AhR ligand production by the gut microbiota could influence gluten immunopathology in nonobese diabetic (NOD) mice expressing DQ8, a celiac disease susceptibility gene. NOD/DQ8 mice, exposed or not exposed to gluten, were subjected to three interventions directed at enhancing AhR pathway activation. These included a high-tryptophan diet, gavage with Lactobacillus reuteri that produces AhR ligands or treatment with an AhR agonist. We investigated intestinal permeability, gut microbiota composition determined by 16S rRNA gene sequencing, AhR pathway activation in intestinal contents, and small intestinal pathology and inflammatory markers. In NOD/DQ8 mice, a high-tryptophan diet modulated gut microbiota composition and enhanced AhR ligand production. AhR pathway activation by an enriched tryptophan diet, treatment with the AhR ligand producer L. reuteri, or pharmacological stimulation using 6-formylindolo (3,2-b) carbazole (Ficz) decreased immunopathology in NOD/DQ8 mice exposed to gluten. We then determined AhR ligand production by the fecal microbiota and AhR activation in patients with active celiac disease compared to nonceliac control individuals. Patients with active celiac disease demonstrated reduced AhR ligand production and lower intestinal AhR pathway activation. These results highlight gut microbiota-dependent modulation of the AhR pathway in celiac disease and suggest a new therapeutic strategy for treating this disorder.
Broad He i 1.08-µm absorption from the obscurer in the active galaxy NGC 5548

The nucleus of the active galaxy NGC 5548 was the target of two intensive spectroscopic monitoring campaigns at X-ray, ultraviolet (UV), and optical frequencies in 2013/2014. These campaigns detected the presence of a massive obscuration event. In 2016/2017, Landt et al. conducted a near-IR spectroscopic monitoring campaign on NGC 5548 and discovered He i 1.08-μm absorption. Here, we decompose this absorption into its components and study its time variability. We attribute the narrow He i absorption lines to the warm absorber (WA) and, as for the newly appeared low-ionization WA lines in the UV, their presence is most likely due to a reduction in ionization parameter caused by the obscurer. The observed variability of the narrow He i absorption is consistent with what is expected for the WA. Most importantly, we also detect fast, broad He i absorption, which we attribute to the obscurer. This He i broad absorption, which is indicative of a high column density gas, is unsaturated and variable on time-scales of a few months. The observed variability of the obscurer is mainly due to changes in ionization, although density changes also play a role. We test the physical cycle model of Dehghanian et al. which proposes that helium recombination can account for how the obscurer influences the physics of the WA gas. Our results support their model, but also indicate that the reality might be more complex.
Visual Search for Circumscribed Interests in Autism Is Similar to That of Neurotypical Individuals

Intense interests are a core symptom of autism spectrum disorders (ASD) and can be all-encompassing for affected individuals. This observation raises the hypothesis that intense interests in ASD are related to pervasive changes in visual processing for objects within that category, including visual search. We assayed visual processing with two novel tasks, targeting category search and exemplar search. For each task, three kinds of stimuli were used: faces, houses, and images personalized to each participant’s interest. 25 children and adults with ASD were compared to 25 neurotypical (NT) children and adults. We found no differences in either visual search task between ASD and NT controls for interests. Thus, pervasive alterations in perception are not likely to account for ASD behavioral symptoms.
Fatty Acids in Veterinary Medicine and Research

Fatty acid regulation is an essential process for all animals. A number of studies have shown that diet affects the levels/availability of fatty acids in the body but increasingly evidence shows that disease states can alter the amounts within the body too. Fatty acid levels and availability have been altered by a number of diseases, disorders and reactions including inflammatory responses, heart disease and heart failure and wound repair. They are also essential during the growth and development stages of animals. The amount of research into the consequences of different fatty acid intake and levels in various disease states and during development has increased in both humans and animals. This review presents an overview of the research undertaken to date and highlights the importance, uses and benefits of understanding the roles of fatty acids in both the healthy animal and under differing disorders and diseases.
Strategy Use in Learning From Multiple Texts: An Investigation of the Integrative Framework of Learning From Multiple Texts

This study examined undergraduates’ strategy use when learning about a complex and controversial topic (i.e., mass incarceration in the United States) based on information presented across multiple texts. Guided by the Integrated Framework of Learning from Multiple Texts, this study directed students to engage in one of three forms of strategy use while learning from multiple texts. In particular, students were asked to identify relevant and important information in texts (i.e., intratextual processing), to form relations or connections across texts (i.e., intertextual processing), or to identify easy or difficult to understand information in texts (i.e., metacognitive processing). In addition to receiving task instructions directing them to engage in these modes of processing, students were also provided with a highlighting tool to scaffold their strategy use (e.g., by allowing important and relevant information to be marked in green, in the intratextual processing condition). This highlighting tool also enabled researchers to collect log data of students’ manifest strategy use. Students were found to demonstrate differential patterns of strategy use in accordance with their assigned processing conditions. Moreover, students’ use of strategies directed toward multiple texts was found to predict multiple text task performance.
Restoration on Private Lands: A Case Study Examining Vegetation Recruitment following Restoration Treatments in an Oak-pine Barrens Ecosystem in Western Michigan, U.S.A.

Abstract. Oak-pine barrens ecosystems provide critical habitat for the federally endangered Karner blue butterfly (Lycaeides melissa samuelis). Wild lupine (Lupinus perennis), an herbaceous perennial in this ecosystem is the only food source for the butterfly's larvae. The range and quality of these ecosystems have declined significantly. Restoration in private lands can be key to expanding these habitats, but often there is limited or no follow-up to assess the recovery of the site following restoration treatments. We conducted a case study in a private property in Newaygo County, Michigan for which prescribed fire had been implemented every 2 y from 2007 through 2011 to promote recruitment of key understory vegetation, but there had been no follow-up recovery assessment. The burn treatment consisted of a section that was not burned, one that was burned twice, and one that was burned three times. We collected data on vegetation groups and site related factors along this fire gradient to examine differences as a function of fire frequency, as well as delineate factors driving patterns of understory plant recruitment. Results show little tree recruitment from seedlings, but high densities of tree saplings recruited via resprouting. Estimated cover of lupine was low across all treatments, whereas Pennsylvania sedge (Carex pensylvanica Lam,) was highest among species in both cover and biomass. Lupine exhibited a negative relationship with Pennsylvania sedge, litter, and sprouted tree saplings, but a positive relationship with moss cover. We make recommendations for additional restoration interventions and highlight the need for continued support of private landowners as they engage in conservation of imperiled species.