Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the linkage between offline collaboration networks and online representational network diversity on social media

ABSTRACT Building on the symbiotic sustainability model, this study investigated how offline collaboration networks are related to organizations’ representational networks on social media. We analyzed survey data from disaster risk reduction organizations in North America, Europe, and Asia-Pacific regions, along with these organizations’ representational networks on Facebook (N = 108) and Twitter (N = 96). Results showed that diverse offline collaboration networks are positively related to diverse representational tie building on Facebook via organizations’ sense of mutuality. By contrast, homogeneous offline collaboration networks are positively related to diverse representational tie building on Twitter via mutuality and openness to collaboration. This study contributes to research on interorganizational networks and social media, particularly concerning the offline–online connection in the field of interorganizational communication.
Temperature Dependences of the Quantum-Mechanical and Semi-Classical Spectral-Line Widths and the Separation 0 of the Impact and Non-Impact Regions for an Ar-Perturbed/K-Radiator System

Quantum-mechanical and semi-classical spectral-line shapes are computed at 𝑇=400, 800, and 1000 K for the line core of the 5802 Å line of the Ar-Perturbed/K-Radiator system. HWHMs (𝑤's) are measured from computed full spectral-line shapes. The final-state pseudopotential is for the 7𝑠2𝑆1/2 state, and the initial-state potential is for the 4𝑝2𝑃3/2,3/2 state. Three high-pressure (P) log(𝑤)—versus—log(𝑃) curves, corresponding to the non-impact region, intersect a similar set of low-P, impact-region curves at intersections, 𝑃0's. Similarly, for two sets of log(𝑤)—versus—log(𝑛) curves, which yield intersections, 𝑛0's, where 𝑛 is the perturber density. These 𝑛0's and 𝑝0's separate the two regions and represent the upper limits of the impact regions. A specific validity condition for the impact region is given by the equation 𝑛≤𝑛0. From an earlier spectroscopic, Fabry-Perot paper, 𝑤expt=0.021 cm−1 at 𝑇=400 K and 𝑃=10 torr. Two theoretical values, 𝑤theor=0.025 and 0.062 cm−1 corresponding to two different pseudo-potentials, are reported. Two 𝑇-dependent figures are given, in which the first shows an increase in the impact region with 𝑇, based on 𝑃 as the basic parameter, and the second which shows a decrease in the impact region with 𝑇, based on 𝑛 as the basic parameter.
Structural characterization of form I of anhydrous rifampicin

Rifampicin is a first-line drug widely used in the treatment of tuberculosis both in the intensive and in the treatment phase. In this work we characterized the crystal structure of form I of anhydrous rifampicin mainly by using X-ray powder diffraction data combined with the Rietveld method. Other complementary techniques such as Fourier transform infrared spectroscopy and thermal analysis were also employed. It crystallized in a monoclinic crystal system with space group C2 and the following unit cell parameters: a = 25.8846(2) A, b = 14.2965(2) A, c = 14.2796(2) A, β = 122.98(1)°, V = 4432.81(7) A3, Z = 4, Z′ = 1 and ρcalc = 1.23310(2) g cm−3. A BFDH model was used to inspect the crystal morphology prediction, and great similarity with crystals observed on an optical microscope was found. The FTIR spectrum confirmed the results obtained by X-ray powder diffraction, which indicates that all the functional groups involved in H bonding are intramolecularly connected. This polymorphic form presented a thermal stability up to approximately 230 °C.
Electrophoretic deposition of negatively charged tetratitanate nanosheets and transformation into preferentially oriented TiO2(B) film

A tetrabutylammonium–H2Ti4O9·xH2O intercalation compound was obtained by a guest exchange reaction between tetrabutylammonium hydroxide and an ethylammonium–H2Ti4O9·xH2O intercalation compound, and its dispersion state in aqueous and non-aqueous solutions were studied. Spontaneous exfoliation of H2Ti4O9·xH2O into colloidal nanosheets occurred when the tetrabutylammonium–H2Ti4O9·xH2O intercalation compound was dispersed in water, methyl alcohol, isopropyl alcohol, acetonitrile, N,N-dimethylformamide, dimethyl sulfoxide, and propylene carbonate, while exfoliation did not occur in tetrahydrofuran. A tetrabutylammonium–H2Ti4O9·xH2O film was obtained by a reassembly process by casting the colloidal suspension containing exfoliated nanosheets, while a H2Ti4O9·xH2O film was directly obtained by electrophoretic deposition. Thermal treatment of the electrophoretically deposited film led to an oriented TiO2(B) film with the (0k0) planes lying perpendicular to the substrate.
Plasma concentrations of progesterone in the preceding estrous cycle are associated with the intensity of estrus and fertility of Holstein cows

The aim of this study was to determine the association between concentrations of progesterone (P4) during previous the estrous cycle with the intensity of spontaneous or estrogen-induced estrous expression and pregnancy per artificial insemination (P/AI). A total of 1,953 AI events from lactating Holstein cows were used, consisting of 1,289 timed AI events from experiment 1 (Exp. 1) and 664 AI events from experiment 2 (Exp. 2). In Exp. 1, cows were bred after a timed AI protocol based on estradiol and P4. In Exp. 2 animals were bred upon spontaneous estrus detection. In both experiments cows were continuously monitored by an automated activity monitor (AAM). The intensity of estrous expression was determined for each event and classified as either high or low intensity using the median of each experiment. Blood samples were collected for P4 analysis in Exp. 1 at –4 d, 0 d, and 7 d relative to timed AI, and in Exp. 2 immediately following estrus (0 d), 7 d, 14 d, and 21 d post-AI. Concentration of P4 was classified as greater or lower according to the median value in each experiment. Cows with lower concentrations of P4 at AI had greater estrous expression in Exp. 1 (363.6 ± 5.2 vs. 275.9 ± 8.0 % relative increase) and Exp. 2 (76.7 ± 1.9 vs. 67.4 ± 4.7 index; and 12.5 ± 0.5 vs. 9.3 ± 1.8 h). Cows with a greater intensity of estrous expression at timed AI had greater concentrations of P4 at –4 d than cows with lower intensity estrus or no estrous expression (4.6 ± 0.2 vs. 3.6 ± 0.2 vs. 3.7 ± 0.2 ng/mL). Cows with greater concentrations of P4 at –4 d had greater P/AI (32.8 ± 4.4 vs. 22.4 ± 4.5 %), whereas cows with lesser concentrations of P4 at d0 for either timed AI (35.2 ± 3.4 vs. 19.6 ± 4.6 %) or spontaneous estrus (31.8 ± 2.8 vs. 23.4 ± 3.2 %) had greater P/AI. Cows with greater concentrations of P4 7 d post-timed AI had greater P/AI compared with cows that had lower concentration of P4 (39.1 ± 2.9 vs. 24.7 ± 2.6 %). Similarly, cows that had lower concentrations of P4 at 7 d, 14 d and 21 d post-spontaneous estrus tended to have lower P/AI when compared with cows with greater concentrations of P4. Overall, concentrations of P4 prior to and at AI were associated with greater estrous intensity and P/AI at both spontaneous and timed AI events.
Intrinsic variability of fluorescence calibrators impacts the assignment of MESF or ERF values to nanoparticles and extracellular vesicles by flow cytometry

Flow cytometry is commonly used to characterize nanoparticles (NPs) and extracellular vesicles (EVs) but results are often expressed in arbitrary units to indicate fluorescence intensity. This hampers interlaboratory and inter-platform comparisons. We investigated the use of molecules of equivalent soluble fluorophores (MESF)-beads for assignment of fluorescence values to NPs and EVs by comparing two FITC-MESF bead sets as calibrators on different flow cytometry platforms (BD Influx™, CytoFLEX LX™ and SORP BD FACSCelesta™). Next, fluorescence signals of NPs and EVs were calibrated using different sets of FITC and PE-MESF beads. Fluorescence calibration using beads designed for cellular flow cytometry allowed inter-platform comparison. However, the intrinsic uncertainty in the fluorescence assignment to these MESF beads impacts the reliable assignment of MESF values to NPs and EVs based on extrapolation into the dim fluorescence range. Our findings demonstrate that the use of the same set of calibration materials (vendor and lot number) and the same number of calibration points, greatly improves robust interlaboratory and inter-platform comparison of fluorescent submicron sized particles.
De novo purine nucleotide biosynthesis mediated by amidophosphoribosyl transferase is required for conidiation and essential for the successful host colonization of Magnaporthe oryzae

Amidophosphoribosyl transferase catalyzes the first step of the purine nucleotide biosynthesis by converting 5-phosphoribosyl-1-pyrophosphate into 5-phosphoribosyl-1-amine. In this study, we identified and characterized the functions of MoAde4, an ortholog of yeast Ade4 in the rice blast fungus. MoAde4 is a 537-amino acid protein containing the GATase_6 and pribosyltran domains. Quantitative real-time PCR analysis showed MoADE4 transcripts were highly expressed during conidiation, early-infection, and late-infection stages of the fungus. Disruption of MoADE4 gene resulted in ΔMoade4 mutant exhibiting adenine, adenosine, and hypoxanthine auxotrophy on MM. Conidia quantification assays showed ΔMoade4 mutant was significantly reduced in sporulation. The conidia of ΔMoade4 mutant could still form appressoria but mostly failed to penetrate the rice cuticle. Pathogenicity test showed ΔMoade4 was completely nonpathogenic on rice and barley leaves which was attributed by failure of its infectious hyphae to colonize the host cells. The ΔMoade4 was defective in induction of strong host immunity and had its purine transporter genes repressed during in planta infection. Addition of exogenous adenine partially rescued conidiation and pathogenicity defects of the ΔMoade4 mutant on the barley and rice leaves. Localization assays showed that MoAde4 is located in the cytoplasm. Taken together, our results demonstrate that purine biosynthesis orchestrated by MoAde4 is required for fungal development, conidiation, more importantly, we found it to be essential for fungal pathogenicity not because of the appressorial formation, but appressorium penetration and host colonization during the plant infection of M. oryzae. Thus this findings suggests that purine biosynthesis could act as an important target for combating recalcitrant plant fungal pathogens.
Arabidopsis ROOT UV-B SENSITIVE 1 and 2 Interact with Aminotransferases to Regulate Vitamin B6 Homeostasis

Pyridoxal-5’-phosphate (PLP), the enzymatic cofactor form of Vitamin B6 (vitB6), is a versatile compound that has essential roles in metabolism. Cellular PLP homeostasic regulation is currently not well understood. Here we report that in Arabidopsis, biosynthesized PLP is sequestered by specific aminotransferases (ATs), and that the proteins ROOT UV-B SENSITIVE 1 (RUS1) and RUS2 function with ATs to regulate PLP homeostasis. The stunted growth phenotypes of rus1 and rus2 mutants were previously shown to be rescuable by exogenously supplied vitB6. Specific residue changes near the PLP-binding pocket in ASPARTATE AMINOTRANSFERASE2 (ASP2) also rescued rus1 and rus2 phenotypes. In this study, saturated suppressor screens identified 14 additional suppressor of rus (sor) alleles in four aminotransferase genes (ASP1, ASP2, ASP3, or ALANIN AMINOTRANSFERASE1 (AAT1)), which suppressed the rus phenotypes to varying degrees. Each of the sor mutations altered an amino acid in the PLP-binding pocket of the protein, and sor proteins were found to have reduced levels of PLP conjugation. Genetic data revealed that the availability of PLP normally requires both RUS1 and RUS2, and that increasing the number of sor mutants additively enhanced the suppression of rus phenotypes. Biochemical results showed that RUS1 and RUS2 physically interacted with ATs. Our studies suggest a mechanism in which RUS1, RUS2 and specific ATs work together to regulate PLP homeostasis in Arabidopsis.
Genetic basis of variation in cocaine and methamphetamine consumption in outbred populations of Drosophila melanogaster

Significance The use of cocaine and methamphetamine presents significant socioeconomic problems. However, identifying the genetic underpinnings that determine susceptibility to substance use is challenging in human populations. The fruit fly, Drosophila melanogaster, presents a powerful genetic model since we can control the genetic background and environment, 75% of disease-causing genes in humans have a fly counterpart, and flies—like humans—exhibit adverse effects upon cocaine and methamphetamine exposure. We showed that the genetic architecture underlying variation in voluntary cocaine and methamphetamine consumption differs between sexes and is dominated by variants in genes associated with connectivity and function of the nervous system. Results obtained from the Drosophila gene discovery model can guide studies on substance abuse susceptibility in human populations. We used Drosophila melanogaster to map the genetic basis of naturally occurring variation in voluntary consumption of cocaine and methamphetamine. We derived an outbred advanced intercross population (AIP) from 37 sequenced inbred wild-derived lines of the Drosophila melanogaster Genetic Reference Panel (DGRP), which are maximally genetically divergent, have minimal residual heterozygosity, are not segregating for common inversions, and are not infected with Wolbachia pipientis. We assessed consumption of sucrose, methamphetamine-supplemented sucrose, and cocaine-supplemented sucrose and found considerable phenotypic variation for consumption of both drugs, in both sexes. We performed whole-genome sequencing and extreme quantitative trait locus (QTL) mapping on the top 10% of consumers for each replicate, sex, and condition and an equal number of randomly selected flies. We evaluated changes in allele frequencies among high consumers and control flies and identified 3,033 variants significantly (P < 1.9 × 10−8) associated with increased consumption, located in or near 1,962 genes. Many of these genes are associated with nervous system development and function, and 77 belong to a known gene–gene interaction subnetwork. We assessed the effects of RNA interference (RNAi) on drug consumption for 22 candidate genes; 17 had a significant effect in at least one sex. We constructed allele-specific AIPs that were homozygous for alternative candidate alleles for 10 single-nucleotide polymorphisms (SNPs) and measured average consumption for each population; 9 SNPs had significant effects in at least one sex. The genetic basis of voluntary drug consumption in Drosophila is polygenic and implicates genes with human orthologs and associated variants with sex- and drug-specific effects.
Distinct sub-cellular autophagy impairments occur independently of protein aggregation in induced neurons from patients with Huntington’s disease

Huntington’s disease (HD) is a neurodegenerative disorder caused by CAG expansions in the huntingtin (HTT) gene. Modelling HD has remained challenging, as rodent and cellular models poorly recapitulate the disease. To address this, we generated induced neurons (iNs) through direct reprogramming of human skin fibroblasts, which retain age-dependent epigenetic characteristics. HD-iNs displayed profound deficits in autophagy, characterised by reduced transport of late autophagic structures from the neurites to the soma. The neurite-specific alterations in autophagy resulted in shorter, thinner and fewer neurites presented by HD-iNs. CRISPRi-mediated silencing of HTT did not rescue this phenotype but rather resulted in additional autophagy alterations in ctrl-iNs, highlighting the importance of wild type HTT in neuronal autophagy. In summary, our work identifies a distinct subcellular autophagy impairment in aged patient derived HD-neurons and provides a new rational for future development of autophagy activation therapies.
miRNA-dependent poly(A) length control in uncoupling transcription and translation of haploid male germ cells

As one of the post-transcriptional regulatory mechanisms, transcription and translation’s uncoupling plays an essential role in development and adulthood physiology. However, it remains elusive how thousands of mRNAs get translationally silenced while stability is maintained for up to hours or even days before translation. In addition to oocytes and neurons, developing spermatids have significant uncoupling of transcription and translation for delayed translation. Therefore, spermiogenesis represents an excellent in vivo model for investigating the mechanism underlying uncoupled transcription and translation. Through full-length poly(A) deep sequencing, we discovered dynamic changes in poly(A) length through deadenylation and re-polyadenylation. Deadenylation appeared to be mediated by microRNAs (miRNAs), and transcripts with shorter poly(A) tails tend to be sequestered into ribonucleoproteins (RNPs) for translational repression and stabilization. In contrast, re-polyadenylation allows for translocation of the translationally repressed transcripts from RNPs to polysomes for translation. Overall, our data suggest that miRNA-dependent poly(A) length control represents a novel mechanism underlying uncoupled translation and transcription in haploid male germ cells.
BMP signaling: A significant player and therapeutic target for osteoarthritis

Objective To investigate the role of BMP signaling in osteoarthritis' pathogenesis and propose a disease-modifying therapy for OA. Methods C57BL6/J mouse line was used to perform ACLT surgery at P120 to study the expression pattern of the BMP signaling readout pSMAD1/5/9. To investigate whether activation of BMP signaling is sufficient and necessary to induce osteoarthritis, we have used conditional GOF and LOF mouse lines in which BMP signaling can be activated or depleted, respectively, upon intra-peritoneal injection of tamoxifen. Finally, we locally inhibited BMP signaling through intra-articular injection of LDN-193189 pre- and post-onset surgically induced OA. Most of the analysis has been done through immunohistochemistry, histopathological staining, and micro-CT to evaluate the status of the pathogenesis of the disease. Results We observed concomitant activation of BMP signaling, as judged by pSMAD1/5/9 immunoreactivity in the articular cartilage, upon induction of osteoarthritis with simultaneous depletion of SMURF1, an intra-cellular BMP signaling inhibitor in articular cartilage. Even without surgical induction of osteoarthritis, only BMP gain-of-function mutation induces OA in mouse articular cartilage. Also, genetic, or pharmacological inhibition of BMP signaling offered significant protection against OA pathogenesis. Interestingly, post-onset of the disease, inhibition of BMP signaling by intra-articular injection of LDN-193189 retarded OA progression with a significant reduction in inflammatory markers. Conclusion Our study demonstrated that BMP signaling plays an essential role in the pathogenesis of OA and that local BMP inhibition can be an effective therapeutic strategy to mitigate osteoarthritis.
Decline in large-seeded species in Danish grasslands over an eight-year period

A time-series analysis of cover data from 236 Danish grassland sites demonstrated community selection on seed mass. Across four grassland habitat types and during an eight-year period there was a significant decline in large-seeded species. In the analysis, the continuous seed size variable was used to group plant species into functional types. This method was chosen in order to account for the sampling process of the abundance data, and is in contrast to most other analyses of trait selection, where the community weighted mean of the traits is used as the dependent variable. Generally, little is known on the causes for seed size community selection in semi-natural grasslands that are not subjected to successional processes.
ksrates: positioning whole-genome duplications relative to speciation events in KS distributions

Summary We present ksrates, a user-friendly command-line tool to position ancient whole-genome duplication (WGD) events with respect to speciation events in a phylogeny by comparing paralog and ortholog KS distributions derived from genomic or transcriptomic sequences, while adjusting for substitution rate differences among the lineages involved. Availability and implementation ksrates is implemented in Python 3 and as a Nextflow pipeline. The source code, Singularity and Docker containers, documentation and tutorial are available via https://github.com/VIB-PSB/ksrates. Contact steven.maere@ugent.vib. be, rolf.lohaus@ugent.vib. be
Geminiviral genomes encode additional proteins with specific subcellular localizations and virulence function

Geminiviruses are plant viruses with limited coding capacity. Geminivirus-encoded proteins were identified applying a 10-kDa arbitrary threshold; however, it is increasingly clear that small proteins play relevant roles in biological systems, which calls for the reconsideration of this criterion. Here, we show that geminiviral genomes contain additional ORFs. Using tomato yellow leaf curl virus, we demonstrate that some of these novel ORFs are expressed during the infection, and that the encoded proteins display specific subcellular localizations. We prove that the largest of these new ORFs, which we name V3, is required for full viral infection, and that the V3 protein localizes in the Golgi apparatus and functions as an RNA silencing suppressor. These results imply that the repertoire of geminiviral proteins can be expanded, and that getting a comprehensive overview of the molecular plant-geminivirus interactions will require the detailed study of small ORFs so far neglected.
A pan-ontology view of machine-derived knowledge representations and feedback mechanisms for curation

Biomedical ontologies are established tools that organize knowledge in specialized research areas. They can also be used to train machine-learning models. However, it is unclear to what extent representations of ontology concepts learned by machine-learning models capture the relationships intended by ontology curators. It is also unclear whether the representations can provide insights to improve the curation process. Here, we investigate ontologies from across the spectrum of biological research and assess the concordance of formal ontology hierarchies with representations based on plain-text definitions. By comparing the internal properties of each ontology, we describe general patterns across the pan-ontology landscape and pinpoint areas with discrepancies in individual domains. We suggest specific mechanisms through which machine-learning approaches can lead to clarifications of ontology definitions. Synchronizing patterns in machine-derived representations with those intended by the ontology curators will likely streamline the use of ontologies in downstream applications.