Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Dissection of Resistance to the Three Fungal Plant Pathogens Blumeria graminis, Zymoseptoria tritici, and Pyrenophora tritici-repentis Using a Multiparental Winter Wheat Population

Bread wheat (Triticum aestivum L.) is one of the world’s most important crop species. The development of new varieties resistant to multiple pathogens is an ongoing task in wheat breeding, especially in times of increasing demand for sustainable agricultural practices. Despite this, little is known about the relations between various fungal disease resistances at the genetic level, and the possible consequences for wheat breeding strategies. As a first step to fill this gap, we analyzed the genetic relations of resistance to the three fungal diseases – powdery mildew (PM), septoria tritici blotch (STB), and tan spot (TS) – using a winter wheat multiparent advanced generation intercross population. Six, seven, and nine QTL for resistance to PM, STB, and TS, respectively, were genetically mapped. Additionally, 15 QTL were identified for the three agro-morphological traits plant height, ear emergence time, and leaf angle distribution. Our results suggest that resistance to STB and TS on chromosome 2B is conferred by the same genetic region. Furthermore, we identified two genetic regions on chromosome 1AS and 7AL, which are associated with all three diseases, but not always in a synchronal manner. Based on our results, we conclude that parallel marker-assisted breeding for resistance to the fungal diseases PM, STB, and TS appears feasible. Knowledge of the genetic co-localization of alleles with contrasting effects for different diseases, such as on chromosome 7AL, allows the trade-offs of selection of these regions to be better understood, and ultimately determined at the genic level.
Structure–Activity Study, Characterization, and Mechanism of Action of an Antimicrobial Peptoid D2 and Its d- and l-Peptide Analogues

Methicillin-resistant Staphylococcus pseudintermedius (MRSP) constitutes an emerging health problem for companion animals in veterinary medicine. Therefore, discovery of novel antimicrobial agents for treatment of Staphylococcus-associated canine infections is urgently needed to reduce use of human antibiotics in veterinary medicine. In the present work, we characterized the antimicrobial activity of the peptoid D2 against S. pseudintermedius and Pseudomonas aeruginosa, which is another common integumentary pathogen in dogs. Furthermore, we performed a structure–activity relationship study of D2, which included 19 peptide/peptoid analogs. Our best compound D2D, an all d-peptide analogue, showed potent minimum inhibitory concentrations (MICs) against canine S. pseudintermedius (2–4 µg/mL) and P. aeruginosa (4 µg/mL) isolates as well as other selected dog pathogens (2–16 µg/mL). Time–kill assays demonstrated that D2D was able to inhibit MRSP in 30 min at 1× MIC, significantly faster than D2. Our results suggest that at high concentrations D2D is rapidly lysing the bacterial membrane while D2 is inhibiting macromolecular synthesis. We probed the mechanism of action at sub-MIC concentrations of D2, D2D, the l-peptide analog and its retro analog by a macromolecular biosynthesis assay and fluorescence spectroscopy. Our data suggest that at sub-MIC concentrations D2D is membrane inactive and primarily works by cell wall inhibition, while the other compounds mainly act on the bacterial membrane.
Function, Architecture, and Biogenesis of Reovirus Replication Neoorganelles

Most viruses that replicate in the cytoplasm of host cells form neoorganelles that serve as sites of viral genome replication and particle assembly. These highly specialized structures concentrate viral proteins and nucleic acids, prevent the activation of cell-intrinsic defenses, and coordinate the release of progeny particles. Reoviruses are common pathogens of mammals that have been linked to celiac disease and show promise for oncolytic applications. These viruses form nonenveloped, double-shelled virions that contain ten segments of double-stranded RNA. Replication organelles in reovirus-infected cells are nucleated by viral nonstructural proteins µNS and σNS. Both proteins partition the endoplasmic reticulum to form the matrix of these structures. The resultant membranous webs likely serve to anchor viral RNA–protein complexes for the replication of the reovirus genome and the assembly of progeny virions. Ongoing studies of reovirus replication organelles will advance our knowledge about the strategies used by viruses to commandeer host biosynthetic pathways and may expose new targets for therapeutic intervention against diverse families of pathogenic viruses.
Two-Dimensional and Three-Dimensional Single Particle Tracking of Upconverting Nanoparticles in Living Cells

Lanthanide-doped upconversion nanoparticles (UCNPs) are inorganic nanomaterials in which the lanthanide cations embedded in the host matrix can convert incident near-infrared light to visible or ultraviolet light. These particles are often used for long-term and real-time imaging because they are extremely stable even when subjected to continuous irradiation for a long time. It is now possible to image their movement at the single particle level with a scale of a few nanometers and track their trajectories as a function of time with a scale of a few microseconds. Such UCNP-based single-particle tracking (SPT) technology provides information about the intracellular structures and dynamics in living cells. Thus far, most imaging techniques have been built on fluorescence microscopic techniques (epifluorescence, total internal reflection, etc.). However, two-dimensional (2D) images obtained using these techniques are limited in only being able to visualize those on the focal planes of the objective lens. On the contrary, if three-dimensional (3D) structures and dynamics are known, deeper insights into the biology of the thick cells and tissues can be obtained. In this review, we introduce the status of the fluorescence imaging techniques, discuss the mathematical description of SPT, and outline the past few studies using UCNPs as imaging probes or biologically functionalized carriers.
Changes in care costs associated with cognitive behavioural therapy for psychosis delivered in routine clinical practice

Abstract Background: Schizophrenia spectrum disorders are long-term disabling conditions placing high economic demands on health services. Aim: To investigate whether cognitive behavioural therapy for psychosis (CBTp), delivered in a specialist psychological therapies service, was associated with a reduction in intensive care costs. Methods: Days using inpatient care and out of hours crisis support were recorded (N = 69). Costs associated with high intensity care use in the 12 months pre-referral were compared to during, and 12 months following cessation of therapy. Results: Despite the majority of participants incurring £0 at all time periods, costs of intensive mental health care more than halved with CBTp delivery, with a significant decrease during therapy, and at trend level after therapy (p = 0.07). Post hoc analysis revealed that offsetting the cost of therapy for those who utilised intensive care services at any time point (N = 18) resulted in therapy being cost neutral during therapy and cost effective (at trend level) 12 months following cessation of therapy. Conclusion: CBTp may reduce costs associated with intensive psychiatric care, even in a population where the minority use these services. Investment in therapy may lead to both clinical and financial benefits.
Study of correlation coefficient for yield and its components in spine gourd (Momordica dioica Roxb.)

Twelve genotype of spine gourd (Momordica dioica Roxb.) were evaluated in a Randomized Block Design with three replications at Horticulture Instructional farm, COA, IGKV, Raipur (C.G) during Kharif 2018. Correlation coefficients were carried out to study the Character association and contribution, respectively for fifteen qualitative characters. Results of correlation coefficient analysis revealed that fruit yield per plant showed the highest significant positive association with number of branches per plant, number of fruits per plant, fruit length, fruit width and average fruit weight at both genotypic and phenotypic levels and had negative and significant association with days to first fruit harvest and fruiting periods. Hence, in selection programme, emphasis should be given on these traits for improvement in fruit yield of spine gourd.
The Immune Deficiency Pathway Regulates Metabolic Homeostasis in Drosophila

Key Points IMD activation in the fat body disrupts growth and energy stores. Inhibition of IMD signaling in Drosophila disrupts metabolic homeostasis. Insulin mutant flies have varied responses to bacterial infection. Immune and metabolic pathways collectively influence host responses to microbial invaders, and mutations in one pathway frequently disrupt activity in another. We used the Drosophila melanogaster model to characterize metabolic homeostasis in flies with modified immune deficiency (IMD) pathway activity. The IMD pathway is very similar to the mammalian TNF-α pathway, a key regulator of vertebrate immunity and metabolism. We found that persistent activation of IMD resulted in hyperglycemia, depleted fat reserves, and developmental delays, implicating IMD in metabolic regulation. Consistent with this hypothesis, we found that imd mutants weigh more, are hyperlipidemic, and have impaired glucose tolerance. To test the importance of metabolic regulation for host responses to bacterial infection, we challenged insulin pathway mutants with lethal doses of several Drosophila pathogens. We found that loss-of-function mutations in the insulin pathway impacted host responses to infection in a manner that depends on the route of infection and the identity of the infectious microbe. Combined, our results support a role for coordinated regulation of immune and metabolic pathways in host containment of microbial invaders.
Decrease in skeletal muscle index one year after radical cystectomy as a prognostic indicator in patients with urothelial bladder cancer

ABSTRACT Purpose The present study aimed to determine whether sarcopenia after radical cystectomy (RC) could predict overall survival (OS) in patients with urothelial bladder cancer (UBC). Materials and Methods The lumbar skeletal muscle index (SMI) of 80 patients was measured before and 1 year after RC. The prognostic significance of sarcopenia and SMI decrease after RC were evaluated using Kaplan–Meier analysis and a multivariable Cox regression model. Results Of 80 patients, 26 (32.5%) experienced sarcopenia before RC, whereas 40 (50.0%) experienced sarcopenia after RC. The median SMI change was -2.2 cm2/m2. Patients with sarcopenia after RC had a higher pathological T stage and tumor grade than patients without sarcopenia. Furthermore, the overall mortality rate was significantly higher in patients with sarcopenia than in those without sarcopenia 1 year after RC. The median follow-up time was 46.2 months, during which 22 patients died. Kaplan-Meier estimates showed a significant difference in OS rates based on sarcopenia (P=0.012) and SMI decrease (P=0.025). Multivariable Cox regression analysis showed that SMI decrease (≥2.2 cm2/m2) was an independent predictor of OS (hazard ratio: 2.68, confidence interval: 1.007-7.719, P = 0.048). Conclusions The decrease in SMI after surgery might be a negative prognostic factor for OS in patients who underwent RC to treat UBC.
Comparative Genomics Reveals the Genetic Mechanisms of Musk Secretion and Adaptive Immunity in Chinese Forest Musk Deer

Abstract The Chinese forest musk deer (Moschus berezovskii; FMD) is an artiodactyl mammal and is both economically valuable and highly endangered. To investigate the genetic mechanisms of musk secretion and adaptive immunity in FMD, we compared its genome to nine other artiodactyl genomes. Comparative genomics demonstrated that eight positively selected genes (PSGs) in FMD were annotated in three KEGG pathways that were related to metabolic and synthetic activity of musk, similar to previous transcriptome studies. Functional enrichment analysis indicated that many PSGs were involved in the regulation of immune system processes, implying important reorganization of the immune system in FMD. FMD-specific missense mutations were found in two PSGs (MHC class II antigen DRA and ADA) that were classified as deleterious by PolyPhen-2, possibly contributing to immune adaptation to infectious diseases. Functional assessment showed that the FMD-specific mutation enhanced the ADA activity, which was likely to strengthen the immune defense against pathogenic invasion. Single nucleotide polymorphism-based inference showed the recent demographic trajectory for FMD. Our data and findings provide valuable genomic resources not only for studying the genetic mechanisms of musk secretion and adaptive immunity, but also for facilitating more effective management of the captive breeding programs for this endangered species.
HLA‐A, B, C, DRB1 and DQB1 allele and haplotype frequencies in volunteer bone marrow donors from Eastern Region of Saudi Arabia

We analyzed HLA allele and haplotype frequencies from donors from the Eastern region of Saudi Arabia. A cross‐sectional study was performed on 2405 bone marrow donors from the Eastern region. HLA typing was carried out by sequencing. The most common HLA allele groups were HLA‐A*02:01:01G (11.08%), A*01:01:01G (10.40%), HLA‐B*52:01:01G (8.79%), B*18:01:01G (8.07%), HLA‐C*04:01:01G (17.88%), C*12:03:01G (10.23%), HLA‐DRB1*10:01 (14.89%), DRB1*03:01:01G (14.10%), HLA‐DQB1*02:01:01G (24.53%) and DQB1*05:01:01G (20.17%). The most frequent HLA‐A~C~B~DRB1~DQB1 haplotypes were HLA‐A*01:03~C*15:05:01G~B*73:01~DRB1*10:01:01~DQB1*05:01:01G (3.11%) and HLA‐A*01:01:01G~C*12:02:01G~B*52:01:01G~DRB1*15:02:01~DQB1*06:01:01G (2.25%). When comparing the allele and haplotype frequencies of the Eastern regions' population to those from the Central region we found significant differences in several allele frequencies including A*01:01:01G (P ≤ 0.0001), B*52:01:01G (P ≤ 0.0001), B*18:01:01G (P = 0.0001), C*12:03:01G (P < 0.0001), DRB1*10:01:01 (P < 0.0001) and DQB1*05:01:01G (P < 0.0001). Our data confirms genetic heterogeneity among the Saudi population.
“Male Hair Cannot Extend Below Plane of the Shoulder” and “No Cross Dressing”: Critical Queer Analysis of High School Dress Codes in the United States

ABSTRACT In this study, we questioned how high school dress codes outlined in official handbooks were written or presented in regard to the gender binary, either/or perspective. We critically analyzed how or if they allowed for flexibility in expression of gender and sexual identity and if they supported, encouraged, or affirmed a variety of expressions, in particular transgender and gender non-conforming expressions, throughout the text or images. The content analysis method was used to analyze 735 handbooks from the 2016 to 2017 school year. Three themes emerged from the data: (1) support of fluid gender expression, yet not overt support; (2) passive marginalization of gender non-conforming or transgender identities or expressions; and (3) active marginalization of gender non-conforming or transgender identities or expressions. The “LGBTQ+ Dress Code Analysis Tool” was developed for policy makers to use to analyze their dress codes.
Low Temperature Synthesis of High-Density Carbon Nanotubes on Insulating Substrate

A method to synthesize high-density, vertically-aligned, multi-wall carbon nanotubes (MWCNTs) on an insulating substrate at low temperature using a complementary metal–oxide–semiconductor (CMOS) compatible process is presented. Two factors are identified to be important in the carbon nanotube (CNT) growth, which are the catalyst design and the substrate material. By using a Ni–Al–Ni multilayer catalyst film and a ZrO2 substrate, vertically-aligned CNTs can be synthesized at 340 °C using plasma-enhanced chemical vapor deposition (PECVD). Both the quality and density of the CNTs can be enhanced by increasing the synthesis temperature. The function of the aluminum interlayer in reducing the activation energy of the CNT formation is studied. The nanoparticle sintering and quick accumulation of amorphous carbon covering the catalyst can prematurely stop CNT synthesis. Both effects can be suppressed by using a substrate with a high surface energy such as ZrO2.
Proliferation-dominant high-grade astrocytoma: survival benefit associated with extensive resection of FLAIR abnormality region.

OBJECTIVEThe aim of this study was to investigate the relationship between extent of resection (EOR) and survival in terms of clinical, molecular, and radiological factors in high-grade astrocytoma (HGA). METHODSClinical and radiological data from 585 cases of molecularly defined HGA were reviewed. In each case, the EOR was evaluated twice: once according to contrast-enhanced T1-weighted images (CE-T1WI) and once according to fluid attenuated inversion recovery (FLAIR) images. The ratio of the volume of the region of abnormality in CE-T1WI to that in FLAIR images (VFLAIR/VCE-T1WI) was calculated and a receiver operating characteristic curve was used to determine the optimal cutoff value for that ratio. Univariate and multivariate analyses were performed to identify the prognostic value of each factor.RESULTSBoth the EOR evaluated from CE-T1WI and the EOR evaluated from FLAIR could divide the whole cohort into 4 subgroups with different survival outcomes (p < 0.001). Cases were stratified into 2 subtypes based on VFLAIR/VCE-T1WI with a cutoff of 10: a proliferation-dominant subtype and a diffusion-dominant subtype. Kaplan-Meier analysis showed a significant survival advantage for the proliferation-dominant subtype (p < 0.0001). The prognostic implication has been further confirmed in the Cox proportional hazards model (HR 1.105, 95% CI 1.078-1.134, p < 0.0001). The survival of patients with proliferation-dominant HGA was significantly prolonged in association with extensive resection of the FLAIR abnormality region beyond contrast-enhancing tumor (p = 0.03), while no survival benefit was observed in association with the extensive resection in the diffusion-dominant subtype (p = 0.86). CONCLUSIONSVFLAIR/VCE-T1WI is an important classifier that could divide the HGA into 2 subtypes with distinct invasive features. Patients with proliferation-dominant HGA can benefit from extensive resection of the FLAIR abnormality region, which provides the theoretical basis for a personalized resection strategy.
Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination

RNA helicases are a class of enzymes that unwind RNA duplexes in vitro but whose cellular functions are largely enigmatic. Here, we provide evidence that the DEAD-box protein Dbp2 remodels RNA-protein complex (RNP) structure to facilitate efficient termination of transcription in Saccharomyces cerevisiae via the Nrd1-Nab3-Sen1 (NNS) complex. First, we find that loss of DBP2 results in RNA polymerase II accumulation at the 3′ ends of small nucleolar RNAs and a subset of mRNAs. In addition, Dbp2 associates with RNA sequence motifs and regions bound by Nrd1 and can promote its recruitment to NNS-targeted regions. Using Structure-seq, we find altered RNA/RNP structures in dbp2∆ cells that correlate with inefficient termination. We also show a positive correlation between the stability of structures in the 3′ ends and a requirement for Dbp2 in termination. Taken together, these studies provide a role for RNA remodeling by Dbp2 and further suggests a mechanism whereby RNA structure is exploited for gene regulation.
CliqueMS: a computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network

Abstract Motivation The analysis of biological samples in untargeted metabolomic studies using LC-MS yields tens of thousands of ion signals. Annotating these features is of the utmost importance for answering questions as fundamental as, e.g. how many metabolites are there in a given sample. Results Here, we introduce CliqueMS, a new algorithm for annotating in-source LC-MS1 data. CliqueMS is based on the similarity between coelution profiles and therefore, as opposed to most methods, allows for the annotation of a single spectrum. Furthermore, CliqueMS improves upon the state of the art in several dimensions: (i) it uses a more discriminatory feature similarity metric; (ii) it treats the similarities between features in a transparent way by means of a simple generative model; (iii) it uses a well-grounded maximum likelihood inference approach to group features; (iv) it uses empirical adduct frequencies to identify the parental mass and (v) it deals more flexibly with the identification of the parental mass by proposing and ranking alternative annotations. We validate our approach with simple mixtures of standards and with real complex biological samples. CliqueMS reduces the thousands of features typically obtained in complex samples to hundreds of metabolites, and it is able to correctly annotate more metabolites and adducts from a single spectrum than available tools. Availability and implementation https://CRAN.R-project.org/package=cliqueMS and https://github.com/osenan/cliqueMS. Supplementary information Supplementary data are available at Bioinformatics online.
Nitrate acts at the Arabidopsis thaliana shoot apical meristem to regulate flowering time

Summary Optimal timing of flowering, a major determinant for crop productivity, is controlled by environmental and endogenous cues. Nutrients are known to modify flowering time; however, our understanding of how nutrients interact with the known pathways, especially at the shoot apical meristem (SAM), is still incomplete. Given the negative side‐effects of nitrogen fertilization, it is essential to understand its mode of action for sustainable crop production. We investigated how a moderate restriction by nitrate is integrated into the flowering network at the SAM, to which plants can adapt without stress symptoms. This condition delays flowering by decreasing expression of SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) at the SAM. Measurements of nitrate and the responses of nitrate‐responsive genes suggest that nitrate functions as a signal at the SAM. The transcription factors NIN‐LIKE PROTEIN 7 (NLP7) and NLP6, which act as master regulators of nitrate signaling by binding to nitrate‐responsive elements (NREs), are expressed at the SAM and flowering is delayed in single and double mutants. Two upstream regulators of SOC1 (SQUAMOSA PROMOTER BINDING PROTEIN‐LIKE3 (SPL3) and SPL5) contain functional NREs in their promoters. Our results point at a tissue‐specific, nitrate‐mediated flowering time control in Arabidopsis thaliana.