GeCKO: user-friendly workflows for genotyping complex genomes using target enrichment capture. A use case on the large tetraploid durum wheat genome.

Background: Genotyping of individuals plays a pivotal role in various biological analyses, with technology choice influenced by multiple factors including genomic constraints, number of targeted loci and individuals, cost considerations, and the ease of sample preparation and data processing. Target enrichment capture of specific polymorphic regions has emerged as a flexible and cost-effective genomic reduction method for genotyping, especially adapted to the case of very large genomes. However, this approach necessitates complex bioinformatics treatment to extract genotyping data from raw reads.

Practical synthesis of 1,3-benzoazaphosphole analogues.

Despite the promising pharmacological activity and material properties of five-membered heterocyclic compounds containing phosphorus and nitrogen, synthetic examples of them have been rather limited due to the instability of phosphorus toward air and water. In this study, 1,3-benzoazaphosphol analogues were selected as target molecules, and various synthetic routes were examined to establish a fundamental technology for the introduction of phosphorus groups into aromatic rings and formation of five-membered rings containing phosphorus and nitrogen by cyclization. As a result, we found that 2-aminophenyl(phenyl)phosphine is an extremely promising synthetic intermediate with high stability and easy handling.

Population Pharmacokinetic and Exposure-Safety Analyses of Ibrutinib for the Treatment of Chronic Graft-Versus-Host Disease.

The population pharmacokinetic (PK) and exposure-response (E-R) analyses for the safety of ibrutinib for the treatment of chronic graft-versus-host disease (cGVHD) is presented. This work aims to develop a population PK model for ibrutinib based on data from clinical studies in subjects with cGVHD, to evaluate the impact of intrinsic and extrinsic factors on PK parameters as well as systemic exposure levels, and to assess an E-R relationship for selected safety end points. Pooled data from 162 subjects with cGVHD enrolled in 4 clinical studies were included in the population PK analysis.

Nanoparticulate System for the Transdermal Delivery of Catechin as an Antihypercholesterol: In Vitro and In Vivo Evaluations.

Gambir (, Roxb.) contains catechins that is often empirically used to treat various diseases. Catechins can reduce cholesterol levels by inhibiting coenzyme HMG-CoA reductase that plays a role in cholesterol metabolism.

The Impact of Distance Education during the COVID-19 Pandemic on Physical Activity and Well-Being of Czech and Polish Adolescents.

Background: The aim of this study was to identify the changes in the structure of weekly physical activity (PA) and well-being among adolescent boys and girls between habitual education (HE) and distance education (DE) during the pandemic in secondary schools.

Methods: The research was carried out in 12 Czech and 18 Polish schools during 2019 to 2020 academic session for HE and 2020 to 2021 academic session for DE. The research involved 723 girls and 626 boys aged 15 to 18 years.

EggLib 3: A python package for population genetics and genomics.

Rapid and repeatable polymorphism analyses have become a necessity with the current amount of genomic data that can be collected in many organisms. Traditionally, such analyses are conducted using a variety of tools in combination, often requiring numerous format translation and manipulation. Here, we present a massively updated version of our previous software package egglib, intended to alleviate such costly and error-prone tinkering with the data.

Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina.

The recent availability of genome-wide sequencing techniques has allowed systematic screening for molecular signatures of adaptation, including in nonmodel organisms. Host-pathogen interactions constitute good models due to the strong selective pressures that they entail. We focused on an adaptive event which affected the poplar rust fungus Melampsora larici-populina when it overcame a resistance gene borne by its host, cultivated poplar.

A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown.

The deployment of plant varieties carrying resistance genes (R) exerts strong selection pressure on pathogen populations. Rapidly evolving avirulence genes (Avr) allow pathogens to escape R-mediated plant immunity through a variety of mechanisms, leading to virulence. The poplar rust fungus Melampsora larici-populina is a damaging pathogen of poplars in Europe.

Evolution of morphological but not aggressiveness-related traits following a major resistance breakdown in the poplar rust fungus, .

Crop varieties carrying qualitative resistance to targeted pathogens lead to strong selection pressure on parasites, often resulting in resistance breakdown. It is well known that qualitative resistance breakdowns modify pathogen population structure but few studies have analyzed the consequences on their quantitative aggressiveness-related traits. The aim of this study was to characterize the evolution of these traits following a resistance breakdown in the poplar rust fungus, .

Identification of biomarkers for drug-resistant endometriosis using clinical proteomics.

Dienogest (DNG), is an effective and widely used progestin used in the treatment of endometriosis, yet clinically, a subset of cases show resistance to DNG treatment. During a previous investigation on the effect of DNG of cytokines and growth factor production, we incidentally found that endometriotic cyst fluid did not demonstrate inhibitory effects to DNG in a subset of cases. To clarify the mechanisms of this resistance to DNG, we performed proteomics analysis to compare the protein expression between DNG-sensitive and resistant cases.

Depth Elemental Imaging during Corrosion of Hot-Dip Galvanized Steel Sheet by Confocal Micro XRF Analysis.

The elucidation of the mechanism for steel corrosion under a coating layer has been attracting research attention. Herein, we utilized a confocal micro-X-ray fluorescence (XRF) analytical instrument to conduct non-destructive elemental analysis near the surface of a steel sheet. Using this method, elemental map images of steel sheet cross sections were obtained without sample destruction.

Synthesis of Aryl Iodides from Arylhydrazines and Iodine.

A metal- and base-free method is developed for the synthesis of aryl iodides from arylhydrazine hydrochlorides and iodine. A wide variety of aryl iodides can be conveniently synthesized by an equimolar reaction of arylhydrazine hydrochlorides and I in dimethyl sulfoxide at 60 °C for 6 h. In the iodination step, arylhydrazines are oxidized by iodine to form arenediazonium salts, which undergo single-electron transfer from iodide anion to give aryl and iodine radicals; subsequent combination of them affords the corresponding aryl iodides.

Effect of the Air/Water Interfacial Properties of Amine Derivatives on the in Situ Fabrication of Microsized Gold Sheets.

Development of new methods for producing large-area nanocrystals with specific shapes is crucial for advancements in various fields. In this study, submillimeter-sized sheet-structured gold crystals with nanoscale thicknesses were fabricated by chemical reduction of HAuCl in the presence of long-chain amidoamine-derived surfactants (C nAOH; n = 12, 14, 16, or 18) in aqueous solutions. Using the C18AOH system at 30 °C, large-area sheet-structured crystals with widths of ∼100 μm and thicknesses of 30 nm were effectively obtained at the air/water interface.

Dienogest suppresses the activation of primordial follicles and preserves the primordial follicle stockpile for fertility in mice.

The aim of the present study was to characterize the effect of long-term usage of dienogest, a fourth-generation progestin that possesses progestogen and anti-androgen activities, on the stockpile of oocytes and fertility after administration. Female ICR mice (100 days old) were divided into a dienogest group and a control group. The mice received 16 consecutive subcutaneous injections of 5 mg dienogest dissolved in corn oil or corn oil as a vehicle control every 4 days.

Structure of Ultrathin Native Oxides on III-Nitride Surfaces.

When pristine material surfaces are exposed to air, highly reactive broken bonds can promote the formation of surface oxides with structures and properties differing greatly from bulk. Determination of the oxide structure is often elusive through the use of indirect diffraction methods or techniques that probe only the outermost layer. As a result, surface oxides forming on widely used materials, such as group III-nitrides, have not been unambiguously resolved, even though critical properties can depend sensitively on their presence.

Dienogest inhibits C-C motif chemokine ligand 20 expression in human endometriotic epithelial cells.

Objective: C-C motif chemokine ligand 20 is thought to contribute to the development of endometriosis by recruiting Th17 lymphocytes into endometriotic foci. The present study investigated the effects of dienogest, a progesterone receptor agonist used to treat endometriosis, on C-C motif chemokine ligand 20 expression by endometriotic cells.

Study Design: Effects of dienogest on mRNA expression and protein secretion of C-C motif chemokine ligand 20 induced by interleukin 1β were assessed in three immortalized endometriotic epithelial cell lines, parental cells (EMosis-CC/TERT1), and stably expressing human progesterone receptor isoform A (EMosis-CC/TERT1/PRA+) or isoform B (EMosis-CC/TERT1/PRA-/PRB+).

The escalatory Red Queen: Population extinction and replacement following arms race dynamics in poplar rust.

Host-parasite systems provide convincing examples of Red Queen co-evolutionary dynamics. Yet, a key process underscored in Van Valen's theory - that arms race dynamics can result in extinction - has never been documented. One reason for this may be that most sampling designs lack the breadth needed to illuminate the rapid pace of adaptation by pathogen populations.

Endometriotic cyst fluid induces reactive oxygen species (ROS) in human immortalized epithelial cells derived from ovarian endometrioma.

Objectives: Endometriotic cyst fluid (ECF) contains a large amount of reactive oxygen species (ROS), and endometriotic cysts are exposed to strong oxidative stress, which may cause malignant transformation. In this study, ROS production by ECF was clinically analysed.

Methods: Human immortalized epithelial cells derived from ovarian endometrioma (EMosis-CC/TERT 1) were treated with ECF.

Genetic signatures of a range expansion in natura: when clones play leapfrog.

The genetic consequences of range expansions have generally been investigated at wide geographical and temporal scales, long after the colonization event. A unique ecological system enabled us to both monitor the colonization dynamics and decipher the genetic footprints of expansion over a very short time period. Each year an epidemic of the poplar rust () expands clonally and linearly along the Durance River, in the Alps.

Intrapopulation genomics in a model mutualist: Population structure and candidate symbiosis genes under selection in Medicago truncatula.

Bottom-up evolutionary approaches, including geographically explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here, we conduct a population genomic analysis in the model legume, Medicago truncatula, to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe.

Population pharmacokinetic modeling and noncompartmental analysis demonstrated bioequivalence between metformin component of metformin/vildagliptin fixed-dose combination products and metformin immediate-release tablet sourced from various countries.

Metformin is the first-line pharmacotherapy choice for treating type-2 diabetes mellitus, alone or in combination with other antidiabetic drugs. During the development of immediate-release (IR) metformin containing novel fixed-dose combination (FDC) products, several health-authorities require sponsors to demonstrate bioequivalence between FDC products and the country-sourced metformin for market approval. Eight bioequivalence studies that compared metformin/vildagliptin FDC product (test) to metformin IR tablet sourced from various countries (reference) were conducted.

miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species.

Background: Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii.

Bioequivalence and food effect assessment for vildagliptin/metformin fixed-dose combination tablets relative to free combination of vildagliptin and metformin in Japanese healthy subjects.

Objective: To assess the bioequivalence of vildagliptin/metformin fixeddose combination (FDC) tablets (50/250 mg and 50/500 mg) to free combinations of vildagliptin and metformin and the effect of food on the pharmacokinetics (PK) of vildagliptin and metformin following administration of 50/500 mg FDC tablets.

Methods: Two openlabel, randomized, single-center, singledose, 2-period crossover studies were conducted in Japanese healthy male volunteers. Participants were administered vildagliptin/ metformin FDC tablets (study I: 50/250 mg, study II: 50/500 mg) or their free combinations under fasted condition.

An explanatory framework of teachers' perceptions of a positive mealtime environment in a preschool setting.

Attending a preschool center may help preschoolers with growth and development that encourage a healthy lifestyle, including sound eating behaviors. Providing a positive mealtime environment (PME) may be one of the keys to fostering a child's healthy eating habits in the classroom. However, a specific definition of a PME, the components of a PME, or directions on how to create one have not been established.