Miracle-dz/UniFAR-FTUs huggingface dataset:
Endocrine Fertility Parameters—Genomic Background and Their Genetic Relationship to Boar Taint in German Landrace and Large White

Simple Summary Breeding against boar taint compounds androstenone and skatole can be an efficient alternative for surgical castration of young piglets during their first week of life to avoid boar taint. Physiological links of androstenone to steroid hormones in the synthesis pathway are documented and they have to be analyzed for their genetic effects on reproduction and fertility. While using boar taint and hormone data from Landrace and Large White pigs (commercial nucleus populations and herd book populations), the effects of breeding against androstenone on fertility were evaluated. Moreover, the genetic foundation of the chosen hormones’ testosterone, 17β-estradiol, luteinizing hormone, follicle-stimulating hormone, and progesterone was analyzed and then checked for possible pleiotropic effects with boar taint compounds. The results showed consistent unfavorable side effects of breeding against androstenone on testosterone and 17β-estradiol in both breeds. The other hormones showed contrary results regarding unfavorable relationships between boar taint and endocrine fertility parameters. The genetic foundation showed a high potential of breeding against boar taint but the impact on fertility potential should be supervised. Abstract The surgical castration of young male piglets without anesthesia is no longer allowed in Germany from 2021. One alternative is breeding against boar taint, but shared synthesis pathways of androstenone (AND) and several endocrine fertility parameters (EFP) indicate a risk of decreasing fertility. The objective of this study was to investigate the genetic background between AND, skatole (SKA), and six EFP in purebred Landrace (LR) and Large White (LW) populations. The animals were clustered according to their genetic relatedness because of their different origins. Estimated heritabilities (h2) of AND and SKA ranged between 0.52 and 0.34 in LR and LW. For EFP, h2 differed between the breeds except for follicle-stimulating hormone (FSH) (h2: 0.28–0.37). Both of the breeds showed unfavorable relationships between AND and testosterone, 17-β estradiol, and FSH. The genetic relationships (rg) between SKA and EFP differed between the breeds. A genome-wide association analysis revealed 48 significant associations and confirmed a region for SKA on Sus Scrofa chromosome (SSC) 14. For EFP, the results differed between the clusters. In conclusion, rg partly confirmed physiologically expected antagonisms between AND and EFP. Particular attention should be spent on fertility traits that are based on EFP when breeding against boar taint to balance the genetic progress in both of the trait complexes.
Acousto-Optic Cells with Phased-Array Transducers and Their Application in Systems of Optical Information Processing

This paper presents the results of theoretical and experimental studies of anisotropic acousto-optic interaction in a spatially periodical acoustic field created by a phased-array transducer with antiphase excitation of adjacent sections. In this case, contrary to the nonsectioned transducer, light diffraction is absent when the optical beam falls on the phased-array cell at the Bragg angle. However, the diffraction takes place at some other angles (called “optimal” here), which are situated on the opposite sides to the Bragg angle. Our calculations show that the diffraction efficiency can reach 100% at these optimal angles in spite of a noticeable acousto-optic phase mismatch. This kind of acousto-optic interaction possesses a number of interesting regularities which can be useful for designing acousto-optic devices of a new type. Our experiments were performed with a paratellurite (TeO2) cell in which a shear acoustic mode was excited at a 9° angle to the crystal plane (001). The piezoelectric transducer had to nine antiphase sections. The efficiency of electric to acoustic power conversion was 99% at the maximum frequency response, and the ultrasound excitation band extended from 70 to 160 MHz. The experiments have confirmed basic results of the theoretical analysis.
Environmental Risk Factors in Bipolar Disorder and Psychotic Depression: A Systematic Review and Meta-Analysis of Prospective Studies.

OBJECTIVE The aim of this systematic review and meta-analysis was to study the association between specific environmental risk factors (ERF) and later development of Bipolar disorder and Psychotic depression. METHODS A systematic search of prospective studies was conducted in MEDLINE, EMBASE and PsycINFO databases, and supplemented by hand searching, according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (registration number: CRD42018092253). Selected ERF included: pre-/peri-natal factors-paternal age at birth, maternal infection, obstetric complications, perinatal stress; early childhood factors-urbanicity at birth, childhood infection, childhood adversity; later life factors-substance misuse, ethnic minority and migration, urbanicity later in life, stressful life events, and traumatic head injury. Pooled effect sizes of the association between these ERF and affective psychoses were calculated from systematically selected studies. When studies examining each ERF were insufficient for meta-analysis, results were presented narratively. RESULTS Forty-six studies were included for quantitative analyses among selected ERF for affective psychosis, with significant association found for paternal age >40 years (OR 1.17, 95%CI 1.12-1.23), early (OR 1.52, 95%CI 1.07-2.17) and late (OR 1.32, 95%CI 1.05-1.67) gestational age, childhood adversity (OR 1.33, 95%CI 1.18-1.50), substance misuse (OR 2.87, 95%CI 1.63-5.50), and being from an ethnic minority (OR 1.99, 95%CI 1.39-2.84). CONCLUSIONS These results suggest some shared environmental load between non-affective and affective psychosis, implying generalized risks for psychosis rather than for specific diagnostic categories. Nonetheless, published studies for some ERF in the affective psychoses are scarce, and further longitudinal studies are needed.
T-Cell Lymphoma Clonality by Copy Number Variation Analysis of T-Cell Receptor Genes

Simple Summary T-cells defend the human body from pathogenic invasion via specific recognition by T-cell receptors (TCRs). The TCR genes undergo recombination (rearrangement) in a myriad of possible ways to generate different TCRs that can recognize a wide diversity of foreign antigens. However, in patients with T-cell lymphoma (TCL), a particular T-cell becomes malignant and proliferates, resulting in a population of genetically identical cells with same TCR rearrangement pattern. To help diagnose patients with TCL, a polymerase chain reaction (PCR)-based assay is currently used to determine if neoplastic cells in patient samples are of T-cell origin and bear identical (monoclonal) TCR rearrangement pattern. Herein, we report the application of a novel segmentation and copy number computation algorithm to accurately identify different TCR rearrangement patterns using data from the whole genome sequencing of patient materials. Our approach may improve the diagnostic accuracy of TCLs and can be similarly applied to the diagnosis of B-cell lymphomas. Abstract T-cell lymphomas arise from a single neoplastic clone and exhibit identical patterns of deletions in T-cell receptor (TCR) genes. Whole genome sequencing (WGS) data represent a treasure trove of information for the development of novel clinical applications. However, the use of WGS to identify clonal T-cell proliferations has not been systematically studied. In this study, based on WGS data, we identified monoclonal rearrangements (MRs) of T-cell receptors (TCR) genes using a novel segmentation algorithm and copy number computation. We evaluated the feasibility of this technique as a marker of T-cell clonality using T-cell lymphomas (TCL, n = 44) and extranodal NK/T-cell lymphomas (ENKTLs, n = 20), and identified 98% of TCLs with one or more TCR gene MRs, against 91% detected using PCR. TCR MRs were absent in all ENKTLs and NK cell lines. Sensitivity-wise, this platform is sufficiently competent, with MRs detected in the majority of samples with tumor content under 25% and it can also distinguish monoallelic from biallelic MRs. Understanding the copy number landscape of TCR using WGS data may engender new diagnostic applications in hematolymphoid pathology, which can be readily adapted to the analysis of B-cell receptor loci for B-cell clonality determination.
Resveratrol benefits the lineage commitment of bone marrow mesenchymal stem cells into osteoblasts via miR‐320c by targeting Runx2

Bone marrow mesenchymal stem cells (BMSCs) are a potential source of osteoblasts and have been widely used in clinical therapies due to their pluripotency. Recent publications have found that resveratrol (RSVL) played a crucial role in the proliferation and differentiation of BMSCs; however, the underlying molecular mechanism of RSVL‐induced BMSCs osteogenic differentiation needs to be fully elucidated. The objective of this study was to explore functions of miRNAs in the RSVL‐treated BMSCs and its effects on the differentiation potentials of BMSCs. The findings demonstrated that RSVL enhanced the osteogenesis and suppressed the adipogenesis of BMSCs in a dose‐dependent manner. Besides, a novel regulatory axis containing miR‐320c, and its target Runx2 was found during the differentiation process of BMSCs under RSVL treatment. Increase of miR‐320c reduced the osteogenic potential of BMSCs, while knockdown of miR‐320c played a positive role in the osteogenesis of BMSCs. In contrast, overexpression of miR‐320c accelerated the adipogenic differentiation, while knockdown of miR‐320c restrained the adipogenic differentiation of BMSCs. The results confirmed that Runx2 might be the direct target of miR‐320c in RSVL‐promoted osteogenic differentiation of BMSCs. This study revealed that RSVL might be used for the treatment of bone loss related diseases and miR‐320c could be regarded as a novel and potential target to regulate the biological functions of BMSCs.
The Wetting of Gold and Platinum by Water

Abstract : When a sessile drop of pure water is placed on a clean surface of pure polished gold or platinum, it will spread spontaneously over the metal and exhibit a zero contact angle. However, in order to rid surfaces of these metals of adsorbed hydrophobic contaminants, it is necessary to heat them to white-hot temperatures in flowing streams of high-purity hydrogen, nitrogen, argon, krypton, or air. Such a treatment gives surfaces which are completely wetted by pure water and exhibit zero contact angles in gases freed from trace contaminants by an adsorbent cold trap. However, prolonged exposure of the metals to these gases renders them nonwetting because of the gradual adsorption of trace hydrophobic contaminants present in the gas streams. (Author)
Assessments of the In Vitro and In Vivo Linker Stability and Catabolic Fate for the Ortho Hydroxy-Protected Aryl Sulfate Linker by Immuno-Affinity Capture Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometric Assay

Antibody–drug conjugate (ADC) linkers play an important role in determining the safety and efficacy of ADC. The Ortho Hydroxy-Protected Aryl Sulfate (OHPAS) linker is a newly developed linker in the form of a di-aryl sulfate structure consisting of phenolic payload and self-immolative group (SIG). In this study, using two bioanalytical approaches (namely “bottom-up” and “middle-up” approaches) via the liquid chromatography-quadrupole time-of-flight mass spectrometric (LC-qTOF-MS) method, in vitro and in vivo linker stability experiments were conducted for the OHPAS linker. For comparison, the valine-citrulline-p-aminobenzyloxycarbonyl (VC-PABC) linker was also evaluated under the same experimental conditions. In addition, the catabolite identification experiments at the subunit intact protein level were simultaneously performed to evaluate the catabolic fate of ADCs. As a result, the OHPAS linker was stable in the in vitro mouse/human plasma as well as in vivo pharmacokinetic studies in mice, whereas the VC-PABC linker was relatively unstable in mice in vitro and in vivo. This is because the VC-PABC linker was sensitive to a hydrolytic enzyme called carboxylesterase 1c (Ces1c) in mouse plasma. In conclusion, the OHPAS linker appears to be a good linker for ADC, and further experiments would be warranted to demonstrate the efficacy and toxicity related to the OHPAS linker.
Experimental Investigation into the Effect of Pyrolysis on Chemical Forms of Heavy Metals in Sewage Sludge Biochar (SSB), with Brief Ecological Risk Assessment

Experimental investigations were carried out to study the effect of pyrolysis temperature on the characteristics, structure and total heavy metal contents of sewage sludge biochar (SSB). The changes in chemical forms of the heavy metals (Zn, Cu, Cr, Ni, Pb and Cd) caused by pyrolysis were analyzed, and the potential ecological risk of heavy metals in biochar (SSB) was evaluated. The conversion of sewage sludge into biochar by pyrolysis reduced the H/C and O/C ratios considerably, resulting in stronger carbonization and a higher degree of aromatic condensation in biochar. Measurement results showed that the pH and specific surface area of biochar increased as the pyrolysis temperature increased. It was found that elements Zn, Cu, Cr and Ni were enriched and confined in biochar SSB with increasing pyrolysis temperature from 300–700 °C; however, the residual rates of Pb and Cd in biochar SSB decreased significantly when the temperature was increased from 600 °C to 700 °C. Measurement with the BCR sequential extraction method revealed that the pyrolysis of sewage sludge at a suitable temperature transferred its bioavailable/degradable heavy metals into a more stable oxidizable/residual form in biochar SSB. Toxicity of heavy metals in biochar SSB could be reduced about four times if sewage sludge was pyrolyzed at a proper temperature; heavy metals confined in sludge SSB pyrolyzed at about 600 °C could be assessed as being low in ecological toxicity.
Severity by National Institute of Health Stroke Scale Score and Clinical Features of Stroke Patients with Patent Foramen Ovale Stroke and Atrial Fibrillation

The comparative severity of patent foramen ovale (PFO)-related stroke in patients without atrial fibrillation (AF) and AF-related stroke in patients without PFO is unknown. Therefore, we compared the severity of PFO-related stroke and AF-related stroke. Twenty-six patients who underwent transesophageal echocardiography (TEE) were diagnosed with cardioembolic stroke from July 2018 to March 2020. Cases with AF detected by electrocardiograms or thrombus in the left atrium or left atrial appendage on TEE were included in the AF-related stroke group. Cases with a positive microbubble test on the Valsalva maneuver during TEE, and with no other factors that could cause stroke, were included in the PFO-related stroke group. This study was designed as a single-center, small population pilot study. The stroke severity of the two groups by the National Institute of Health Stroke Scale (NIHSS) score was compared by statistical analysis. Of the 26 cases, five PFO-related stroke patients and 21 AF-related stroke patients were analyzed. The NIHSS score was 2.2 ± 2.8 and 11.5 ± 9.2 (p-value < 0.01), the rate of hypertension was 20.0% and 85.7% (p-value = 0.01), and the HbA1c value was 5.5 ± 0.2% and 6.3 ± 1.3% (p-value = 0.02) in the PFO-related and AF-related stroke groups, respectively. Compared with AF-related stroke patients, stroke severity was low in PFO-related stroke patients.
Genomic Features of MCR-1 and Extended-Spectrum β-Lactamase-Producing Enterobacterales from Retail Raw Chicken in Egypt

Colistin is considered as a last resort agent for treatment of severe infections caused by carbapenem-resistant Enterobacterales (CRE). Recently, plasmid-mediated colistin resistance genes (mcr type) have been reported, mainly corresponding to mcr-1 producers. Those mcr-1-positive Enterobacterales have been identified not only from human isolates, but also from food samples, from animal specimens and from environmental samples in various parts of the world. Our study focused on the occurrence and characterization of mcr-1-positive Enterobacterales recovered from retail raw chicken in Egypt. From the 345 retail chicken carcasses collected, a total of 20 samples allowed to recover mcr-1-positive isolates (Escherichia coli, n = 19; Citrobacter freundii, n = 1). No mcr-2- to mcr-10-positive isolate was identified from those samples. The colistin resistance trait was confirmed for all those 20 isolates with a positivity of the Rapid Polymyxin NP (Nordmann-Poirel) test. Minimum inhibitory concentrations (MICs) of colistin for all MCR-1-producing isolates ranged between 4 and 16 μg/mL. Noticeably, 9 out of the 20 mcr-1-positive isolates produced an extended-spectrum β-lactamase (ESBL), respectively producing CTX-M-9 (n = 2), CTX-M-14 (n = 4), CTX-M-15 (n = 2), and SHV-12 (n = 1). Noteworthy, the fosA4 gene encoding resistance to fosfomycin was found in a single mcr-1-positive E. coli isolate, in which both genes were located on different conjugative plasmids. The pulsed-field gel electrophoresis (PFGE) patterns were identified, corresponding to 10 different sequence types (STs), highlighting the genetic diversity of those different E. coli. Whole-genome sequencing revealed three major types of mcr-1-bearing plasmids, corresponding to IncI2, IncX4, and IncHI2 scaffolds. The occurrence of MCR-1-producing multidrug-resistant Enterobacterales in retail raw chicken is of great concern, considering the possibility of transmission to humans through the food chain.
Profiling Thimet Oligopeptidase‐Mediated Proteolysis in Arabidopsis thaliana

Proteostasis is essential for proper cellular function, including the production of peptides with biological functions via the breakdown of proteins/peptides through controlled proteolysis. Proteostasis contributes to the maintenance of cellular functions and plant‐environment interactions under physiological conditions. Plant stress continues to reduce agricultural yields resulting in significant economic losses; thus, it is crucial to understand how plants perceive stress signals to elicit responses for survival. As previously shown in Arabidopsis thaliana, thimet oligopeptidases (TOPs) are essential components in plant response to oxidative stress triggered by pathogens. However, further characterization of TOP1 (also referred to as organellar oligopeptidase), TOP2 (also referred to as cytosolic oligopeptidase) and their peptide substrates is required to understand their contributions to stress perception and defense signaling. Label‐free peptidomics via liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) was used to differentially quantify 1111 peptides, originating from 369 proteins, between the Arabidopsis Col‐0 wild type and top1top2 knock‐out mutant. This revealed 350 peptides as significantly more abundant in the mutant, representing accumulation of these potential TOP substrates. Ten direct substrates were validated using in vitro enzyme assays and electrospray ionization mass spectrometry (ESI‐MS) with recombinant TOPs and synthetic candidate peptides. The TOP substrates discovered are derived from proteins involved in photosynthesis, biogenesis, glycolysis, protein folding, and antioxidant defense, implicating TOP involvement in processes beyond defense signaling. Identification of these substrates provides a framework for TOP signaling networks, through which the interplay between proteolytic pathways and defense signaling can be further characterized.
Exposure Route Affects the Toxicity Class of Thiamethoxam for the Predatory Bug, Orius albidipennis (Hemiptera: Anthocoridae) by Changing Its Fitness

Abstract In many cases, pesticides' side effects on natural enemies have closely related to their exposure route. We assessed long-term lethal and sublethal effects of thiamethoxam (TMX) on the predatory bug, Orius albidipennis (Reuter), fed on Aphis gossypii Glover (Hemiptera: Aphididae), through three exposure routes. First-instar nymphs were treated with the maximum field recommended concentration (MFRC), ½ MFRC, and ¼ MFRC of TMX for 24 h. Based on the results, the soil-application treatment (bottom-up effect: plant-aphid-predator) led to the lowest survival reduction. In contrast, leaf-dip (residual contact) and aphid-dip (oral exposure route) treatments decreased the survival severely. While the soil-application treatment had no significant effect on adult longevity and egg production, all tested concentrations of TMX in the leaf-dip and aphid-dip treatments negatively affected both traits. The egg hatchability was not affected by the insecticide in all exposure routes. Among all treatments, ¼ MFRC of TMX in the residual contact and oral treatments shortened the egg incubation period compared to control, but others failed to affect it. Finally, based on the criteria provided by the International Organization for Biological and Integrated Control (IOBC) regarding toxicity classification, systemic (soil) application of TMX was harmless for this predator. However, it was moderately harmful and harmful (depending on concentration) to the predator through the residual contact and oral exposures, even at ¼ MFRC. Given our results, the soil-application of TMX is compatible with O. albidipennis, and it can improve conservation approaches of the predator in the integrated management of A. gossypii.
Synthesis and Characterisation of [Re(CO)3(SS)(P)] Complexes: A [2+1] Concept for 99mTc‐ and 188Re‐Radiopharmaceutical Applications

A new (SS)(P) coordination set based on the concurrent use of a dithiocarbamate and a functionalised phosphane is reported. The (SS)(P) fashion is achieved by applying the [2+1] mixed-ligand concept and makes it possible to obtain stable rhenium tricarbonyl complexes without employing tripodal bifunctional chelating agents (BFCAs). The coordination chemistry of the simple sodium N,N-dimethyldithiocarbamate and new functionalised phosphanes L1–L3 [L1 = Ph2PCH2CH2C(O)OCH3, L2 = Ph2PCH2CH2C(O)NHCH2C(O)OCH3, L3 = Ph2PCH2CH2C(O)NHCH2CH2C(O)OCH3] was studied by reaction with the rhenium complex [NEt4]2[fac-Re(CO3)Br3]. The rhenium tricarbonyl core was found to be stabilised by the SS chelation of dithiocarbamate and by the P coordination of the phosphane. Two synthetic pathways leading to the complexes [fac-Re(CO)3(L)(MDTC)] (L = L1, L2, L3; MDTC = N,N-dimethyldithiocarbamate) are described. The structural characterisation of the isolated complexes by spectroscopic methods is reported, including X-ray crystallographic analysis for rhenium complexes with ligands L1 and L3. The homologous Tc-99m compounds with the same (SS)(P) coordination set were prepared at tracer level with the L2 and L3 ligands, and characterised by HPLC methods. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)