Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Gene Rearrangement Pattern in Pachycrepoideus vindemmiae Mitochondrial Genome: New Gene Order in Pteromalidae (Hymenoptera: Chalcidoidea)

Simple Summary The mitochondrial genome is a reliable genetic marker for reconstructing phylogeny and Pteromalidae is a diverse and complex family of chalcid wasps, but its evolutionary history is still poorly understood. In this study, we sequenced the mitochondrial genomes of four species (Muscidifurax similadanacus, M. sinesensilla, Nasonia vitripennis, and Pachycrepoideus vindemmiae) of Pteromalidae. Additionally, a phylogenetic hypothesis was reconstructed for the subfamilies of Pteromalidae that includes newly acquired mitogenomes and those deposited in NCBI. We used pairwise breakpoint distances to infer this phylogeny. Our study enriches the overall knowledge on gene rearrangement in Pteromalidae, reveals the evolutionary relationships among several major groups of Pteromalidae, accumulates molecular data for a Pteromalidae phylogeny, and provides a genetic background basis for biological control in agriculture and forestry. Abstract The mitochondrial genomes of Muscidifurax similadanacus, M. sinesensilla, Nasonia vitripennis, and Pachycrepoideus vindemmiae were sequenced to better understand the structural evolution of Pteromalidae mitogenomes. These newly sequenced mitogenomes all contained 37 genes. Nucleotide composition was AT-biased and the majority of the protein-coding genes exhibited a negative AT skew. All 13 protein-coding genes (PCGs) initiated with the standard start codon of ATN, excepted for nad1 of N. vitripennis, which started with TTG, and terminated with a typical stop codon TAA/TAG or an incomplete stop codon T. All transfer RNA (tRNA) genes were predicted to fold into the typical clover-leaf secondary structures, except for trnS1, which lacks the DHU arm in all species. In P. vindemmiae, trnR and trnQ lack the DHU arm and TΨC arm, respectively. Although most genes evolved under a strong purifying selection, the Ka/Ks value of the atp8 gene of P. vindemmiae was greater than 1, indicating putative positive selection. A novel transposition of trnR in P. vindemmiae was revealed, which was the first of this kind to be reported in Pteromalidae. Two kinds of datasets (PCG12 and AA) and two inference methods (maximum likelihood and Bayesian inference) were used to reconstruct a phylogenetic hypothesis for the newly sequenced mitogenomes of Pteromalidae and those deposited in GenBank. The topologies obtained recovered the monophyly of the three subfamilies included. Pachyneurinae and Pteromalinae were recovered as sister families, and both appeared sister to Sycophaginae. The pairwise breakpoint distances of mitogenome rearrangements were estimated to infer phylogeny among pteromalid species. The topology obtained was not totally congruent with those reconstructed using the ML and BI methods.
StackTHPred: Identifying Tumor-Homing Peptides through GBDT-Based Feature Selection with Stacking Ensemble Architecture

One of the major challenges in cancer therapy lies in the limited targeting specificity exhibited by existing anti-cancer drugs. Tumor-homing peptides (THPs) have emerged as a promising solution to this issue, due to their capability to specifically bind to and accumulate in tumor tissues while minimally impacting healthy tissues. THPs are short oligopeptides that offer a superior biological safety profile, with minimal antigenicity, and faster incorporation rates into target cells/tissues. However, identifying THPs experimentally, using methods such as phage display or in vivo screening, is a complex, time-consuming task, hence the need for computational methods. In this study, we proposed StackTHPred, a novel machine learning-based framework that predicts THPs using optimal features and a stacking architecture. With an effective feature selection algorithm and three tree-based machine learning algorithms, StackTHPred has demonstrated advanced performance, surpassing existing THP prediction methods. It achieved an accuracy of 0.915 and a 0.831 Matthews Correlation Coefficient (MCC) score on the main dataset, and an accuracy of 0.883 and a 0.767 MCC score on the small dataset. StackTHPred also offers favorable interpretability, enabling researchers to better understand the intrinsic characteristics of THPs. Overall, StackTHPred is beneficial for both the exploration and identification of THPs and facilitates the development of innovative cancer therapies.
Contemporary Knowledge on the Assessment of Temperament in Cattle and Its Impact on Production and Reproduction Including Some Immunological, Genetic and Metabolic Parameters

Simple Summary The assessment of temperament has a long history in cattle. However, the tests used to evaluate it are often difficult and time-consuming and, therefore, rarely used in practice. Meanwhile, temperament affects many of the breeding parameters of cattle. The aim of the article is to present known and lesser-known methods of temperament assessment and to indicate its relationship and influence on production and reproductive parameters as well as on some immunological, genetic and metabolic parameters in cattle. The article presents the most commonly used methods of temperament assessment and discusses some of the issues surrounding them. Abstract Temperament is associated with the well-being, health, production and reproduction of cattle. In order to increase the population of individuals with the desired temperament, its evaluation should be standardized and be made one of the obligatory elements of breeding and veterinary examination. A number of different tests are used for temperament assessment. In this article, the importance of temperament correlation with some metabolic, genetic, immunological, production and reproductive parameters have been shown, pointing at its influence on the economy and cattle handling. The most common methods for assessing the temperament of cattle are presented, including long-time scales of temperament assessment. At the same time, the relationship of the temperament of cattle with production efficiency, immunity and reproductive indicators has been shown, indicating that its correct assessment is an important aspect of the proper development of the herd and the associated economic growth.
Current Status Regarding Immunosuppressive Treatment in Patients after Renal Transplantation

Renal transplantation is now the best treatment for end-stage renal failure. To avoid rejection and prolong graft function, organ recipients need immunosuppressive therapy. The immunosuppressive drugs used depends on many factors, including time since transplantation (induction or maintenance), aetiology of the disease, and/or condition of the graft. Immunosuppressive treatment needs to be personalised, and hospitals and clinics have differing protocols and preparations depending on experience. Renal transplant recipient maintenance treatment is mostly based on triple-drug therapy containing calcineurin inhibitors, corticosteroids, and antiproliferative drugs. In addition to the desired effect, the use of immunosuppressive drugs carries risks of certain side effects. Therefore, new immunosuppressive drugs and immunosuppressive protocols are being sought that exert fewer side effects, which could maximise efficacy and reduce toxicity and, in this way, reduce both morbidity and mortality, as well as increase opportunities to modify individual immunosuppression for renal recipients of all ages. The aim of the current review is to describe the classes of immunosuppressive drugs and their mode of action, which are divided by induction and maintenance treatment. An additional aspect of the current review is a description of immune system activity modulation by the drugs used in renal transplant recipients. Complications associated with the use of immunosuppressive drugs and other immunosuppressive treatment options used in kidney transplant recipients have also been described.
Evaluation of soil moisture derived from FY3B microwave brightness temperature over the Tibetan Plateau

ABSTRACT In recent years, remote sensing has become one newest technology for deriving soil moisture at large scales. Using a radiative transfer algorithm, we have derived soil moisture over the Tibetan Plateau from the brightness temperature of the microwave radiometer imager (MWRI) onboard China’s Fengyun 3B (FY3B) satellite. The derived FY3B soil moisture data are evaluated with in situ observations, the ERA-Interim reanalysis and the retrievals from microwave imager (TMI) onboard the Tropical Rainforest Measuring Mission (TRMM). The FY3B and the TMI data are found to have both overestimated the soil moisture magnitudes against in situ observations. The FY3B data significantly outperform the TMI retrievals and particularly the ERA-Interim data with respect to their temporal dynamics, which is more important in soil moisture applications. This finding suggests the promising potential for using FY3B microwave brightness temperature to derive soil moisture over the Tibetan Plateau.
The Relationship between Metacognitive Beliefs with Clinical Belongingness and Resilience among Novice Nurses in Neonatal Intensive Care Units

Background The neonatal intensive care unit (NICU) is a sensitive ward for nurses. However, the low nurse-to-patient ratio has led to the hiring of novice nurses into the critical areas such as NICUs. These nurses are in need of help in the clinical environment as they have no much experience caring the neonates in the real clinical setting. Therefore, it is necessary to address the individual and psychological capacities with the help of which a person can overcome the difficult situations. This study aimed to investigate the relationship between metacognitions, clinical belongingness, and resilience of novice nursing staff in NICU wards. Method This study is a descriptive-analytical study, and the research samples were composed of 78 novice nursing staff of Neonatal Intensive Care Units from teaching hospitals. Samples were selected via a purposive sampling method. Research tools included demographic, Wells and Hatton metacognitive beliefs, Jones Levitt belonging, and Connor–Davidson resilience questionnaires. SPSS 22 software was used for data analysis. Results The mean score of metacognitive beliefs in novice nursing staff was 92.67 ± 13.69, and it was 116.69 ± 19.11 for belongingness and 78.78 ± 14.73 for resilience. There is positive and significant relationship between metacognitive beliefs and belongingness (p < 0.019, r = 0.265). In addition, the relationship between metacognitive beliefs and resilience in novice nursing staff was positive and significant (p < 0.001, r = 0.359). Conclusion There is a positive relationship between metacognitive beliefs with belongingness and resilience of novice nurses; nursing managers can consider educational metacognition workshops to enhance the sense of belongingness and resilience of novice nursing staff leading to improve their clinical performance in neonatal care.
A Comparative Proteomic Analysis to Explore the Influencing Factors on Endometritis Using LC-MS/MS

The inflammatory system activated by uterine infection is associated with decreased fertility. Diseases can be detected in advance by identifying biomarkers of several uterine diseases. Escherichia coli is one of the most frequent bacteria that is involved in pathogenic processes in dairy goats. The purpose of this study was to investigate the effect of endotoxin on protein expression in goat endometrial epithelial cells. In this study, the LC–MS/MS approach was employed to investigate the proteome profile of goat endometrial epithelial cells. A total of 1180 proteins were identified in the goat Endometrial Epithelial Cells and LPS-treated goat Endometrial Epithelial Cell groups, of which, 313 differentially expressed proteins were accurately screened. The proteomic results were independently verified by WB, TEM and IF techniques, and the same conclusion was obtained. To conclude, this model is suitable for the further study of infertility caused by endometrial damage caused by endotoxin. These findings may provide useful information for the prevention and treatment of endometritis.
Theratyping of the Rare CFTR Genotype A559T in Rectal Organoids and Nasal Cells Reveals a Relevant Response to Elexacaftor (VX-445) and Tezacaftor (VX-661) Combination

Despite the promising results of new CFTR targeting drugs designed for the recovery of F508del- and class III variants activity, none of them have been approved for individuals with selected rare mutations, because uncharacterized CFTR variants lack information associated with the ability of these compounds in recovering their molecular defects. Here we used both rectal organoids (colonoids) and primary nasal brushed cells (hNEC) derived from a CF patient homozygous for A559T (c.1675G>A) variant to evaluate the responsiveness of this pathogenic variant to available CFTR targeted drugs that include VX-770, VX-809, VX-661 and VX-661 combined with VX-445. A559T is a rare mutation, found in African-Americans people with CF (PwCF) with only 85 patients registered in the CFTR2 database. At present, there is no treatment approved by FDA (U.S. Food and Drug Administration) for this genotype. Short-circuit current (Isc) measurements indicate that A559T-CFTR presents a minimal function. The acute addition of VX-770 following CFTR activation by forskolin had no significant increment of baseline level of anion transport in both colonoids and nasal cells. However, the combined treatment, VX-661-VX-445, significantly increases the chloride secretion in A559T-colonoids monolayers and hNEC, reaching approximately 10% of WT-CFTR function. These results were confirmed by forskolin-induced swelling assay and by western blotting in rectal organoids. Overall, our data show a relevant response to VX-661-VX-445 in rectal organoids and hNEC with CFTR genotype A559T/A559T. This could provide a strong rationale for treating patients carrying this variant with VX-661-VX-445-VX-770 combination.
Astrocytes Differentiated from LRRK2-I1371V Parkinson’s-Disease-Induced Pluripotent Stem Cells Exhibit Similar Yield but Cell-Intrinsic Dysfunction in Glutamate Uptake and Metabolism, ATP Generation, and Nrf2-Mediated Glutathione Machinery

Owing to the presence of multiple enzymatic domains, LRRK2 has been associated with a diverse set of cellular functions and signaling pathways. It also has several pathological mutant-variants, and their incidences show ethnicity biases and drug-response differences with expression in dopaminergic-neurons and astrocytes. Here, we aimed to assess the cell-intrinsic effect of the LRRK2-I1371V mutant variant, prevalent in East Asian populations, on astrocyte yield and biology, involving Nrf2-mediated glutathione machinery, glutamate uptake and metabolism, and ATP generation in astrocytes derived from LRRK2-I1371V PD patient iPSCs and independently confirmed in LRRK2-I1371V-overexpressed U87 cells. Astrocyte yield (GFAP-immunopositive) was comparable between LRRK2-I1371V and healthy control (HC) populations; however, the astrocytic capability to mitigate oxidative stress in terms of glutathione content was significantly reduced in the mutant astrocytes, along with a reduction in the gene expression of the enzymes involved in glutathione machinery and nuclear factor erythroid 2-related factor 2 (Nrf2) expression. Simultaneously, a significant decrease in glutamate uptake was observed in LRRK2-I1371V astrocytes, with lower gene expression of glutamate transporters SLC1A2 and SLC1A3. The reduction in the protein expression of SLC1A2 was also directly confirmed. Enzymes catalyzing the generation of γ glutamyl cysteine (precursor of glutathione) from glutamate and the metabolism of glutamate to enter the Krebs cycle (α-ketoglutaric acid) were impaired, with significantly lower ATP generation in LRRK2-I1371V astrocytes. De novo glutamine synthesis via the conversion of glutamate to glutamine was also affected, indicating glutamate metabolism disorder. Our data demonstrate for the first time that the mutation in the LRRK2-I1371V allele causes significant astrocytic dysfunction with respect to Nrf2-mediated antioxidant machinery, AT -generation, and glutamate metabolism, even with comparable astrocyte yields.
Unveiling the Prognostic Significance of BCL6+/CD10+ Mantle Cell Lymphoma: Meta-Analysis of Individual Patients and Systematic Review

Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma (NHL) characterized by a hallmark translocation of t (11; 14). CD10 negativity has been used to differentiate MCL from other NHL types; however, recently, there has been an increase in the number of reported cases of CD10-positive MCL. This warrants further investigation into this rarer immunophenotype and its clinical significance. BCL6, which is a master transcription factor for the regulation of cell proliferation and key oncogene in B cell lymphomagenesis, has been reported to have co-expression with CD10 in MCL. The clinical significance of this aberrant antigen expression remains unknown. We conducted a systematic review by searching four databases and selected five retrospective analyses and five case series. Two survival analyses were conducted to determine if BCL6 positivity conferred a survival difference: 1. BCL6+ vs. BCL6− MCL. 2. BCL6+/CD10+ vs. BCL6−/CD10+ MCL. Correlation analysis was conducted to determine if BCL6 positivity correlated with the Ki67 proliferation index (PI). Overall survival (OS) rates were performed by the Kaplan–Meier method and log-rank test. Our analyses revealed that BCL6+ MCL had significantly shorter overall survival (median OS: 14 months vs. 43 months; p = 0.01), BCL6+/CD10+ MCL had an inferior outcome vs. BCL6+/CD10− MCL (median OS: 20 months vs. 55 months p = 0.1828), BCL6+ MCL had significantly higher percentages of Ki67% (Ki67% difference: 24.29; p = 0.0094), and BCL6 positivity had a positive correlation with CD10+ status with an odds ratio 5.11 (2.49, 10.46; p = 0.0000286). Our analysis showed that BCL6 expression is correlated with CD10 positivity in MCL, and BCL6 expression demonstrated an inferior overall survival. The higher Ki67 PI in BCL6+ MCL compared to BCL6− MCL further supports the idea that the BCL6+ immunophenotype may have prognostic value in MCL. MCL management should consider incorporating prognostic scoring systems adjusted for BCL6 expression. Targeted therapies against BCL6 may offer potential therapeutic options for managing MCL with aberrant immunophenotypes.
ON ISOMORPHIC GROUPS AND HOMEOMORPHIC SPACES

Suppose X and Y are topological spaces, and H(X) is the group of all homeomorphisms of X onto itself. We are concerned, in this paper, with the following question: (a) if p is a group isomorphism between H(X) and H(Y), does there exist a homeomorphism w of X onto Y such that (p(h) = h-1 for all h e H(X)? A more restricted question, which is also of interest, would be: (b) is every group automorphism of H(X) inner? The answer to (a) is, in general, no, for we may let X be the closed interval [0, 1], Y= (0, 1), and, for each h e H(X), 9(h) be the restriction of h to Y. To show that (b) also has a negative answer in general, let X = [O, 1] U (2, 3), w be a homeomorphic mapping of (0, 1) onto (2, 3) and (2, 3) onto (0, 1), and 9(h) be the extension of wha-v to X. Then 9 is an outer automorphism of H(X), for w can not be extended to an element of H(X). If X and Y are discrete spaces, then the answer to both questions is known to be yes, except in (b) when X has six elements (cf. [2] for a short historical survey). Question (a) has been studied in a more general setting by Gerstenhaber [2]. Fine and Schweigert [1] proved that (b) has an affirmative answer when X is a 1-cell, either open or closed, and Gerstenhaber [4] proved the same when X is a closed 2-cell. In the present paper, we will show that (a) has an affirmative answer when X and Y are compact, locally euclidean manifolds, with or without boundary. By setting X= Y, we also obtain an affirmative answer to (b) for the same class of spaces. The results obtained actually show that an isomorphism between any two sufficiently large subgroups of H(X) and H( Y) implies that X and Y are homeomorphic. In the course of this work, we develop a representation for the minimal normal subgroups of any sufficiently large subgroup of H(X).
Occurrence of Carbapenemases, Extended-Spectrum Beta-Lactamases and AmpCs among Beta-Lactamase-Producing Gram-Negative Bacteria from Clinical Sources in Accra, Ghana

Beta-lactamase (β-lactamase)-producing Gram-negative bacteria (GNB) are of public health concern due to their resistance to routine antimicrobials. We investigated the antimicrobial resistance and occurrence of carbapenemases, extended-spectrum β-lactamases (ESBLs) and AmpCs among GNB from clinical sources. GNB were identified using matrix-assisted laser desorption/ionization time of flight–mass spectrometry (MALDITOF-MS). Antimicrobial susceptibility testing was performed via Kirby–Bauer disk diffusion and a microscan autoSCAN system. β-lactamase genes were determined via multiplex polymerase chain reactions. Of the 181 archived GNB analyzed, Escherichia coli and Klebsiella pneumoniae constituted 46% (n = 83) and 17% (n = 30), respectively. Resistance to ampicillin (51%), third-generation cephalosporins (21%), and ertapenem (21%) was observed among the isolates, with 44% being multi-drug resistant (MDR). β-lactamase genes such as AmpCs ((blaFOX-M (64%) and blaDHA-M and blaEDC-M (27%)), ESBLs ((blaCTX-M (81%), other β-lactamase genes blaTEM (73%) and blaSHV (27%)) and carbapenemase ((blaOXA-48 (60%) and blaNDM and blaKPC (40%)) were also detected. One K. pneumoniae co-harbored AmpC (blaFOX-M and blaEBC-M) and carbapenemase (blaKPC and blaOXA-48) genes. blaOXA-48 gene was detected in one carbapenem-resistant Acinetobacter baumannii. Overall, isolates were resistant to a wide range of antimicrobials including last-line treatment options. This underpins the need for continuous surveillance for effective management of infections caused by these pathogens in our settings.
Porcine Follicular Fluid-Derived Exosome: The Pivotal Material for Porcine Oocyte Maturation in Lipid Antioxidant Activity

Several studies have examined exosomes derived from porcine follicular fluid (FF), but few have reported their application in controlled experiments. The main concern in the field of embryology may be that controlled conditions, such as using a defined medium intermittently, cause poor results in mammalian oocyte maturation and embryo development. The first reason is the absence of the FF, which copes with the majority of the processes emerging in oocytes and embryos. Therefore, we added exosomes derived from porcine FF to the maturation medium of porcine oocytes. For morphological assessment, cumulus cell expansion and subsequent embryonic development were evaluated. Moreover, several stainings, such as glutathione (GSH) and reactive oxygen species (ROS), fatty acid, ATP, and mitochondrial activity, as well as evaluations of gene expression and protein analysis, were used for the functional verification of exosomes. When the oocytes were treated with exosomes, the lipid metabolism and cell survival of the oocytes were fully recovered, as well as morphological evaluations compared to the porcine FF-excluded defined medium. Therefore, controlled experiments may produce reliable data if the exosomes are treated with the desired amounts, and we suggest applying FF-derived exosomes to promote experimental data when performing controlled experiments in embryology.