Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of necroptosis and its association with pyroptosis in organ damage in experimental pulmonary arterial hypertension

In this study, a role of cell loss due to necroptosis and its linkage with pyroptosis in organ damage under the conditions of pulmonary arterial hypertension (PAH) was examined. Monocrotaline (MCT) was used to induce PAH in Wistar rats, and depending on the severity of the disease progression, they were further divided into two subgroups: MCT group—sacrificed 4 weeks after MCT administration and ptMCT group—prematurely sacrificed due to rapid deterioration in vital functions (on Day 24,11 ± 0,7). The elevation of respiratory rate and right ventricular (RV) hypertrophy were more evident in ptMCT group, while the heart rate and cardiac haemodynamic stress markers were comparably higher in both diseased groups. Detailed immunoblotting analysis revealed that the upregulation of pThr231/Ser232‐RIP3 proceeded into necroptosis execution in the RVs, unlike in the lungs of both PAH stages. The elevated pulmonary pThr231/Ser232‐RIP3 levels in both PAH subgroups were associated rather with GSDMD‐mediated pyroptosis. On the contrary, other inflammasome forms, such as AIM2 and NLRC4, were higher in the RV, unlike in the lungs, of diseased groups. The PAH‐induced increase in the plasma RIP3 levels was more pronounced in ptMCT group, and positively correlated with RV hypertrophy, but not with haemodynamic stress. Taken together, we indicated for the first time that pThr231/Ser232‐RIP3 upregulation resulting in two different necrosis‐like cell death modes might underlie the pathomechanisms of PAH and that the plasma RIP3 might serve as an additional diagnostic and prognostic marker of cardiac injury under these conditions.
A Biomass Pyrolysis Oil as a Novel Insect Growth Regulator Mimic for a Variety of Stored Product Beetles

Abstract As fumigants face increasing regulatory restrictions, resistance, and consumer pushback, it is vital to expand the integrated pest management (IPM) chemical toolkit for stored products. The production of biomass derived insecticides (e.g., bio-oil fraction) from byproducts of biofuel production may be a promising alternative source of chemistries for controlling stored product insects. These potential insecticidal bio-oils were fractionated based on boiling points (ranging from 115 to 230°C in one series and 245–250°C in another). Fractions were analyzed using GC-MS, and were found to be unique in composition. The lethality of these fractions was tested on Tribolium castaneum, Tribolium confusum, and Oryzaephilus surinamensis (L.) (Coleoptera: Silvanidae). Fractions were tested at concentrations ranging from 5–260 mg/ml to screen for efficacy against adults for durations of 2–8 hr sprayed on concrete arenas. In addition, a separate assay evaluated adult emergence of larvae after 6 wk with supplemental food in arenas, while repellency was evaluated against four stored product insect species in a laminar wind tunnel. A greenhouse gas (GHG) emissions life cycle assessment was also performed, which found the use of the bio-oil fraction could reduce GHG emissions associated with the insecticide supply chain by 25–61% relative to a fossil-fuel based insecticide or pyrethroid. While adults were largely unaffected, we found that larval emergence was significantly suppressed compared to controls by roughly half or more. We also determined that there was minimal repellency to most fractions by most species. We conclude that the use of bio-oil fractions is a climate-friendly choice that may support IPM programs. Graphical Abstract
Interfering Hsa_circRNA_0060640 Suppresses TGF-β2-Induced Proliferation, Motility and EMT in Human Lens Epithelium Cells by Targeting miR-214-3p and Collagen Type I alpha2 Chain

Abstract Background Circular RNA (circRNA) is a novel star factor in the research of ocular diseases including cataract and the most common postoperative complication posterior capsule opacification (PCO). Hsa_circRNA_0060640 (circ_0060640) is an age-related cataract-related circRNA. However, its role in cataractogenesis is unrevealed yet. Methods PCO in vitro model was established in human lens epithelium cells (hLECs) induced by transforming growth factor-beta2 (TGF-β2). RNA and protein expressions were respectively detected by quantitative PCR and western blotting. Direct interaction between two RNAs was predicted by Starbase tool and confirmed by dual-luciferase reporter assay. MTS and EdU assays measured cell proliferation; Transwell, starch wound and western blotting assays evaluated cell motility and epithelial-mesenchymal transition (EMT). Results Circ_0060640 expression is higher in anterior lens capsule tissues from human cataractous eyes and TGF-β2-stimulated hLECs cells line SRA01/04. RNA interference of circ_0060640 could prevent SRA01/04 cells from TGF-β2-induced cell proliferation, migration and invasion, accompanied with decreased N-cadherin and α-smooth muscle actin and increased E-cadherin. Mechanistically, circ_0060640 directly controls microRNA (miR)-214-3p expression and then regulates gene expression of collagen type I alpha2 chain (COL1A2). Notably, COL1A2 inhibition is underlying the protective role of circ_0060640 silencing and miR-214-3p ectopic expression in TGF-β2-stimulated SRA01/04 cells. Conclusion Circ_0060640 is a novel cataract-related gene and its silencing could block TGF-β2-evoked hLECs proliferation, motility and EMT in vitro via targeting miR-214-3p-COL1A2 axis. Therefore, targeting circ_0060640 via RNA interference might be a treatment strategy for PCO development.
Abnormal dynamic functional connectivity in first‐episode, drug‐naïve adolescents with major depressive disorder

Previous neuroimaging studies have identified disrupted large‐scale functional brain networks in major depressive disorder (MDD); however, most of them focused on adult patients and were based on static functional connectivity (FC). Thus, we aimed to investigate the patterns of change in dynamic FC in depressed adolescents. Resting‐state functional magnetic resonance imaging data were acquired from 60 first‐episode, drug‐naïve adolescents with MDD and 60 matched healthy controls (HCs). Then, the dynamic FC properties were analyzed using a sliding windows approach, k‐means clustering, and graph theory methods. The intrinsic brain FC were clustered into two configuration states—a more frequent and relatively sparsely connected State 1 and a less frequent and more strongly interconnected State 2. Compared with HCs, depressed adolescents had higher reoccurrence fraction and dwell time in State 1, and lower reoccurrence fraction and dwell time in State 2, and higher total number of transitions between the two states. Depressed adolescents showed decreased FC within the default mode network (DMN) and between the DMN and other networks in State 1. Additionally, the MDD group showed higher variances in the global and local efficiency. Furthermore, the duration of illness was positively correlated with the number of state transitions, and the 17‐item Hamilton Depression Rating Scale score was positively correlated with the mean dwell time in State 1. This study demonstrated abnormal dynamic FC in depressed adolescents, which provided new insights into the pathophysiological mechanisms of adolescent‐onset depression.
Design of ZigBee-Based Monitoring System for Alkali Concentration in Mercerized Cotton Fabric

Aimed at the real-time monitoring of alkali concentration in mercerizing cotton goods,a monitor system based on ZigBee technology was established,including the network structure,the procedure flow and communication data formats of master node and data collection node and network protocol.The results show the stability and reliability,and low power and small size and low-cost of this system in monitoring the mercerization process of cotton goods.
Developmental Hypothyroidism Influences the Development of the Entorhinal-Dentate Gyrus Pathway of Rat Offspring

Background Developmental hypothyroidism impairs learning and memory in offspring, which depend on extensive neuronal circuits in the entorhinal cortex, together with the hippocampus and neocortex. The entorhinal-dentate gyrus pathway is the main entrance of memory circuits. We investigated whether developmental hypothyroidism impaired the morphological development of the entorhinal-dentate gyrus pathway. Methods We examined the structure and function of the entorhinal-dentate gyrus pathway in response to developmental hypothyroidism induced using 2-mercapto-1-methylimidazole. Results 1,1´-Dioctadecyl-3,3,3´,3´-tetramethylindocarbocyanine perchlorate tract tracing indicated that entorhinal axons showed delayed growth in reaching the outer molecular layer of the dentate gyrus at postnatal days 2 and 4 in hypothyroid conditions. The proportion of fibers in the outer molecular layer was significantly smaller in the hypothyroid group than in the euthyroid group at postnatal day 4. At postnatal day 10, the pathway showed a layer-specific distribution in the outer molecular layer, similar to the euthyroid group. However, the projected area of entorhinal axons was smaller in the hypothyroid group than in the euthyroid group. An electrophysiological examination showed that hypothyroidism impaired the long-term potentiation of the perforant and the cornu ammonis 3–cornu ammonis 1 pathways. Many repulsive axon guidance molecules were involved in the formation of the entorhinaldentate gyrus pathway. The hypothyroid group had higher levels of erythropoietin-producing hepatocyte ligand A3 and semaphorin 3A than the euthyroid group. Conclusion We demonstrated that developmental hypothyroidism might influence the development of the entorhinal-dentate gyrus pathway, contributing to impaired long-term potentiation. These findings improve our understanding of neural mechanisms for memory function.
Endometrial organoids derived from Mayer–Rokitansky–Küster–Hauser syndrome patients provide insights into disease-causing pathways

The uterus is responsible for the nourishment and mechanical protection of the developing embryo and fetus and is an essential part in mammalian reproduction. The Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by agenesis of the uterus and upper part of the vagina in females with normal ovarian function. Although heavily studied, the cause of the disease is still enigmatic. Current research in the field of MRKH mainly focusses on DNA-sequencing efforts and, so far, failed to decipher the nature and heterogeneity of the disease, thereby holding back scientific and clinical progress. Here, we developed long-term expandable organoid cultures from endometrium found in uterine rudiment horns of MRKH patients. Phenotypically, they share great similarity with healthy control organoids and are surprisingly fully hormone responsive. Transcriptome analyses, however, identified an array of dysregulated genes that point at potentially disease-causing pathways altered during the development of the female reproductive tract. We consider the endometrial organoid cultures to be a powerful research tool that promise to enable an array of studies into the pathogenic origins of MRKH syndrome and possible treatment opportunities to improve patient quality of life.
The expression of virulence genes increases membrane permeability and sensitivity to envelope stress in Salmonella Typhimurium

Virulence gene expression can represent a substantial fitness cost to pathogenic bacteria. In the model entero-pathogen Salmonella Typhimurium (S.Tm), such cost favors emergence of attenuated variants during infections that harbor mutations in transcriptional activators of virulence genes (e.g., hilD and hilC). Therefore, understanding the cost of virulence and how it relates to virulence regulation could allow the identification and modulation of ecological factors to drive the evolution of S.Tm toward attenuation. In this study, investigations of membrane status and stress resistance demonstrate that the wild-type (WT) expression level of virulence factors embedded in the envelope increases membrane permeability and sensitizes S.Tm to membrane stress. This is independent from a previously described growth defect associated with virulence gene expression in S.Tm. Pretreating the bacteria with sublethal stress inhibited virulence expression and increased stress resistance. This trade-off between virulence and stress resistance could explain the repression of virulence expression in response to harsh environments in S.Tm. Moreover, we show that virulence-associated stress sensitivity is a burden during infection in mice, contributing to the inherent instability of S.Tm virulence. As most bacterial pathogens critically rely on deploying virulence factors in their membrane, our findings could have a broad impact toward the development of antivirulence strategies.
Single Position Lateral Lumbar Interbody Fusion With Posterior Instrumentation Utilizing Computer Navigation and Robotic Assistance: Retrospective case review and surgical technique considerations

Study Design Retrospective cohort study. Objective To determine safety and short-term outcomes of single-position lateral lumbar interbody fusion (LLIF) with bilateral posterior instrumentation and robotic assistance. The article also describes surgical technique considerations for the procedure. Methods 20 patients underwent single-position LLIF with posterior instrumentation and robotic assistance. The patients were followed for a minimum of 3 months post-operatively. Results Average operative time was 211 ± 34 minutes, average blood loss was 51.25 ± 17 cc’s, and average length of stay was 1.4 ± . 75 days. There were no intraoperative complications, readmissions, revision surgeries, and no incidence of hardware malposition. Significant improvement in pain and ODI scores was noted at 3 month follow up. Conclusions The study demonstrated safety and short-term clinical efficacy of minimally invasive single-position lateral lumbar interbody fusion with bilateral posterior instrumentation utilizing robotic assistance and navigation. There are certain surgical technique considerations that must be followed to ensure optimal surgical workflow and predictable outcomes.
Effects of clinical and metabolic variables and hormones on the expression of immune protein biomarkers in the endometrium of women with polycystic ovary syndrome and normal-cycling controls

Abstract Background Women with polycystic ovary syndrome (PCOS) are at an elevated risk of endometrial cancer, which may be associated with the continuous proliferative state caused by the interaction between hormones and metabolic factors. Objective To investigate the impact of hormones and metabolic factors in the proliferation and death of endometrium during the proliferative phase. Methods Cross-sectional study with 11 women with PCOS and eight normal-cycling non-PCOS controls at the Federal University of the State of Rio de Janeiro from February 2011 to June 2019. Clinical, biochemical, and hormonal data were collected to analyze their influence on the expression of biomarkers related to the endometrial tissue breakdown. Hysteroscopy and endometrial biopsies were conducted, and the endometrial samples underwent immunohistochemistry for markers of apoptosis B-cell lymphoma 2 (BCL2), cleaved caspase-3 (CASP3), fas cell surface death receptor (FAS), FAS ligand (FASLG), BCL2 associated X (BAX), marker of proliferation Ki-67 (MKI67), and cell death using terminal deoxynucleotidyl transferase dUTP nick and labeling (TUNEL). Results CASP3 and TUNEL expressions were lower in both stroma and endometrium gland of PCOS women than in controls. MKI67 and homeostasis indexes (BCL2/BAX; FASLG/FAS) in the endometrium of the PCOS group were significantly higher. Body mass index (BMI) values were positively correlated with the expression of MKI67 and MKI67/TUNEL ratio in the endometrial stroma compartment. Fasting insulin levels were positively correlated with the expression of BCL2, and DHEA-S levels were negatively correlated with the expression of CASP3 of women with PCOS. Conclusion BMI, insulin, and DHEA-S influence the endometrial homeostasis breakdown in PCOS in the endometrium stroma.
Identification of differentially expressed genes and pathways in diquat and paraquat poisoning using bioinformatics analysis

Abstract Objective In this study, differentially expressed genes (DEGs) and signaling pathways involved in diquat (DQ) and paraquat (PQ) poisoning were identified via bioinformatics analysis, in order to inform the development of novel clinical treatments. Methods Raw data from GSE153959 were downloaded from the Gene Expression Omnibus database. DEGs of the DQ vs. control (CON) and PQ vs. CON comparison groups were identified using R, and DEGs shared by the two groups were identified using TBtools. Subsequently, the shared DEGs were searched in the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, using the Database for Annotation, Visualization, and Integrated Discovery. A protein–protein interaction (PPI) network was constructed, and hub genes were identified using the cytoHubba plug-in in Cytoscape software. Finally, circos and contrast plots showing the DEGs shared between mouse and human chromosomes were constructed using TBtools. Results Thirty-one DEGs shared by the DQ and PQ groups were identified. Enriched biological process terms included positive regulation of cell proliferation and translation. Enriched cellular component terms included extracellular region, intracellular membrane-bounded organelle and mitochondrion. Enriched molecular function terms included transcription factor activity and sequence-specific double-stranded DNA binding. Enriched KEGG pathways included the interleukin-17 signaling pathway, tumor necrosis factor signaling pathway, and human T-cell leukemia virus 1 infection. The top 10 hub genes in the PPI network were prostaglandin-endoperoxide synthase 2 (Ptgs2), chemokine (C-X-C motif) ligand 2 (Cxcl2), colony-stimulating factor 2 (granulocyte-macrophage) (Csf2), matrix metallopeptidase 13 (Mmp13), amphiregulin (Areg), plasminogen activator, urokinase receptor (Plaur), fos-like antigen 1 (Fosl1), epiregulin (Ereg), activating transcription factor 3 (Atf3), and transferrin receptor (Tfrc). Cxcl2, Csf2, and Atf3 played important roles in the mitogen-activated protein kinase (MAPK) signaling pathway. Conclusions These pathways and DEGs may serve as targets for gene therapy.
Cnot8 eliminates naïve regulation networks and is essential for naïve-to-formative pluripotency transition

Abstract Mammalian early epiblasts at different phases are characterized by naïve, formative, and primed pluripotency states, involving extensive transcriptome changes. Here, we report that deadenylase Cnot8 of Ccr4-Not complex plays essential roles during the transition from naïve to formative state. Knock out (KO) Cnot8 resulted in early embryonic lethality in mice, but Cnot8 KO embryonic stem cells (ESCs) could be established. Compared with the cells differentiated from normal ESCs, Cnot8 KO cells highly expressed a great many genes during their differentiation into the formative state, including several hundred naïve-like genes enriched in lipid metabolic process and gene expression regulation that may form the naïve regulation networks. Knockdown expression of the selected genes of naïve regulation networks partially rescued the differentiation defects of Cnot8 KO ESCs. Cnot8 depletion led to the deadenylation defects of its targets, increasing their poly(A) tail lengths and half-life, eventually elevating their expression levels. We further found that Cnot8 was involved in the clearance of targets through its deadenylase activity and the binding of Ccr4-Not complex, as well as the interacting with Tob1 and Pabpc1. Our results suggest that Cnot8 eliminates naïve regulation networks through mRNA clearance, and is essential for naïve-to-formative pluripotency transition.
Bioinformatics detection of modulators controlling splicing factor‐dependent intron retention in the human brain

Alternative RNA splicing is an important means of genetic control and transcriptome diversity. However, when alternative splicing events are studied independently, coordinated splicing modulated by common factors is often not recognized. As a result, the molecular mechanisms of how splicing regulators promote or repress splice site recognition in a context‐dependent manner are not well understood. The functional coupling between multiple gene regulatory layers suggests that splicing is modulated by additional genetic or epigenetic components. Here, we developed a bioinformatics approach to identify causal modulators of splicing activity based on the variation of gene expression in large RNA sequencing datasets. We applied this approach in a neurological context with hundreds of dorsolateral prefrontal cortex samples. Our model is strengthened with the incorporation of genetic variants to impute gene expression in a Mendelian randomization‐based approach. We identified novel modulators of the splicing factor SRSF1, including UIMC1 and the long noncoding RNA CBR3‐AS1, that function over dozens of SRSF1 intron retention splicing targets. This strategy can be widely used to identify modulators of RNA‐binding proteins involved in tissue‐specific alternative splicing.
Leaf water potential measurements using the pressure chamber: Synthetic testing of assumptions towards best practices for precision and accuracy

Abstract Leaf water potential (ψ leaf), typically measured using the pressure chamber, is the most important metric of plant water status, providing high theoretical value and information content for multiple applications in quantifying critical physiological processes including drought responses. Pressure chamber measurements of ψ leaf (ψ leafPC) are most typical, yet, the practical complexity of the technique and of the underlying theory has led to ambiguous understanding of the conditions to optimize measurements. Consequently, specific techniques and precautions diversified across the global research community, raising questions of reliability and repeatability. Here, we surveyed specific methods of ψ leafPC from multiple laboratories, and synthesized experiments testing common assumptions and practices in ψ leafPC for diverse species: (i) the need for equilibration of previously transpiring leaves; (ii) leaf storage before measurement; (iii) the equilibration of ψ leaf for leaves on bagged branches of a range of dehydration; (iv) the equilibration of ψ leaf across the lamina for bagged leaves, and the accuracy of measuring leaves with artificially ‘elongated petioles’; (v) the need in ψ leaf measurements for bagging leaves and high humidity within the chamber; (vi) the need to avoid liquid water on leaf surfaces; (vii) the use of ‘pulse’ pressurization versus gradual pressurization; and (viii) variation among experimenters in ψ leafPC determination. Based on our findings we provide a best practice protocol to maximise accuracy, and provide recommendations for ongoing species‐specific tests of important assumptions in future studies.