Miracle-dz/UniFAR-FTUs huggingface dataset:
In Silico Identification of a BRCA1:miR-29:DNMT3 Axis Involved in the Control of Hormone Receptors in BRCA1-Associated Breast Cancers

Germline inactivating mutations in the BRCA1 gene lead to an increased lifetime risk of ovarian and breast cancer (BC). Most BRCA1-associated BC are triple-negative tumors (TNBC), aggressive forms of BC characterized by a lack of expression of estrogen and progesterone hormone receptors (HR) and HER2. How BRCA1 inactivation may favor the development of such a specific BC phenotype remains to be elucidated. To address this question, we focused on the role of miRNAs and their networks in mediating BRCA1 functions. miRNA, mRNA, and methylation data were retrieved from the BRCA cohort of the TCGA project. The cohort was divided into a discovery set (Hi-TCGA) and a validation set (GA-TCGA) based on the platform used for miRNA analyses. The METABRIC, GSE81002, and GSE59248 studies were used as additional validation data sets. BCs were differentiated into BRCA1-like and non-BRCA1-like based on an established signature of BRCA1 pathway inactivation. Differential expression of miRNAs, gene enrichment analysis, functional annotation, and methylation correlation analyses were performed. The miRNAs downregulated in BRCA1-associated BC were identified by comparing the miRNome of BRCA1-like with non-BRCA1-like tumors from the Hi-TCGA discovery cohort. miRNAs:gene-target anticorrelation analyses were then performed. The target genes of miRNAs downregulated in the Hi-TCGA series were enriched in the BRCA1-like tumors from the GA-TCGA and METABRIC validation data sets. Functional annotation of these genes revealed an over-representation of several biological processes ascribable to BRCA1 activity. The enrichment of genes related to DNA methylation was particularly intriguing, as this is an aspect of BRCA1 functions that has been poorly explored. We then focused on the miR-29:DNA methyltransferase network and showed that the miR-29 family, which was downregulated in BRCA1-like tumors, was associated with poor prognosis in these BCs and inversely correlated with the expression of the DNA methyltransferases DNMT3A and DNMT3B. This, in turn, correlated with the methylation extent of the promoter of HR genes. These results suggest that BRCA1 may control the expression of HR via a miR-29:DNMT3:HR axis and that disruption of this network may contribute to the receptor negative phenotype of tumors with dysfunctional BRCA1.
l-Alanine Exporter AlaE Functions as One of the d-Alanine Exporters in Escherichia coli

d-amino acids have recently been found to be present in the extracellular milieu at millimolar levels and are therefore assumed to play a physiological function. However, the pathway (or potential pathways) by which these d-amino acids are secreted remains unknown. Recently, Escherichia coli has been found to possess one or more energy-dependent d-alanine export systems. To gain insight into these systems, we developed a novel screening system in which cells expressing a putative d-alanine exporter could support the growth of d-alanine auxotrophs in the presence of l-alanyl–l-alanine. In the initial screening, five d-alanine exporter candidates, AlaE, YmcD, YciC, YraM, and YidH, were identified. Transport assays of radiolabeled d-alanine in cells expressing these candidates indicated that YciC and AlaE resulted in lower intracellular levels of d-alanine. Further detailed transport assays of AlaE in intact cells showed that it exports d-alanine in an expression-dependent manner. In addition, the growth constraints on cells in the presence of 90 mM d-alanine were mitigated by the overexpression of AlaE, implying that AlaE could export free d-alanine in addition to l-alanine under conditions in which intracellular d/l-alanine levels are raised. This study also shows, for the first time, that YciC could function as a d-alanine exporter in intact cells.
A method for the efficient evaluation of substrate-based cholinesterase imaging probes for Alzheimer’s disease

Abstract Cholinesterase (ChE) enzymes have been identified as diagnostic markers for Alzheimer disease (AD). Substrate-based probes have been synthesised to detect ChEs but they have not detected changes in ChE distribution associated with AD pathology. Probes are typically screened using spectrophotometric methods with pure enzyme for specificity and kinetics. However, the biochemical properties of ChEs associated with AD pathology are altered. The present work was undertaken to determine whether the Karnovsky-Roots (KR) histochemical method could be used to evaluate probes at the site of pathology. Thirty thioesters and esters were synthesised and evaluated using enzyme kinetic and KR methods. Spectrophotometric methods demonstrated all thioesters were ChE substrates, yet only a few provided staining in the brain with the KR method. Esters were ChE substrates with interactions with brain ChEs. These results suggest that the KR method may provide an efficient means to screen compounds as probes for imaging AD-associated ChEs.
Optogenetic and Chemogenic Control of Pain Signaling: Molecular Markers

Pain is a complex experience that involves physical, emotional, and cognitive aspects. This review focuses specifically on the physiological processes underlying pain perception, with a particular emphasis on the various types of sensory neurons involved in transmitting pain signals to the central nervous system. Recent advances in techniques like optogenetics and chemogenetics have allowed researchers to selectively activate or inactivate specific neuronal circuits, offering a promising avenue for developing more effective pain management strategies. The article delves into the molecular targets of different types of sensory fibers such as channels, for example, TRPV1 in C-peptidergic fiber, TRPA1 in C-non-peptidergic receptors expressed differentially as MOR and DOR, and transcription factors, and their colocalization with the vesicular transporter of glutamate, which enable researchers to identify specific subtypes of neurons within the pain pathway and allows for selective transfection and expression of opsins to modulate their activity.
Prolactin Regulates Ovine Ovarian Granulosa Cell Apoptosis by Affecting the Expression of MAPK12 Gene

Prolactin (PRL) has been reported to influence reproductive performance and cell apoptosis. However, its mechanism remains unclear. Hence, in the present study, ovine ovarian granulosa cells (GCs) were used as a cell model to investigate the relationship between PRL concentration and GC apoptosis, as well as its possible mechanisms. We examined the relationship between serum PRL concentration and follicle counts in sexually mature ewes. GCs were isolated from adult ewes and treated with different concentrations of PRL, while 500 ng/mL PRL was selected as the high concentration of prolactin (HPC). Then, we applied the transcriptome sequencing (RNA-Seq) combined with a gene editing approach to explore the HPC contributing to cell apoptosis and steroid hormones. The apoptosis of GCs gradually increased at PRL concentrations above 20 ng/mL, while 500 ng/mL PRL significantly decreased the secretion of steroid hormones and the expression of L-PRLR and S-PRLR. The results indicated that PRL regulates GC development and steroid hormones mainly through the target gene MAPK12. The expression of MAPK12 was increased after knocked-down L-PRLR and S-PRLR, while it decreased after overexpressed L-PRLR and S-PRLR. Cell apoptosis was inhibited and the secretion of steroid hormones increased after interfering with MAPK12, while the overexpression of MAPK12 showed the opposite trend. Overall, the number of follicles gradually decreased with increasing PRL concentration. HPCs promoted apoptosis and inhibited steroid hormone secretion in GCs by upregulating MAPK12 through reducing L-PRLR and S-PRLR.
The Influence of Carious Lesion and Bleeding Time on the Success of Partial Pulpotomy in Permanent Molars with Irreversible Pulpitis: A Prospective Study

This prospective study aimed to evaluate the success rate of partial pulpotomy using mineral trioxide aggregate (MTA), in permanent molars with symptomatic irreversible pulpitis. Moreover, this study aimed to investigate the effect of carious lesion depth and activity and bleeding time on the outcome of partial pulpotomy. Forty permanent molars with deep and extremely deep carious lesions clinically diagnosed with symptomatic irreversible pulpitis were included. The status of the carious lesion was evaluated clinically and radiographically to determine its activity (rapidly or slowly progressing) and depth (deep or extremely deep). A partial pulpotomy was performed and MTA was used. Clinical and radiographic analysis were performed at 3, 6 and 12 months. Chi-square analysis and Fisher’s exact test were used. Scanning electron microscope and energy dispersive X-rays were used to investigate the crystalline structures and their chemical composition onto MTA surfaces after immersion in several conditions. The partial pulpotomy was 88.9% successful, with no significant difference in outcome between deep and extremely deep carious lesions (p = 0.22) or between rapidly and slowly progressing lesions (p = 0.18). Nevertheless, all failed cases were associated with rapidly progressing lesions and extremely deep lesions. All failures occurred when the bleeding time was more than 3 min (p = 0.10). Different crystalline structures were detected on MTA surfaces, with higher calcium percentages in PBS conditions. Within the limitations of the present study, favorable results demonstrated that MTA might be recommended as a suitable agent for partial pulpotomy in permanent molars with irreversible pulpitis. The depth and activity of the carious lesion as well as the bleeding time are important factors in the success of partial pulpotomy treatment. The prolonged bleeding time and the extremely deep rapidly progressing caries could be related with the failure cases in partial pulpotomy treatment of irreversible pulpitis.
The Changes in Mitochondrial Morphology and Physiology Accompanying Apoptosis in Galleria mellonella (Lepidoptera) Immunocompetent Cells during Conidiobolus coronatus (Entomophthorales) Infection

Mitochondria have been shown to play an important role in apoptosis using mammalian cell lines. However, their role in insects is not fully understood; thus, more indepth studies of insect cell apoptosis are necessary. The present study investigates mitochondrial involvement during Conidiobolus coronatus-induced apoptosis in Galleria mellonella hemocytes. Previous research has shown that fungal infection could induce apoptosis in insect hemocytes. Our findings indicate that mitochondria undergo several morphological and physiological changes during fungal infection, e.g., loss of mitochondrial membrane potential, megachannel formation, disturbances in intracellular respiration, increased nonrespiratory oxygen consumption in mitochondria, decreased ATP-coupled oxygen consumption and increased non-ATP–coupled oxygen consumption, decreased extracellular and intracellular oxygen consumption, and increased extracellular pH. Our findings confirm that G. mellonella immunocompetent cells demonstrate Ca2+ overload in mitochondria, translocation of cytochrome c-like protein from mitochondrial to cytosol fraction, and higher activation of caspase-9-like protein after C. coronatus infection. Most importantly, several of the changes observed in insect mitochondria are similar to those accompanying apoptosis in mammalian cells, suggesting that the process is evolutionarily conserved.
Nicotine and Microvascular Responses in Skeletal Muscle from Acute Exposure to Cigarettes and Vaping

Despite claims of safety or harm reduction for electronic cigarettes (E-cig) use (also known as vaping), emerging evidence indicates that E-cigs are not likely safe, or necessarily safer than traditional cigarettes, when considering the user’s risk of developing vascular dysfunction/disease. E-cigs are different from regular cigarettes in that E-cig devices are highly customizable, and users can change the e-liquid composition (such as the base solution, flavors, and nicotine level). Since the effects of E-cigs on the microvascular responses in skeletal muscle are poorly understood, we used intravital microscopy with an acute (one-time 10 puff) exposure paradigm to evaluate the individual components of e-liquid on vascular tone and endothelial function in the arterioles of the gluteus maximus muscle of anesthetized C57Bl/6 mice. Consistent with the molecular responses seen with endothelial cells, we found that the peripheral vasoconstriction response was similar between mice exposed to E-cig aerosol or cigarette smoke (i.e., 3R4F reference cigarette); this response was not nicotine dependent, and endothelial cell-mediated vasodilation was not altered within this acute exposure paradigm. We also report that, regardless of the base solution component [i.e., vegetable glycerin (VG)-only or propylene glycol (PG)-only], the vasoconstriction responses were the same in mice with inhalation exposure to 3R4F cigarette smoke or E-cig aerosol. Key findings from this work reveal that some component other than nicotine, in inhaled smoke or aerosol, is responsible for triggering peripheral vasoconstriction in skeletal muscle, and that regardless of one’s preference for an E-cig base solution composition (i.e., ratio of VG-to-PG), the acute physiological response to blood vessels appears to be the same. The data suggest that vaping is not likely to be ‘safer’ than smoking towards blood vessels and can be expected to produce and/or result in the same adverse vascular health outcomes associated with smoking cigarettes.
User Real-Time Influence Ranking Algorithm of Social Networks Considering Interactivity and Topicality

At present, the existing influence evaluation algorithms often ignore network structure attributes, user interests and the time-varying propagation characteristics of influence. To address these issues, this work comprehensively discusses users’ own influence, weighted indicators, users’ interaction influence and the similarity between user interests and topics, thus proposing a dynamic user influence ranking algorithm called UWUSRank. First, we determine the user’s own basic influence based on their activity, authentication information and blog response. This improves the problem of poor objectivity of initial value on user influence evaluation when using PageRank to calculate user influence. Next, this paper mines users’ interaction influence by introducing the propagation network properties of Weibo (a Twitter-like service in China) information and scientifically quantifies the contribution value of followers’ influence to the users they follow according to different interaction influences, thereby solving the drawback of equal value transfer of followers’ influence. Additionally, we analyze the relevance of users’ personalized interest preferences and topic content and realize real-time monitoring of users’ influence at various time periods during the process of public opinion dissemination. Finally, we conduct experiments by extracting real Weibo topic data to verify the effectiveness of introducing each attribute of users’ own influence, interaction timeliness and interest similarity. Compared to TwitterRank, PageRank and FansRank, the results show that the UWUSRank algorithm improves the rationality of user ranking by 9.3%, 14.2%, and 16.7%, respectively, which proves the practicality of the UWUSRank algorithm. This approach can serve as a guide for research on user mining, information transmission methods, and public opinion tracking in social network-related areas.
HnRNP Pathologies in Frontotemporal Lobar Degeneration

Frontotemporal dementia (FTD) is the second most common form of young-onset (<65 years) dementia. Clinically, it primarily manifests as a disorder of behavioural, executive, and/or language functions. Pathologically, frontotemporal lobar degeneration (FTLD) is the predominant cause of FTD. FTLD is a proteinopathy, and the main pathological proteins identified so far are tau, TAR DNA-binding protein 43 (TDP-43), and fused in sarcoma (FUS). As TDP-43 and FUS are members of the heterogeneous ribonucleic acid protein (hnRNP) family, many studies in recent years have expanded the research on the relationship between other hnRNPs and FTLD pathology. Indeed, these studies provide evidence for an association between hnRNP abnormalities and FTLD. In particular, several studies have shown that multiple hnRNPs may exhibit nuclear depletion and cytoplasmic mislocalisation within neurons in FTLD cases. However, due to the diversity and complex association of hnRNPs, most studies are still at the stage of histological discovery of different hnRNP abnormalities in FTLD. We herein review the latest studies relating hnRNPs to FTLD. Together, these studies outline an important role of multiple hnRNPs in the pathogenesis of FTLD and suggest that future research into FTLD should include the whole spectrum of this protein family.
Translation of the Modified Polycystic Ovary Syndrome Questionnaire (mPCOSQ) and the Polycystic Ovary Syndrome Quality of Life Tool (PCOSQOL) in Dutch and Flemish Women with PCOS

This study aims to determine the test–retest reliability and to confirm the domain structures of the Dutch version of the modified polycystic ovary syndrome questionnaire (mPCOSQ) and the Polycystic Ovary Syndrome Quality of Life Scale (PCOSQOL) in Dutch and Flemish women with Polycystic Ovary Syndrome (PCOS). PCOS patients were contacted with a request to complete both questionnaires (including additional demographic questions) online in their home environment on T0 and on T1. The study was approved by the Ethics Committee of Erasmus Medical Centre and of Ghent University Hospital. In this study, 245 participants were included between January and December 2021. The mPCOSQ has excellent internal consistency (α: 0.95) and a high to excellent Intraclass Correlation Coefficient (ICC) for all six domains (ICC: 0.88–0.96). The PCOSQOL demonstrates excellent internal consistency (α: 0.96) and ICC (ICC: 0.91–0.96) for all four domains. The original six-factor structure of the mPCOSQ is partly confirmed. An extra domain is added to the PCOSQOL which included coping items. Most women have no preference for one of the two questionnaires (55.9%). In conclusion, The Dutch mPCOSQ and PCOSQOL are reliable and disease-specific QoL measures for women with PCOS. Both questionnaires are recommended for clinical practice.
Neuroprotective Efficacy of a Nanomicellar Complex of Carnosine and Lipoic Acid in a Rat Model of Rotenone-Induced Parkinson’s Disease

Oxidative stress, accompanied by mitochondrial dysfunction, is a key mechanism involved in the pathogenesis of Parkinson’s disease (PD). Both carnosine and lipoic acid are potent antioxidants, the applicability of which in therapy is hindered by their limited bioavailability. This study aimed to evaluate the neuroprotective properties of a nanomicellar complex of carnosine and lipoic acid (CLA) in a rotenone-induced rat model of PD. Parkinsonism was induced via the administration of 2 mg/kg rotenone over the course of 18 days. Two doses of intraperitoneal CLA (25 mg/kg and 50 mg/kg) were administered alongside rotenone to assess its neuroprotective effect. At 25 mg/kg CLA decreased muscle rigidity and partially restored locomotor activity in animals that received rotenone. Furthermore, it caused an overall increase in brain tissue antioxidant activity, accompanied by a 19% increase in neuron density in the substantia nigra and increased dopamine levels in the striatum relative to animals that only received rotenone. Based on the acquired results, it may be concluded that CLA have neuroprotective properties and could potentially be beneficial in PD treatment when used in conjunction with the base therapy.
Value of Left Atrial Strain in Predicting Recurrence after Atrial Fibrillation Ablation

This study tested the relationship between left atrial (LA) function parameters and the results of pulmonary vein isolation (PVI) in patients with atrial fibrillation (AF). Consecutive patients undergoing PVI for the first time between 2019 and 2021 were included. Patients underwent radiofrequency ablation using contact force catheters and an electroanatomical system. Follow-up consisted of ambulatory visits/televisits and 7-day Holter monitoring (at 6 and 12 months after ablation). On the day of ablation, all patients underwent transesophageal and transthoracic echocardiography with LA strain analysis. The primary endpoint was atrial tachyarrhythmia recurrence during the follow-up period. Of 221 patients, 22 did not meet the echocardiographic quality criteria, leaving 199 patients. The median follow-up period was 12 months, and 12 patients were lost to follow-up. Recurrences were observed in 67 patients (35.8%) after a mean of 1.06 procedures per patient. The patients were divided into a sinus rhythm (SR, n = 109) group and an AF (n = 90) group based on their cardiac rhythm at the time of echocardiography. In the SR group, univariable analysis showed that LA reservoir strain, LA appendage emptying velocity (LAAV), and LA volume index predicted AF recurrence, with only LAAV being significant in the multivariable analysis. In AF patients, univariable analysis revealed no LA strain parameters predicting AF recurrence.
Dietary Probiotics Modulate Gut Barrier and Immune-Related Gene Expression and Histomorphology in Broiler Chickens under Non- and Pathogen-Challenged Conditions: A Meta-Analysis

Simple Summary The supplementation of diets for broiler chickens has increased due to the increasing demand of consumers for antibiotic-free broiler products. Nevertheless, the benefits of probiotics for intestinal barrier and immune functions, as well as on growth performance in chickens, are still controversially discussed. In performing a meta-analysis, we found that dietary supplementation with probiotics of various genera/species can enforce intestinal barrier function. Moreover, our meta-regressions indicated that in pathogen-challenged birds, probiotics might effectively help reduce gut inflammation by suppressing the expression of pro-inflammatory cytokines. Probiotics further sustained the intestinal histomorphology and hence digestive and absorptive processes in challenged and non-challenged chickens. Abstract Data published in the literature about the favorable effects of dietary probiotics on gut health in broiler chickens are inconsistent. To obtain a more comprehensive understanding, we conducted a meta-analysis to assess the effects of probiotics on the gut barrier and immune-related gene expression, histomorphology, and growth in chickens that were either challenged or non-challenged with pathogens. From the 54 articles published between 2012 and 2022, subsets of data, separately for non-challenged and challenged conditions, for response variables were created. The mean dietary probiotic concentrations ranged from 4.7 to 6.2 and 4.7 to 7.2 log10 colony-forming unit/kg under non-challenged and challenged conditions, respectively. Probiotics increased the expression of genes for mucins and tight junction proteins in the jejunum and ileum at weeks 3 and 6. The stimulatory effect of probiotics on tight junction protein expression was partly stronger in challenged than in non-challenged birds. Meta-regressions also showed an anti-inflammatory effect of probiotics under challenged conditions by modulating the expression of cytokines. Probiotics improved villus height at certain ages in the small intestine while not influencing growth performance. Dietary metabolizable energy, crude protein, and days post-infection modified the effects of probiotics on the observed variables. Overall, meta-regressions support the beneficial effects of probiotics on gut integrity and structure in chickens.