Miracle-dz/UniFAR-FTUs huggingface dataset:
Definition of erythroid cell‐positive blood transcriptome phenotypes associated with severe respiratory syncytial virus infection

Abstract Biomarkers to assess the risk of developing severe respiratory syncytial virus (RSV) infection are needed. We conducted a meta‐analysis of 490 unique profiles from six public RSV blood transcriptome datasets. A repertoire of 382 well‐characterized transcriptional modules was used to define dominant host responses to RSV infection. The consolidated RSV cohort was stratified according to four traits: “interferon response” (IFN), “neutrophil‐driven inflammation” (Infl), “cell cycle” (CC), and “erythrocytes” (Ery). We identified eight prevalent blood transcriptome phenotypes, of which three Ery+ phenotypes comprised higher proportions of patients requiring intensive care. This finding confirms on a larger scale data from one of our earlier reports describing an association between an erythrocyte signature and RSV disease severity. Further contextual interpretation made it possible to associate this signature with immunosuppressive states (late stage cancer, pharmacological immunosuppression), and with a population of fetal glycophorin A+ erythroid precursors. Furthermore, we posit that this erythrocyte cell signature may be linked to a population of immunosuppressive erythroid cells previously described in the literature, and that overabundance of this cell population in RSV patients may underlie progression to severe disease. These findings outline potential priority areas for biomarker development and investigations into the immune biology of RSV infection. The approach that we developed and employed here should also permit to delineate prevalent blood transcriptome phenotypes in other settings.
Proteomic and microRNA-omic profiles and potential mechanisms of dysfunction in pancreatic islet cells primed by inflammation

Diabetes is an inflammatory disease that induces pancreatic islet dysfunction. However, to the best of our knowledge, the potential underlying molecular mechanisms of this inflammatory process remains unknown. The present study investigated microRNA (miRNA/miR) and protein expression profiles through proteomics and miRNA-omics. Lipopolysaccharide-induced macrophage cell medium (LRM) was used to stimulate inflammation in mouse Beta-TC-6 islet cells. Protein analysis revealed that 87 proteins were upregulated and 42 proteins were downregulated in LRM-treated Beta-TC-6 cells compared with control cells. Additionally, miRNA analysis revealed that 11 miRNAs were upregulated, while 28 miRNAs were downregulated in LRM-treated Beta-TC-6 cells compared with control cells. Islet cells exposed to inflammation exhibited markedly downregulated protein levels of transcription factor MafA, pancreatic and duodenal homeobox 1, paired box 6, homeobox protein Nkx-2.2, synaptosomal-associated protein 25, glucagon and insulin-2, while the expression of miR-146a-5p and miR-21a-5p were upregulated. It was also determined that upregulated miR-146a-5p and miR-21a-5p levels may be mediated by NF-κB activation. The downregulation of islet functional factor mRNA was partially reversed by treating islet cells with an inhibitor of miR-21a-5p. However, treatment with an miR-146a-5p inhibitor did not exert the same effect. Overall, the present study determined the molecular profiles of islet cell inflammation based on proteomics and miRNA-omics, and indicated that the proteins and miRNAs with altered expressions may form a large network that serves a role in islet dysfunction. Particularly, miR-21a-5p upregulation in response to inflammation may contribute to islet cell dysfunction. However, how these miRNAs regulated the expression of certain mRNAs and proteins in islet cell inflammation requires further investigation.
Modulation of Astrocytes on Mode Selection of Neuron Firing Driven by Electromagnetic Induction

Both of astrocytes and electromagnetic induction are magnificent to modulate neuron firing by introducing feedback currents to membrane potential. An improved astro-neuron model considering both of the two factors is employed to investigate their different roles in modulation. The mixing mode, defined by combination of period bursting and depolarization blockage, characterizes the effect of astrocytes. Mixing mode and period bursting alternatively appear in parameter space with respect to the amplitude of feedback current on neuron from astrocyte modulation. However, magnetic flux obviously plays a role of neuron firing inhibition. It not only repels the mixing mode but also suppresses period bursting. The mixing mode becomes period bursting mode and even resting state when astrocytes are hyperexcitable. Abnormal activities of astrocytes are capable to induce depolarization blockage to compose the mixing mode together with bursting mode. But electromagnetic induction shows its strong ability of inhibition of neuron firing, which is also illustrated in the bifurcation diagram. Indeed, the combination of the two factors and appropriate choice of parameters show the great potential to control disorder of neuron firing like epilepsy.
Does Method Matter? Assessing the Correspondence between Experimental and Nonexperimental Results from a School Voucher Program Evaluation

Background. Randomized Controlled Trials are the “gold-standard” for estimating causal impacts of education programs. They are not always feasible, however, and may not generalize to the population of interest. Generally, researchers cannot measure selection bias in quasi-experimental estimates, leaving us uncertain about the true program impact. Objective. This study assesses the performance of propensity score matching, kernel matching, and multivariate regression in replicating the experimental results of a District of Columbia school voucher evaluation. Research Design. We assess whether nonexperimental methods can replicate experimental results among two samples: the experimental sample, in which treated and nontreated students are similar in terms of their eligibility status and desire to apply for the program, and a broader nonexperimental sample that includes geographically similar comparison units who did not apply for the program. Results. Nonexperimental methods more closely replicate experimental estimates when the sample is limited to program applicants. Little evidence suggests that a particular nonexperimental method performs better than other approaches. The direction of the bias in the quasi-experimental estimates tends to be positive when the sample is limited to program applicants, but negative when expanded to non-applicants. This pattern suggests that voucher program applicants are negatively selected on unmeasured characteristics but voucher users are positively selected on unmeasured factors.
Schizophrenia EEG Signal Classification Based on Swarm Intelligence Computing

One of the serious mental disorders where people interpret reality in an abnormal state is schizophrenia. A combination of extremely disordered thinking, delusion, and hallucination is caused due to schizophrenia, and the daily functions of a person are severely disturbed because of this disorder. A wide range of problems are caused due to schizophrenia such as disturbed thinking and behaviour. In the field of human neuroscience, the analysis of brain activity is quite an important research area. For general cognitive activity analysis, electroencephalography (EEG) signals are widely used as a low-resolution diagnosis tool. The EEG signals are a great boon to understand the abnormality of the brain disorders, especially schizophrenia. In this work, schizophrenia EEG signal classification is performed wherein, initially, features such as Detrend Fluctuation Analysis (DFA), Hurst Exponent, Recurrence Quantification Analysis (RQA), Sample Entropy, Fractal Dimension (FD), Kolmogorov Complexity, Hjorth exponent, Lempel Ziv Complexity (LZC), and Largest Lyapunov Exponent (LLE) are extracted initially. The extracted features are, then, optimized for selecting the best features through four types of optimization algorithms here such as Artificial Flora (AF) optimization, Glowworm Search (GS) optimization, Black Hole (BH) optimization, and Monkey Search (MS) optimization, and finally, it is classified through certain classifiers. The best results show that, for normal cases, a classification accuracy of 87.54% is obtained when BH optimization is utilized with Support Vector Machine-Radial Basis Function (SVM-RBF) kernel, and for schizophrenia cases, a classification accuracy of 92.17% is obtained when BH optimization is utilized with SVM-RBF kernel.
Evaluation of the Antimicrobial Activity of Caesalpinia pulcherrima (L) Swartz Extract against Microbes that Cause Dental and Oral Infections and Determination of the Total Flavonoid and Total Phenolic Contents of the Plant

In Indonesia, Caesalpinia pulcherrima (L) Swartz is widely grown as an ornamental, whereas it is used as a medicinal herb in Mexico as an alternative treatment for dental and oral infections. At present, only fruit and root parts of the plant are used. The aim of this study was is evaluate the anti-microbial activity of ethanol extract of fruit, leaves, flowers and stems against microbes that cause dental and oral infections and determination of the total flavonoid and total phenolic contents of C. pulcherrima (L) Swartz. Porphyromonas gingivalis, Sterptococcus mutans, Enterococcus faecalis and Candida albicans are microbes that cause dental and oral infections. All parts of the plant were extracted by maceration using 70% ethanol for 24 hours at 150-300C, and extracts were concentrated using a reflux method and dried over a water bath. The total flavonoid contents were determined using the aluminium chloride colorimetric assay at 415 nm. The total phenolic content was determined using Folin–Ciocalteu reagent in a 1:4 ratio at a wavelength of 750 nm using a microplate reader. Antimicrobial activity was determined by the diffusion method. The total flavonoid content was expressed as milligram quercetin equivalent (QE) per gram of plant extract. The highest total flavonoid content per gram of plant extract was found in the flowers (10.06 ± 0.08 mg QE/g), and the lowest total content was found in the leaves (0.34 ± 0.02 mg QE/g). The highest phenolic content was also found in the flowers (498.52 ± 1.96 mg gallic acid equivalent [GAE]/g), and the lowest total phenolic content was detected in the leaves (216.76 ± 1.00 mg GAE/g). A 100% crude ethanol extract of the flower and fruit parts exhibited antimicrobial activity against bacteria P. gingivalis, S. mutans, E. faecalis and C. albicans) that cause dental and oral infections. A 2% crude flower extract showed the highest antimicrobial activity against P. gingivalis (14.49 ± 0.465 mm), S. mutans (9.02 ± 0.607 mm), E. faecalis (9.67 ± 0.297 mm) and C. albicans (19.44 ± 0.207 mm). The ethanol extract of the flowers had the highest contents of total flavonoids and total phenols and the most antimicrobial activity against the studied compared to the other parts. This results of the present study revealed valuable information and also support the continued sustainable use of C. pulcherrima (L) Swartz in a traditional system of medicine
Turn Back Elevation of Once Reduced IOP After Trabeculotomy Ab Externo and Kahook Dual Blade Surgeries Combined with Cataract Surgery

Purpose To evaluate the surgical outcome of internal trabeculectomy by Kahook dual blade (KDB) with that of external trabeculotomy, each combined with phaco-lensectomy and intraocular lens implantation (Phaco). Patients and Methods This is a retrospective comparative study. The primary and secondary outcome measures are postsurgical intraocular pressure and postsurgical hyphema. One eye each of 76 primary open angle glaucoma (POAG), pseudoexfoliation glaucoma (PEG) and ocular hypertension (OH) patients underwent external phaco-trabeculotomy, and that of 40 POAG, PEG and OH patients underwent phaco-KDB surgery. Results Reduction of the intraocular pressure (IOP) by phaco-KDB at one and two years was 28.4 and 27.8%, respectively, and was not significantly different from that by external phaco-trabeculotomy of 32.7% (P=0.256) and 31.5% (P=0.468), respectively. Three months postsurgical IOP after phaco-KDB and external phaco-trabeculotomy was 16.1 and 15.9 mmHg, respectively. There was a significant turn back elevation of once reduced IOP to 17.1 (P=0.0207) and 17.0 mmHg (P=0.0096) at 24 months, respectively. There were no differences in success probability to achieve IOP below 17 mmHg (P=0.120), 21 mmHg (P=0.719) and >20% IOP reduction (P=0.309) with medication(s) at two years between the phaco-KDB and external phaco-trabeculotomy cohorts. Younger age was a significant (P<0.001) risk factor for failure; however, presurgical IOP (P=0.466), the type of surgery (P=0.219) and presence of postsurgical IOP spike (P=0.737) were not significant risk factors by the Cox proportional hazard model. Hyphema and spike of the IOP in phaco-KDB and external phaco-trabeculotomy cohorts were 40% and 88% (P<0.001), and 53% and 41% (P=0.238), respectively. Conclusion The IOP reduction by the phaco-KDB was equivalent to that by external phaco-trabeculotomy up to two years. In both cohorts, once reduced postsurgical IOP tend to increase up to 24 months.
Research Progress on the Anti-Cancer Molecular Mechanisms of Huaier

Abstract Huaier (Trametes robiniophila Murr), a Chinese traditional herb of medicine, has demonstrated promising curative effects in clinical treatment for various tumors. There are documented experiments showing the biological functions of Huaier with its antineoplastic molecular mechanisms: restraining proliferation and metastasis, arresting cell cycle, inducing apoptosis, pyrosis, and autophagy, anti-intratumoral angiogenesis, attenuating characteristics of tumor stem-like cells, interfering with the function of the tumor-related immune system, reversing drug resistance, and enhancing the sensitivity to chemotherapeutic drugs, etc. In addition, studies suggest that non-coding RNA (ncRNA) acts a pivotal part in cancer occurrence and development, and demonstrates that Huaier adjusts the performance of certain lncRNA (long non-coding RNA) and proceeds to affect the microRNA and its target genes, rendering an anti-tumor effect. Huaier also modulates the expression of lncRNA to attenuate the activity of ncRNA-sponged microRNA and then inhibits the expression of downstream target genes. We summarize and illustrate the experimentally confirmed anti-cancer molecular mechanisms of Huaier, to inspire new ideas for researchers in relevant fields.
Post-Fundamentals Drift in Stock Prices: A Regression Regularization Perspective

Regression regularization techniques show that deviations of accounting fundamentals from their preceding moving averages forecast drifts in equity market prices. The deviations-based predictability survives a comprehensive set of prominent anomalies. The profitability applies strongly to the long-leg and survives value-weighting and excluding microcaps. We provide evidence that the predictability arises because investors anchor to recent means of fundamentals. A factor based on our fundamentals-based index yields economically significant intercepts after controlling for a comprehensive set of other factors, including those based on profit margins and earnings drift.
Distributive Leadership Within an Emerging Network of Integrated Youth Health Centres: A Case Study of Foundry

Background: Distributive leadership has been proposed as an effective means towards achieving integrated health services. This study draws from the case of Foundry, a network of integrated youth health centres in British Columbia, Canada, and explores the function and impact of distributive leadership in the context of a large-scale effort towards integrated service delivery for youth experiencing mental health and substance use challenges. Methods: Qualitative data was obtained from a developmental evaluation of Foundry using a longitudinal, ethnographic approach. Over 150 participants involved in the development of six Foundry centres were interviewed individually or in focus groups. Purposive and theoretical sampling strategies were used to maximize the diversity of perspectives represented in the data set. Results and Discussion: Distributive leadership was observed to be a facilitator for achieving service and system-level integration. Distributive leadership was effective in promoting streamlined service provision, and coordinating efforts towards optimized access to care. A new culture of leadership emerged through collaboration and relationship-building based on a common value system to prioritize youth needs. Conclusion: As Foundry, and other integrated youth services, continues to expand, distributive leadership shows promise in assuring diverse and coordinated input for integrating services.
Heritable gene expression variability governs clonal heterogeneity in circadian period

A ubiquitous feature of circadian clocks across life forms is its organization as a network of coupled cellular oscillators. Individual cellular oscillators of the network often exhibit a considerable degree of heterogeneity in their intrinsic periods. While the interaction of coupling and heterogeneity in circadian clock networks is hypothesized to influence clock’s entrainability, our knowledge of mechanisms governing network heterogeneity remains elusive. In this study, we aimed to explore the principles that underlie inter-cellular period variation in circadian clock networks (clonal period-heterogeneity). To this end, we employed a laboratory selection approach and derived a panel of 25 clonal cell populations exhibiting circadian periods ranging from 22 h to 28 h. We report that while a single parent clone can produce progeny clones with a wide distribution of circadian periods, heterogeneity is not entirely stochastically driven but has a strong heritable component. By quantifying the expression of 20 circadian clock and clock-associated genes across our panel, we found that inheritance of different expression patterns in at least three clock genes might govern clonal period-heterogeneity in circadian clock networks. Furthermore, we provide preliminary evidence suggesting that epigenetic variation might underlie such gene expression variation.
Study of the Properties of a Biodegradable Polymer Filled with Different Wood Flour Particles

Lignocellulosic wood flour particles with three different sizes were used to reinforce Solanyl® type bioplastic in three compositions (10, 20, and 30 wt.%) and further processed by melt-extrusion and injection molding to simulate industrial conditions. The wood flour particles were morphologically and granulometric analyzed to evaluate their use as reinforcing filler. The Fuller method on wood flour particles was successfully applied and the obtained results were subsequently corroborated by the mechanical characterization. The rheological studies allowed observing how the viscosity was affected by the addition of wood flour and to recover information about the processing conditions of the biocomposites. Results suggest that all particles can be employed in extrusion processes (shear rate less than 1000 s−1). However, under injection molding conditions, biocomposites with high percentages of wood flour or excessively large particles may cause an increase in defective injected-parts due to obstruction of the gate in the mold. From a processing point of view and based on the biocomposites performance, the best combination resulted in Solanyl® type biopolymer reinforced with wood flour particles loaded up to 20 wt. % of small and medium particles size. The obtained biocomposites are of interest for injected molding parts for several industrial applications.
RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow

RNA-Seq enables the identification and quantification of RNA molecules, often with the aim of detecting differentially expressed genes (DEGs). Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data’s computational analysis. On top of that, previous studies proved the irreproducibility of RNA-Seq studies. Here, we present a portable, scalable, and parallelizable Nextflow RNA-Seq pipeline to detect DEGs, which assures a high level of reproducibility. The pipeline automatically takes care of common pitfalls, such as ribosomal RNA removal and low abundance gene filtering. Apart from various visualizations for the DEG results, we incorporated downstream pathway analysis for common species as Homo sapiens and Mus musculus. We evaluated the DEG detection functionality while using qRT-PCR data serving as a reference and observed a very high correlation of the logarithmized gene expression fold changes.
Trabectedin Plus Radiotherapy for Advanced Soft-Tissue Sarcoma: Experience in Forty Patients Treated at a Sarcoma Reference Center

Simple Summary Active therapeutic options in advanced sarcomas, able to induce durable objective responses, are scarce beyond first line. New strategies for disease and symptomatic control are thus needed. Our aim was to analyze the activity of the combination of trabectedin and palliative radiotherapy in the real-life setting, in patients with pretreated metastatic sarcoma. Our findings on 40 pretreated metastatic soft-tissue sarcoma patients, in terms of objective responses (overall response rate by RECIST of 32.5%) and outcome (median progression-free survival of 7.5 months and median overall survival of 23.5 months), confirm the activity of this regimen, which is a valuable option to consider, especially in patients in which a dimensional response could help for symptomatic control. Abstract Symptomatic control and tumoral shrinkage is an unmet need in advanced soft-tissue sarcoma (STS) patients beyond first-line. The combination of trabectedin and radiotherapy showed activity in a recently reported clinical trial in this setting. This retrospective series aims to analyze our experience with the same regimen in the real-life setting. We retrospectively reviewed advanced sarcoma patients treated with trabectedin concomitantly with radiotherapy with palliative intent. Growth-modulation index (GMI) was calculated as a surrogate of efficacy. Forty metastatic patients were analyzed. According to RECIST, there was one (2.5%) complete response, 12 (30%) partial responses, 18 (45%) disease stabilizations, and nine (22.5%) progressions. After a median follow-up of 15 months (range 2–38), median progression-free survival (PFS) and overall survival (OS) were 7.5 months (95% CI 2.8–12.2) and 23.5 months (95% CI 1.1–45.8), respectively. Median GMI was 1.42 (range 0.19–23.76), and in 16 (53%) patients, it was >1.33. In patients with GMI >1.33, median OS was significantly longer than in those with GMI 0–1.33 (median OS 52.1 months (95% CI not reached) vs. 8.9 months (95% CI 6.3–11.6), p = 0.028). The combination of trabectedin plus radiotherapy is an active therapeutic option in patients with advanced STS, especially when tumor shrinkage for symptomatic relief is needed.