Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of T-cell exhaustion-related genes and prediction of their immunotherapeutic role in lung adenocarcinoma

Background: Lung adenocarcinoma ranks as the second most widespread form of cancer globally, accompanied by a significant mortality rate. Several studies have shown that T cell exhaustion is associated with immunotherapy of tumours. Consequently, it is essential to comprehend the possible impact of T cell exhaustion on the tumor microenvironment. The purpose of this research was to create a TEX-based model that would use single-cell RNA-seq (scRNA-seq) and bulk-RNA sequencing to explore new possibilities for assessing the prognosis and immunotherapeutic response of LUAD patients. Methods: RNA-seq data from LUAD patients was downloaded from the Cancer Genome Atlas (TCGA) database and the National Center for Biotechnology Information (GEO). 10X scRNA sequencing data, as reported by Bischoff P et al., was utilized for down-sampling clustering and subgroup identification using TSNE. TEX-associated genes were identified through gene set variance analysis (GSVA) and weighted gene correlation network analysis (WGCNA). We utilized LASSO-Cox analysis to establish predicted TEX features. External validation was conducted in GSE31210 and GSE30219 cohorts. Immunotherapeutic response was assessed in IMvigor210, GSE78220, GSE35640 and GSE100797 cohorts. Furthermore, we investigated differences in mutational profiles and immune microenvironment between various risk groups. We then screened TEXRS key regulatory genes using ROC diagnostic curves and KM survival curves. Finally, we verified the differential expression of key regulatory genes through RT-qPCR. Results: Nine TEX genes were identified as highly predictive of LUAD prognosis and strongly correlated with disease outcome. Univariate and multivariate analysis revealed that patients in the low-risk group had significantly better overall survival rates compared with those in the high-risk group, highlighting the model's ability to independently predict LUAD prognosis. Our analysis revealed significant variation in the biological function, mutational landscape, and immune cell infiltration within the tumor microenvironment of both high-risk and low-risk groups. Additionally, immunotherapy was found to have a significant impact on both groups, indicating strong predictive efficacy of the model. Conclusions: The TEX model showed good predictive performance and provided a new perspective for evaluating the efficacy of preimmunization, which provides a new strategy for the future treatment of lung adenocarcinoma.
Comment on ‘The influence of geological–morphological and land-use settings on shallow landslides in the Pogliaschina T. basin (northern Apennines, Italy)’ by Bartelletti et al. (2017)

ABSTRACT Bartelletti, Giannecchini, D’Amato Avanzi, Galanti, & Mazzali [(2017). The influence of geological–morphological and land use settings on shallow landslides in the Pogliaschina T. basin (northern Apennines, Italy). Journal of Maps, 13, 142–152] analyse the main features of the landslides triggered by an intense rainstorm in a small basin of northern Apennines (Italy). This comment discusses the assessment of event rainfall and its implications for the interpretation of landslide distribution.
Light-driven methane conversion: unveiling methanol using a TiO2/TiOF2 photocatalyst

A TiO2/TiOF2 composite has been synthesized through a hydrothermal method and characterized using X-ray diffraction, Raman spectroscopy, UV-vis diffuse reflectance, SEM-EDX, TEM, and N2 adsorption–desorption isotherms. The percentage of exposed facet [001] and the composition of TiO2/TiOF2 in the composite were controlled by adjusting the amount of HF and hydrothermal temperature synthesis. Three crucial factors in the photocatalytic conversion of methane to methanol, including the photocatalyst, electron scavenger (FeCl2), and H2O2 were evaluated using a statistical approach. All factors were found to have a significant impact on the photocatalytic reaction and exhibited a synergistic effect that enhanced methanol production. The highest methanol yield achieved was 0.7257 μmole h−1 gcat−1. The presence of exposed [001] and fluorine (F) in the catalyst is believed to enhance the adsorption of reactant molecules and provide a more oxidative site. The Fenton cycle reaction between FeCl2 and H2O2 was attributed to reducing recombination and extending the charge carrier lifetime. Incorporating Ag into the TiO2/TiOF2 catalyst results in a significant 2.2-fold enhancement in methanol yield. Additionally, the crucial involvement of hydroxyl radicals in the comprehensive reaction mechanism highlights their importance in influencing the process of photocatalytic methane-to-methanol conversion.
Routine closed-suction drainage reduces seromas following totally extraperitoneal (TEP) inguinal hernia repair: A meta-analysis

Background: The value of prophylactic closed-suction drainage in totally extraperitoneal inguinal hernia repair (TEP) is still a matter of controversy. We conducted a meta-analysis of studies examining postoperative seroma rates in patients with or without routine placement of closed-suction drainage tubes. Methods: A systematic literature search was conducted for trials comparing the outcome of TEP with or without routine drainage placement. Data regarding postoperative outcomes were extracted and compared by meta-analysis. The odds ratio and standardized mean differences with 95% confidence intervals were calculated. Results: Four studies were identified, involving a total of 1626 cases (Drain: n = 1251, no Drain: n = 375). There was a statistically significant difference noted between the 2 groups regarding postoperative seroma formation favoring the Drain group (odds ratio = 0.12; 95% confidence intervals [0.05, 0.29]; P < .001; 4 studies; I2 = 72%). For the remaining secondary endpoints postoperative urinary retention, recurrence, mesh infection and in-hospital length of stay no statistically significant difference was noted between the 2 study groups. Conclusion: Current evidence suggests that patients who underwent TEP with routine closed-suction drain placement developed significantly fewer seromas without any additional morbidity or prolongation of in-hospital stay.
Field-based molecular detection of Batrachochytrium dendrobatidis in critically endangered Atelopus toads and aquatic habitats in Ecuador

Batrachochytrium dendrobatidis (Bd) is a lethal fungal species that parasitizes vertebrates and is associated with the worldwide decline of amphibian populations. The development of sensitive, rapid detection methods, particularly DNA-based techniques, is critical for effective management strategies. This study evaluates the efficacy of DNA extraction and a portable PCR device in a mountable field laboratory setup for detecting Bd near the habitats of three critically endangered Atelopus toad species in Ecuador. We collected skin swabs from Atelopus balios, A. nanay, and A. bomolochos, and environmental DNA (eDNA) samples from streams in Andean and coastal regions of Ecuador. For eDNA, a comparison was made with duplicates of the samples that were processed in the field and in a standard university laboratory. Our findings revealed Bd detection in eDNA and swabs from 6 of 12 water samples and 10 of 12 amphibian swab samples. The eDNA results obtained in the field laboratory were concordant with those obtained under campus laboratory conditions. These findings highlight the potential of field DNA-based monitoring techniques for detecting Bd in amphibian populations and their aquatic habitats, particularly in remote areas. Furthermore, this research aligns with the National Action Plan for the Conservation of Ecuadorian Amphibians and contributes to the global effort to control this invasive and deadly fungus.
Development of an immune-related diagnostic predictive model for oral lichen planus

Oral lichen planus (OLP) was a chronic inflammatory disease of unknown etiology with a 1.4% chance of progressing to malignancy. However, it has been suggested in several studies that immune system disorders played a dominant role in the onset and progression of OLP. Therefore, this experiment aimed to develop a diagnostic prediction model for OLP based on immunopathogenesis to achieve early diagnosis and treatment and prevent cancer. In this study, 2 publicly available OLP datasets from the gene expression omnibus database were filtered. In the experimental group (GSE52130), the level of immune cell infiltration was assessed using MCPcounter and ssGSEA algorithms. Subsequently, differential expression analysis and gene set enrichment analysis were performed between the OLP and control groups. The resulting differentially expressed genes were intersected with immunologically relevant genes provided on the immunology database and analysis portal database (ImmPort) website to obtain differentially expressed immunologically relevant genes (DEIRGs). Furthermore, the gene ontology and kyoto encyclopedia of genes and genomes analyses were carried out. Finally, protein–protein interaction network and least absolute shrinkage and selection operator regression analyses constructed a model for OLP. Receiver operating characteristic curves for the experimental and validation datasets (GSE38616) were plotted separately to validate the model’s credibility. In addition, real-time quantitative PCR experiment was performed to verify the expression level of the diagnostic genes. Immune cell infiltration analysis revealed a more significant degree of inflammatory infiltration in the OLP group compared to the control group. In addition, the gene set enrichment analysis results were mainly associated with keratinization, antibacterial and immune responses, etc. A total of 774 differentially expressed genes was obtained according to the screening criteria, of which 65 were differentially expressed immunologically relevant genes. Ultimately, an immune-related diagnostic prediction model for OLP, which was composed of 5 hub genes (BST2, RNASEL, PI3, DEFB4A, CX3CL1), was identified. The verification results showed that the model has good diagnostic ability. There was a significant correlation between the 5 hub diagnostic biomarkers and immune infiltrating cells. The development of this model gave a novel insight into the early diagnosis of OLP.
A novel CD8+ T cell-related gene signature as a prognostic biomarker in hepatocellular carcinoma

CD8+ T cells have great roles in tumor suppression and elimination of various tumors including hepatocellular carcinoma (HCC). Nonetheless, potential prognostic roles of CD8+ T cell-related genes (CD8Gs) in HCC remains unknown. In our study, 416 CD8Gs were identified in HCC, which were enriched in inflammatory and immune signaling pathways. Using The Cancer Genome Atlas dataset, a 5-CD8Gs risk model (KLRB1, FYN, IL2RG, FCER1G, and DGKZ) was constructed, which was verified in International Cancer Genome Consortium and gene expression omnibus datasets. Furthermore, we found that overall survival was independently correlated with the CD8Gs signature, and it was associated with immune- and cancer-related signaling pathways and immune cells infiltration. Finally, drug sensitivity data indicated that 10 chemotherapeutic drugs held promise as therapeutics for HCC patients with high-risk. In conclusion, multi-databases analysis showed that 5-CD8Gs and their signature could be an indicator to predict candidate drugs for HCC therapy.
World Journal of Gastrointestinal Endoscopy

Endoscopic ultrasound-guided gastroenterostomy (EUS-GE) has been transformed from an innovative technique, into a viable alternative to enteral stenting and surgical gastrointestinal anastomosis for patients with gastric outlet obstruction. Even EUS-GE guided ERCP and EUS-guided gastrointestinal anastomosis for the treatment of afferent loop syndrome have been performed, giving patients more less invasive options. However, EUS-GE is still a technically challenging procedure. In order to improve EUS-GE, several techniques have been reported to improve the technical details. With EUS-GE widely performed, more data about EUS-GE’s clinical outcomes have been reported. The aim of the current review is to describe technical details updates, clinical outcomes, and adverse events of EUS-GE.
Scholarly Commons @ Baptist Health South Florida Scholarly Commons @ Baptist Health South Florida

Background The Multi-Ethnic Study of Atherosclerosis (MESA) showed that the addition of coronary artery calcium (CAC) to traditional risk factors improves risk classification, particularly in intermediate risk asymptomatic patients with LDL cholesterol levels < 160 mg/dL. However, the cost-effectiveness of incorporating CAC into treatment decision rules has yet to be clearly delineated. Objective To model the cost-effectiveness of CAC for cardiovascular risk stratification in asymptomatic, intermediate risk patients not taking a statin
Behavioral and Brain Functions

Background: Recent research has shown that errors seem to influence the patterns of brain activity. Additionally current notions support the idea that similar brain mechanisms are activated during acting and observing. The aim of the present study was to examine the patterns of brain activity of actors and observers elicited upon receiving feedback information of the actor's response. Methods: The task used in the present research was an auditory identification task that included both acting and observing settings, ensuring concurrent ERP measurements of both participants. The performance of the participants was investigated in conditions of varying complexity. ERP data were analyzed with regards to the conditions of acting and observing in conjunction to correct and erroneous responses. Results: The obtained results showed that the complexity induced by cue dissimilarity between trials was a demodulating factor leading to poorer performance. The electrophysiological results suggest that feedback information results in different intensities of the ERP patterns of observers and actors depending on whether the actor had made an error or not. The LORETA source localization method yielded significantly larger electrical activity in the supplementary motor area (Brodmann area 6), the posterior cingulate gyrus (Brodmann area 31/23) and the parietal lobe (Precuneus/Brodmann area 7/5). Conclusion: These findings suggest that feedback information has a different effect on the intensities of the ERP patterns of actors and observers depending on whether the actor committed an error. Certain neural systems, including medial frontal area, posterior cingulate gyrus and precuneus may mediate these modulating effects. Further research is needed to elucidate in more detail the neuroanatomical and neuropsychological substrates of these systems. Published: 20 January 2009 Behavioral and Brain Functions 2009, 5:5 doi:10.1186/1744-9081-5-5 Received: 26 June 2008 Accepted: 20 January 2009 This article is available from: http://www.behavioralandbrainfunctions. com/content/5/1/5 © 2009 Karanasiou et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Measurement of Cotton Transpiration

There are a few field methods available to directly measure water evapotranspiration (ET) along with its two components, evaporation from the soil (E) and from the crop (T). One such technique that measures T, uses sensors to calculate the sap flow (F) of water through the plant stem and is based on the conservation of mass and energy, i.e., the stem heat balance method. This instrument consists of a flexible heater that is wrapped around the plant stem with temperature sensors to measure the difference in temperature of F below and above the heater. This is a null method, where all inputs and outputs are known and the calculated F is a direct measure of T. This method has been used to measure T in a variety of crops, including cotton, grapes, olive trees, soybean, ornamental and horticultural crops. A new version of the EXO-SkinTM is the Stem Gauge Dual Channel Design (SGDCTM), which was commercially introduced and had a radically new design resulting in a different energy balance, compared to the original design, which needed experimental verification. An initial evaluation was done with potted cotton (Gossypium hirsutum, L.) plants in a greenhouse experiment showing that values of cotton-T measured with the new sensor were accurate; however, this comparison was limited to daily T T in the 2 - 7 mm/d range, representative of the semiarid Texas High Plains. For this purpose, cotton was planted on 12 June 2017 on a 1000 m2 plot in a soil classified in the Amarillo series at the facilities of the USDA-ARS, Lubbock, TX. For a period of 15 days, 2 to 16 Sep 2017, we measured hourly cotton-T with the new sensors and with portable growth chambers (0.75 m × 1 m cross-section, and 1 m height) where water vapor flux was measured at a 10 Hz frequency using an infrared gas analyzer. We used three chambers and, in each chamber, the new sensors were installed on four cotton plants. We used linear regression analysis to compare hourly and daily values of cotton-T measured with the sap flow gauges against T measured by the chambers. Using a t-test (p T for a wide range of environmental conditions.
Who needs education on LGBTQIA+ healthcare inclusion?

ABSTRACT The topic of education on healthcare needs and equity of care for LGBTQIA+ populations is an extremely current issue. There is a demand for education on these topics not only from medical and other health sciences students but also from established healthcare professionals. Given this widespread educational deficiency, it is natural to ask whether the teaching class is prepared to satisfy these requests or in turn needs training on these issues and above all whether it is capable of transmitting attention and sensitivity on the issues of inclusion and equality in needs of healthcare.
The one-carbon metabolism as an underlying pathway for placental DNA methylation – a systematic review

ABSTRACT Epigenetic modifications, including DNA methylation, are proposed mechanisms explaining the impact of parental exposures to foetal development and lifelong health. Micronutrients including folate, choline, and vitamin B12 provide methyl groups for the one-carbon metabolism and subsequent DNA methylation processes. Placental DNA methylation changes in response to one-carbon moieties hold potential targets to improve obstetrical care. We conducted a systematic review on the associations between one-carbon metabolism and human placental DNA methylation. We included 22 studies. Findings from clinical studies with minimal ErasmusAGE quality score 5/10 (n = 15) and in vitro studies (n = 3) are summarized for different one-carbon moieties. Next, results are discussed per study approach: (1) global DNA methylation (n = 9), (2) genome-wide analyses (n = 4), and (3) gene specific (n = 14). Generally, one-carbon moieties were not associated with global methylation, although conflicting outcomes were reported specifically for choline. Using genome-wide approaches, few differentially methylated sites associated with S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), or dietary patterns. Most studies taking a gene-specific approach indicated site-specific relationships depending on studied moiety and genomic region, specifically in genes involved in growth and development including LEP, NR3C1, CRH, and PlGF; however, overlap between studies was low. Therefore, we recommend to further investigate the impact of an optimized one-carbon metabolism on DNA methylation and lifelong health.
The biogenesis and maintenance of photosystem II: recent advances and current challenges.

The growth of plants, algae and cyanobacteria relies on the catalytic activity of the oxygen-evolving photosystem two (PSII) complex which uses solar energy to extract electrons from water to feed into the photosynthetic electron transport chain. PSII is proving to be an excellent system to study how large multi-subunit membrane-protein complexes are assembled in the thylakoid membrane and subsequently repaired in response to photooxidative damage. Here we summarize recent developments in understanding the biogenesis of PSII, with an emphasis on recent insights obtained from biochemical and structural analysis of cyanobacterial PSII assembly/repair intermediates. We also discuss how chlorophyll synthesis is synchronized with protein synthesis and suggest a possible role for photosystem I in PSII assembly. Special attention is paid to unresolved and controversial issues that could be addressed in future research.
Experimental Rearing of the Golden Gray Mullet Liza Aurata (Risso, 1810) in a Recirculating System at the Black Sea

Abstract Recirculating Aquaculture Systems (RAS) used in aquatic research and production are a viable alternative to traditional open-sea mariculture. The rearing of marine living resources in controlled environments is one of NIMRD’s constant concerns. Golden gray mullet Liza aurata (Risso, 1810) is spread in the Mediterranean, Black and Caspian Seas, as well as along the Atlantic coast, and culture in extensive and semi-intensive enclosures has been practiced worldwide for centuries, especially in the Far East and the Mediterranean, reaching a global production of 134,329 tons in 2010. The species’ potential for aquaculture is enhanced by its eurihalyne and eurithermal adaptability, allowing it to grow in a variety of ecosystems. The biological material used for the experiment was represented by golden gray mullet fingerlings fished using the beach seine from the Black Sea. They were monitored for health state, growth rythm (mean length and weight determinations), behavior under RAS conditions, survival rate and overall adaptability. The growth of juveniles after 90 days was 89.2% for total length and 246% for mean biomass. Concerning overall adaptability, after approximately one month, the golden gray mullet individuals fully adapted to rearing in the RAS tanks and handling during measurements. Moreover, the food administered (Skretting Classic K) was easily accepted, active feeding behavior being observed even in the presence of NIMRD’s staff. The fish’s health state was good, with no mortalities caused by infections or parasites. The survival rate upon completion of the two monitoring months was 76.66% (23 of the 30 individuals included in the experiment). The preliminary results obtained showed a good adaptability and a normal growth rate, which makes Liza aurata a potential candidate for aquaculture targeting the national and regional market.