Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of Selenoprotein Genes and Association with Selenium Status in Colorectal Adenoma and Colorectal Cancer

Dietary selenium (Se) intake is essential for synthesizing selenoproteins that are important in countering oxidative and inflammatory processes linked to colorectal carcinogenesis. However, there is limited knowledge on the selenoprotein expression in colorectal adenoma (CRA) and colorectal cancer (CRC) patients, or the interaction with Se status levels. We studied the expression of seventeen Se pathway genes (including fifteen of the twenty-five human selenoproteins) in RNA extracted from disease-normal colorectal tissue pairs, in the discovery phase of sixty-two CRA/CRC patients from Ireland and a validation cohort of a hundred and five CRC patients from the Czech Republic. Differences in transcript levels between the disease and paired control mucosa were assessed by the Mann-Whitney U-test. GPX2 and TXNRD3 showed a higher expression and GPX3, SELENOP, SELENOS, and SEPHS2 exhibited a lower expression in the disease tissue from adenomas and both cancer groups (p-values from 0.023 to <0.001). In the Czech cohort, up-regulation of GPX1, SELENOH, and SOD2 and down-regulation of SELENBP1, SELENON, and SELENOK (p-values 0.036 to <0.001) was also observed. We further examined the correlation of gene expression with serum Se status (assessed by Se and selenoprotein P, SELENOP) in the Irish patients. While there were no significant correlations with both Se status markers, SELENOF, SELENOK, and TXNRD1 tumor tissue expression positively correlated with Se, while TXNRD2 and TXNRD3 negatively correlated with SELENOP. In an analysis restricted to the larger Czech CRC patient cohort, Cox regression showed no major association of transcript levels with patient survival, except for an association of higher SELENOF gene expression with both a lower disease-free and overall survival. Several selenoproteins were differentially expressed in the disease tissue compared to the normal tissue of both CRA and CRC patients. Altered selenoprotein expression may serve as a marker of functional Se status and colorectal adenoma to cancer progression.
Ergosterol interacts with Sey1p to promote atlastin‐mediated endoplasmic reticulum membrane fusion in Saccharomyces cerevisiae

Sterols play critical roles in various membrane fusion events, including soluble NSF attachment protein receptor‐mediated membrane fusion, mainly by modulating the physical properties of biologic membranes; however, it remains unclear whether they also function in atlastin‐mediated endoplasmic reticulum (ER) membrane fusion. Although ergosterol, the major sterol in yeast, is essential for fusion of Sey1p (yeast atlastin)‐containing liposomes with an ER‐mimicking lipid composition, fusion of phosphatidylcholine/phosphatidylserine liposomes does not require sterols. Here, we examined whether sterols are important for Sey1p‐mediated ER fusion in Saccharomyces cerevisiae using an in vitro ER fusion assay with isolated yeast ER microsomes. Ergosterol‐specific ligands inhibited microsome fusion, indicating that ergosterol is critical for ER fusion. However, microsomes isolated from yeast strains lacking genes that encode enzymes involved in synthesis of ergosterol from lanosterol still fused, suggesting that other sterols can replace ergosterol and support Sey1p‐mediated ER fusion. Importantly, disruption of sterol‐binding motifs in the transmembrane regions of Sey1p markedly reduced ER fusion. Sey1p physically interacted with Erg11p and Erg4p, which function in ergosterol biosynthesis, suggesting that Sey1p recruits ergosterol‐synthesizing enzymes to fusion sites and thereby enriches ergosterol, which, in turn, may recruit more Sey1p. This positive feedback loop may facilitate ER membrane fusion by concentrating fusion factors at fusion sites. —Lee, M. , Moon, Y. , Lee, S. , Lee, C. , Jun, Y. Ergosterol interacts with Sey1p to promote atlastin‐mediated endoplasmic reticulum membrane fusion in Saccharomyces cerevisiae. FASEB J. 33, 3590–3600 (2019). www.fasebj. org
Coriander essential oil and linalool – interactions with antibiotics against Gram‐positive and Gram‐negative bacteria

The aim of this study was to evaluate the antibacterial activity of coriander essential oil and its major constituent, linalool, in combination with antibiotics against Gram‐positive (methicillin‐susceptible and methicillin‐resistant Staphylococcus aureus, S. epidermidis) and Gram‐negative bacteria (Pseudomonas aeruginosa, Escherichia coli). The chemical composition of coriander essential oil was analyzed by gas chromatography with flame ionization and mass spectrometry detection. The antibacterial activity of coriander essential oil, linalool and their combinations with antibiotics were assessed by the broth microdilution and checkerboard assays respectively. Thirty‐four compounds were identified in coriander essential oil, linalool (70·11%) being predominant. Coriander essential oil and linalool showed synergistic interactions with antibiotics (oxacillin, amoxicillin, gentamicin, ciprofloxacin, tetracycline) against both Gram‐positive and Gram‐negative bacteria. In these synergistic combinations, minimum inhibitory concentrations of antibiotics were markedly reduced; even antibiotic resistance reversal activity was recorded. These findings are very promising for the development of new therapeutic options for bacterial infections.
Re-Identification With Consistent Attentive Siamese Networks

We propose a new deep architecture for person re-identification (re-id). While re-id has seen much recent progress, spatial localization and view-invariant representation learning for robust cross-view matching remain key, unsolved problems. We address these questions by means of a new attention-driven Siamese learning architecture, called the Consistent Attentive Siamese Network. Our key innovations compared to existing, competing methods include (a) a flexible framework design that produces attention with only identity labels as supervision, (b) explicit mechanisms to enforce attention consistency among images of the same person, and (c) a new Siamese framework that integrates attention and attention consistency, producing principled supervisory signals as well as the first mechanism that can explain the reasoning behind the Siamese framework’s predictions. We conduct extensive evaluations on the CUHK03-NP, DukeMTMC-ReID, and Market-1501 datasets and report competitive performance.
Downregulation of PIM1 regulates glycolysis and suppresses tumor progression in gallbladder cancer

Background PIM1, a serine/threonine kinase, plays an essential role in tumorigenesis of multiple types of tumors. However, the expression pattern and functions of PIM1 in gallbladder cancer (GBC) remain largely unknown. Materials and methods Immunohistochemistry, quantitative real-time PCR, and western blot analysis were performed to measure the expression of PIM1. Tissue microarray analysis was used to confirm the relationship between PIM1 expression and clinical outcomes of GBC patients. Finally, in vivo and in vitro functional studies were performed to detect the inhibition of PIM1 by RNAi or specific inhibitor in GBC cells. Results We observed that PIM1 was dramatically overexpressed in GBC tissues, and its expression levels were positively related with clinical malignancies and a poor prognosis. Inhibition of PIM1 via RNAi or enzyme-specific inhibitor could suppress GBC cell proliferation, migration, and invasion both in vitro and vivo. Additionally, flow cytometry assays and cell cycle assays indicated that PIM1 inhibition promoted cell apoptosis and induced cell cycle arrest. Remarkably, inhibition of PIM1 could drive a metabolic shift from aerobic glycolysis to oxidative phosphorylation. We found that inhibition of PIM1 mechanistically reduced glucose consumption by regulating key molecules in aerobic glycolysis. Conclusion PIM1 may serve as an oncogene in GBC and be involved in the regulation of glycolysis. PIM1 is a promising therapeutic target for the treatment of human GBC.
Long-term intake of vegetables and fruits and subjective cognitive function in US men

Objective To evaluate the prospective association of long-term intake of vegetables and fruits with late-life subjective cognitive function (SCF). Methods Among 27,842 men with a mean age of 51 years in 1986, we used multinomial logistic regression to examine the relation of vegetable and fruit consumption to future SCF. Average dietary intake was calculated from 5 repeated food frequency questionnaires collected every 4 years until 2002. SCF score was assessed twice (2008 and 2012) using a 6-item questionnaire; validity was supported by strong associations with APO ε4 genotype. We categorized the average of the 2 scores as good, moderate, and poor SCF. Results Higher intakes of total vegetables, total fruits, and fruit juice were each significantly associated with lower odds of moderate or poor SCF after controlling for major nondietary factors and total energy intake. The association with total fruit intake was weaker after further adjusting for major dietary factors. In this model, the multivariate odds ratios (95% confidence intervals) for vegetable intake (top vs bottom quintile) were 0.83 (0.76–0.92), p trend <0.001 for moderate SCF and 0.66 (0.55–0.80), p trend <0.001 for poor SCF. For orange juice, compared to <1 serving/mo of intake, daily consumption was associated with a substantially lower odds of poor SCF (0.53 [0.43–0.67], p trend <0.001). Higher consumption of vegetables and fruits 18 to 22 years before SCF assessment was associated with lower odds of poor SCF independent of more proximal intake. Conclusion Our findings support a long-term beneficial role of vegetable, fruit, and orange juice consumption on SCF.
IoT-Based Strawberry Disease Prediction System for Smart Farming

Crop diseases cannot be accurately predicted by merely analyzing individual disease causes. Only through construction of a comprehensive analysis system can users be provided with predictions of highly probable diseases. In this study, cloud-based technology capable of handling the collection, analysis, and prediction of agricultural environment information in one common platform was developed. The proposed Farm as a Service (FaaS) integrated system supports high-level application services by operating and monitoring farms as well as managing associated devices, data, and models. This system registers, connects, and manages Internet of Things (IoT) devices and analyzes environmental and growth information. In addition, the IoT-Hub network model was constructed in this study. This model supports efficient data transfer for each IoT device as well as communication for non-standard products, and exhibits high communication reliability even in poor communication environments. Thus, IoT-Hub ensures the stability of technology specialized for agricultural environments. The integrated agriculture-specialized FaaS system implements specific systems at different levels. The proposed system was verified through design and analysis of a strawberry infection prediction system, which was compared with other infection models.
Exploiting serological data to understand the epidemiology of bluetongue virus serotypes circulating in Libya

Abstract The epidemiological patterns of Bluetongue (BT) in North Africa and Mediterranean Basin (MB) dramatically changed by emergence of subsequent episodes of novel bluetongue virus (BTV) serotypes with highly pathogenic indexes and socio‐economic impacts. The objective of the study was to investigate the sero‐prevalence and serotype distribution of BTV in Libya. During 2015‐2016, a total of 826 serum samples were collected from domestic ruminants in Libya. All sera were assayed by competitive enzyme‐linked immunosorbent assays (c‐ELISA). C‐Elisa‐positive samples (43.3%; 173/400) were further analyzed by virus neutralization assay to identify BTV serotypes and determine the antibody titre of positive samples. An overall BTV sero‐prevalence was 48.4% (95% CI: 45.0%‐51.8%). Neutralizing antibodies were detected against the following BTV serotypes namely: BTV‐1, BTV‐2, BTV‐3, BTV‐4, BTV‐9 and BTV‐26. While BTV‐1, BTV‐2, BTV‐4 and BTV‐9 circulation was unsurprising as they have been responsible of the last year outbreaks in Northern African Countries, the detection of BTV‐3 and BTV‐26 was definitely new and concerning for the animal health of the countries facing the Mediterranean Basin. It is crucial that European and Northern African authorities collaborate in organizing common surveillance programmes to early detect novel strains or emerging serotypes in order to set up proper preventive measures, and, in case, develop specific vaccines and plan coordinated vaccination campaigns.
Peptide T7-modified polypeptide with disulfide bonds for targeted delivery of plasmid DNA for gene therapy of prostate cancer

Background Vectors are essential for successful gene delivery. In the present study, a tumor-targeting cationic gene vector, known as the disulfide cross-linked arginine-aspartic acid peptide modified by HAIYPRH (T7) peptide (CRD-PEG-T7), was designed for targeted delivery of plasmid DNA (pDNA) for gene therapy of prostate cancer (PCa). Methods The structure of CRD-PEG-T7 was determined and the cellular uptake efficacy, gene transfection efficacy, cytotoxicity, and the targeting effect of the CRD-PEG-T7–plasmid DNA complex were examined. Results The results demonstrated that the CRD-PEG-T7–plasmid DNA complex was nanosized and had a positively charged surface, good cellular uptake efficacy, minimal cytotoxicity, and a dual-targeting effect as compared with the CRD-PEG–plasmid DNA complex. The peptide T7-modifed new delivery system was able to target the highly expressed transferrin receptor (TfR) on tumor cells with an efficiency four-fold higher than that of the non-modified system. Conclusion The results above indicatd that the CRD-PEG-T7–plasmid DNA complex may prove to be a promising gene delivery system targeting bone-metastatic tumor.
Pulmonary impact of titanium dioxide nanorods: examination of nanorod-exposed rat lungs and human alveolar cells

Background Titanium dioxide nanoparticles have numerous applications, resulting in human exposure. Nonetheless, available toxicological and safety data are insufficient regarding aspherical particles, such as rod-shaped nanoparticles. Methods In a combined in vitro–in vivo approach, cultured A549 lung alveolar adenocarcinoma cells were treated with approximately 15×65 nm TiO2 nanorod-containing medium, while young adult rats received the same substance by intratracheal instillation for 28 days in 5 and 18 mg/kg body-weight doses. Nanoparticle accumulation in the lungs and consequent oxidative stress, cell damage, and inflammation were assessed by biochemical and histopathological methods. Results Titanium was detected in tissue samples by single-particle inductively coupled plasma mass spectrometry. Nanoparticles were visualized inside cultured A549 cells, within pulmonary macrophages, and in hilar lymph nodes of the rats. A549 cells showed dose-dependent oxidative stress and lethality, and the observed nanoparticle-laden endosomes suggested deranged lysosomal function and possible autophagy. Strongly elevated Ti levels were measured in the lungs of nanorod-treated rats and moderately elevated levels in the blood of the animals. Numerous cytokines, indicating acute and also chronic inflammation, were identified in the lung samples of TiO2-exposed rodents. Conclusion Several signs of cell and tissue damage were detected in both the cultured alveolar cells and in treated rats’ lungs. Rod-shaped nanoparticulate TiO2 may consequently be more harmful than has generally been supposed. The occupational health risk suggested by the results calls for improved safety measures.
A Systematic Mapping Review of Memory Leak Detection Techniques

Numerous problems investigated in Software Aging and Rejuvenation (SAR) research are also of interest of other research communities. One of these problems is memory leak detection, which is one of the most recurrent topic in the SAR literature in its twenty-three years. Due to this major interest of SAR researchers on memory leak detection techniques, naturally a question emerges: how other areas deal with this problem? To answer this question we surveyed the main scientific digital libraries, from 1982 to 2017, looking for studies on memory-leak detection that were not originated in the SAR community. We found 105 papers that matched our inclusion and exclusion criteria. Our method was based on the systematic mapping review approach. The empirical findings revealed several intersections of SAR research with studies conducted in other areas, offering interesting insights on different research cooperation opportunities.
Anticoagulant therapies for acute venous thromboembolism among a cohort of patients discharged from Canadian urban and rural hospitals

Objective To determine anticoagulant therapy at hospital discharge for patients with acute venous thromboembolism (VTE) and secondarily, to describe factors affecting choice of therapy. Design A retrospective chart review. Setting Canadian hospitals in Edmonton, Alberta (n=4), Regina, Saskatchewan (n=2) and rural Alberta (n=3) from April 2014 to March 2015. Participants All patients discharged with an acute VTE were screened. Those with atypical clots, another indication for anticoagulation, pregnancy/breast feeding or lifespan <3 months were excluded. Primary and secondary outcomes Primarily, we identified the proportion of patients discharged from hospital with acute VTE that were prescribed either traditional therapy (parenteral anticoagulant±warfarin) or a direct oral anticoagulant (DOAC). Secondarily, management based on setting, therapy choice based on deep vein thrombosis (DVT) versus pulmonary embolism (PE), clot burden and renal function was compared. DOAC dosing was assessed (when prescribed), length of hospital stay based on therapy was compared and planned follow-up in the community was described. Results Among the 695 patients included, most were discharged following a diagnosis of PE (82.9%) on traditional therapy (parenteral anticoagulant±warfarin) (70.2%) with follow-up by either a family doctor (51.5%) or specialist/clinic (46.9%) postdischarge. Regional variation was most evident between urban and rural sites. Of those prescribed a DOAC (28.3%), the majority were dosed appropriately (85.8%). DOAC use did not differ between those with DVT and PE, was proportionately higher for less severe clots and declined with worsening renal function. Patients prescribed DOACs versus traditional therapy had a shorter length of stay (4 vs 7 days, respectively). Conclusions Uptake of DOAC therapy for acute VTE was modest and may have been influenced by the timing of the audit in relation to the approval of these agents for this indication. Future audits should occur to assess temporal changes and ongoing appropriateness of care delivery.
Tissue‐engineered nanoclay‐based 3D in vitro breast cancer model for studying breast cancer metastasis to bone

Breast cancer (BrCa) preferentially spreads to bone and colonises within the bone marrow to cause bone metastases. To improve the outcome of patients with BrCa bone metastasis, we need to understand better the mechanisms underlying bone metastasis. Researchers have relied heavily upon in vivo xenografts due to limited availability of human bone metastasis samples. A significant limitation of these is that they do not have a human bone microenvironment. To address this issue, we have developed a nanoclay‐based 3D in vitro model of BrCa bone metastasis using human mesenchymal stem cells (MSCs) and human BrCa cells mimicking late stage of BrCa pathogenesis at the metastatic site. This 3D model can provide a microenvironment suitable for cell–cell and cell–matrix interactions whilst retaining the behaviour of BrCa cells with different metastasis potential (i.e., highly metastatic MDA‐MB‐231 and low metastatic MCF‐7) as shown by the production of alkaline phosphatase and matrix metalloproteinase‐9. The sequential culture of MSCs with MCF‐7 exhibited 3D tumouroids formation and also occurrence of mesenchymal to epithelial transition of cancer metastasis as evidenced by gene expression and immunocytochemistry. The unique and distinct behaviour of highly metastatic MDA‐MB‐231 and the low metastatic MCF‐7 was observed at the bone metastasis site. The changes to migratory capabilities and invasiveness in MDA‐MB‐231 in comparison with tumour growth with MCF‐7 was observed. Together, a novel bone‐mimetic 3D in vitro BrCa model has been developed that could be used to study mechanisms governing the later stage of cancer pathogenesis in bone.
Risk factors for surgical site infection following lumbar spinal surgery: a meta-analysis

Objective To identify risk factors for surgical site infection (SSI) in patients who had undergone lumbar spinal surgery. Methods Studies published in PubMed, Web of Science, and Embase were systematically reviewed to determine risk factors for SSI following lumbar spinal surgery. Results are expressed as risk ratios (RRs) with 95% CIs and weighted mean difference (WMD) with 95% CI. A fixed-effect or random-effect model was used to pool the estimates according to heterogeneity among the studies included. Results Sixteen studies involving 13,393 patients were included in this meta-analysis. Pooled estimates suggested that diabetes (RR 2.19, 95% CI 1.43–3.36; P<0.001), obesity (RR 2.87, 95% CI 1.62–5.09; P<0.001), BMI (WMD 1.32 kg/m2, 95% CI 0.39–2.25; P=0.006), prolonged operating time (WMD 24.96 minutes, 95% CI 14.77–35.15; P<0.001), prolonged hospital stay (WMD 2.07 days, 95% CI 0.28–3.87; P=0.024), hypertension (RR 1.28, 95% CI 1.08–1.52; P=0.005), and previous surgery (RR 2.06, 95% CI 1.39–3.06; P<0.001) were independent risk factors for SSI in patients who had undergone lumbar spine surgery. Current smoking (RR 0.89, 95% CI 0.75–1.06; P=0.178), American Society of Anesthesiologists grade >2 (RR 2.63, 95% CI 0.84–8.27; P=0.098), increased age (WMD 1.43 years, 95% CI −1.15 to 4.02; P=0.278), COPD (RR 1.21, 95% CI 0.68–2.17; P=0.521), cardiovascular disease (RR 1.63, 95% CI 0.40–6.70; P=0.495), rheumatoid arthritis (RR 1.76, 95% CI 0.53–5.90; P=0.359), and osteoporosis (RR 1.91, 95% CI 0.79–4.63; P=0.152) were not risk factors for postoperative SSI. Conclusion Our results identified several important factors that increased the risk of postoperative SSI. Knowing these risk factors, surgeons could adequately analyze and evaluate risk factors in patients and then develop prevention measurements to reduce the rate of SSI.