Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic analysis of Asian honeybee populations in China reveals evolutionary relationships and adaptation to abiotic stress

Abstract The geographic and biological diversity of China has resulted in the differential adaptation of the eastern honeybee, Apis cerana, to these varied habitats. A. cerana were collected from 14 locations in China. Their genomes were sequenced, and nucleotide polymorphisms were identified at more than 9 million sites. Both STRUCTURE and principal component analysis placed the bees into seven groups. Phylogenomic analysis groups the honeybees into many of the same clusters with high bootstrap values (91%–100%). Populations from Tibet and South Yunnan are sister taxa and together represent the earliest diverging lineage included in this study. We propose that the evolutionary origin of A. cerana in China was in the southern region of Yunnan Province and expanded from there into the southeastern regions and into the northeastern mountain regions. The Cold‐Temperate West Sichuan Plateau and Tropical Diannan populations were compared to identify genes under adaptive selection in these two habitats. Pathway enrichment analysis showing genes under selection, including the Hippo signaling pathway, GABAergic pathway, and trehalose‐phosphate synthase, indicates that most genes under selection pressure are involved in the process of signal transduction and energy metabolism. qRT‐PCR analysis reveals that one gene under selection, the AcVIAAT gene, involved in the GABAergic pathway, is responding to cold temperature stress. Through homologous recombination, we show that the AcVIAAT gene is able to replace the CNAG_01904 gene in the fungus Cryptococcus neoformans and that it makes the fungus less sensitive to conditions of oxidative stress and variations in temperature. Our results contribute to our understanding of the evolutionary origin of A. cerana in China and the molecular basis of environmental adaptation.
Comparative patterns in taxonomic and functional spider diversities between tropical vs. temperate forests

Abstract High diversity in tropical compared to temperate regions has long intrigued ecologists, especially for highly speciose taxa like terrestrial arthropods in tropical rainforests. Previous studies showed that arthropod herbivores account for much tropical diversity, yet differences in the diversity of predatory arthropods between tropical and temperate systems have not been properly quantified. Here, we present the first standardized tropical–temperate forest quantification of spider diversities, a dominant and mega‐diverse taxon of generalist predators. Spider assemblages were collected using a spatially replicated protocol including two standardized sampling methods (vegetation sweep netting and beating). Fieldwork took place between 2010 and 2015 in metropolitan (Brittany) and overseas (French Guiana) French territories. We found no significant difference in functional diversity based on hunting guilds between temperate and tropical forests, while species richness was 13–82 times higher in tropical versus temperate forests. Evenness was also higher, with tropical assemblages up to 55 times more even than assemblages in temperate forests. These differences in diversity far surpass previous estimates and exceed tropical–temperate ratios for herbivorous taxa.
Characteristics and outcomes of hemodialysis patients with COVID-19: a retrospective single center study

Background The coronavirus 19 (COVID-19) pandemic has heightened the threat to the health and lives of patients with comorbid diseases. Infection by COVID-19 is especially detrimental to patients on hemodialysis. In this study, we evaluated the clinical characteristics, laboratory findings, treatments and prognoses of hemodialysis patients with COVID-19. Methods A total of 16 hemodialysis patients with COVID-19 were recruited from Wuhan Fourth Hospital from 5 February to 20 March 2020 for a retrospective, single-center study. A total of 62 non-dialysis patients with COVID-19 were the control group. We collected data on the clinical characteristics, laboratory findings, treatments, and clinical outcomes of patients affected by the virus. Results Hemodialysis patients with COVID-19 had a lower incidence of fever (P = 0.001) and relatively higher incidence of pre-admission comorbidities and shortness of breath than non-dialysis patients with COVID-19 (75% vs. 61%, P = 0.467 50% vs. 33.87%, P = 0.248 ). Hemodialysis patients had lower levels of hemoglobin (P < 0.001), white blood cell counts (P = 0.015), neutrophils (P = 0.016), AST (P = 0.037), ALT (P < 0.001) and procalcitonin (P < 0.001), and higher levels of D-dimer (P < 0.001) and thrombin time (P < 0.001). Hemodialysis patients had a higher incidence of pulmonary effusion, cord-like high-density shadows, pleural thickening, and atelectasis (P < 0.05). Hemodialysis patients also had relatively higher rates of mortality and prolonged hospital stays compared with the control group. Conclusions Hemodialysis patients typically present with multiple comorbidities and are considered to be a high-risk group for COVID-19 infections. Hemodialysis patients with COVID-19 may have prolonged hospital stays and unfavorable prognoses and should be closely monitored.
High levels of human epididymis protein 4 mRNA and protein expression are associated with chemoresistance and a poor prognosis in pancreatic cancer

Pancreatic cancer is associated with an exceedingly poor prognosis, warranting the development of novel therapeutic strategies and discovery of prognostic predictors. Given that chemoresistance-related molecules are reportedly associated with the poor prognosis of pancreatic cancer, the present study aimed to identify molecules that could be efficacious therapeutic targets for pancreatic cancer. First, 10 patient-derived xenografts (PDXs) were established from patients with pancreatic cancer. Subsequently, after treating tumor tissue generated from the PDXs with standard drugs, next-generation sequencing (NGS) was performed using these tissues. The results of NGS analysis and immunohistochemical analysis on 80 pancreatic cancer tissues revealed that human epididymis protein 4 (HE4) expression in the anticancer drug-treated PDX group was higher than that in the untreated PDXs. In addition, chemoresistance ability was observed in tumor cell lines overexpressing HE4. Furthermore, Kaplan-Meier analysis of tumor tissues from 80 patients with pancreatic cancer was performed and it was found that patients with a high HE4 expression level had a poor survival rate compared with those who had a low HE4 expression level. Multivariate analysis also indicated the high expression level of HE4 was an independent poor prognostic biomarker. Thus, it was concluded that high gene and protein expression levels of HE4 mediate chemoresistance and are independent prognostic factors for pancreatic cancer.
The Spectrum of Non-ischemic Cardiac Magnetic Resonance Imaging Findings: A Retrospective Analysis

Introduction Since cardiac pathologies remain ubiquitous, their prompt diagnosis through the means of innovative technologies, such as cardiac magnetic resonance imaging, remains pivotal. The spectrum of these pathologies varies widely, ranging from ischemic etiologies to rare cardiac malignancies. This study evaluates the prevalence of nonischemic cardiac pathologies, such as infiltrative heart diseases, that often warrant meticulous diagnostic evaluation through the means of cardiac magnetic resonance imaging. Methods We performed a retrospective study in order to analyse the cardiac magnetic resonance imaging records of 250 patients over a period of six months with previously remarkable cardiac histories. Patients with a prior history of ischemic cardiac disease, as determined from past medical and surgical records, were excluded from the study. The prevalence of various nonischemic findings was ascertained. The demographic characteristics and comorbidities of the patients were also tabulated. Results In the present study, 250 patients were included, of which 115 were females and 135 were males, with the mean age hovering at 48.21 ± 11.49 years. The top two most prevalent cardiac magnetic resonance imaging findings were concentric moderate-to-severe left ventricular hypertrophy and patchy subendocardial late gadolinium enhancement of the left ventricle; these were observed in 62.2% and 23.7% of the patients, respectively. Cardiac magnetic resonance imaging also divulged findings typical of rarer pathologies, including cardiac sarcoidosis and primary cardiac lymphoma. Conclusion Pathologies of the heart often mandate extensive diagnostic workup through the means of radiological modalities such as cardiac magnetic resonance imaging. In patients with indications of nonischemic cardiac pathologies, cardiac magnetic resonance imaging can be employed as part of the initial radiological armamentarium. Furthermore, cardiac magnetic resonance remains the imaging modality of choice for detecting infrequent cardiac pathologies, such as cardiac sarcoidosis.
A signature of tumor DNA repair genes associated with the prognosis of surgically-resected lung adenocarcinoma

Background Lung cancer has the highest morbidity and mortality of cancers worldwide. Lung adenocarcinoma (LUAD) is the most common pathological subtype of lung cancer and surgery is its most common treatment. The dysregulated expression of DNA repair genes is found in a variety of cancers and has been shown to affect the origin and progression of these diseases. However, the function of DNA repair genes in surgically-treated LUAD is unclear. Methods We sought to determine the association between the signature of DNA repair genes for patients with surgical LUAD and their overall prognosis. We obtained gene expression data and corresponding clinical information of LUAD from The Cancer Genome Atlas (TCGA) database. The differently expressed DNA repair genes of surgically-treated LUAD and normal tissues were identified using the Wilcoxon rank-sum test. We used uni- and multivariate Cox regression analyses to shrink the aberrantly expressed genes, which were then used to construct the prognostic signature and the risk score formula associated with the independent prognosis of surgically-treated LUAD. We used Kaplan–Meier and Cox hazard ratio analyses to confirm the diagnostic and prognostic roles. Two validation sets (GSE31210 and GSE37745) were downloaded from the Gene Expression Omnibus (GEO) and were used to externally verify the prognostic value of the signature. OSluca online database verifies the hazard ratio for the DNA repair genes by which the signature was constructed. We investigated the correlation between the signature of the DNA repair genes and the clinical parameters. The potential molecular mechanisms and pathways of the prognostic signature were explored using Gene Set Enrichment Analysis (GSEA). Results We determined the prognostic signature based on six DNA repair genes (PLK1, FOXM1, PTTG1, CCNO, HIST3H2A, and BLM) and calculated the risk score based on this formula. Patients with surgically-treated LUAD were divided into high-risk and low-risk groups according to the median risk score. The high-risk group showed poorer overall survival than the low-risk group; the signature was used as an independent prognostic indicator and had a greater prognostic value in surgically-treated LUAD. The prognostic value was replicated in GSE31210 and GSE37745. OSluca online database analysis shows that six DNA repair genes were associated with poor prognosis in most lung cancer datasets. The prognostic signature risk score correlated with the pathological stage and smoking status in surgically-treated LUAD. The GSEA of the risk signature in high-risk patients showed pathways associated with the cell cycle, oocyte meiosis, mismatch repair, homologous recombination, and nucleotide excision repair. Conclusions A six-DNA repair gene signature was determined using TCGA data mining and GEO data verification. The gene signature may serve as a novel prognostic biomarker and therapeutic target for surgically-treated LUAD.
Hemorrhagic complications after percutaneous nephrolithotomy: angiographic diagnosis and management by transcatheter arterial embolization

Objective To identify the main hemorrhagic complications after percutaneous nephrolithotomy, as well as the results obtained with transcatheter arterial embolization (TAE) at an interventional radiology center. Materials and Methods This was a retrospective analysis of patients undergoing TAE for the treatment of hemorrhagic complications after percutaneous nephrolithotomy. All patients underwent computed tomography angiography (CTA). Results We evaluated a total of nine patients. At emergency department readmission, the most common symptom was macroscopic hematuria, which was seen in five patients. Three patients had an isolated pseudoaneurysm, two had a pseudoaneurysm together with active bleeding (perirenal hematoma), and one had a pseudoaneurysm together with arteriocalyceal fistula. Arteriovenous fistula was diagnosed in three patients and was not seen in combination with other vascular lesions. We did not identify arteriocalyceal fistula in isolation. Five patients underwent TAE with 6 × 15 mm and 6 × 20 mm microcoils. Four patients underwent TAE with n-butyl-2-cyanoacrylate and ethiodized oil. Follow-up CTAs revealed no complications. Conclusion Because of its high diagnostic accuracy, CTA provides the interventional radiologist with valuable data for individualized therapeutic planning. The TAE procedure is safe and effective. It can therefore be used as a first-line treatment for hemorrhagic complications resulting from percutaneous renal procedures.
QTc-interval prolongation and increased risk of sudden cardiac death associated with hydroxychloroquine

Abstract Aims: Hydroxychloroquine and chloroquine ([hydroxy]chloroquine) are drugs used to treat malaria and rheumatological disorders and were recently suggested as beneficial for prevention and treatment of patients with coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 infection. However, longitudinal studies to assess the electrocardiographic and cardiotoxic effects of these drugs are limited. In this study, we aimed to investigate the effect of these drugs on QTc-interval and incidence of sudden cardiac death (SCD). Methods We designed a longitudinal follow-up study of individuals within the prospective population-based Rotterdam Study. Eligible individuals had available data on medication and repeated ECG measurements. The study period was between 1 January 1991 and 1 January 2014. We studied on current and past use of [hydroxy]chloroquine as a time-varying exposure; high versus low daily dose of [hydroxy]chloroquine. QTc-interval duration, and the occurrence of SCD were the main outcomes. SCD was defined as an unexpected and sudden death due to cardiac arrhythmia within one hour of the onset of acute symptoms, and in patients without cardiac symptoms within 24 hours before death. Results Among the study population of 14 594 individuals (58.8% women) with an average age of 65 years, 346 patients used [hydroxy]chloroquine at any time during follow-up. The total number of SCD cases was 609. In a multiple linear mixed model analysis, the current use of [hydroxy]chloroquine was associated with a significantly increased duration of the QTc-interval of 8.1 ms (95% CI: 3.6; 12.6) compared with non-users. The association was stronger among current-high daily dosage [15.3 (95%CI: 7.0; 23.6)] compared with current-low daily dosage [5.5 (95%CI: 0.4; 10.7)] users. In a Cox proportional hazard regression analysis, the risk of SCD was significantly higher in participants who were current users of [hydroxy]chloroquine than in non-users [adjusted hazard ratio; 3.7 (95%CI: 1.1; 12.6)]. Conclusions In this longitudinal study, persons who received [hydroxy]chloroquine had an increased QTc-interval duration and the association was dose-dependent. [Hydroxy]chloroquine was associated with a significantly increased risk of SCD. As long as their activity against COVID-19 is controversial, cardiotoxicity is a strong argument against using these drugs to treat COVID-19 infections.
Volatile composition and nutritional quality of the edible mushroom Polyporus tenuiculus grown on different agro-industrial waste.

Summary The volatile composition and the nutritional value of Polyporus tenuiculus grown on supplemented and nonsupplemented wheat straw and willow sawdust were determined. Thirty-nine volatile compounds were detected, including acids, esters, alcohols, hydrocarbons, aldehydes and ketones. The main volatile compound in all samples was 1-octen-3-ol, with increasing levels in mushrooms cropped on supplemented substrate. In addition, several precursors of this alcohol were identified in lower percentages. Mushrooms grown on supplemented substrates showed lower fat (5.2–5.7%) and carbohydrate contents (48.2%) and higher protein content (22–22.5%). Fibre and ash contents showed some variations between types of substrates. Compared to other edible fungi, P. tenuiculus high fibre and protein contents point to this species as a healthy nutritional alternative of interest for the food industry. Moreover, the wide spectrum of volatile compounds of P. tenuiculus reveals great potential for biotechnological applications such as the production of “non artificial” mushroom flavour.
Rearrangement Reactions for the Synthesis of Some Oxa- and Aza-tricyclic Rings Heterocyclic Compounds

This review article describes the main results of our research during the last 5-6 years. A series of new rearrangement reactions was discovered and used for the synthesis of novel heterocyclic compounds: furo[2,3-f]isoquinolines, furo[3,2 -f] quinolines, benzo[c]xanthene, benzo[h]chromene, benzo[a]xanthene, benzo[f]chromene, furo[2,3-f]isoquinoline, spirofuro[3,2-f]quinoline, cycloalkanoindoles, and benzotriazines.
Contact angles on quartz induced by adsorption of heteropolar hydrocarbons

The wetting behavior induced by the adsorption of crude oil components onto mineral substrates initially covered with brine is of special importance to petroleum engineering. The wettability of reservoir rock is a controlling factor in the efficiency of oil recovery from the swept zone of a waterflood. The effect of the adsorption of polar components from crude oil on the wetting properties of quartz plates was investigated by the dynamic Wilhelmy plate technique. Force-distance relationships were measured for treated quartz plates passing through oleic-aqueous interfaces. Water receding and advancing contact angles under dynamic conditions were obtained. Changes in the wetting of the quartz plate from a completely water-wet state were induced by adsorption from crude oil or solutions of its components. Different wetting states were developed by varying the oil composition, aqueous phase pH. temperature, time of adsorption, the solvents used to remove excess crude oil, and the probe oil used in contact angle measurements. Some important features of wetting, contact angle hysteresis and slippage of the three-phase contact line, are presented. Organic films adsorbed from the crude oil were examined by atomic force microscopy.
Kinetics of the dissolution of ilmenite in oxalic and sulfuric acid solutions

In this study, the effects of particle size, type and concentration of acid solution on dissolution kinetics of ilmenite are investigated. The results showed that both oxalic and sulfuric acid and their concentrations had relatively high effects on the dissolution rate of titanium, which increased with an increase in acid concentration. About 86.4% of titanium could be leached in 10 h when using 4 M oxalic acid, 1 : 20 solid/liquid ratio, 90 °C temperature and particle size less than 45 µm. Under similar experimental conditions with the exception of sulfuric acid concentrations of 4, 8 and 12 M, the titanium solubilization was 16.1%, 48.2% and 52.0%, respectively. The experimental data followed reaction kinetics and indicated that the shrinking particle model controlled the chemical reaction. The observed titanium dissolution rates could be expressed as 1 − (1 − x)1/3 = 0.0092C1. 2022t for oxalic acid for concentration varying between 1 and 4 M and 1 − (1 − x)1/3 = 0.0006C1. 5977t for sulfuric acid for concentration varying between 2 and 12 M, respectively. The fitted models for estimating the titanium dissolution rate from the experimental data indicated good accuracy with coefficient of determination (R2) higher than 0.96. © 2013 Curtin University of Technology and John Wiley & Sons, Ltd.
Direct stochastic optical reconstruction microscopy (dSTORM) imaging of cellular structures

The diffraction limit restricts conventional light microscopes to approximately 250 nm laterally and 500 nm axially, these limits being first proposed by Abbe in 1873. Despite this, optical microscopes have found many applications in biological research and single cells that are 10 - 100 um in size. Furthermore by coupling the non-invasive nature of a light microscope with highly sensitive fluorescent probes, fluorescence microscopy has also become a standard imaging technique. Recent advances in fluorescence microscopy now provide a number of methods to circumvent the Abbe diffraction limit, with many techniques becoming prevalent over the last 10 years including direct Stochastic Optical Reconstruction Microscopy (dSTORM). A dSTORM system has been constructed and calibrated using a commercially available inverted florescence microscope and total internal reflection florescence (TIRF) imaging. dSTORM relies on the ability to switch sparse subsets of fluorophores and temporally separate them. Provided the spatial separation is sufficient between any member of a subset, the average error with which the emission can be localized is much less than size of the emission profile itself. The underlying mechanism for this switching is detailed based on the principle of photoinduced electron transfer (PET). The switching characteristics of the common florescent dye Alexa Fluor 568 are investigated and shown to be controlled by a number of factors including the excitation intensity and concentration of the primary thiol cysteamine beta-MEA. A number of parameters are defined, including the dye switching rate, for a given set of physical parameters. U2OS cells are labelled for the microtubule protein Tubulin using immunofluorescent labelling strategies. A direct comparison is made between diffraction limited TIRF images and dSTORM reconstructed images, with an average width for microtubules determined to (58.2 � 8.1) nm. Further measurements are made by labelling the Rab5 effector Early Endosome Antigen 1 (EEA1). From this the aspect ratio for early endosomes is determined to be 1.68 � 0.7 with an average radius of (45.8 � 18.8) nm. The point spatial distribution of EEA1 is investigated by using the linearised form of Ripley's K-function H(r) and the null hypothesis of complete spatial randomness tested. EEA1 is shown to cluster at radius of 58.7 nm on individual endosomes, thought to be due to the well defined binding domains present on early endosomes for EEA1. Further evidence suggests that clustering is also exhibited at another maximum of approximately 500 nm when looking at an ensemble of EEA1 and early endosomes.