Miracle-dz/UniFAR-FTUs huggingface dataset:
Uptake and speciation of zinc in edible plants grown in smelter contaminated soils

Heavy metal accumulation in edible plants grown in contaminated soils poses a major environmental risk to humans and grazing animals. This study focused on the concentration and speciation of Zn in different edible plants grown in soils contaminated with smelter wastes (Spelter, WV, USA) containing high levels of the metals Zn, Cu, Pb, Cd. Their accumulation was examined in different parts (roots, stem, and leaves) of plants and as a function of growth stage (dry seed, sprouting seed, cotyledon, and leaves) in the root vegetables radish, the leafy vegetable spinach and the legume clover. Although the accumulation of metals varied significantly with plant species, the average metal concentrations were [Zn] > [Pb] > [Cu] > [Cd]. Metal uptake studies were complemented with bulk and micro X-ray absorption spectroscopy (XAS) at Zn K-edge and micro X-ray fluorescence (μXRF) measurements to evaluate the speciation and distribution of Zn in these plant species. Dynamic interplay between the histidine and malate complexation of Zn was observed in all plant species. XRF mapping of spinach leaves at micron spatial resolution demonstrated the accumulation of Zn in vacuoles and leaf tips. Radish root showed accumulation of Zn in root hairs, likely as ZnS nanoparticles. At locations of high Zn concentration in spinach leaves, μXANES suggests Zn complexation with histidine, as opposed to malate in the bulk leaf. These findings shed new light on the dynamic nature of Zn speciation in plants.
Heterozygosity at 9 CODIS STR Loci and Risk of Schizophrenia.

Faculty of Medical Laboratory, Dalian Medical University, Dalian, P.R. China Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, P.R. China Department of Neurology, Shenyang Brain Institute, Shenyang First People's Hospital, Shenyang, P.R. China Entry-exit Inspection & Quarantine of Liaoning Province, Dalian, P.R. China Dalian Seventh Hospital, Dalian, P.R. China Dalian Blood Center, Dalian, P.R. China
Variation in plasma 25-hydroxyvitamin D2 and D3 in normal pregnancy with gestational age, sampling season, and complications: A longitudinal cohort study

Introduction Low levels of vitamin D in pregnancy have been associated with the risk of a variety of pregnancy outcomes. Few studies have investigated vitamin D concentrations throughout pregnancy in healthy women, and most guidelines recommend high vitamin D levels. In the present study, we investigated 25-hydroxyvitamin D concentrations in healthy Caucasian Danish women in relation to season, gestational age and possible vitamin D-linked complications. Materials and methods Eight hundred and one healthy Caucasian Danish women with an expected normal pregnancy were recruited among 2147 women attending first trimester screening. Seven blood samplings were planned throughout the pregnancy and delivery period. The 25-hydroxyvitamin D2 (25(OH)D2) and 25-hydroxyvitamin D3 (25(OH)D3) concentrations were measured by LC-MS/MS and total 25-hydroxyvitamin D (25(OH)D) were calculated. Results A total of 3304 samples from 694 women were available for 25(OH)D measurements. The mean (25th-75th percentiles) concentrations of 25(OH)D, 25(OH)D3, and 25(OH)D2 were 54.6 (38.8–68.6) nmol/L, 52.2 (36.4–66.4) nmol/L, and 2.4 (2.2–2.2) nmol/L, respectively. Season was the strongest predictor of 25(OH)D concentration, with the lowest values observed in winter and spring, where only 42% and 41% of samples, respectively, were above 50 nmol/L. Nearly all women had values below the suggested optimal level of 75 nmol/L, independent of season. 25(OH)D peaked at gestational weeks 21–34. Plasma 25(OH)D2 levels were low in all seasons. Women with complications during pregnancy had higher 25(OH)D (estimated difference 9.8 nmol/L, standard error 2.7, p<0.001) than did women without complications, and women giving birth vaginally had lower 25(OH)D than did those delivering via elective (10.0 nmol/L, standard error 2.1, p<0.001) or emergency cesarean section (6.8 nmol/L, standard error 2.2, p<0.001). Conclusion The 25(OH)D concentrations vary with both season and gestational age. Healthy women had lower 25(OH)D concentrations than recommended, without an association with an increased risk of pregnancy complications. Guidelines for vitamin D in pregnancy may require revision.
The Safety of Oral Ketoconazole in the Treatment of Skin Diseases (Single Blinded, Therapeutic, Comparative Study)

Background: Ketoconazole was introduced in 1981 as the first in a series of antifungal agents that are characterized by nitrogen-containing ring. Ketoconazole acts against many different kinds of fungi such as candida, dermatophytes and as pergillus. Also oral ketoconazole had proved its effectiveness in the treatment of cutaneous Leishmaniasis. Objective: To evaluate the safety of oral ketoconazole in the treatment of different skin diseases like cutaneous Leishmaniasis (CL), tineacapitis, tineacorporis and tineaversicolor. Patients and Methods: This is a single, blinded, therapeutic, controlled study that was carried out in the Department of Dermatology, Baghdad Teaching Hospital, Baghdad, Iraq, during the time, January 2015 to July 2016. In total, 951 patients with acute cutaneous leishmaniasis, tineacapitis, tineacorporis and tineaversicolor were enrolled in this study. The diagnosis was confirmed by smear and histopathology. Patients were divided into two groups: 51 patients in Group 1; 24 of them were treated with oral ketoconazole tablets 200 mg twice daily for 6 weeks and 27 of them were treated orally with a combination of zinc sulfate 10 mg/kg/day and ketoconazole for 6 weeks. All patients were seen regularly every 2 weeks for 6 weeks of treatment period, then monthly for the next three months as follow up period. Liver enzymes monitoring was done for every patient in this study every two weeks. Elevated liver enzymes were considered as features of hepatotoxicity in the examined patients. While group 2 included 900 patients and was divided into 3 subgroups: A: 600 patients with tineacapitis and tineacorporis, B: 100 patients with tineaversicolor, and C: 200 patients with CL. All patients in group 2 were treated with oral KC tablets 200 mg twice daily for 6 weeks. The dose of oral KC in children is 3.3 - 6.6 mg/Kg/day. All patients in group 2 were not investigated for ketoconazole biochemical side effects but watched for any clinical symptoms and signs of any side effects. Results: After six weeks, 951 patients had completed the treatment. In the first group (51 patients), only two out 27 patients (7.4%) from the combined group showed elevated liver enzymes while the ketoconazole treated group showed no increase in liver enzymes, hence only 3.9% showed elevated liver enzymes that went to normal during follow up. In the second group (900 patients) there were no clinical symptoms and signs in favor of hepatic toxicity or other related organs. Conclusion: Ketoconazole has been used tremendously in treating of different skin diseases including fungal and Leishmania infection but without side effects, accordingly this drug seems safe to be used in treatment of different skin diseases whether adults or children.
Risk and protective factors for post-traumatic stress among New Zealand military personnel: A cross sectional study

Background Post-traumatic stress (PTS) is prevalent among military personnel. Knowledge of the risk and protective factors associated with PTS in this population may assist with identifying personnel who would benefit from increased or targeted support. Aims To examine factors associated with PTS among New Zealand military personnel. Methods For this cross-sectional study, currently serving and retired military personnel were invited to complete a questionnaire. The questionnaire included a measure of PTS (the Military Post-traumatic Stress Disorder Checklist; PCL-M), where scores ≥30 indicate the experience of significant PTS symptoms and scores ≥45 indicate a presumptive clinical diagnosis of post-traumatic stress. Potential risk and protective factors associated with PTS were examined using logistic regression modelling. Results 1817 military personnel completed the questionnaire. PCL-M scores were ≥30 for 549 (30%) participants and ≥45 for 179 (10%) participants. Factors associated with higher PCL-M scores were trauma exposure, older age, male sex, and Māori ethnicity. Factors associated with lower PCL-M scores were greater length of service, psychological flexibility, and better quality sleep. Conclusions PTS was found to be prevalent among New Zealand military personnel. The experience of trauma was strongly associated with PTS. However, factors such as psychological flexibility (the ability to adapt to changes in circumstances) and good sleep were protective, suggesting that these factors could be key targets for interventions designed to reduce PTS among military personnel in New Zealand.
The Turnip mosaic virus and its effects on Arabidopsis thaliana gene expression

Turnip mosaic virus (TuMV) strain UK1 usually causes severely stunted growth in Arabidopsis thaliana plants (Columbia-0 ecotype). The molecular basis of this stunted growth phenotype, which is caused by a variety of plant viruses, remains poorly understood. Previous 24 reports show that suites of genes with functions associated with cell wall extensibility and growth are down regulated during viral infection. These genes encode proteins that are predicted or known to possess the following biochemical functions: pectin methylesterases, xyloglucan endotransglucosylase/hydrolase, expansins, and the brassinolide biosynthesis enzyme DWARF1 (DWF1). In order to test the functions of these genes in the stunted growth phenotype, CaMV 35S over-expression lines were generated. However, when over-expression lines were infected with TuMV, they all showed stunted growth phenotypes similar to TuMV-infected wild type plants. Analysis of mRNA expression demonstrated that the transcript levels of these genes were still down regulated as they were in wild type plants infected by TuMV. The activity of the 35S promoter was not reduced by TuMV infection, implying that cell wall function and hormone biosynthesis genes are down regulated by a post-transcriptional mechanism. Down-regulation of these genes in response to TuMV was perturbed in dcl1, dcl3, and rdr1/rdr2/rdr6 silencing mutants. Using a publicly available deep-sequencing dataset, small RNAs (sRNAs) associated with these genes were quantified. The data suggest the sRNAs associated with the downregulated genes of interest are in low abundance and their levels inversely correlate with expression of their targets. In addition, 15 sRNAs were identified that share sequence identity with the A. thaliana and TuMV genomes. GAL2, a gene involved in leaf morphogenesis and positive regulation of flower development was also found to be down-regulated in a manner similar to the cell wall and hormone biosynthesis genes. These data suggest that TuMV infection activates an RNA silencing mechanism that can target endogenous host genes.
Preclinical validation of a novel metastasis‐inhibiting Tie1 function‐blocking antibody

The angiopoietin (Ang)–Tie pathway has been intensely pursued as candidate second‐generation anti‐angiogenic target. While much of the translational work has focused on the ligand Ang2, the clinical efficacy of Ang2‐targeting drugs is limited and failed to improve patient survival. In turn, the orphan receptor Tie1 remains therapeutically unexplored, although its endothelial‐specific genetic deletion has previously been shown to result in a strong reduction in metastatic growth. Here, we report a novel Tie1 function‐blocking antibody (AB‐Tie1‐39), which suppressed postnatal retinal angiogenesis. During primary tumor growth, neoadjuvant administration of AB‐Tie1‐39 strongly impeded systemic metastasis. Furthermore, the administration of AB‐Tie1‐39 in a perioperative therapeutic window led to a significant survival advantage as compared to control‐IgG‐treated mice. Additional in vivo experimental metastasis and in vitro transmigration assays concurrently revealed that AB‐Tie1‐39 treatment suppressed tumor cell extravasation at secondary sites. Taken together, the data phenocopy previous genetic work in endothelial Tie1 KO mice and thereby validate AB‐Tie1‐39 as a Tie1 function‐blocking antibody. The study establishes Tie1 as a therapeutic target for metastasis in a perioperative or neoadjuvant setting.
A novel voluntary weightlifting model in mice promotes muscle adaptation and insulin sensitivity with simultaneous enhancement of autophagy and mTOR pathway

Our understanding of the molecular mechanisms underlying adaptations to resistance exercise remains elusive despite the significant biological and clinical relevance. We developed a novel voluntary mouse weightlifting model, which elicits squat‐like activities against adjustable load during feeding, to investigate the resistance exercise‐induced contractile and metabolic adaptations. RNAseq analysis revealed that a single bout of weightlifting induced significant transcriptome responses of genes that function in posttranslational modification, metabolism, and muscle differentiation in recruited skeletal muscles, which were confirmed by increased expression of fibroblast growth factor‐inducible 14 (Fn14), Down syndrome critical region 1 (Dscr1) and Nuclear receptor subfamily 4, group A, member 3 (Nr4a3) genes. Long‐term (8 weeks) voluntary weightlifting training resulted in significantly increases of muscle mass, protein synthesis (puromycin incorporation in SUnSET assay) and mTOR pathway protein expression (raptor, 4e‐bp‐1, and p70S6K proteins) along with enhanced muscle power (specific torque and contraction speed), but not endurance capacity, mitochondrial biogenesis, and fiber type transformation. Importantly, weightlifting training profound improved whole‐body glucose clearance and skeletal muscle insulin sensitivity along with enhanced autophagy (increased LC3 and LC3‐II/I ratio, and decreased p62/Sqstm1). These data suggest that resistance training in mice promotes muscle adaptation and insulin sensitivity with simultaneous enhancement of autophagy and mTOR pathway.
Both Enolase and the DEAD-Box RNA Helicase CrhB Can Form Complexes with RNase E in Anabaena sp. Strain PCC 7120

In all domains of life, RNA turnover is important for gene regulation and quality control. The process of RNA metabolism is regulated by many RNA-processing enzymes and assistant proteins, where these proteins usually exist as complexes. However, there is little known about the RNA metabolism, as well as about the RNA degradation complex. In the present study, we described an RNA degradosome-like complex in cyanobacteria and revealed an assembly mechanism different from that of E. coli. Moreover, CrhB could help RNase E in Anabaena sp. strain PCC 7120 degrade double-stranded RNA with a 5′ tail. In addition, CrhB and AnaRne have similar cytoplasm localizations, in contrast to the membrane localization in E. coli. ABSTRACT At present, little is known about the RNA metabolism driven by the RNA degradosome in cyanobacteria. RNA helicase and enolase are the common components of the RNA degradosome in many bacteria. Here, we provide evidence that both enolase and the DEAD-box RNA helicase CrhB can interact with RNase E in Anabaena (Nostoc) sp. strain PCC 7120 (referred to here as PCC 7120). Furthermore, we found that the C-terminal domains of CrhB and AnaEno (enolase of PCC 7120) are required for the interaction, respectively. Moreover, their recognition motifs for AnaRne (RNase E of PCC 7120) turned out to be located in the N-terminal catalytic domain, which is obviously different from those identified previously in Proteobacteria. We also demonstrated in enzyme activity assays that CrhB can induce AnaRne to degrade double-stranded RNA with a 5′ tail. Furthermore, we investigated the localization of CrhB and AnaRne by green fluorescent protein (GFP) translation fusion in situ and found that they both localized in the center of the PCC 7120 cytoplasm. This localization pattern is also different from the membrane binding of RNase E and RhlB in Escherichia coli. Together with the previous identification of polynucleotide phosphorylase (PNPase) in PCC 7120, our results show that there is an RNA degradosome-like complex with a different assembly mechanism in cyanobacteria. IMPORTANCE In all domains of life, RNA turnover is important for gene regulation and quality control. The process of RNA metabolism is regulated by many RNA-processing enzymes and assistant proteins, where these proteins usually exist as complexes. However, there is little known about the RNA metabolism, as well as about the RNA degradation complex. In the present study, we described an RNA degradosome-like complex in cyanobacteria and revealed an assembly mechanism different from that of E. coli. Moreover, CrhB could help RNase E in Anabaena sp. strain PCC 7120 degrade double-stranded RNA with a 5′ tail. In addition, CrhB and AnaRne have similar cytoplasm localizations, in contrast to the membrane localization in E. coli.
γ-Mangostin isolated from Garcinia mangostana L. suppresses inflammation and alleviates symptoms of osteoarthritis via modulating miR-124-3p/IL-6/NF-κB signaling

Osteoarthritis (OA) a disease associated with joints and become severe with age, due to softening, inflammation and degradation of cartilage in joints. The agents that can target OA is needed, specifically without any side effects. Garcinia mangostana L. (Mangosteen) a tropical fruit used to treat many skin and stomach associated ailments. γ- Mangostin (γ-MS) a key bioactive substance present in mangosteen. Here, we aimed to explore γ-MS potential in targeting the pro-inflammatory cytokine, factors and miRs in OA progression. Significantly, γ-MS suppresses the inflammatory cytokines (IL-6, TNF-α, and INF- γ) and factors (NF-κB, STAT3, and COX-2) which regulates/participate in the catabolic process of cartilage destruction. Result of Hematoxylin-eosin (H&E) staining of tissue sections of OA joints of γ-MS treated and non-treated mice confirm γ-MS improves the signs of injuries, and maintains the structural integrity of the articular cartilage (epiphyseal disk joints and bone marrow) and reduces inflammation. Mechanistically, γ-MS targets miR-98-5p and miR-124-3p which are found to suppress the expression IL-6 and NF-κB, respectively. But in OA these miRs are inhibited, especially miR-124-3p which regulates not only NF-κB but also TNF-α, IL-6 and MMP7. With a further investigation underway, γ-MS represents an important source for treating and managing OA.
Cyanopeptide co-production dynamics beyond microcystins and effects of growth stages and nutrient availability.

Intensified cyanobacterial bloom events are of increasing global concern because of adverse effects associated with the release of bioactive compounds including toxic cyanopeptides. Cyanobacteria can produce a variety of cyanopeptides, yet our knowledge about their abundance and co-production remains limited. We applied a suspect-screening approach including 700 structurally known cyanopeptides and identified 11 cyanopeptides in Microcystis aeruginosa and 17 in Dolichospermum flos-aquae. Total cyanopeptide concentrations ranged from high nmol to µmol gdry-1 with slightly higher cell quotas in the mid-exponential growth phase. Relative cyanopeptide profiles were unchanged throughout the growth cycle. We demonstrate that quantification based on microcystin-LR equivalents can introduce an error of up to 6-fold and recommend a class-equivalent approach instead. In M. aeruginosa, rarely studied cyclamides dominated (>80%) over cyanopeptolins and microcystins. While all nutrient reductions caused less growth, only lowering phosphorous and micronutrients reduced cyanopeptide production by M. aeruginosa. Similar trends were observed for D. flos-aquae and only lowering nitrogen decreased cyanopeptide production while the relative abundance of individual cyanopeptides remained stable. The synchronized production of other cyanopeptides along with microcystins emphasizes the need to make them available as reference standards to encourage more studies on their occurrence in blooms, persistence and potential toxicity.
Value of prognostic scores in antineutrophil cytoplasmic antibody (ANCA) associated vasculitis patients in intensive care unit: a multicenter retrospective cohort study from Turkey

Background/aim There is a need for a scoring system for predicting ICU prognosis of patients with ANCA-associated vasculitis (AAV), but there are limited data on it in the literature. Therefore, we aimed to determine the scores that can estimate the prognosis of patients with AAV during intensive care follow up. Materials and methods All adult patients admitted to the medical ICUs of 4 reference university hospitals in Turkey due to AAV activation and/or disease/treatment complications in the last 10 years were included in this study. Demographic data, treatments before ICU, the Birmingham Vasculitis Activity Score (BVAS) score at the time of vasculitis diagnosis, and BVAS, APACHE II, SOFA, and SAPS II scores at the ICU admission, treatments, procedures, and complications during ICU stay were recorded for all AAV patients. Results Thirty-four patients were included in the study. The median age of the patients was 60 (42–70) years, and 64.7% were male. Twenty-five patients were diagnosed with Granulomatosis with polyangiitis, and 9 were diagnosed with Microscopic polyangiitis. The most common ICU admission causes were hemorrhage (85.3%) and sepsis/septic shock (67.6%). Twenty patients (58.8%) died in the ICU follow up. There were significant differences in APACHE II (P = 0.004) and SAPS II (P = 0.044) scores between survivors and nonsurvivors, while there were no significant differences in BVAS (during diagnosis P = 0.089 and ICU admission P = 0.539) and SOFA (P = 0.097) scores. APACHE II score was found to be an independent risk factor for ICU mortality (OR = 1.231, CI 95% = 1.011–1.498, P = 0.038) according to logistic regression analysis. An APACHE II score of greater than 20.5 predicted ICU mortality with 80% sensitivity and 70% specificity (AUC = 0.8, P = 0.004, Likelihood ratio = 2.6) according to the ROC curve analysis. Conclusion APACHE II score can be used for the prediction of ICU mortality in AAV patients.
Unusual Structure of a Human Middle Repetitive DNA

Unusual Structure of a Human Middle Repetitive DNA by Duminda D, Ratnasinghe The L2Hs sequences are a polymorphic, interspersed, middle repetitive DNA family unique to human genomes. Genomic fingerprinting indicates that these DNAs vary from one individual to another and between tissues of the same individual. Sequence analysis reveals that they are AT-rich {76%) and contain many unusual sequence arrangements (palindromes, inverted and direct repeats). These sequence properties confer on the L2Hs elements the potential to fold into non-B-form structures, a characteristic of recombination hot spots. To test this hypothesis carbodiimide, osmium tetroxide and Sx nuclease were used as single-strand specific probes to study a recombinant plasmid, pN6.4. 39, containing a single L2Hs segment. Different forms of the plasmid substrate were analyzed, including linear molecules and circular forms of low, intermediate and high superhelical densities. In addition, plasmid DNA in growing E, coli cells were analyzed. Modified plasmid DNA was analyzed by primer extension in a sequencing-type reaction format. These studies demonstrate that the L2Hs sequences: 1. assume non-B-form structures both in vitro and in vivo, 2. map to predicted cruciform structures, 3. behave as C-type extrusion sequences and 4. that these unusual DNA structures are dependent on plaBmid superhelicity.