Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of binary mixtures of zinc, copper, cadmium, and nickel on the growth of the freshwater diatom Navicula pelliculosa and comparison with mixture toxicity model predictions

The authors investigated the effect of binary mixtures of zinc (Zn), copper (Cu), cadmium (Cd), and nickel (Ni) on the growth of a freshwater diatom, Navicula pelliculosa. A 7 × 7 full factorial experimental design (49 combinations in total) was used to test each binary metal mixture. A 3‐d fluorescence microplate toxicity assay was used to test each combination. Mixture effects were predicted by concentration addition and independent action models based on a single‐metal concentration–response relationship between the relative growth rate and the calculated free metal ion activity. Although the concentration addition model predicted the observed mixture toxicity significantly better than the independent action model for the Zn–Cu mixture, the independent action model predicted the observed mixture toxicity significantly better than the concentration addition model for the Cd–Zn, Cd–Ni, and Cd–Cu mixtures. For the Zn–Ni and Cu–Ni mixtures, it was unclear which of the 2 models was better. Statistical analysis concerning antagonistic/synergistic interactions showed that the concentration addition model is generally conservative (with the Zn–Ni mixture being the sole exception), indicating that the concentration addition model would be useful as a method for a conservative first‐tier screening‐level risk analysis of metal mixtures. Environ Toxicol Chem 2016;35:2765–2773. © 2016 SETAC
Dysfunctional HDL and Cardiovascular Disease Risk in Individuals with Diabetic Dyslipidemia

Cardiovascular disease (CVD) remains the leading cause of morbidity and mortality in individuals with diabetes mellitus despite advances in the prevention and management of CVD. A number of studies have shown that the prospective risk of adverse cardiovascular events in diabetic individuals without previous myocardial infarctionis comparable to non-diabetic individuals with myocardial infarction, with comparatively worse clinical outcomes for diabetic individuals following an adverse cardiovascular event [1-4]. Furthermore, population studies indicate that diabetes amplifies the effects of other common CVD risk factors, including hypertension, hypercholesterolemia, and smoking [5,6]. Consequently, diabetes has been considered in some prevention guidelines as a coronary artery disease-risk equivalent [7,8].
Analysis of Ground Level Ozone and Nitrogen Oxides in the City of Dar es Salaam and the Rural Area of Bagamoyo, Tanzania

From 2012 to 2015, we measured surface ozone, NOx, NO2, and NO levels at three urban sites (Mapipa, Ubungo, and Posta) and two suburban sites (Kunduchi and Vijibweni) in the city of Dar es Salaam and in the village of Mwetemo, a rural area of Bagamoyo, Tanzania. The average hourly O3 concentrations at all sites were between 9 ppb and 30 ppb during our sampling periods. O3 levels at suburban sites were generally higher than at urban sites. The average hourly concentrations in Dar es Salaam were 10 - 32 ppb, while in Bagamoyo they were 9 - 15 ppb. We observed a strong diurnal variation in Dar es Salaam while measurements from Bagamoyo showed little variation. At Dar es Salaam, the surface O3 concentrations increased from their minimum level at sunrise (around 6:00 a.m.) to a maximum in the late afternoon (around 4:00 p.m.), and then decreased toward 11:00 p.m. Another secondary ozone peak appeared between midnight and ~4:00 a.m., after which the surface ozone concentrations decreased to a minimum around 7:00 a.m. NO2 concentrations were higher at the urban sites of Ubungo and Posta, and their weekly average NO2 concentrations were 246 ppb and 118 ppb, respectively. Weekly average NOx concentrations ranged from 39.4 ppb at the Kunduchi site (suburban) to 738 ppb at the Ubungo site (urban). To our knowledge, there were few continuous measurements of ozone and nitrogen oxides concentrations in Tanzania. Since high NOx concentrations were observed, continuous air quality monitoring and effective air pollution control measures are required in Dar es Salaam to prevent further deterioration of air quality and limit the possible negative impacts on humans and vegetation.
Business Cycles Synchronization Assessment : AnEBA-Wavelets Approach

This paperuses an Extreme Bound Analysis (EBA) and Wavelet Transformation (WT) to provide a detailed characterization of the Business Cycle Synchronization (BCS) within the selected countries belonging to the Euro Area (EA) and Gulf Cooperation Council countries (GCC). In addition, a cross wavelets transformation and wavelets coherency transformation analysis is introduced in order to understand how wavelets could be used in BCS leading likely to achieve high levels of economic activity integration betweencountries or groups
Convolutional 2D Knowledge Graph Embeddings

Link prediction for knowledge graphs is the task of predicting missing relationships between entities. Previous work on link prediction has focused on shallow, fast models which can scale to large knowledge graphs. However, these models learn less expressive features than deep, multi-layer models — which potentially limits performance. In this work we introduce ConvE, a multi-layer convolutional network model for link prediction, and report state-of-the-art results for several established datasets. We also show that the model is highly parameter efficient, yielding the same performance as DistMult and R-GCN with 8x and 17x fewer parameters. Analysis of our model suggests that it is particularly effective at modelling nodes with high indegree — which are common in highly-connected, complex knowledge graphs such as Freebase and YAGO3. In addition, it has been noted that the WN18 and FB15k datasets suffer from test set leakage, due to inverse relations from the training set being present in the test set — however, the extent of this issue has so far not been quantified. We find this problem to be severe: a simple rule-based model can achieve state-of-the-art results on both WN18 and FB15k. To ensure that models are evaluated on datasets where simply exploiting inverse relations cannot yield competitive results, we investigate and validate several commonly used datasets — deriving robust variants where necessary. We then perform experiments on these robust datasets for our own and several previously proposed models, and find that ConvE achieves state-of-the-art Mean Reciprocal Rank across all datasets.
Effects of two fungicide formulations on microbial and macroinvertebrate leaf decomposition under laboratory conditions

Aquatic fungi contribute significantly to the decomposition of leaves in streams, a key ecosystem service. Little is known, however, about the effects of fungicides on aquatic fungi and macroinvertebrates involved with leaf decomposition. Red maple (Acer rubrum) leaves were conditioned in a stream to acquire microbes (bacteria and fungi) or leached in tap water (unconditioned) to simulate potential reduction of microbial biomass by fungicides. Conditioned leaves were exposed to fungicide formulations QUILT (azoxystrobin + propiconazole) or PRISTINE (boscalid + pyraclostrobin) in the presence and absence of the leaf shredder, Hyalella azteca (amphipods; 7‐d old at start of exposures) for 14 d at 23 °C. The QUILT formulations (∼0.3 μg/L, 1.8 μg/L, and 8 μg/L) tended to increase leaf decomposition by amphipods (not significant) without a concomitant increase in amphipod biomass, indicating potential increased consumption of leaves with reduced nutritional value. The PRISTINE formulation (∼33 μg/L) significantly reduced amphipod growth and biomass (p < 0.05), effects similar to those observed with unconditioned controls. The significant suppressive effects of PRISTINE on amphipod growth and the trend toward increased leaf decomposition with increasing QUILT concentration indicate the potential for altered leaf decay in streams exposed to fungicides. Further work is needed to evaluate fungicide effects on leaf decomposition under conditions relevant to stream ecosystems, including temperature shifts and pulsed exposures to pesticide mixtures. Environ Toxicol Chem 2016;35:2834–2844. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.
Egg‐laying sequence influences egg mercury concentrations and egg size in three bird species: Implications for contaminant monitoring programs

Bird eggs are commonly used in contaminant monitoring programs and toxicological risk assessments, but intraclutch variation and sampling methodology could influence interpretability. The authors examined the influence of egg‐laying sequence on egg mercury concentrations and burdens in American avocets, black‐necked stilts, and Forster's terns. The average decline in mercury concentrations between the first and last eggs laid was 33% for stilts, 22% for terns, and 11% for avocets, and most of this decline occurred between the first and second eggs laid (24% for stilts, 18% for terns, and 9% for avocets). Trends in egg size with egg‐laying order were inconsistent among species, and overall differences in egg volume, mass, length, and width were <3%. The authors summarized the literature, and among 17 species studied, mercury concentrations generally declined by 16% between the first and second eggs laid. Despite the strong effect of egg‐laying sequence, most of the variance in egg mercury concentrations still occurred among clutches (75–91%) rather than within clutches (9%–25%). Using simulations, the authors determined that accurate estimation of a population's mean egg mercury concentration using only a single random egg from a subset of nests would require sampling >60 nests to represent a large population (10% accuracy) or ≥14 nests to represent a small colony that contained <100 nests (20% accuracy). Environ Toxicol Chem 2016;35:1458–1469. Published 2015 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.
Effects of Novel Isoform-Selective Phosphoinositide 3-Kinase Inhibitors on Natural Killer Cell Function

Phosphoinositide 3-kinases (PI3Ks) are promising targets for therapeutic development in cancer. The class I PI3K isoform p110α has received considerable attention in oncology because the gene encoding p110α (PIK3CA) is frequently mutated in human cancer. However, little is known about the function of p110α in lymphocyte populations that modulate tumorigenesis. We used recently developed investigational inhibitors to compare the function of p110α and other isoforms in natural killer (NK) cells, a key cell type for immunosurveillance and tumor immunotherapy. Inhibitors of all class I isoforms (pan-PI3K) significantly impaired NK cell-mediated cytotoxicity and antibody-dependent cellular cytotoxicity against tumor cells, whereas p110α-selective inhibitors had no effect. In NK cells stimulated through NKG2D, p110α inhibition modestly reduced PI3K signaling output as measured by AKT phosphorylation. Production of IFN-γ and NK cell-derived chemokines was blocked by a pan-PI3K inhibitor and partially reduced by a p110δinhibitor, with lesser effects of p110α inhibitors. Oral administration of mice with MLN1117, a p110α inhibitor in oncology clinical trials, had negligible effects on NK subset maturation or terminal subset commitment. Collectively, these results support the targeting of PIK3CA mutant tumors with selective p110α inhibitors to preserve NK cell function.
Relation of locus 1p13 rs646776 polymorphism with the risk of preeclampsia

ABSTRACT Objective: This study aimed to assess the relation of locus 1p13 rs646776 (T/C) polymorphism with preeclampsia in Egyptian women. Methods: The study included 100 healthy pregnant female subjects and 100 preeclampsia patients. The genotypes of the polymorphisms were assessed. Endothelin-1 level was determined in plasma. Results: The major T allele of the 1p13.3 genomic region rs646776 polymorphism had a higher frequency in preeclampsia patients. Carriers of C allele had significantly lower endothelin-1 levels, lower systolic and diastolic blood pressure, decreased proteinuria, and increased HDL-C in the patients. Conclusion: The rare C allele of rs646776 polymorphism in chromosomal locus 1p13.3 is associated with decreased risk of preeclampsia.
A Review of the Common Models Used in Mechanistic Studies on Demineralization-Remineralization for Cariology Research

Mechanistic studies on demineralization-remineralization play a critical role in investigating caries pathogenicity, testing effects of new caries prevention methods, and developing new caries-preventing products. Simulating the cariogenic challenges in the mouth, various demineralization-remineralization models have been used for cariology research. This review aimed to provide an overview of the common mechanistic studies on demineralization-remineralization for cariology research in recent literature. Most mechanistic studies were in vitro studies (n = 294, 84%) among the 350 cariology studies indexed in the Web of Science from 2014 to 2016. Among these in vitro studies, most studies (257/294, 87%) used chemical models that could be classified as simple mineralization models (159/257, 62%) or pH-cycling models (98/257, 38%). In vitro studies consumed less expense and time than in vivo studies. Furthermore, in vitro conditions were easier to control. However, they could hardly imitate the complex structures of oral cavities, the microbiological effect of oral biofilm, and the hydrodynamic instability of saliva. The advantages of chemical models included simplicity of the study, low cost, efficiency (time saving), reproducibility, and stability of experiments. However, the “caries” generated were not biological. Moreover, the chemical models were generally basic and could not mimic a carious lesion in the complex oral environment.
Age Is Not a Limiting Factor in Interventional Radiotherapy (Brachytherapy) for Patients with Localized Cancer

This review examines the role of interventional radiotherapy (IRT otherwise known as brachytherapy) in cancer treatment for elderly patients. Despite their advanced age and associated comorbidities, elderly patients should receive definitive cancer therapies, including surgery and radiotherapy (RT). In fact, RT becomes first-line option for patients who are not eligible for surgery (due to comorbidities, anticoagulant drugs, and risk of disfigurement) or those who refuse it. It emerged from this review of the literature as effective, simple, safe, and comfortable and was associated with good local control, low toxicity rates, and excellent cosmesis and provided a cost benefit. IRT may be used as sole treatment for small cancers or as a useful adjunct to surgery or external beam radiotherapy (EBRT) in more advanced (or lymph node positive) cases, especially when the aim is local control with adequate preservation of normal tissue function. As palliative treatment, IRT preserves quality of life and/or improves survival. It is to be hoped that this review will serve as a helpful guide for members of multidisciplinary teams that are involved in treating elderly patients with cancer.
CPAP Does Not Reduce Inflammatory Biomarkers in Patients With Coronary Artery Disease and Nonsleepy Obstructive Sleep Apnea: A Randomized Controlled Trial

Objectives Obstructive sleep apnea (OSA) and enhanced vascular inflammation coexist in patients with coronary artery disease (CAD). Continuous positive airway pressure (CPAP) is first-line treatment for OSA with daytime sleepiness. This analysis of data from the RICCADSA (Randomized Intervention with CPAP in Coronary Artery Disease and Sleep Apnea) trial investigated the effects of CPAP on inflammatory markers in patients with CAD and nonsleepy OSA. Methods This single-center, randomized, controlled, open-label trial enrolled consecutive revascularized patients with nonsleepy OSA (apnea-hypopnea index >15/h; Epworth Sleepiness Scale score <10). Levels of high-sensitivity C-reactive protein (hs-CRP), interleukin (IL)-6, IL-8, and tumor necrosis factor-α (TNF-α) were measured in blood samples taken at baseline (median 94 days after revascularization) and after 1 year of follow-up in patients randomized to CPAP or no-CPAP. Results A total of 220 patients with analyzable blood samples at baseline and 1 year were included. Baseline IL-6 levels were significantly lower in the CPAP versus no-CPAP group (median 3.1 pmol/L [interquartile range 1.3-5.7] vs. 4.2 pmol/L [2.0-8.9], respectively; p = .005). At 1-year follow-up, median IL-6 levels were significantly reduced in both groups (to 2.2 pmol/L [1.2-3.9] in the CPAP group and to 2.2 [1.2-4.7] in no-CPAP group; both p < .001 vs. baseline). IL-8, hs-CRP, and TNF-α did not change significantly from baseline. There was no association between CPAP adherence and changes in inflammatory marker levels. Conclusions In patients with stable CAD and nonsleepy OSA, inflammatory biomarkers did not change significantly over time except for IL-6 levels, which reduced to the same extent in the CPAP and no-CPAP groups. Clinical Trial Registration ClinicalTrials.gov, ID: NCT00519597; researchweb.org, VGSKAS-4731.
Genetic and Environmental Models of Circadian Disruption Link SRC-2 Function to Hepatic Pathology

Circadian rhythmicity is a fundamental process that synchronizes behavioral cues with metabolic homeostasis. Disruption of daily cycles due to jet lag or shift work results in severe physiological consequences including advanced aging, metabolic syndrome, and even cancer. Our understanding of the molecular clock, which is regulated by intricate positive feedforward and negative feedback loops, has expanded to include an important metabolic transcriptional coregulator, Steroid Receptor Coactivator-2 (SRC-2), that regulates both the central clock of the suprachiasmatic nucleus (SCN) and peripheral clocks including the liver. We hypothesized that an environmental uncoupling of the light-dark phases, termed chronic circadian disruption (CCD), would lead to pathology similar to the genetic circadian disruption observed with loss of SRC-2. We found that CCD and ablation of SRC-2 in mice led to a common comorbidity of metabolic syndrome also found in humans with circadian disruption, non-alcoholic fatty liver disease (NAFLD). The combination of SRC-2–/– and CCD results in a more robust phenotype that correlates with human non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) gene signatures. Either CCD or SRC-2 ablation produces an advanced aging phenotype leading to increased mortality consistent with other circadian mutant mouse models. Collectively, our studies demonstrate that SRC-2 provides an essential link between the behavioral activities influenced by light cues and the metabolic homeostasis maintained by the liver.
Circadian gene methylation profiles are associated with obesity, metabolic disturbances and carbohydrate intake

ABSTRACT The circadian clock regulates the daily rhythms of several physiological and behavioral processes. Disruptions in clock genes have been associated with obesity and related comorbidities. This study aimed to analyze the association of DNA methylation signatures at circadian rhythm pathway genes with body mass index (BMI), metabolic profiles and dietary intakes. DNA methylation profiling was determined by microarray in white blood cells from 474 adults from the Methyl Epigenome Network Association (MENA) project. Kyoto Encyclopedia of Genes and Genomes database was used to identify the genes integrating the circadian rhythm pathway. Network enrichment analyses were performed with the PathDIP platform. Associations between circadian methylation patterns with anthropometric measurements, the metabolic profile, clinical data and dietary intakes were analyzed. DNA methylation patterns of nine CpG sites at six circadian rhythm pathway genes were strongly correlated with BMI (false discovery rates <0.0001). These CpGs encompassed cg09578018 (RORA), cg20406576 (PRKAG2), cg10059324 (PER3), cg01180628 (BHLHE40), cg23871860 (FBXL3), cg16964728 (RORA), cg14129040 (CREB1), cg07012178 (PRKAG2) and cg24061580 (PRKAG2). Interestingly, network enrichment analyses revealed that the six BMI-associated genes statistically contributed to the regulation of the circadian rhythm pathway (p = 1.9E-10). In addition, methylation signatures at cg09578018 (RORA), cg24061580 (PRKAG2), cg01180628 (BHLHE40) and cg10059324 (PER3) also correlated with insulin resistance (p < 0.0001) and mean arterial blood pressure (p < 0.0001). Furthermore, relevant correlations (p < 0.05) between methylation at cg09578018 (RORA) and cg01180628 (BHLHE40) with total energy and carbohydrate intakes were found. This investigation revealed potential associations of DNA methylation profiles at circadian genes with obesity, metabolic disturbances and carbohydrate intake, with potential impact on weight homeostasis.
Branched pattern of regulatory interactions between late sporulation genes in Bacillus subtilis

We measured the synthesis of dipicolinic acid (DPA) during sporulation in spo mutants of Bacillus subtilis by a sensitive biological assay based on cross-feeding of a spoVF mutant strain and also chemically. Many spo mutations, including several that block sporulation at stage III, did not prevent synthesis of DPA but instead prevented its incorporation into the spore. In general, strains with mutations in loci that are expressed in the spore compartment synthesized DPA, whereas strains with mutations in most of the loci that are expressed in the mother-cell compartment did not. Transcription of the gerE gene, as measured by DNA-RNA hybridization, followed a dependence pattern very similar to that of DPA synthesis. However, the dependence patterns of the two operons show that at about stage IV of sporulation there is a branch in the sequence of operon expression in the mother cell. One branch leads through spoVC to synthesis of DPA synthetase, and the other leads through spoVD to expression of gerE.
Freeze concentration of lime juice

The main objective of this research was to study the effects of processing conditions, i.e. cooling medium temperature (-6, -12 and -18C) and scraper blade rotational speed (50, 100 and 150 rpm) on the freeze concentration of lime juice. The initial soluble solid content of lime juice was 7.6 Brix. Results showed that soluble solid content of lime juice increased as cooling medium temperature decreased while scraper blade rotational speed increased. It was also found that the processing condition with -18˚C cooling medium temperature and 150 rpm rotational speed of the scraper blade was the best among all studied conditions, although the loss of the soluble solids with ice crystals during ice separation was relatively high at 35%.
Biofilm removal potential of neutral electrolysed water on pathogen and spoilage bacteria in dairy model systems

This study aimed to investigate the efficacy of neutral electrolysed water (NEW) on biofilm and planktonic forms of Listeria monocytogenes, Escherichia coli and Pseudomonas aeruginosa in Luria–Bertani (LB) broth, 0·5 and 3% w/w fat pasteurized and ultra high temperature (UHT) milk.
Piezoelectric polymeric bicomponent fibers produced by melt spinning

Melt spinning of a novel piezoelectric bicomponent fiber, with poly(vinylidene fluoride) as the electroactive sheath component, has been demonstrated. An electrically conductive compound of carbon black (CB) and high density polyethylene was used as core material, working as an inner electrode. A force sensor consisting of a number of fibers embedded in a soft CB/polyolefin elastomer matrix was manufactured for characterization. The fibers showed a clear piezoelectric effect, with a voltage output (peak-to-peak) of up to 40 mV under lateral compression. This continuous all-polymer piezoelectric fiber introduces new possibilities toward minimal single fiber sensors as well as large area sensors produced in standard industrial weaving machines.