Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effect of VPA on Increasing Radiosensitivity in Osteosarcoma Cells and Primary-Culture Cells from Chemical Carcinogen-Induced Breast Cancer in Rats

This study explored whether valproic acid (VPA, a histone deacetylase inhibitor) could radiosensitize osteosarcoma and primary-culture tumor cells, and determined the mechanism of VPA-induced radiosensitization. The working system included osteosarcoma cells (U2OS) and primary-culture cells from chemical carcinogen (DMBA)-induced breast cancer in rats; and clonogenic survival, immunofluorescence, fluorescent in situ hybridization (FISH) for chromosome aberrations, and comet assays were used in this study. It was found that VPA at the safe or critical safe concentration of 0.5 or 1.0 mM VPA could result in the accumulation of more ionizing radiation (IR)-induced DNA double strand breaks, and increase the cell radiosensitivity. VPA-induced radiosensitivity was associated with the inhibition of DNA repair activity in the working systems. In addition, the chromosome aberrations including chromosome breaks, chromatid breaks, and radial structures significantly increased after the combination treatment of VPA and IR. Importantly, the results obtained by primary-culture cells from the tissue of chemical carcinogen-induced breast cancer in rats further confirmed our findings. The data in this study demonstrated that VPA at a safe dose was a radiosensitizer for osteosarcoma and primary-culture tumor cells through suppressing DNA-double strand breaks repair function.
Characterization of Wastewater Treatment Plant Microbial Communities and the Effects of Carbon Sources on Diversity in Laboratory Models

We are developing a laboratory-scale model to improve our understanding and capacity to assess the biological risks of genetically engineered bacteria and their genetic elements in the natural environment. Our hypothetical scenario concerns an industrial bioreactor failure resulting in the introduction of genetically engineered bacteria to a downstream municipal wastewater treatment plant (MWWTP). As the first step towards developing a model for this scenario, we sampled microbial communities from the aeration basin of a MWWTP at three seasonal time points. Having established a baseline for community composition, we investigated how the community changed when propagated in the laboratory, including cell culture media conditions that could provide selective pressure in future studies. Specifically, using PhyloChip 16S-rRNA-gene targeting microarrays, we compared the compositions of sampled communities to those of inocula propagated in the laboratory in simulated wastewater conditionally amended with various carbon sources (glucose, chloroacetate, D-threonine) or the ionic liquid 1-ethyl-3-methylimidazolium chloride ([C2mim]Cl). Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in both aeration basin and laboratory-cultured communities. Laboratory-cultured communities were enriched in γ-Proteobacteria. Enterobacteriaceae, and Aeromonadaceae were enriched by glucose, Pseudomonadaceae by chloroacetate and D-threonine, and Burkholderiacea by high (50 mM) concentrations of chloroacetate. Microbial communities cultured with chloroacetate and D-threonine were more similar to sampled field communities than those cultured with glucose or [C2mim]Cl. Although observed relative richness in operational taxonomic units (OTUs) was lower for laboratory cultures than for field communities, both flask and reactor systems supported phylogenetically diverse communities. These results importantly provide a foundation for laboratory models of industrial bioreactor failure scenarios.
Suboptimal Acclimation of Photosynthesis to Light in Wheat Canopies[CC-BY]

High-resolution 3D reconstruction and ray tracing combined with an empirical model of photosynthesis reveals suboptimal photosynthetic acclimation in wheat canopies. Photosynthetic acclimation (photoacclimation) is the process whereby leaves alter their morphology and/or biochemistry to optimize photosynthetic efficiency and productivity according to long-term changes in the light environment. The three-dimensional architecture of plant canopies imposes complex light dynamics, but the drivers for photoacclimation in such fluctuating environments are poorly understood. A technique for high-resolution three-dimensional reconstruction was combined with ray tracing to simulate a daily time course of radiation profiles for architecturally contrasting field-grown wheat (Triticum aestivum) canopies. An empirical model of photoacclimation was adapted to predict the optimal distribution of photosynthesis according to the fluctuating light patterns throughout the canopies. While the photoacclimation model output showed good correlation with field-measured gas-exchange data at the top of the canopy, it predicted a lower optimal light-saturated rate of photosynthesis at the base. Leaf Rubisco and protein contents were consistent with the measured optimal light-saturated rate of photosynthesis. We conclude that, although the photosynthetic capacity of leaves is high enough to exploit brief periods of high light within the canopy (particularly toward the base), the frequency and duration of such sunflecks are too small to make acclimation a viable strategy in terms of carbon gain. This suboptimal acclimation renders a large portion of residual photosynthetic capacity unused and reduces photosynthetic nitrogen use efficiency at the canopy level, with further implications for photosynthetic productivity. It is argued that (1) this represents an untapped source of photosynthetic potential and (2) canopy nitrogen could be lowered with no detriment to carbon gain or grain protein content.
Modified aging of elite athletes revealed by analysis of epigenetic age markers

Recent progress in epigenomics has led to the development of prediction systems that enable accurate age estimation from DNA methylation data. Our objective was to track responses to intense physical exercise of individual age-correlated DNA methylation markers and to infer their potential impact on the aging processes. The study showed accelerated DNA hypermethylation for two CpG sites in TRIM59 and KLF14. Both markers predicted the investigated elite athletes to be several years older than controls and this effect was more substantial in subjects involved in power sports. Accordingly, the complete 5-CpG model revealed age acceleration of elite athletes (P=1.503x10-7) and the result was more significant amongst power athletes (P=1.051x10-9). The modified methylation of TRIM59 and KLF14 in top athletes may be accounted for by the biological roles played by these genes. Their known anti-tumour and anti-inflammatory activities suggests that intense physical training has a complex influence on aging and potentially launches signalling networks that contribute to the observed lower risk of elite athletes to develop cardiovascular disease and cancer.
BART miRNAs: an unimaginable force in the development of nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a head and neck cancer that represents a major health burden in Southern China and Southeast Asia. Although the close association of NPC with Epstein–Barr virus (EBV) infection has been demonstrated, its exact role in the pathogenesis of this malignancy is still unclear. The expression of EBV-encoded microRNAs, especially BART miRNAs, which are encoded from the BamHI-A region of the viral genome, is detected at a high level in NPC. miRNAs are small noncoding mRNAs that can positively regulate the virus to ensure accurate expression of viral genomes and to modify the gene expression of host cells by negative regulation. Accumulating evidence suggests that ebv-mir-BARTs play a critical role in host cell survival, immune escape, cell proliferation, cell apoptosis, and cancer metabolism, promoting the generation of NPC. This review will summarize our current understanding of the nature and function of ebv-mir-BARTs in NPC.
Germline variation in inflammation-related pathways and risk of Barrett's oesophagus and oesophageal adenocarcinoma

Objective Oesophageal adenocarcinoma (OA) incidence has risen sharply in Western countries over recent decades. Local and systemic inflammation is considered an important contributor to OA pathogenesis. Established risk factors for OA and its precursor, Barrett's oesophagus (BE), include symptomatic reflux, obesity and smoking. The role of inherited genetic susceptibility remains an area of active investigation. Here, we explore whether germline variation related to inflammatory processes influences susceptibility to BE/OA. Design We used data from a genomewide association study of 2515 OA cases, 3295 BE cases and 3207 controls. Our analysis included 7863 single-nucleotide polymorphisms (SNPs) in 449 genes assigned to five pathways: cyclooxygenase (COX), cytokine signalling, oxidative stress, human leucocyte antigen and nuclear factor-κB. A principal components-based analytic framework was employed to evaluate pathway-level and gene-level associations with disease risk. Results We identified a significant signal for the COX pathway in relation to BE risk (p=0.0059, false discovery rate q=0.03), and in gene-level analyses found an association with microsomal glutathione-S-transferase 1 (MGST1); (p=0.0005, q=0.005). Assessment of 36 MGST1 SNPs identified 14 variants associated with elevated BE risk (q<0.05). Four of these were subsequently confirmed (p<5.5×10−5) in a meta-analysis encompassing an independent set of 1851 BE cases and 3496 controls, and are known strong expression quantitative trait loci for MGST1. Three such variants were associated with similar elevations in OA risk. Conclusions This study provides the most comprehensive evaluation of inflammation-related germline variation in relation to risk of BE/OA and suggests that variants in MGST1 influence disease susceptibility.
Foreign Direct Investment and Economic Growth in Cote D'Ivoire: A Time Series Analysis

This paper investigates the impact of foreign direct investment (FDI) inflows on economic growth in Cote Di¯Ivoire during the 1975-2011 period. The selection of this African nation is motivated by the rapid inflows it has experienced over the past decade. Using unit root and cointegration analysis, the resulting error correction model (ECM) suggests that gross fixed capital formation (GFCF) has a short-run positive impact on economic growth, while FDI, the repatriation of net income abroad, and periods involving structural breaks, have a negative effect on economic growth in Cote Di¯Ivoire. In addition, the negative error correction term indicates that deviations from long-run per capita growth during the current year are corrected relatively quickly in the following year, ceteris paribus. The unexpected negative effect of FDI on economic growth may be due to the significant repatriation of profits and dividends the country has experienced in recent years.
Effects of Biochar-Derived Sewage Sludge on Heavy Metal Adsorption and Immobilization in Soils

The object of this study was to evaluate the effect of sewage sludge biochar on adsorption and mobility of Cr, Mn, Cu, and Zn. Biochar (BC400) was produced via pyrolysis of municipal sewage sludge at 400 °C. Maximum adsorption capacities (qm) for Zn, Cr, Mn, and Cu were 5.905, 5.724, 5.681, and 5.342 mg·g−1, respectively, in the mono-metal solution and 2.475, 8.204, 1.01, and 5.415 mg·g−1, respectively, in the multi-metal solution. The adsorption capacities for Mn, Cu, and Zn decreased in the multi-metal solution due to competitive adsorption, whereas the capacity for Cr increased. Surface precipitation is an important mechanism in the sorption of these metals on BC400. The 360-day incubation experiment showed that BC400 application reduced metal mobility in contaminated soils, which was attributed to the substantial decreases in the acid-soluble fractions of Cr, Mn, Cu, and Zn (72.20%, 70.38%, 50.43%, and 29.78%, respectively). Furthermore, the leaching experiment using simulated acid rain indicated that the addition of BC400 enhanced the acid buffer capacity of contaminated soil, and the concentration of Cr, Mn, Cu, and Zn in the leachate was lower than in untreated soil. Overall, this study indicates that sewage sludge biochar application reduces the mobility of heavy metal in co-contaminated soil, and this adsorption experiment is suitable for the evaluation of biochar properties for remediation.
Activation of nuclear factor kappa B and mitogen activated protein kinases in psoriatic arthritis before and after etanercept treatment.

OBJECTIVE To study activation of intracellular pathways depending on nuclear factor kappa B (NFkappaB) and mitogen activated kinases (MAPK) in the synovium of patients with psoriatic arthritis before and after treatment with etanercept. METHODS Synovial biopsies were obtained by needle arthroscopy of the knee in 9 patients with active psoriatic arthritis before the initiation of etanercept. Follow-up biopsies were taken in the same knee after 6 months. Synovitis was studied by histology. Pathway activation was studied by immunofluorescense for phosphorylated ERK, phosphorylated p38, phosphorylated JNK or phosphorylated inhibitor of kappa B (IkappaBalpha) using digital image analysis. RESULTS Histological severity scores were significantly reduced after etanercept treatment. Activation of NFkappaB signaling was found in the lining layer, and in infiltrating and peri-vascular cells in the sublining zone. Activated p38 was present in both lining and sublining layer. In the sublining layer, positive cells were found in inflammatory infiltrates, in perivascular zones and in the endothelium. Activated ERK was mainly present in the sublining layer, both in mononuclear cell infiltrates and perivascularly. Occasional positive cells were found in the lining layer. Activation of JNK was recognized in cells of the lining layer, in some of the sublining cell infiltrates and the perivascular compartment. CONCLUSIONS Etanercept therapy resulted in a significant decrease in NFkappaB, JNK and ERK, but not in p38 activation. Persistent activation of these pathways, albeit reduced, may trigger positive feedback loops and flares of arthritis after cessation of etanercept.
Best Practices in Counseling Young Female Cancer Survivors on Reproductive Health

Abstract In the United States, there are more than 400,000 girls and young women of reproductive-age with a history of cancer. Cancer treatments including surgery, chemotherapy, targeted therapy, and radiation can adversely impact their reproductive health. This review discusses infertility, contraception, and adverse pregnancy and child health outcomes in reproductive-aged cancer survivors, to increase awareness of these health risks for survivors and their health care providers. Infertility rates are modestly higher, while rates of using contraception and using highly effective contraceptive methods are lower in cancer survivors than in women without a history of cancer. During pregnancy, preterm births are also more common in survivors, resulting in more low-birth-weight offspring. Children of cancer survivors do not have more childhood cancers, birth defects, or chromosomal abnormalities than the general population, with the exception of families with hereditary cancer. Reproductive risks in survivors depend on cancer treatment exposures. For example, women with prior abdominal or pelvic radiation have additional risks of spontaneous abortions, small-for-gestational-age offspring and stillbirths, while those with prior chest radiation or anthracycline exposures have higher risks of cardiomyopathy. To help survivors achieve their reproductive goals safely, family planning and preconception counseling are central to survivorship care.
Gradient Descent Learns One-hidden-layer CNN: Don't be Afraid of Spurious Local Minima

We consider the problem of learning a one-hidden-layer neural network with non-overlapping convolutional layer and ReLU activation, i.e., $f(\mathbf{Z}, \mathbf{w}, \mathbf{a}) = \sum_j a_j\sigma(\mathbf{w}^T\mathbf{Z}_j)$, in which both the convolutional weights $\mathbf{w}$ and the output weights $\mathbf{a}$ are parameters to be learned. When the labels are the outputs from a teacher network of the same architecture with fixed weights $(\mathbf{w}^*, \mathbf{a}^*)$, we prove that with Gaussian input $\mathbf{Z}$, there is a spurious local minimizer. Surprisingly, in the presence of the spurious local minimizer, gradient descent with weight normalization from randomly initialized weights can still be proven to recover the true parameters with constant probability, which can be boosted to probability $1$ with multiple restarts. We also show that with constant probability, the same procedure could also converge to the spurious local minimum, showing that the local minimum plays a non-trivial role in the dynamics of gradient descent. Furthermore, a quantitative analysis shows that the gradient descent dynamics has two phases: it starts off slow, but converges much faster after several iterations.
Association of insulin-like growth factor-1 and IGF binding protein-3 with 25-hydroxy vitamin D in pre-pubertal and adolescent Indian girls

Abstract Background: There is a high prevalence of vitamin D deficiency (VDD) in India. Molecular mechanisms suggest a strong relationship between vitamin D and growth factors. However, there is a paucity of literature with regard to a relationship between insulin-like growth factor-1 (IGF-1), insulin-like growth factor binding protein-3 (IGFBP-3) and vitamin D particularly in subjects with VDD. The objective of the study was to assess the relationship between growth factors and serum vitamin D-parathormone (PTH) status in school girls and study the impact of vitamin D supplementation on growth factors in pre-pubertal girls with VDD. Methods: Our study subjects were apparently healthy school girls aged 6–18 years. The baseline height, weight, body mass index (BMI), pubertal status, serum 25-hydroxy vitamin D (25OHD), PTH, IGF-1 and IGFBP-3 were assessed in 847 girls aged 6–18 years and in 190 pre-pubertal girls with VDD following supplementation. Results: The mean age, BMI and serum 25OHD of girls were 11.5±3.2 years, 18.7±4.8 kg/m2 and 9.9±5.6 ng/mL, respectively. VDD was observed in 94.6% of girls. Unadjusted serum IGF-1 levels and IGF-1/IGFBP-3 molar ratio were significantly higher in girls with severe VDD as compared to girls with mild-to-moderate VDD. However, these differences disappeared when adjusted for age, height or sexual maturation. The serum IGF-1 and IGFBP-3 levels increased significantly post supplementation with vitamin D. Conclusions: There were no differences in serum IGF-1 levels and the IGF-1/IGFBP-3 molar ratio among VDD categories when adjusted for age, height and sexual maturation in girls. Vitamin D supplementation resulted in a significant increase in serum IGF-1 levels in VDD pre-pubertal girls.
Patterns of Dental Macrowear in Subfossil Lemur catta from Ankilitelo Cave, Madagascar: Indications of Ecology and Habitat Use over Time

The Ankilitelo cave site, Madagascar, contains a large collection of extant and recently extinct subfossil lemurs including the extant taxa Lemur catta and Eulemur rufifrons, which today are rarely found in sympatry. Dates for this assemblage range from 300 to 13,000 BP, though known dates for extinct primate specimens range between ∼500 and ∼600 BP. Data from Ankilitelo L. catta and E. rufifrons were compared to assess tooth wear in sympatric, related forms. Wear was scored using an ordinal scale from 0 to 5. For P4, M1 and M2, E. rufifrons displays significantly more wear than L. catta. Ankilitelo represents one of the most southerly samples of E. rufifrons, and wear data suggest that in the recent (i.e. Holocene) past, their diet near the edges of their geographic range included mechanically challenging foods. In contrast, sympatric L. catta was using foods in this transitional humid-dry forest with succulent woodlands that were not significantly impacted by recent human actions, and for which they were dentally adapted. Results also suggest that this non-gallery forest habitat may be the ‘adaptive home' of L. catta, given the lack of notable tooth wear when compared to populations currently living in tamarind-dominated riverine gallery forests.
DNA Methylation Profiling in Inflammatory Bowel Disease Provides New Insights into Disease Pathogenesis.

BACKGROUND AND AIMS Inflammatory bowel diseases (IBDs) are heterogeneous disorders with complex aetiology. Quantitative genetic studies suggest that only a small proportion of the disease variance observed in IBD is accounted for by genetic variation, indicating a potential role for differential epigenetic regulation in disease aetiology. The aim of this study was to assess genome-wide DNA methylation changes specifically associated with ulcerative colitis (UC), Crohn's disease (CD) and IBD activity. METHODS DNA methylation was quantified in peripheral blood mononuclear cells (PBMCs) from 149 IBD cases (61 UC, 88 CD) and 39 controls using the Infinium HumanMethylation450 BeadChip. Technical and functional validation was performed using pyrosequencing and the real-time polymerase chain reaction. Cross-tissue replication of the top differentially methylated positions (DMPs) was tested in colonic mucosa tissue samples obtained from paediatric IBD cases and controls. RESULTS A total of 3196 probes were differentially methylated between CD cases and controls, while 1481 probes were differentially methylated between UC cases and controls. There was considerable (45%) overlap between UC and CD DMPs. The top-ranked IBD-associated PBMC differentially methylated region (promoter region of TRIM39-RPP2) was also significantly hypomethylated in colonic mucosa from paediatric UC patients. In addition, we confirmed TRAF6 hypermethylation using pyrosequencing and found reduced TRAF6 gene expression in PBMCs of IBD patients. CONCLUSIONS Our data provide new insights into differential epigenetic regulation of genes and molecular pathways, which may contribute to the pathogenesis and activity of IBD.
Generation and phenotypic characterization of Pde1a mutant mice

It has been proposed that a reduction in intracellular calcium causes an increase in intracellular cAMP and PKA activity through stimulation of calcium inhibitable adenylyl cyclase 6 and inhibition of phosphodiesterase 1 (PDE1), the main enzymes generating and degrading cAMP in the distal nephron and collecting duct, thus contributing to the development and progression of autosomal dominant polycystic kidney disease (ADPKD). In zebrafish pde1a depletion aggravates and overexpression ameliorates the cystic phenotype. To study the role of PDE1A in a mammalian system, we used a TALEN pair to Pde1a exon 7, targeting the histidine-aspartic acid dipeptide involved in ligating the active site Zn++ ion to generate two Pde1a null mouse lines. Pde1a mutants had a mild renal cystic disease and a urine concentrating defect (associated with upregulation of PDE4 activity and decreased protein kinase A dependent phosphorylation of aquaporin-2) on a wild-type genetic background and aggravated renal cystic disease on a Pkd2WS25/- background. Pde1a mutants additionally had lower aortic blood pressure and increased left ventricular (LV) ejection fraction, without a change in LV mass index, consistent with the high aortic and low cardiac expression of Pde1a in wild-type mice. These results support an important role of PDE1A in the renal pathogenesis of ADPKD and in the regulation of blood pressure.