Miracle-dz/UniFAR-FTUs huggingface dataset:
Global DNA 5‐Hydroxymethylcytosine and 5‐Formylcytosine Contents Are Decreased in the Early Stage of Hepatocellular Carcinoma

Methylation of the fifth position of cytosine (5mC) is an important epigenetic modification of DNA. It has been shown that the oxidized derivatives of 5mC, namely 5‐hydroxymethylcytosine (5hmC), 5‐formylcytosine (5fC), and 5‐carboxylcytosine (5caC), are in dynamic existence and have distinct regulatory functions. In the current study, we investigated whether there are changes in the contents of all three 5mC‐oxidized derivatives in the hepatocellular carcinoma (HCC) genome and further explored the underlying mechanisms. We showed that both global genomic 5hmC and 5fC contents were decreased significantly in the very early stage (stage 0, Barcelona Clinic Liver Cancer [BCLC] staging) of HCC compared with those of paratumor tissues. Noteworthily, 5fC content continued to decrease in the late stage (BCLC staging from 0 to A) of HCC. The 5caC content in HCC tissues was below the detection threshold. Hepatitis B virus (HBV) infection was associated with 5mC, 5hmC, or 5fC decrease in HCC; and measurements in cell lines integrated with or without HBV DNA showed consistent results. On the other hand, both the expression level of ten‐eleven translocation enzyme 2 (TET2) and α‐ketoglutarate content were decreased significantly in HCC. The significantly positive correlations among the expression levels of DNA methylation–related enzymes in paratumor tissues were generally attenuated or even disappeared in HCC tumor tissues. The decreases of both 5hmC and 5fC contents in genomic DNA were associated with poor prognosis of HCC patients. Conclusion: Global 5hmC and 5fC contents were decreased significantly in the very early stage of HCC; the decrease of 5hmC and 5fC was mainly due to the decrease of 5mC and associated with HBV infection, decreased TET enzyme activity, and uncoordinated expression of DNA methylation–related enzymes.
An author keyword analysis for mapping Sport Sciences

Scientific production has increased exponentially in recent years. It is necessary to find methodological strategies for understanding holistic or macro views of the major research trends developed in specific fields. Data mining is a useful technique to address this task. In particular, our study presents a global analysis of the information generated during last decades in the Sport Sciences Category (SSC) included in the Web of Science database. An analysis of the frequency of appearance and the dynamics of the Author Keywords (AKs) has been made for the last thirty years. Likewise, the network of co-occurrences established between words and the survival time of new words that have appeared since 2001 has also been analysed. One of the main findings of our research is the identification of six large thematic clusters in the SSC. There are also two major terms that coexist ('REHABILITATION' and 'EXERCISE') and show a high frequency of appearance, as well as a key behaviour in the calculated co-occurrence networks. Another significant finding is that AKs are mostly accepted in the SSC since there has been high percentage of new terms during 2001–2006, although they have a low survival period. These results support a multidisciplinary perspective within the Sport Sciences field of study and a colonization of the field by rehabilitation according to our AK analysis.
Cyclic AMP Signaling Promotes the Differentiation of Human Induced Pluripotent Stem Cells into Intestinal Epithelial Cells

To develop a novel in vitro system for predicting intestinal drug absorption using human induced pluripotent stem (iPS) cell–derived intestinal epithelial cells, the cells need to have sufficient drug-metabolizing enzyme and drug transporter activities. We found that cyclic adenosine monophosphate (cAMP) signaling plays an important role in the differentiation of human iPS cells into intestinal epithelial cells. In this study, we aimed to demonstrate the effects of signaling activation in the intestinal differentiation of human iPS cells and the pharmacokinetic characteristics of human iPS cell–derived intestinal epithelial cells. Human iPS cells were differentiated into intestinal stem cells using activin A and fibroblast growth factor 2. Subsequently, the intestinal stem cells were maturated into intestinal epithelial cells by treatment with 8-bromo-cyclic adenosine monophosphate (8-Br-cAMP) and 3-isobutyl-1-methylxanthine (IBMX), which activate cAMP signaling. The expression levels of intestinal markers and pharmacokinetics-related genes in the differentiated cells were markedly increased by using 8-Br-cAMP and IBMX. In the cells differentiated with the compound we observed cytochrome P450 (CYP) 3A4 inducibility via pregnane X receptor and vitamin D receptor. The metabolic activities of CYP2C9, CYP2C19, CYP2D6, CYP3A4/5, and UDP-glucuronosyltransferase, which are expressed in the human small intestine, were also markedly increased. Furthermore, uptake of glycylsarcosine via peptide transporter 1 was markedly increased. The cells differentiated with the compounds also had drug transporter activities via organic anion transporters and P-glycoprotein. This study is the first to report that the activation of cAMP signaling promotes differentiation of human iPS cell–derived intestinal epithelial cells.
Adolescent Isolation Interacts With DISC1 Point Mutation to Impair Adult Social Memory and Synaptic Functions in the Hippocampus

Disrupted-in-schizophrenia 1 (DISC1) is a strong candidate susceptibility gene for a spectrum of neuropsychiatric diseases including schizophrenia, bipolar disorder and major depression, all of which are thought to result from interactions between gene mutations and environmental risk factors such as influenza, trauma and stress. Adolescence is a key period susceptible to stress and stress-related mental illnesses. In a previous study, we found that although DISC1 L100P point mutation mice shows object recognition deficits, their sociability and social memory are relatively normal. Therefore, in this article, we investigated whether the interaction between adolescent stress and DISC1 L100P point mutation affects adult social memory, and we explored the underlying mechanisms. We found that adolescent stress (isolation from 5 weeks to 8 weeks of age) specifically impaired social memory of adult DISC1 L100P mice but not that of WT littermates, which could be rescued by administration of atypical antipsychotic drug clozapine. On the other hand, it did not induce anxiety or depression in adult mice. Adolescent isolation exacerbated adult neurogenesis deficits in the hippocampus of DISC1 L100P mice, while it had no effect on WT mice. In addition, we found that adolescent isolation led to long lasting changes in synaptic transmission and plasticity in the hippocampal circuits, some of which are specific for DISC1 L100P mice. In summary, we identified here the specific interaction between genetic mutation (DISC1 L100P) and adolescence social stress that damages synaptic function and social memory in adult hippocampal circuits. Highlights – Adolescent isolation (from 5 weeks to 8 weeks of age) impairs adult social memory when combined with DISC1 L100P point mutation. – Adolescent isolation exacerbates adult neurogenesis deficit in the hippocampus of L100P mice but has no similar effect on WT mice. – Adolescent isolation causes long lasting changes in synaptic transmission and plasticity of the hippocampal network in DISC1 L100P mice.
Meta-Analysis Results on the Association Between TP53 Codon 72 Polymorphism With the Susceptibility to Oral Cancer

Objectives: TP53 is an important tumor suppressor gene to maintain genomic integrity, and its mutations increase the susceptibility to oral carcinoma. Previous published studies have reported the relation of TP53 codon 72 polymorphism with the risk of oral carcinoma, but the results remain controversial and inconclusive. Methods: We therefore utilized meta-analysis based on a comprehensive search in PubMed, EMBASE, and Google of Scholar databases up to August 19, 2017. Results: Total 3,525 cases and 3,712 controls from 21 case-control studies were selected. We found no significant association between TP53 codon 72 polymorphism and oral carcinoma susceptibility in all genetic contrast models, including subgroup analysis based on control source and ethnicity. Furthermore, TP53 codon 72 polymorphism was not significant associated with oral carcinoma susceptibility in tobacco or alcohol use, and HPV infection status. Our results were confirmed by sensitivity analysis and no publication bias was found. Conclusions: Taken together, our data indicate that TP53 codon 72 polymorphism is not associated with the susceptibility to oral carcinoma.
Trends in avoidable mortality over the life course in Mexico, 1990–2015: a cross-sectional demographic analysis

Objective To analyse average lifespan and quantify the effect of avoidable/amenable mortality on the difference between state-specific mortality and a low-mortality benchmark in Mexico during 1990–2015. Design Retrospective cross-sectional demographic analysis using aggregated data. Setting Vital statistics from the Mexican civil registration system. Participants Aggregated national data (from 91.2 million people in 1995 to 119.9 in 2015) grouped in 64 populations (32 Mexican states (including Mexico City) by sex) with cause-of-death data. Main outcome measures Cause-specific contributions to the gap in life expectancy with a low-mortality benchmark in three age groups (0–14, 15–49 and 50–84 years). Results Infants and children under the age of 15 years show improvements towards maximal survival in all states. However, adult males aged 15 to 49 years show deterioration after 2006 in almost every state due to increasing homicides, and a slow recovery thereafter. Out of 35 potential years, females and males live on average 34.57 (34.48 to 34.67) and 33.80 (33.34 to 34.27), respectively. Adults aged 50 to 84 years show an unexpected decrease in the low mortality benchmark, indicating nationwide deterioration among older adults. Females and males in this age group show an average survival of 28.59 (27.43 to 29.75) and 26.52 (25.33 to 27.73) out of 35 potential years, respectively. State gaps from the benchmark were mainly caused by ischaemic heart diseases, diabetes, cirrhosis and homicides. We find large health disparities between states, particularly for the adult population after 2005. Conclusions Mexico has succeeded in reducing mortality and between-state inequalities in children. However, adults are becoming vulnerable as they have not been able to reduce the burden of violence and conditions amenable to health services and behaviours, such as diabetes, ischaemic heart diseases and cirrhosis. These trends have led to large health disparities between Mexican states in the last 25 years.
Gastric cooling and menthol cause an increase in cardiac parasympathetic efferent activity in healthy adult human volunteers

What is the central question of this study? How do gastric stretch and gastric cooling stimuli affect cardiac autonomic control? What is the main finding and its importance? Gastric stretch causes an increase in cardiac sympathetic activity. Stretch combined with cold stimulation result in an elimination of the sympathetic response to stretch and an increase in cardiac parasympathetic activity, in turn resulting in a reduction in heart rate. Gastric cold stimulation causes a shift in sympathovagal balance towards parasympathetic dominance. The cold‐induced bradycardia has the potential to decrease cardiac workload, which might be significant in individuals with cardiovascular pathologies.
Cognitive Techniques for Early Detection of Cybersecurity Events

The early detection of cybersecurity events such as attacks is challenging given the constantly evolving threat landscape. Even with advanced monitoring, sophisticated attackers can spend as many as 146 days in a system before being detected. This paper describes a novel, cognitive framework that assists a security analyst by exploiting the power of semantically rich knowledge representation and reasoning with machine learning techniques. Our Cognitive Cybersecurity system ingests information from textual sources, and various agents representing host and network-based sensors, and represents this information in a knowledge graph. This graph uses terms from an extended version of the Unified Cybersecurity Ontology. The system reasons over the knowledge graph to derive better actionable intelligence to security administrators, thus decreasing their cognitive load and increasing their confidence in the system. We have developed a proof of concept framework for our approach and demonstrate its capabilities using a custom-built ransomware instance that is similar to WannaCry.
Oxidative stress in asthma: Part of the puzzle

An imbalance between the production of reactive oxygen species and the capacity of antioxidant defense mechanisms favoring oxidants is called oxidative stress and is implicated in asthmatic inflammation and severity. Major reactive oxygen species that are formed endogenously include hydrogen peroxide, superoxide anion, hydroxyl radical, and hypohalite radical; and the major antioxidants that fight against the endogenous and environmental oxidants are superoxide dismutase, catalase, and glutathione. Despite the well‐known presence of oxidative stress in asthma, studies that target oxidative burden using a variety of nutritional, pharmacological, and environmental approaches have generally been disappointing. In this review, we summarize the current knowledge on oxidative stress and antioxidant imbalance in asthma. In addition, we focus on possible biomarkers of oxidative stress in asthma and on current and future treatment strategies using the modulation of oxidative stress to treat asthma patients.
L. S. Vygotsky and Contemporary Developmental Psychology.

Central themes from L. S. Vygotsky's writings that have particular relevance for contemporary developmental psychology are outlined, and these ideas are extended in light of recent theoretical advances in the social sciences and humanities. The discussion focuses primarily on Vygotsky's claims about the social origins and social nature of higher (i.e., uniquely human) mental functioning and on his understanding of culture. His claims about the social origins of individual mental functioning have implications for the definition of terms such as "cognition" and " memory" as well as for how empirical research on these processes can be pursued. His understanding of culture is shown to be derivative of his account of the "psychological tools" that mediate human mental functioning. It is argued that efforts need to be made to elaborate a notion of culture within a Vygotskian framework that takes into account contemporary ideas and findings in the social sciences and humanities.
Detection of pesticides on navel orange skin by surface-enhanced Raman spectroscopy coupled with Ag nanostructures

Residual pesticides such as phosmet and chlorpyrifos in fruit have become a public concern problem in recent years. In this study, surface-enhanced Raman spectroscopy (SERS) was used to detect and characterize pesticides extracted from navel orange surfaces. Silver colloid was prepared for getting the SERS of phosmet and chlorpyrifos. Enhanced Raman signals of phosmet over a concentration range of 5 mg/L to 30 mg/L and chlorpyrifos over a concentration range of 5 mg/L to 20 mg/L were acquired. Partial least squares (PLS) regression combined with different data preprocessing methods was used to develop quantitative models. With the second derivative data preprocessing, the best prediction model of phosmet pesticide was achieved with a correlation coefficient (r) of 0.852 and the root mean square error of prediction (RMSEP) of 5.177 mg/L. The best prediction model of chlorpyrifos pesticide was achieved with r of 0.843 and the RMSEP of 2.992 mg/L using the multiplicative scatter correction (MSC) and first derivative data preprocessing. This study indicated that SERS coupled with Ag nanostructures is a potential tool for analysis of phosmet and chlorpyrifos pesticide residues. Keywords: pesticides residues, detection, silver colloid, surface enhanced Raman spectroscopy, navel orange, food safety DOI: 10.3965/j.ijabe. 20160902.1960 Citation: Liu Y D, Zhang Y X, Wang H Y, Ye B. Detection of pesticides on navel orange skin by surface-enhanced Raman spectroscopy coupled with Ag nanostructures. Int J Agric & Biol Eng, 2016; 9(2): 179－185.
Inhibitory effect of antagonistic bio-agents and chitosan on the growth of tomato root rot pathogens In vitro

Fungal and bacterial bio-agents and the by-product chitosan as fungicides alternatives were evaluated for their inhibitory effect against the growth of tomato root rot pathogenic fungi under laboratory conditions. The tested pathogenic fungi were Fusarium oxysporum radicisycopersici, F. oxysporum lycopersici, F. solani, Rhizoctonia solani, Sclerotium rolfsii, Macrophomina phaseolinae, Pythium sp. and Phytophthora sp. , Meanwhile, isolates of the antagonistic microorganisms, i.e. T. harzianum, T. viride, Bacillus subtilis, and P. fluorescens. Mycelial growth of pathogenic fungi was significantly reduced by the inhibitor action produced by all antagonistic agents tested. The antagonistic fungi had a greater effect on the retardation of growth (75.5--100%) compared with the bacterial agents (57.7—83.3%). The inhibitor effect of the two tested chitosan (High and Low molecular weight) was increased as chitosan concentration is increased in growth medium to reach its maximum at the highest concentration (5 g/L). Complete inhibition of tested fungal growth was observed at the concentration of 4 g/L of LMW chitosan, while the highest fungal growth reduction was recorded in PDA-amended with HMW at the same concentration. On the light of the present study, it could be suggested that the use of chitosan as natural safe materialsalone or in combination with bio agents is considered one of low cost and effective applicable methods for controlling such soil-borne plant pathogens causing plant diseases.
Serum biochemistry and native protein electrophoresis in diarrheic calves with arthritis.

In this study, serum biochemistry and native protein electrophoresis in newborn calves with diarrhea and arthritis, were performed in order to evaluate the changes along with clinical findings for their possible application in the diagnosis and prognosis of disease. Based on clinical examination, animals were allotied into two groups comprising either diseased or healthy animals. Urea, creatinine, ALT, AST, LDH, albumin, total protein, glucose, total cholesterol, uric acid and iron levels were determined in the sera. Serum protein native polyacrilamide gel electrophoresis (nPAGE) was performed followed by protein band ratio estimation supported with densitometry at 596 nm. Differences between the average mean of healthy and diseased animals were compared statistically (Kruskal-Walley test). In this study a decrease in serum glucose and cholesterol values (p<0.001), increase in urea, LDH levels and 1-and 2-globulin levels (p<0.01 and p<0.05 respectively) were found to be associated with the disease. As a result, the observed significant changes in biochemical parameters and clinical investigation in calves, suggesting acute inflammation causing the decrease in glucose and increase in -globulins, may be of prognostic value.
Treatment of domestic wastewater by anaerobic denitrification: Influence of the type of support media on the production of extracellular polymer substances

Eighteen Erlenmeyer flask containing six different support media [pozzolan, polyvinyl chloride1 (PVC1), polyvinyl chloride2 (PVC2), foam, polyethylene terephthalate (PET) and polystyrene (PS)] were subject to identical volumetric organic loadings and hydraulic retention time in treating synthetic protein ± carbohydrate waste. The objective was to examine the influence of support media on performance of anaerobic denitrification and retention and their resulting impact on system performance and failure. According to the results relative to every control support media, it was noticed that the best support media were the ones in PVC1 and PVC2, with successive reduction rates of 68.33 and 61.93% for chemical oxygen demand (COD), and 55 and 49% for nitrate. On the other hand, in two submerged anaerobic biofilter reactor packed with the support media of PVC1 and PVC2, the reactor with PVC1 media exhibited 89.93% COD and 78.75% nitrate removal efficiency attributable to its higher production of EPSp and EPSc. Key words: Wastewater, anaerobic biofilm, extracellular polymeric substances (EPS), extraction, support media.
Meridional circulation in turbulent protoplanetary disks

Context. Based on the viscous disk theory, a number of recent studies have suggested there is large-scale meridional circulation in protoplanetary disks. Such a flow could account for the presence of crystalline silicates, including calcium- and aluminum-rich inclusions (CAIs), at large distances from the sun. Aims. This paper aims at examining whether such large-scale flows exist in turbulent protoplanetary disks. Methods. High-resolution global hydrodynamical and magnetohydrodynamical (MHD) numerical simulations of turbulent protoplanetary disks were used to infer the properties of the flow in such disks. Results. By performing hydrodynamic simulations using explicit viscosity, we demonstrate that our numerical setup does not suffer from any numerical artifact. The aforementioned meridional circulation is easily recovered in viscous and laminar disks and is quickly established. In MHD simulations, the magnetorotational instability drives turbulence in the disks. Averaging out the turbulent fluctuations on a long timescale, the results fail to show any large-scale meridional circulation. A detailed analysis of the simulations show that this lack of meridional circulation is due to the turbulent stress tensor having a vertical profile different from the viscous stress tensor. A simple model is provided that successfully accounts for the structure of the flow in the bulk of the disk. In addition to those results, possible deviations from standard vertically averaged α disk models are suggested by the simulations and should be the focus of future work. Conclusions. Global MHD numerical simulations of fully ionized and turbulent protoplanetary disks are not consistent with the existence of a large-scale meridional flow. As a consequence, the presence of crystalline silicates at large distance of the central star cannot be accounted for by that process as suggested by recent models based on viscous disk theory.
The effect of Ramadan fasting on endocrine system.

In the religion of Islam, fasting is obligatory for healthy adults during Ramadan. Millions of Muslims around the world practice fasting in this holy month which may cause different metabolic and hormonal changes due to the restrictions in regular caloric intake. This article was aimed to review some possible effects of Ramadan fasting on the endocrine system which has a great impact on physiological and cellular processes through a wide variety of hormones. Despite various studies regarding the impact of Islamic fasting on a number of hormonal values, yet there is not any obvious consensus on its impact on human health. In conclusion, this article recommended normal people to continue fasting during this holy month because despite the modifications that occur in the secretion pattern of some hormones, it causes no major alteration in the health of normal subjects; it is also effective for maintenance of remission in some diseases.