Miracle-dz/UniFAR-FTUs huggingface dataset:
Histone modification alteration coordinated with acquisition of promoter DNA methylation during Epstein-Barr virus infection

Aberrant DNA hypermethylation is a major epigenetic mechanism to inactivate tumor suppressor genes in cancer. Epstein-Barr virus positive gastric cancer is the most frequently hypermethylated tumor among human malignancies. Herein, we performed comprehensive analysis of epigenomic alteration during EBV infection, by Infinium HumanMethylation 450K BeadChip for DNA methylation and ChIP-sequencing for histone modification alteration during EBV infection into gastric cancer cell line MKN7. Among 7,775 genes with increased DNA methylation in promoter regions, roughly half were “DNA methylation-sensitive” genes, which acquired DNA methylation in the whole promoter regions and thus were repressed. These included anti-oncogenic genes, e.g. CDKN2A. The other half were “DNA methylation-resistant” genes, where DNA methylation is acquired in the surrounding of promoter regions, but unmethylated status is protected in the vicinity of transcription start site. These genes thereby retained gene expression, and included DNA repair genes. Histone modification was altered dynamically and coordinately with DNA methylation alteration. DNA methylation-sensitive genes significantly correlated with loss of H3K27me3 pre-marks or decrease of active histone marks, H3K4me3 and H3K27ac. Apoptosis-related genes were significantly enriched in these epigenetically repressed genes. Gain of active histone marks significantly correlated with DNA methylation-resistant genes. Genes related to mitotic cell cycle and DNA repair were significantly enriched in these epigenetically activated genes. Our data show that orchestrated epigenetic alterations are important in gene regulation during EBV infection, and histone modification status in promoter regions significantly associated with acquisition of de novo DNA methylation or protection of unmethylated status at transcription start site.
Impact of HLA Allele-KIR Pairs on HIV Clinical Outcome in South Africa.

BACKGROUND HLA class I contributes to HIV immune control through antigen presentation to cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. In contrast to investigations of CTL, studies of NK cells in HIV control through HLA-killer immunoglobulin-like receptor (KIR) interactions remain sparse in African cohorts. METHODS Treatment-naive, chronically HIV-infected adults (N = 312) were recruited from South Africa, and the effects of HLA-KIR pairs on clinical outcome were analyzed. RESULTS There was no significant difference in viral load among all subjects with HLA alleles from the HLA-C1 group (P = .1). However, differences in HLA-C type significantly influenced viremia among 247 KIR2DL3 positives (P = .04), suggesting that specific HLA-KIR interactions contribute to immune control. Higher viral load (P = .02) and lower CD4+ T-cell counts (P = .008) were observed in subjects with HLA-C*16:01+KIR2DL3+. Longitudinal analysis showed more rapid progression to AIDS among HLA-C*16:01+KIR2DL3+ subjects (adjusted hazard ratio 1.9, P = .03) than those without this genotype, independent of CD4+ T-cell count and viral load. CONCLUSIONS These results highlight the existence of unique anti-HIV innate immunity within distinct populations and the contribution of KIR on NK cells and some CTLs to the well-described HLA-mediated impact on HIV disease progression.
The Effect of Warm-Up on High-Intensity, Intermittent Running Using Nonmotorized Treadmill Ergometry

The aim of this study was to investigate the effect of previous warming on high-intensity intermittent running using nonmotorized treadmill ergometry. Ten male soccer players completed a repeated sprint test (10 × 6-second sprints with 34-second recovery) on a nonmotorized treadmill preceded by an active warm-up (10 minutes of running: 70% &OV0312;o2max; mean core temperature (Tc) 37.8 ± 0.2°C), a passive warm-up (hot water submersion: 40.1 ± 0.2°C until Tc reached that of the active warm-up; 10 minutes ± 23 seconds), or no warm-up (control). All warm-up conditions were followed by a 10-minute static recovery period with no stretching permitted. After the 10-minute rest period, Tc was higher before exercise in the passive trial (38.0 ± 0.2°C) compared to the active (37.7 ± 0.4°C) and control trials (37.2 ± 0.2°C; p < 0.05). There were no differences in pre-exercise oxygen consumption and blood lactate concentration; however, heart rate was greater in the active trial (p < 0.05). The peak mean 1-second maximum speed (MxSP) and group mean MxSP were not different in the active and passive trials (7.28 ± 0.12 and 7.16 ± 0.10 m·s−1, respectively, and 7.07 ± 0.33 and 7.02 ± 0.24 m·s−1, respectively; p > 0.05), although both were greater than the control. The percentage of decrement in performance fatigue was similar between all conditions (active, 3.4 ± 1.3%; passive, 4.0 ± 2.0%; and control, 3.7 ± 2.4%). We conclude that there is no difference in high-intensity intermittent running performance when preceded by an active or passive warm-up when matched for post-warm-up Tc. However, repeated sprinting ability is significantly improved after both active and passive warm-ups compared to no warm-up.
Validity of the Mediterranean Diet and Culinary Index (MediCul) for Online Assessment of Adherence to the ‘Traditional’ Diet and Aspects of Cuisine in Older Adults

The Mediterranean diet is associated with multiple health benefits. Yet, no tool has been specifically developed to assess adherence to the ‘traditional’ Mediterranean diet and cuisine within a Western cohort, and validated for online use. We tested the reliability and validity of online administration of the Mediterranean Diet and Culinary Index (MediCul) among middle-aged and older adults. Participants were recruited in January–March 2017 from the 45 and Up Study, completing MediCul twice. Test-retest reliability was assessed using the paired t-test, intra-class correlation coefficient (ICC) and Bland-Altman plot. Validity was tested against a three-day food record (FR)-derived MediCul score using Bland-Altman and nutrient trends across the MediCul score tertiles. Participants (n = 84; 60% female; 65.4 years (SD = 5.9)), were overweight (BMI 26.1; SD = 4.0) with 1.7 (SD = 1.5) chronic illnesses/conditions. Sequential MediCul tool scores were 56.1/100.0 and 56.8/100.0, respectively (t = −1.019; p = 0.311). Reliability via ICC (ICC = 0.86, 95% CI: 0.789, 0.910, p < 0.0001) and Bland-Altman was good. In Bland-Altman validity analyses, the tool over-reported FR MediCul score by 5.6 points with no systematic bias ((y = 8.7 − 0.06*x) (95% CI: −0.278, 0.158, p = 0.584)). Nutrient trends were identified for MediCul consistent with expected Mediterranean patterns. Online MediCul administration demonstrated good reliability and moderate validity for assessing adherence to a ‘traditional’ Mediterranean pattern among older Australians.
Laparoscopic reversible occlusion of uterine arteries and cornuostomy for advanced interstitial pregnancy

Abstract During laparoscopic enucleation of an interstitial pregnancy, adequate hemostatic control is of paramount importance due to the high vascularization of the uterine cornus. However, no consensus or guidance exists regarding the optimal hemostatic technique. We report laparoscopic reversible uterine arteries occlusion as hemostatic technique during laparoscopic enucleation by cornuostomy of an interstitial pregnancy at advanced gestational age (46 × 40 mm gestational sac). Preliminary identification of the uterine arteries and bilateral reversible occlusion by Hem-o-Lok clips allowed bleeding control during surgery. The laparoscopic procedure was performed without complications and with limited blood loss. The reported case reinforces the feasibility of this minimally invasive technique in interstitial pregnancy.
Wiring and Plumbing in the Brain

No one with common sense would believe that in a house, water movements in pipes could tell you how many lamps are on and how much fuel is used for heat-ing. Surprisingly most neuroscientists are convinced that in the brain monitoring local cerebral blood ﬂ ow (CBF) what I call plumbing, is a reliable surrogate method to localize electrical neuronal activity and monitor metabolic events. This is usually done by functional magnetic resonance imaging (fMRI) a technique that meas-ures haemodynamic changes. In fMRI, the blood-oxygen-level-dependent (BOLD) signal resulting from the paramagnetic properties of deoxyhaemoglobin in red blood cells is measured with precise local and time resolution. In most neuroimaging fMRI studies, activation of the brain with cognitive tasks or sensory stimuli results in a local functional hyperaemia, most of the time accompanied by an increase in the local ﬁ eld potentials (LFP) ( Logothetis, 2008). How activation of the brain trans-mutes in functional hyperaemia is the topic of intense debate among neuroscientists with two hypothesis, the “metabolic” and the “neurogenic” (Estrada and DeFelipe, 1998; Hamel, 2006). The metabolic hypothesis assumes a causal link between neuronal energy demand and the regulation of local CBF. The general assumption, which is supported by PET ﬁ ndings showing comparable functional increases in blood ﬂ ow and glucose uptake (Raichle and Mintun, 2006), is that CBF is coupled to regional glucose utilization, which in turn is directly related to neuronal activ-ity (Magistretti, 2006). Excitatory neuronal activity releases glutamate which activates glia through metabotropic glutamate recep-tors. The activation of glial cells will induce at the same time an increase in the diameter of nearby blood vessels and stimulation of glucose uptake. In this metabolic hypothesis, the activity- dependent regulation of local CBF is a feedback mechanism that does not anticipate possible demand.The metabolic hypothesis was supported by the original observation by Zonta et al. (2003) that astrocytic endfeet surrounding brain blood vessels were releasing vasodi-lating substances; since then other observa-tions have shown that astrocytes could also provoke vasoconstrictions. These opposite observations were conﬁ rmed: activation of astrocytes triggers the formation of ara-chidonic acid that is either converted to 20-hydroxyeicosatetraenoic acid (20-HETE) in smooth muscle causing vasocontrac-tion or to prostaglandin E
Elevated platelet activation in patients with atopic dermatitis and psoriasis: increased plasma levels of beta-thromboglobulin and platelet factor 4.

BACKGROUND Beyond their role in hemostasis and thrombosis, platelets are important for modulating inflammatory reactions. Activated platelets play a role in the pathomechanism of inflammatory diseases such as asthma, but little is known about platelet activation in chronic skin inflammation, including atopic dermatitis (AD) and psoriasis. Furthermore, the relationship between platelet activation and disease severity is not understood. This work was performed to investigate plasma levels of beta-thromboglobulin (beta-TG) and platelet factor 4 (PF4) as platelet activation markers in patients with AD or psoriasis, and to determine the relationships between these markers and disease severity. METHODS Plasma levels of beta-TG and PF4 were measured by enzyme-linked immunoassay in 22 healthy controls, 44 patients with AD, and 16 patients with psoriasis. The relationships between these markers and the scoring AD (SCORAD) index, blood eosinophilia, serum IgE and serum lactate dehydrogenase were investigated in AD patients, and relationships with the psoriasis area and severity index (PASI) score were examined in psoriatic patients. RESULTS Plasma beta-TG and PF4 levels were significantly higher in patients with AD or psoriasis compared with healthy controls. beta-TG and PF4 levels correlated with the SCORAD index, and PF4 levels correlated with PASI scores. Elevated beta-TG and PF4 levels were significantly reduced after treatments. CONCLUSIONS Our results show that blood platelets are activated in patients with AD or psoriasis, suggesting that activated platelets play a role in the pathomechanism of chronic skin inflammation. Furthermore, plasma beta-TG and PF4 may be markers for the severity of AD and psoriasis.
Plasma donor-derived cell-free DNA kinetics after kidney transplantation using a single tube multiplex PCR assay

Background After transplantation, cell-free DNA derived from the donor organ (ddcfDNA) can be detected in the recipient’s circulation. We aimed to quantify ddcfDNA levels in plasma of kidney transplant recipients thereby investigating the kinetics of this biomarker after transplantation and determining biological variables that influence ddcfDNA kinetics in stable and non-stable patients. Materials and methods From 107 kidney transplant recipients, plasma samples were collected longitudinally after transplantation (day 1–3 months) within a multicenter set-up. Cell-free DNA from the donor was quantified in plasma as a fraction of the total cell-free DNA by next generation sequencing using a targeted, multiplex PCR-based method for the analysis of single nucleotide polymorphisms. A subgroup of stable renal transplant recipients was identified to determine a ddcfDNA threshold value. Results In stable transplant recipients, plasma ddcfDNA% decreased to a mean (SD) ddcfDNA% of 0.46% (± 0.21%) which was reached 9.85 (± 5.6) days after transplantation. A ddcfDNA threshold value of 0.88% (mean + 2SD) was determined in kidney transplant recipients. Recipients that did not reach this threshold ddcfDNA value within 10 days after transplantation showed a higher ddcfDNA% on the first day after transplantation and demonstrated a higher individual baseline ddcfDNA%. Conclusion In conclusion, plasma ddcfDNA fractions decreased exponentially within 10 days after transplantation to a ddcfDNA threshold value of 0.88% or less. To investigate the role of ddcfDNA for rejection monitoring of the graft, future research is needed to determine causes of ddcfDNA% increases above this threshold value.
Assessment of anti-MDA5 antibody as a diagnostic biomarker in patients with dermatomyositis-associated interstitial lung disease or rapidly progressive interstitial lung disease

Anti-melanoma differentiation-associated protein 5 (MDA5) antibody have been found in dermatomyositis (DM)-associated interstitial lung disease (DM-ILD) and DM-associated rapidly progressive ILD (DM-RPILD). Due to the conflicting results regarding the association between anti-MDA5 antibody and DM-ILD or DM-RPILD and the diagnostic value of this antibody for DM-ILD and DM-RPILD, we performed this meta-analysis. A systematic search was performed to identify studies published to January 14, 2017. Sixteen publications with 491 DM with ILD versus 605 DM without ILD, as well as eighteen publications with 186 DM with RPILD and 790 DM without RPILD were included. The pooled sensitivity, specificity, and area under the curve (AUC) values of anti-MDA5 antibody for DM-ILD were 0.47 (95% CI: 0.37–0.57), 0.96 (95% CI, 0.92–0.97), and 0.90 (95% CI: 0.88–0.93), respectively, with a low sensitivity value. The pooled sensitivity, specificity, and AUC values were 0.83 (95% CI: 0.77–0.88), 0.86 (95% CI: 0.80–0.91), and 0.87 (95% CI: 0.84–0.90) for DM with RPILD versus without RPILD with good sensitivity and specificity values. Trial sequential analysis showed sufficient evidence to support that anti-MDA5 antibody was associated with DM-ILD and DM-RPILD. The statistical power of this study calculated using G*Power version 3.1. 9.2 was more than 99% (α = 0.05). Taken together, these findings suggest that anti-MDA5 antibody has a potential useful ability as a noninvasive biomarker in the diagnosis of RPILD in patients with DM.
The preventive effect of aqueous extract of Rosemary (Rosmarinus officinalis) leaves against the nephrotoxicity of carbon tetrachloride in mice

Abstract The present study aimed to evaluate the performance effect of aqueous extract of Rosmarinus officinalis (AERO) against the kidney toxicity induced by CCl4 in mice. The results showed that the renal damage induced by CCl4 was associated with a rise in oxidative stress monitored by a significant increase of TBARS and PCO levels (+89% and +136% respectively, p < .001) and a significant decrease of GSH level (–68%, p < .001) and antioxidants enzymes such as SOD, CAT, and GPX activities (–41.7%, –47.8%, and –50.5%; p < .001, respectively). Also, the nephropathology parameters including creatinine, BUN, and urea (+68.9%, +47%, +48·6% respectively, p < .05) were remarkably increased. These findings were substantiated by histological study. Pretreatment with Rosemary extract significantly attenuated the CCl4 related toxic effects via more than one mechanism such as the inhibition of lipid peroxidation, the stimulation of the synthesis of cellular antioxidants, the decrease of the biomarker kidney and the correction of the kidney structure. We can conclude that the Rosemary is efficient in the prevention of kidney function against CCl4 toxicity.
A Study of the Effects of Hf and Sn on the Microstructure, Hardness and Oxidation of Nb-18Si Silicide Based Alloys without Ti Addition

The paper presents the results of an experimental study of large (≈0.6 kg) arc melted buttons of four Ti free Nb-silicide based alloys with Sn addition with nominal compositions (at.%) Nb-18Si-5Hf-5Sn (EZ1), Nb-18Si-5Al-5Sn (EZ7), Nb-18Si-5Cr-5Hf-5Sn (EZ3) and Nb-18Si-5Al-5Hf-5Sn (EZ4). The alloys were studied in the as-cast and heat treated conditions. In all the alloys there was macrosegregation of Si (MACSi). Among the single element additions Hf had the weakest and Sn the strongest effect on MACSi. The simultaneous presence of Cr and Hf in the alloy EZ3 had the strongest effect on MACSi. In all the alloys the βNb5Si3 was the primary phase and was present after the heat treatment(s), the Nb3Si silicide was suppressed and the A15-Nb3Sn intermetallic was stable. The Nbss was not stable in the alloys EZ7 and EZ4 and the C14-NbCr2 Laves phase was stable in the alloy EZ3. Very Hf-rich Nb5Si3 was stable in the alloy EZ4 after prolonged heat treatments. Eutectics were observed in all the alloys. These were binary eutectics in the alloys EZ1 and EZ7, where respectively they consisted of the Nbss and βNb5Si3, and βNb5Si3 and A15-Nb3Sn phases. Most likely ternary eutectics consisting of the Nbss, C14-NbCr2 and βNb5Si3, and Nbss, βNb5Si3 and A15-Nb3Sn phases were observed, respectively in the alloys EZ3 and EZ4. The addition of Al increased the vol% of the Nb5Si3 and A15-Nb3Sn phases, particularly after the heat treatment(s). The lattice parameter of Nb respectively increased and decreased with the addition of Hf, and Al or Cr and the latter element had the stronger negative effect. Pest oxidation was not suppressed in the alloys of this study.
Effect of Bednets and Indoor Residual Spraying on Spatio-Temporal Clustering of Malaria in a Village in South Ethiopia: A Longitudinal Study

Background Understanding the spatio-temporal pattern of malaria transmission where prevention and control measures are in place will help to fine-tune strategies. The objective of this study was to assess the effect of mass distribution of bednets and indoor residual spraying (IRS) with insecticides on the spatio-temporal clustering of malaria in one malaria endemic village in south Ethiopia. Methods A longitudinal study was conducted from April 2009 to April 2011. The average population was 6631 in 1346 locations. We used active and passive searches for malaria cases for 101 weeks. SatScan v9.1. 1 was used to identify statistically significant retrospective space–time clusters. A discrete Poisson based model was applied with the aim of identifying areas with high rates. PASW Statistics 18 was used to build generalized Poisson loglinear model. Results The total number of both types of malaria episodes was 622, giving 45.1 episodes per 1000 persons per year; among these, episodes of Plasmodium falciparum and vivax infection numbered 316 (22.9 per 1000 per year) and 306 (22.2 per 1000 per year), respectively. IRS with Dichlorodiphenyltrichloroethane (DDT) and later with Deltamethrin and free mass distribution of insecticide-treated nets (ITNs) were carried out during the study period. There was space–time clustering of malaria episodes at a household level. The spatio-temporal clustering of malaria was not influenced by free mass distribution of ITNs; however, the time-span of the spatio-temporal clustering of malaria cases ended after IRS with Deltamethrin. The presence of clusters on the south-east edge of the village was consistent with the finding of an increasing risk of acquiring malaria infection for individuals who lived closer to the identified vector breeding site. Conclusion The risk of getting malaria infection varied significantly within one village. Free mass distribution of ITNs did not influence the spatio-temporal clustering of malaria, but IRS might have eliminated malaria clustering.
Older Worker Identity and Job Performance: The Moderator Role of Subjective Age and Self-Efficacy

Older Worker Identity consists of the internalization of negative beliefs and attitudes towards aged employees by these same people. This research aims to explore the moderator role both of subjective age and self-efficacy in the relationship between older worker identity and job performance. The study was conducted with a panel design, including a sample of +40 Spanish workers (n = 200), with two waves (4-months interval). The findings supported the moderator role of subjective age in the relationship, while it failed to support the moderator role of self-efficacy. These findings underline that workers who actively manage their subjective age perceptions could age successfully at work. The implications of this study for counseling practices are discussed.
Risk factors for inpatient violence and self-harm in forensic psychiatry: the role of head injury, schizophrenia and substance misuse

ABSTRACT Objective: To investigate factors relevant to violence and self-harm in forensic psychiatric inpatients the cross-sectional association between four potential contributory factors; head injury, schizophrenia, drug and alcohol misuse, and self-harm or violence-related outcomes was examined. Methodology: Data were extracted from an existing dataset of routinely collected data on all patients under the care of Scotland’s Forensic Mental Health Managed Care Network, of whom (n = 432) met inclusion criteria. A Factorial MANOVA and Pearson’s chi-square tests were conducted to assess the relationship between potential contributory factors and self-harm and violence. Results: Forty-seven individuals had a documented head injury (10.9%). The presence of head injury was significantly associated with inpatient violence and assessed violence risk. Number of historic violent offences was significantly associated with a history of drug misuse and co-morbid alcohol misuse and schizophrenia. Self-harm was significantly associated with drug misuse and a diagnosis of schizophrenia. Conclusion: These findings highlight a significant association between head injury and actual/assessed risk in forensic psychiatry, over and above that of substance misuse and a diagnosis of schizophrenia, emphasising the need for routine assessment of head injury in clinical practice. Further examination of the impact of head injury in forensic psychiatric populations is needed.