Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of folic acid fortification on global DNA methylation and one-carbon biomarkers in the Women's Health Initiative Observational Study cohort

DNA methylation is an epigenetic mechanism that regulates gene expression and can be modified by one-carbon nutrients. The objective of this study was to investigate the impact of folic acid (FA) fortification of the US food supply on leukocyte global DNA methylation and the relationship between DNA methylation, red blood cell (RBC) folate, and other one-carbon biomarkers among postmenopausal women enrolled in the Women's Health Initiative Observational Study. We selected 408 women from the highest and lowest tertiles of RBC folate distribution matching on age and timing of the baseline blood draw, which spanned the pre- (1994–1995), peri- (1996–1997), or post-fortification (1998) periods. Global DNA methylation was assessed by liquid chromatography-tandem mass spectrometry and expressed as a percentage of total cytosine. We observed an interaction (P = 0.02) between fortification period and RBC folate in relation to DNA methylation. Women with higher (vs. lower) RBC folate had higher mean DNA methylation (5.12 vs. 4.99%; P = 0.05) in the pre-fortification period, but lower (4.95 vs. 5.16%; P = 0.03) DNA methylation in the post-fortification period. We also observed significant correlations between one-carbon biomarkers and DNA methylation in the pre-fortification period, but not in the peri- or post-fortification period. The correlation between plasma homocysteine and DNA methylation was reversed from an inverse relationship during the pre-fortification period to a positive relationship during the post-fortification period. Our data suggest that (1) during FA fortification, higher RBC folate status is associated with a reduction in leukocyte global DNA methylation among postmenopausal women and; (2) the relationship between one-carbon biomarkers and global DNA methylation is dependent on folate availability.
Geometry of the Carotid Bifurcation Predicts Its Exposure to Disturbed Flow

Background and Purpose— That certain vessels might be at so-called geometric risk of atherosclerosis rests on assumptions of wide interindividual variations in disturbed flow and of a direct relationship between disturbed flow and lumen geometry. In testing these often-implicit assumptions, the present study aimed to determine whether investigations of local risk factors in atherosclerosis can indeed rely on surrogate geometric markers of disturbed flow. Methods— Computational fluid dynamics simulations were performed on carotid bifurcation geometries derived from MRI of 25 young adults. Disturbed flow was quantified as the surface area exposed to low and oscillatory shear beyond objectively-defined thresholds. Interindividual variations in disturbed flow were contextualized with respect to effects of uncertainties in imaging and geometric reconstruction. Relationships between disturbed flow and various geometric factors were tested via multiple regression. Results— Relatively wide variations in disturbed flow were observed among the 50 vessels. Multiple regression revealed a significant (P<0.002) relationship between disturbed flow and both proximal area ratio (&bgr;≈0.5) and bifurcation tortuosity (&bgr;≈−0.4), but not bifurcation angle, planarity, or distal area ratio. These findings were shown to be insensitive to assumptions about the flow conditions and to the choice of disturbed flow indicator and threshold. Conclusions— Certain geometric features of the young adult carotid bifurcation are robust surrogate markers of its exposure to disturbed flow. It may therefore be reasonable to consider large-scale retrospective or prospective imaging studies of local risk factors for atherosclerosis without the need for time-consuming and expensive flow imaging or CFD studies.
Genetic Characteristics Of An Ancient Nomadic Group In Northern China

Nomadic populations have played a significant role in the history of not only China but also in many nations worldwide. Because they had no written language, an important aspect in the study of these people is the discovery of their tombs. It has been generally accepted that Xiongnu was the first empire created by nomadic tribe in the 3rd century B.C. However, little population genetic information is available concerning the Donghu, another flourishing nomadic tribe at the same period because of the restriction of materials until Jinggouzi site was excavated. In order to test the genetic characteristics of ancient people in this site and explore the relationship between Jinggouzis and Donghus, two uniparentally inherited markers were analyzed from 42 human remains in this site, which located in northern China, dated approximately 2,500 years ago. With ancient DNA technology, four mtDNA haplogroups (D, G, C and M10) and one Y chromosome haplogroup (C) were identified using mitochondrial DNA and Y-chromosome single nucleotide polymorphisms (Y-SNPs). Those haplogroups are common in North Asia and East Asia. And the Jinggouzi people were genetically closest to the Xianbeis in ancient populations and to the Oroqens among extant populations, who were all pastoralists. This might indicate that ancient Jinggouzi people were nomads. Meanwhile, according to the genetic data and the evidences in archaeology, we inferred that Jinggouzi people were associated with Donghu. It is of much value to trace the history of Donghu tribe and might show some insight into the ancient nomadic society.
CD40 on salivary gland epithelial cells: high constitutive expression by cultured cells from Sjögren’s syndrome patients indicating their intrinsic activation

CD40 has been identified in an expanding list of haematopoietic and non‐haematopoietic cells and has received an increased interest based on its role in a variety of cell‐mediated responses and its potential to participate in the pathogenesis of chronic inflammatory disorders. Sjögren’s syndrome (SS) is an autoimmune exocrinopathy, which is characterized by chronic lymphocytic infiltration of exocrine glands and aberrant activation of epithelial tissues. We studied the expression of CD40 protein in cultured non‐neoplastic salivary gland epithelial cell (SGEC) lines as well as in minor SG biopsies obtained from 17 SS patients and 12 controls. Immunocytochemical and flow cytometric analyses had revealed the occurrence of constitutively expressed CD40 molecules on the surface of long‐term cultured SGEC lines, which could be further induced by interferon‐gamma (IFN‐γ) and IL‐1β cytokines, but not tumour necrosis factor‐alpha (TNF‐α), IL‐4, IL‐6, granulocyte‐macrophage colony‐stimulating factor (GM‐CSF) or IFN‐α. Triggering of SGEC through CD40 enhanced the surface expression of the adhesion molecule intercellular adhesion molecule‐1 (ICAM‐1)/CD54, but not MHC class I and class II (HLA‐DR) molecules. Spontaneous CD40 expression was significantly higher in SGEC lines derived from SS patients, compared with controls (P < 0·001), which is suggestive of their intrinsically activated status. In SG biopsies, CD40 was constitutively expressed by lymphocytes, ductal epithelial cells and endothelial cells but not by other glandular cell types, such as acinar cells, myoepithelial cells and fibroblasts. In addition, CD40L staining was also detected in 30–50% of the infiltrating lymphocytes in the biopsies of SS patients. Our findings indicate the immunoregulatory potential of SGEC and lend further support to a model of intrinsic activation in salivary epithelia in SS, whereby these cells actively participate in the induction and maintenance of lymphocytic infiltrates of patients.
HIV-1 Tat RNA silencing suppressor activity is conserved across kingdoms and counteracts translational repression of HIV-1

The RNA silencing pathway is an intracellular innate response to virus infections and retro-transposons. Many plant viruses counter this host restriction by RNA silencing suppressor (RSS) activity of a double-stranded RNA-binding protein, e.g., tomato bushy stunt virus P19. Here, we demonstrate P19 and HIV-1 Tat function across the plant and animal kingdoms and suppress a common step in RNA silencing that is downstream of small RNA maturation. Our experiments reveal that RNA silencing in HIV-1 infected human cells severely attenuates the translational output of the unspliced HIV-1 gag mRNA, and possibly all HIV-1 transcripts. The attenuation in gag mRNA translation is exacerbated by K51A substitution in the Tat double-stranded RNA-binding domain. Tat, plant virus RSS, or Dicer downregulation rescues robust gag translation and bolsters HIV-1 virion production. The reversal of HIV-1 translation repression by plant RSS supports the recent finding in Arabidopsis that plant miRNAs operate by translational inhibition. Our results identify common features between RNA silencing suppression of plant and animal viruses. We suggest that RNA silencing-mediated translation repression plays a strategic role in determining the viral set-point in a newly HIV-1-infected patient.
Algorithms for Scanned Probe Microscope Image Simulation, Surface Reconstruction, and Tip Estimation

To the extent that tips are not perfectly sharp, images produced by scanned probe microscopies (SPM) such as atomic force microscopy and scanning tunneling microscopy are only approximations of the specimen surface. Tip-induced distortions are significant whenever the specimen contains features with aspect ratios comparable to the tip’s. Treatment of the tip-surface interaction as a simple geometrical exclusion allows calculation of many quantities important for SPM dimensional metrology. Algorithms for many of these are provided here, including the following: (1) calculating an image given a specimen and a tip (dilation), (2) reconstructing the specimen surface given its image and the tip (erosion), (3) reconstructing the tip shape from the image of a known “tip characterizer” (erosion again), and (4) estimating the tip shape from an image of an unknown tip characterizer (blind reconstruction). Blind reconstruction, previously demonstrated only for simulated noiseless images, is here extended to images with noise or other experimental artifacts. The main body of the paper serves as a programmer’s and user’s guide. It includes theoretical background for all of the algorithms, detailed discussion of some algorithmic problems of interest to programmers, and practical recommendations for users.
Improvement in Small Progress Measures

Small Progress Measures is one of the classical parity game solving algorithms. For games with n vertices, m edges and d different priorities, the original algorithm computes the winning regions and a winning strategy for one of the players in O(dm.(n/floor(d/2))^floor(d/2)) time. Computing a winning strategy for the other player requires a re-run of the algorithm on that player's winning region, thus increasing the runtime complexity to O(dm.(n/ceil(d/2))^ceil(d/2)) for computing the winning regions and winning strategies for both players. We modify the algorithm so that it derives the winning strategy for both players in one pass. This reduces the upper bound on strategy derivation for SPM to O(dm.(n/floor(d/2))^floor(d/2)). At the basis of our modification is a novel operational interpretation of the least progress measure that we provide.
Differential modulation for two-user cooperative diversity systems

This paper introduces a novel differential modulation scheme for a two-user cooperative diversity system which does not require channel state information at either the users or the destination. The performance of fixed decode-and-forward and selection relaying protocols is evaluated in both symmetric and asymmetric interuser-channel cases. The lower bound on the performance of the decode-and-forward protocol is given, while the exact bit-error probability of the selection relaying protocol is thoroughly derived. The decode-and-forward relaying protocol achieves a performance gain when the signal-to-noise ratios in the interuser channels are symmetric and sufficiently high. The selection relaying protocol shows a larger performance gain and does not exhibit an error floor like in the case of the decode-and-forward protocol. In addition, it is robust to the asymmetric interuser channels.
Quantitative Seasonal Changes in the Leaf Phenolic Content Related to the Alternate-Bearing Patterns of Olive (Olea europaea L. cv. Gemlik)

Using HPLC, the seasonal changes in the phenolic compound content of the leaves of the Gemlik olive cultivar ( Olea europaea L) has been investigated with respect to the effects on the alternate bearing of the cultivar. For this purpose, the leaf concentrations of oleuropein, chlorogenic acid, caffeic acid, 3-hydroxycinnamic acid, scopolin and pcoumaric acid were analyzed at 10 day intervals around the years. The quantity and distribution of these phenolics in the leaves showed significant differences in 2008 (off year) and 2009 (on year). In the “on” year, the levels of chlorogenic and p-coumaric acids were high, whereas the abundance of other phenolic compounds was low. In contrast, during the “off” year, the chlorogenic and p-coumaric acid levels were at low levels, whereas the levels of the other phenolics were high. We found a negative relationship between the chlorogenic acid and caffeic acid concentrations in the “on” and “off” years: the amount of caffeic acid in the leaves was high, and the chlorogenic acid level was low. The contents of chlorogenic acid, caffeic acid, 3-hydroxycinnamic acid and p-coumaric acid were significantly different in the “on” and “off” years. These findings indicated that these compounds and the other phenolics examined in this study were related to alternate bearing. Interestingly, the levels of all of the phenolic compounds examined in this study were at their highest during the dormant season.
The Smartphone Psychology Manifesto

By 2025, when most of today’s psychology undergraduates will be in their mid-30s, more than 5 billion people on our planet will be using ultra-broadband, sensor-rich smartphones far beyond the abilities of today’s iPhones, Androids, and Blackberries. Although smartphones were not designed for psychological research, they can collect vast amounts of ecologically valid data, easily and quickly, from large global samples. If participants download the right “psych apps,” smartphones can record where they are, what they are doing, and what they can see and hear and can run interactive surveys, tests, and experiments through touch screens and wireless connections to nearby screens, headsets, biosensors, and other peripherals. This article reviews previous behavioral research using mobile electronic devices, outlines what smartphones can do now and will be able to do in the near future, explains how a smartphone study could work practically given current technology (e.g., in studying ovulatory cycle effects on women’s sexuality), discusses some limitations and challenges of smartphone research, and compares smartphones to other research methods. Smartphone research will require new skills in app development and data analysis and will raise tough new ethical issues, but smartphones could transform psychology even more profoundly than PCs and brain imaging did.
Listeria monocytogenes, a down-to-earth pathogen

Listeria monocytogenes is the causative agent of the food-borne life threatening disease listeriosis. This pathogenic bacterium received much attention in the endeavor of deciphering the cellular mechanisms that underlie the onset of infection and its ability to adapt to the food processing environment. Although information is available on the presence of L. monocytogenes in many environmental niches including soil, water, plants, foodstuff and animals, understanding the ecology of L. monocytogenes in outdoor environments has received less attention. Soil is an environmental niche of pivotal importance in the transmission of this bacterium to plants and animals. Soil composition, microbial communities and macrofauna are extrinsic edaphic factors that direct the fate of L. monocytogenes in the soil environment. Moreover, farming practices may further affect its incidence. The genome of L. monocytogenes presents an extensive repertoire of genes encoding transport proteins and regulators, a characteristic of the genome of ubiquitous bacteria. Postgenomic analyses bring new insights in the process of soil adaptation. In the present paper focussing on soil, we review these extrinsic and intrinsic factors that drive environmental adaptation of L. monocytogenes.
Glycated albumin and glycated albumin/ glycated haemoglobin ratio decrease with increasing BMI compared to Glycated haemoglobin in Type 2 diabetes patients

Background: Obese T2DM patients are more prone to develop accelerated complications which burdens the global health systems with undue expenditure. Glycated haemoglobin (A1c) had been settled as a gold standard glycemic indicator though it's levels must be prudently interpreted in some patients. Glycatedalbumin (GA) as an alternative, intermediate glycemic indicator is gaining much attention. Aim: assessing the correlation of each of glycated albumin and glycated haemoglobin to body mass index (BMI) in T2DM patients Hypothesis: negative correlation existsbetween BMI & glycated albumin. Subjects and methods: Cross sectional study into which 62 participants- aged 25-60 years - who are T2DM on insulin were recruited at Suez Canal University hospital.None of them was smoker or known to be CLD or DKD patient, none was on regular statins, aspirin or metformin. All had normal CBC and albumin indices, they underwent thorough history taking & examination. anthropometric measurements namely body mass index (BMI) were taken.They were grouped into a non-obese group with BMI <25 Kg/m 2 & obese group whose BMI ≥25 Kg/m 2 , each with a sample size of 31 participants. FPG,PPPG, HbA1c, CBC,
Excess child mortality after discharge from hospital in Kilifi, Kenya: a retrospective cohort analysis.

OBJECTIVE To explore excess paediatric mortality after discharge from Kilifi District Hospital, Kenya, and its duration and risk factors. METHODS Hospital and demographic data were used to describe post-discharge mortality and survival probability in children aged < 15 years, by age group and clinical syndrome. Cox regression models were developed to identify risk factors. FINDINGS In 2004-2008, approximately 111,000 children were followed for 555,000 person-years. We analysed 14,971 discharges and 535 deaths occurring within 365 days of discharge. Mortality was higher in the post-discharge cohort than in the community cohort (age-adjusted rate ratio, RR: 7.7; 95% confidence interval, CI: 6.6-8.9) and declined little over time. An increased post-discharge mortality hazard was found in children aged < 5 years with the following: weight-for-age Z score < -4 (hazard ratio, HR: 6.5); weight-for-age Z score > -4 but < -3 (HR: 3.4); hypoxia (HR: 2.3); bacteraemia (HR: 1.8); hepatomegaly (HR: 2.3); jaundice (HR: 1.8); hospital stay > 13 days (HR: 1.8). Older age was protective (reference < 1 month): 6-23 months, HR: 0.8; 2-4 years, HR: 0.6. Children with at least one risk factor accounted for 545 (33%) of the 1655 annual discharges and for 39 (47%) of the 83 discharge-associated deaths. CONCLUSION Hospital admission selects vulnerable children with a sustained increased risk of dying. The risk factors identified provide an empiric basis for effective outpatient follow-up.
Modality‐specific hyper‐responsivity of regenerated cat cutaneous nociceptors

1 Experiments were performed on anaesthetized cats to investigate the receptive properties of regenerated cutaneous tibial nerve nociceptors, and to obtain evidence for coupling between them and other afferent fibres as being possible peripheral mechanisms involved in neuropathic pain. These properties were studied 6‐7 months after nerve section and repair. 2 Recordings were made from 25 regenerated nociceptors; 14 were A fibres and the remainder were C fibres. Their receptive field sizes and conduction velocities were similar to controls. There was no significant difference between their mechanical thresholds and those of a control population of nociceptors. 3 Regenerated nociceptors were significantly more responsive to suprathreshold mechanical stimuli than were uninjured control fibres. This increase in mechanical sensitivity occurred in both A and C fibres, although A fibres showed a greater increase in mechano‐sensitivity than C fibres. Over half of the regenerated nociceptors (13/25) showed after‐discharge to mechanical stimuli which was never seen in controls; the mean firing rate during this period of after‐discharge was significantly related to both stimulus intensity and stimulus area. 4 There was no significant difference between the heat encoding properties of regenerated nociceptors and control nociceptors. Cold sensitivity was similarly unchanged. Thus, abnormal peripheral sprouting was unlikely to account for the increased mechanical sensitivity of the regenerated fibres. None of the regenerated nociceptors were found to be coupled to other fibres. 5 These results suggest that the clinical observation of mechanical hyperalgesia in patients after nerve injury may have a peripheral basis. Based on this model, other signs of neuropathic pain (i.e. tactile or thermal allodynia) are more likely to be due to altered central processing.
Multi-Sensor Fusion and Fault Detection using Hybrid Estimation for Air Traffic Surveillance

Data fusion for multiple surveillance sensors in air traffic control (ATC) is studied. The goal is to build up software redundancy for better target tracking accuracy and robustness against sensor faults. A set of hybrid estimation algorithms for different sensors is designed to run in parallel for tracking aircraft with changing flight modes. The proposed sensor fusion algorithm combines the estimates from each hybrid estimation algorithm and identifies potential sensor faults.
A Novel Context-aware Modeling and Reasoning Method based on OWL

Computing is moving toward a pervasive context-aware environment. This paper proposes an approach to model and reason the Context-aware knowledge using Web Ontology Language (OWL) that towards the problem of uncertain model and lack of automatic reasoning support. It suggests a novel context model framework in the semantic restrictions of the ontology, which dividing the context model into two-level structure: Meta Ontology and Domain-specific Ontology, according to the abstract hierarchy. A key component in our framework is the explicit context model defined in OWL, and the objective of our model is to provide flexible extensibility to add specific concepts in different application domains. After that, the paper proposes an algorithm which converting the OWL model to Description Logic to implement automatic context reasoning. Finally, a case study is given to illustrate the practicality of the method.