Miracle-dz/UniFAR-FTUs huggingface dataset:
A cross-study analysis of prenatal exposures to environmental contaminants and the epigenome: support for stress-responsive transcription factor occupancy as a mediator of gene-specific CpG methylation patterning

Abstract A biological mechanism by which exposure to environmental contaminants results in gene-specific CpG methylation patterning is currently unknown. We hypothesize that gene-specific CpG methylation is related to environmentally perturbed transcription factor occupancy. To test this hypothesis, a database of 396 genes with altered CpG methylation either in cord blood leukocytes or placental tissue was compiled from 14 studies representing assessments of six environmental contaminants. Subsequently, an in silico approach was used to identify transcription factor binding sites enriched among the genes with altered CpG methylation in relationship to the suite of environmental contaminants. For each study, the sequences of the promoter regions (representing −1000 to +500 bp from the transcription start site) of all genes with altered CpG methylation were analyzed for enrichment of transcription factor binding sites. Binding sites for a total of 56 unique transcription factors were identified to be enriched within the promoter regions of the genes. Binding sites for the Kidney-Enriched Krupple-like Factor 15, a known responder to endogenous stress, were enriched ( P < 0.001–0.041) among the genes with altered CpG methylation associated for five of the six environmental contaminants. These data support the transcription factor occupancy theory as a potential mechanism underlying environmentally-induced gene-specific CpG methylation.
Children's experiences of domestic violence

This paper describes the key findings of a two year project focused on children's experiences of domestic violence. It draws on 107 interviews with children in Greece, Italy, Spain and the UK. The paper explores children's capacity to articulate their experiences, and highlights that they are not 'witnesses' to intimate partner violence, but experience it directly and make meaning of it, as members of a family affected by violence. I argue that children need to be recognised as direct victims of domestic violence and of coercive control.
Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage

RNA polymerase (Pol) I contains a 10-subunit catalytic core that is related to the core of Pol II and includes subunit A12.2. In addition, Pol I contains the heterodimeric subcomplexes A14/43 and A49/34.5, which are related to the Pol II subcomplex Rpb4/7 and the Pol II initiation factor TFIIF, respectively. Here we used lysine-lysine crosslinking, mass spectrometry (MS) and modeling based on five crystal structures, to extend the previous homology model of the Pol I core, to confirm the location of A14/43 and to position A12.2 and A49/34.5 on the core. In the resulting model of Pol I, the C-terminal ribbon (C-ribbon) domain of A12.2 reaches the active site via the polymerase pore, like the C-ribbon of the Pol II cleavage factor TFIIS, explaining why the intrinsic RNA cleavage activity of Pol I is strong, in contrast to the weak cleavage activity of Pol II. The A49/34.5 dimerization module resides on the polymerase lobe, like TFIIF, whereas the A49 tWH domain resides above the cleft, resembling parts of TFIIE. This indicates that Pol I and also Pol III are distantly related to a Pol II–TFIIS–TFIIF–TFIIE complex.
The Role of Toll-Like Receptors in Hematopoietic Malignancies

Toll-like receptors (TLRs) are a family of pattern recognition receptors that shape the innate immune system by identifying pathogen-associated molecular patterns and host-derived damage-associated molecular patterns. TLRs are widely expressed on both immune cells and non-immune cells, including hematopoietic stem and progenitor cells, effector immune cell populations, and endothelial cells. In addition to their well-known role in the innate immune response to acute infection or injury, accumulating evidence supports a role for TLRs in the development of hematopoietic and other malignancies. Several hematopoietic disorders, including lymphoproliferative disorders and myelodysplastic syndromes, which possess a high risk of transformation to leukemia, have been linked to aberrant TLR signaling. Furthermore, activation of TLRs leads to the induction of a number of proinflammatory cytokines and chemokines, which can promote tumorigenesis by driving cell proliferation and migration and providing a favorable microenvironment for tumor cells. Beyond hematopoietic malignancies, the upregulation of a number of TLRs has been linked to promoting tumor cell survival, proliferation, and metastasis in a variety of cancers, including those of the colon, breast, and lung. This review focuses on the contribution of TLRs to hematopoietic malignancies, highlighting the known direct and indirect effects of TLR signaling on tumor cells and their microenvironment. In addition, the utility of TLR agonists and antagonists as potential therapeutics in the treatment of hematopoietic malignancies is discussed.
Serum parathyroid hormone (PTH) levels in smokers and non-smokers. The fifth Tromsø study.

OBJECTIVE Smoking is associated with reduced bone density and calcium absorption, and reduced serum levels of vitamin D. A compensatory increase in serum parathyroid hormone (PTH) would therefore be expected as a result of an altered calcium balance. However, reports on PTH levels in smokers are conflicting. As serum PTH levels give important information on the calcium balance, the PTH levels in smokers are of interest. SUBJECTS AND METHODS In the fifth Tromsø study, smoking status was recorded and serum PTH measured in 7896 subjects. Intakes of calcium and vitamin D were evaluated with a food-frequency questionnaire. In a follow-up study on 205 subjects, serum 25-hydroxyvitamin D, calcium absorption, and renal excretion of calcium were measured in addition. RESULTS The serum PTH levels were significantly lower in smokers than non-smokers (3.1+/-1.4 vs 3.6+/-1.9 pmol/l in males; 3.1+/-1.5 vs 3.6+/-1.8 pmol/l in females (P < 0.001) after correcting for confounding variables, linear regression). In the smokers, there was no association between number of cigarettes smoked and serum PTH. One year after quitting smoking, serum PTH levels were similar to those of people who had never smoked. The smokers had significantly lower intake of vitamin D, lower serum levels of 25-hydroxyvitamin D and lower calcium absorption. The intake of calcium and the renal excretion of calcium were similar to that in non-smokers. CONCLUSIONS Smokers have lower serum PTH levels than non-smokers. This cannot be explained by the predictors of serum PTH measured in our study.
Effects of Job Stress on Employees Job Performance A Study on Banking Sector of Pakistan

Currently Bankers are under a great transaction of stress and due to many backgrounds of stress such as Excess, Role doubt, Role conflict, Concern for people, Contribution, Lack of feedback, possession up with rapid technologicalchange. Being in an inventive role, Career development, Organizational structure and climate, and recent episodic events. The thing which find out is stress. This study examines the relationship between job stress and job performance on bank employees of banking sector in Pakistan. The study examines the purpose model in relation of job stress and its impact on job performance by using sample of 144 participants. In participant the data ofsenior, graduate employees including customer services officers and managers of well reputed rising bank in Pakistan. The data were obtained through close ended questionnaire. A statistical test of regression, correlation and reliabilities were also confirmed. The results are significant with negative correlation between job stress and job performances and shows that job stress significantly reduces the performance of an individual. The results suggest to the organization that they have sustained a very health, cooperative and friendly environment within the team for better performance. Keywords: Job performance, Job stress, Effects of stress
The effect of low-nitrogen and low-calorie parenteral nutrition combined with enteral nutrition on inflammatory cytokines and immune functions in patients with gastric cancer: a double blind placebo trial.

OBJECTIVE The aim of this study is to investigate the effect of low-nitrogen and low-calorie parenteral nutrition (PN) combined with enteral nutrition (EN) on the inflammatory cytokines and immune function in patients with gastric cancer. PATIENTS AND METHODS Between May 2012 and May 2014, 90 patients undergoing surgery for gastric cancer in our institution were involved in this double blind placebo study and randomly divided into experimental group and control group, 45 patients of each group. Patients in the control group would receive total parenteral nutrition (TPN) whereas patients in the experimental group would be supported with low-nitrogen and low-calorie PN combined with EN. RESULTS On the 7th postoperative day 7, levels of IgA, IgM and IgG in experimental group were significantly higher than those in the control group and preoperative values (p < 0.05). CRP level was significantly lower than that of controls and preoperatively (p < 0.05). Levels of IL-2 and TNF-α were significantly higher than those of controls and preoperatively (p < 0.05). CONCLUSIONS As low-nitrogen and low-calorie PN combined with EN can effectively improve the immune function, reduce the inflammatory reactions and improve the postoperative quality of life (QoL) and prognosis in patients with gastric cancer, it is suitable for clinical application.
The effects of interfacial sub-oxide transition regions and monolayer level nitridation on tunneling currents in silicon devices

Direct tunneling (D-T) in Si metal-oxide-semiconductor (MOS) devices having 1.8 to 3 nm thick gate oxides is reduced approximately tenfold by monolayer Si-dielectric interface nitridation with respect to devices with nonnitrided interfaces. The reduction is independent of gate oxide-equivalent thickness, and gate or substrate injection, and extends into the Fowler-Nordheim tunneling (F-N-T) regime for thicker oxides as well. A barrier layer model, including sub-oxide transition regions, has been developed for the interface electronic structure for tunneling calculations using X-ray photoelectron spectroscopy data. These calculations provide a quantitative explanation for the observed tunneling current reductions.
Laboratory Evaluation and Field Application of Roadside Oral Fluid Collectors and Drug Testing Devices

This study was a part of a collaborative U.S./E.U. international research effort (Roadside Testing Assessment, ROSITA II) to assess illegal drug use among motor vehicle operators suspected of driving while under the influence of drugs and to evaluate the effectiveness of point-of-collection oral fluid drug detection technologies. A goal of the study was to assess commercial oral fluid drug testing devices for potential use in law enforcement. Ten devices were evaluated in the laboratory for their ability to meet manufacturers' claimed (and proposed) cutoff concentrations for the detection of amphetamine(s), cocaine/metabolite, opiates, cannabinoids, and benzodiazepines (2 devices). The field study portion of the research was conducted in major cities in the United States and Western Europe by teams of scientists working in collaboration with the local police. In Salt Lake City, Utah, the Drugwipe, Securetec, Ottobrunn, Germany (Securetec) oral fluids drug testing device was also evaluated in the field by testing suspected drug-impaired drivers. During the initial phase of the field study, 40 subjects were recruited. Drugwipe results were compared with laboratory-based immunoassay and mass spectrometry results and demonstrated that calculated sensitivities were between 75% and 100% depending on drug class. Specificities varied from 36% for cannabinoids to over 95% for opiates. During the second phase of the field study, 267 subjects were recruited. The Drugwipe sensitivities were 36.4%, 35.9%, 42.9%, and 7.7%, respectively, for amphetamine(s), cocaine, opiates, and cannabinoids. The Drugwipe specificities were 99.2%, 97.4%, 99.6%, and 99.6%, respectively, for amphetamine(s), cocaine, opiates, and cannabinoids. Drugwipe failed to meet the study criteria for acceptable device performance, required performance sensitivities, and specificities 90% or greater.
Mechanisms of Viral Infections Associated with HIV

HIV infection is commonly associated with activation and dissemination of several other viral pathogens, including herpes simplex virus 1/2, human cytomegalovirus, human herpesvirus 8, Epstein-Barr virus, Varicella Zoster virus, and human papillomavirus, which behave as opportunistic agents and cause various diseases in immunocompromised hosts. The increased frequency and severity of diseases caused by these viruses in HIV-infected individuals is due mainly to dysfunction of both the adaptive and innate immune responses to viral pathogens. In addition, molecular interactions between HIV and these opportunistic viruses are likely to play critical roles in the progression of disease, including neoplasia. This report reviews the critical aspects of HIV interaction with opportunistic viruses, including Epstein-Barr virus, human cytomegalovirus, herpes simplex virus, Varicella Zoster virus, human herpesvirus 8, and human papillomavirus.
A Paraperspective Factorization Method for Shape and Motion Recovery

The factorization method, first developed by Tomasi and Kanade (1992), recovers both the shape of an object and its motion from a sequence of images, using many images and tracking many feature points to obtain highly redundant feature position information. The method robustly processes the feature trajectory information using singular value decomposition (SVD), taking advantage of the linear algebraic properties of orthographic projection. However, an orthographic formulation limits the range of motions the method can accommodate. Paraperspective projection, first introduced by Ohta et al. (1981), is a projection model that closely approximates perspective projection by modeling several effects not modeled under orthographic projection, while retaining linear algebraic properties. Our paraperspective factorization method can be applied to a much wider range of motion scenarios, including image sequences containing motion toward the camera and aerial image sequences of terrain taken from a low-altitude airplane.
A 12-year follow-up study of ankle muscle function in older adults.

The purpose of this study was to examine changes in strength over time in a cohort of healthy elderly people who underwent assessments of ankle muscle function 12 years earlier. The isometric strength and contractile characteristics of the dorsiflexors and plantarflexors were studied in 11 male and 11 female subjects, ranging from 73-97 yrs (mean age 84 +/- 7.1 yrs). The same footplate apparatus was used as during the original testing. From 1982 to 1994, plantarflexor strength decreased 2.1% per year in females, and 2.5% per year in males (p < .01). The loss was relatively less in the dorsiflexor muscles; strength decreased 0.3% per year in females, and 0.8% per year in male (p > .05). There were no significant changes in evoked twitch torque in either muscle group, which may be due to the fact that passive tension of the connective tissue increased (p < .01) over the 12-year period. We conclude from this longitudinal assessment of ankle muscle function that the rate of loss of voluntary strength can vary considerably between antagonistic muscle groups. Factors influencing this variable loss warrant further investigation.
Linguistic Summaries of Time Series via a Quantifier Based Aggregation Using the Sugeno Integral

Linguistic summaries as descriptions of trends in time series data are proposed. Two general types of such summaries are discussed. The point of departure are linguistic summaries of databases due to Yager. The specificity of time series summarization requires a more general approach to linguistic quantifier based aggregation. Sugeno integrals are employed to address this problem.
Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization

Abstract The seven APOBEC3 (A3) enzymes in primates restrict HIV/SIV replication to differing degrees by deaminating cytosine in viral (−)DNA, which forms promutagenic uracils that inactivate the virus. A polymorphism in human APOBEC3C (A3C) that encodes an S188I mutation increases the enzymatic activity of the protein and its ability to restrict HIV-1, and correlates with increased propensity to form dimers. However, other hominid A3C proteins only have an S188, suggesting they should be less active like the common form of human A3C. Nonetheless, here we demonstrate that chimpanzee and gorilla A3C have approximately equivalent activity to human A3C I188 and that chimpanzee and gorilla A3C form dimers at the same interface as human A3C S188I, but through different amino acids. For each of these hominid A3C enzymes, dimerization enables processivity on single-stranded DNA and results in higher levels of mutagenesis during reverse transcription in vitro and in cells. For increased mutagenic activity, formation of a dimer was more important than specific amino acids and the dimer interface is unique from other A3 enzymes. We propose that dimerization is a predictor of A3C enzyme activity.
Computational Methods for Mild Traumatic Brain Injury

Awareness of mild traumatic brain injury and its potential long term effects has increased dramatically in recent years. Currently, there is a lack of computational methods for the evaluation of mild traumatic brain injury (mTBI) from magnetic resonance imaging (MRI). Further, the development of automated analyses has been hindered by the subtle nature of mTBI abnormalities, which appear as low contrast MR regions. In manual estimation a train operator must spend a copious amount of time locating and delineating the lesions. We have developed three innovations to aid in the analysis of mTBI by automatically detecting lesion in MR images. (1) A high level Bayesian network based contextual model, which is able to estimate the progression of lesion over time given basic information about the subject. The generative contextual model is fused with a discriminative visual model that estimates the lesion using 3D features extracted from T2maps. (2) Low level dynamic and static contextual features are developed that take advantage of sequential imaging to improve detection as an iterative post processing step. After the initial estimate by a discriminative classifier, the context features are estimated from the posterior marginal to describe spatio-temporal information about the lesion to the classifier. (3) Multi-Modal features are developed to further improve the visual model. A temporal generative tissue model is developed to model tissue type probabilities within the brain over the course of the injury in the T2map modality. Maximum a posterior edge features are developed to take advantage of the susceptibility weighted imaging (SWI) channel. All of the proposed methods have been evaluated on a temporal mTBI dataset with manually evaluated ground truth and have been shown to outperform the current state-of-the-art approaches.
Chondroitin sulfate proteoglycan specific to retinal horizontal neurons

Proteoglycans (PGs) are a diverse group of highly glycosylated macromolecules that are implicated in the development and maintenance of neuronal circuitry. With its highly ordered, layered structure, the retina ideally serves to define the synthesis, processing, and distribution of these molecules within a specific cellular subpopulation. In retinal sections, monoclonal antibody (MAb) 6A2 immunostained a horizontal cell‐specific antigen. Antigen 6A2 was expressed within abundant processes in the outer plexiform layer and in rare neurites that extend across the inner nuclear layer to the inner plexiform layer. Ultrastructurally, the antigen was localized to cisternae within horizontal cell somata, along tubulovesicular structures in dendrites, and in the perisynaptic space encircling presynaptic terminals of the cone photoreceptor triad. These findings suggest that this PG is synthesized within the horizontal cells, transported to the terminals, and released into the extracellular spaces just proximal to the synapse. Based on the focal stain in the adjacent photoreceptor cell, it is possible that antigen is pinocytosed by this cell and is concentrated at the ribbon synapse. In Western immunoblots of retinal homogenates, MAb 6A2 recognized a heterogeneous chondroitin sulfate (CS) PG (CSPG) of approximately 400–500 kDa. After sequential enzymatic removal of CS glycosaminoglycans, a major broad band of 300–500 kDa was identified by MAb 1B5, which detects CSPGs that bear uronic acid linked to unsulfated N‐acetylgalactosamine as the initial disaccharide in the CS chain. Localization of this PG around presynaptic terminals of the horizontal neuron and at the ribbon synapse suggests that it may play a modulatory and sustaining role at the synapse. J. Comp. Neurol. 390:268–277, 1998. © 1998 Wiley‐Liss, Inc.
Differences in flooding tolerance between species from two wetland habitats with contrasting hydrology: implications for vegetation development in future floodwater retention areas.

BACKGROUND AND AIMS Plants need different survival strategies in habitats differing in hydrological regimes. This probably has consequences for vegetation development when former floodplain areas that are currently confronted with soil flooding only, will be reconnected to the highly dynamical river bed. Such changes in river management are increasingly important, especially at locations where increased water retention can prevent flooding events in developed areas. It is therefore crucial to determine the responses of plant species from relatively low-dynamic wetlands to complete submergence, and to compare these with those of species from river forelands, in order to find out what the effects of such landscape-scale changes on vegetation would be. METHODS To compare the species' tolerance to complete submergence and their acclimation patterns, a greenhouse experiment was designed with a selection of 19 species from two contrasting sites: permanently wet meadows in a former river foreland, and frequently submerged grasslands in a current river foreland. The plants were treated with short (3 weeks) and long (6 weeks) periods of complete submergence, to evaluate if survival, morphological responses, and changes in biomass differed between species of the two habitats. KEY RESULTS All tested species inhabiting river forelands were classified as tolerant to complete submergence, whereas species from wet meadows showed either relatively intolerant, intermediate or tolerant responses. Species from floodplains showed in all treatments stronger shoot elongation, as well as higher production of biomass of leaves, stems, fine roots and taproots, compared with meadow species. CONCLUSIONS There is a strong need for the creation of temporary water retention basins during high levels of river discharge. However, based on the data presented, it is concluded that such reconnection of former wetlands (currently serving as meadows) to the main river bed will strongly influence plant species composition and abundance.