The Igf2/H19 imprinting control region exhibits sequence-specific and cell-type-dependent DNA methylation-mediated repression

Methylation of CpGs is generally thought to repress transcription without significant influence from the sequence surrounding the methylated dinucleotides. Using the mouse Igf2/H19 imprinting control region (ICR), Igf2r differentially methylated region 2 (DMR2) and bacterial sequences, we addressed how methylation-dependent repression (MDR) from a distance varies with CpG number, density and surrounding sequence. In stably transfected F9 cells, the methylated ICR repressed expression from a CpG-free reporter plasmid more than 1000-fold compared with its unmethylated control. A segment of pBluescript, with a CpG number equal to the ICR's but with a higher density, repressed expression only 70-fold when methylated. A bacteriophage lambda fragment and the Igf2r DMR2 showed minimal MDR activity, despite having CpG numbers and densities similar to or greater than the ICR. By rearranging or deleting CpGs, we identified CpGs associated with three CTCF sites in the ICR that are necessary and sufficient for sequence-specific MDR. In contrast to F9 cells, the methylated ICR and pBS fragments exhibited only 3-fold reporter repression in Hela cells and none in Cos7. Our results show that the strength of MDR from a distance can vary a 1000-fold between different cell types and depends on the sequence surrounding the methylated CpGs, but does not necessarily increase with CpG number or density

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes

Using propensity score adjustment method in genetic association studies

[[abstract]]Background The statistical tests for single locus disease association are mostly under-powered. If a disease associated causal single nucleotide polymorphism (SNP) operates essentially through a complex mechanism that involves multiple SNPs or possible environmental factors, its effect might be missed if the causal SNP is studied in isolation without accounting for these unknown genetic influences. In this study, we attempt to address the issue of reduced power that is inherent in single point association studies by accounting for genetic influences that negatively impact the detection of causal variant in single point association analysis. In our method we use propensity score (PS) to adjust for the effect of SNPs that influence the marginal association of a candidate marker. These SNPs might be in linkage disequilibrium (LD) and/or epistatic with the target-SNP and have a joint interactive influence on the disease under study. We therefore propose a propensity score adjustment method (PSAM) as a tool for dimension reduction to improve the power for single locus studies through an estimated PS to adjust for influence from these SNPs while regressing disease status on the target-genetic locus. The degree of freedom of such a test is therefore always restricted to 1. Results We assess PSAM under the null hypothesis of no disease association to affirm that it correctly controls for the type-I-error rate (70%) and shows an average of 15% improvement in power as compared with commonly-used logistic regression method and PLINK under most simulated scenarios. Using the open-access multifactor dimensionality reduction dataset, PSAM displays improved significance for all disease loci. Through a whole genome study, PSAM was able to identify 21 SNPs from the GAW16 NARAC dataset by reducing their original trend-test p-values from within 0.001 and 0.05 to p-values less than 0.0009, and among which 6 SNPs were further found to be associated with immunity and inflammation. Conclusions PSAM improves the significance of single-locus association of causal SNPs which have had marginal single point association by adjusting for influence from other SNPs in a dataset. This would explain part of the missing heritability without increasing the complexity of the model due to huge multiple testing scenarios. The newly reported SNPs from GAW16 data would provide evidences for further research to elucidate the etiology of rheumatoid arthritis. PSAM is proposed as an exploratory tool that would be complementary to other existing methods. A downloadable user friendly program, PSAM, written in SAS, is available for public use. Graphical abstract The proposed propensity score adjustment method (PSAM) is a tool to improve power for single locus association studies through an estimated propensity-score (PS) by adjusting for SNPs that might be in linkage disequilibrium (LD) and/or epistatic with the target-SNP while regressing disease status on target SNP. The degree of freedom is always restricted to 1.[[notice]]補正完

Influence of an adiabatic square cylinder on hydrodynamic and thermal characteristics in a two-dimensional backward-facing step channel

The work demonstrates numerically the influence of an adiabatic cylinder of square cross section on the flow and heat transfer characteristics within a two-dimensional backward-facing step channel. The study was conducted for a Reynolds number range of 1−200 (in the steady laminar regime) with a fixed Prandtl number of 0.71 (air). Additionally, simulations are also conducted for Reynolds numbers of 104 and 2·104 (unsteady turbulent regime). The numerical simulation is performed by deploying a finite volume-based commercial solver FLUENT. Different cross stream positions of the cylinder are considered to show the positional effect of an obstacle on the overall flow and heat transfer pattern. The flow and thermal fields are demonstrated through the streamlines and isotherm profiles for different Reynolds numbers and cylinder positions. The global flow and heat transfer quantities such as the reattachment length, drag coefficient, local and average Nusselt numbers are computed and presented. A significant heat transfer augmentation due to the presence of the cylinder is observed as compared to the unobstructed case (without a cylinder). Furthermore, it is observed that the heat transfer augmentation is stronger for the case of a square cylinder in comparison with a circular one introduced into the same channel. Finally, correlations are devised for the drag coefficient and Nusselt number for the above range of conditions

Analysis of Single Nucleotide Polymorphisms of PRNP Gene in twenty-four Ethnic Groups of India

Human prion protein (PRNP), a copper binding sialoglycoprotein, is the causative agent for transmissible spongiform encephalopathies (TSEs), a group of neurodegenerative diseases that are generally associated with aggregation of amyloid plaques within the central nervous system disrupting the normal tissue structure (Liberski et al. 2001; Aguzzi et al. 2008). While more than 20 PRNP pathogenic mutations have been reported in patients, polymorphisms in the gene have been suggested to influence the incidence of the diseases with a Met129Val polymorphism (rs1799990) being the most important among them (Soldevila et al. 2006). This particular variant has been found to be associated with different prion related diseases as well as cognitive behaviour and long-term memory. Here, as a part of the effort from Indian Genome Variation Consortium (IGVC), we attempt to establish the baseline allele and genotype frequency of four PRNP SNPs including rs1799990 among 24 ethnic groups representing the Indian population. The allele and genotype frequency of rs1799990 is found to be different among different ethnic groups. This pilot study would serve as a platform for future epidemiologicalworks with respect to PRNP SNPs in India

Seasonal Migration, Social Change and Migrants? Rights: Lessons from West Bengal

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Seasonal Migration and Welfare/Illfare in Eastern India: A Social Analysis

Over 500,000 people are regularly engaged in seasonal migration for rice work into southern West Bengal. This paper analyses social processes at work in the interactions between employers and workers, and the welfare/illfare outcomes. Group identities based on religion and ethnicity are strengthened through the experience of migration and deployed by some migrants to make this form of employment less degrading. In West Bengal seasonal migration can involve practical welfare gains. Importantly, an informal wage floor has been put into place and managed by the peasant union allied to the largest party in the Left Front regime. However, the costs and risks of migration remain high

A study of knowledge, attitude and practice regarding administration of pediatric dosage forms and allied health literacy of caregivers for children

Context: Caregivers of sick children have to be careful with medicine dosing and giving medicines to a reluctant child can be challenging. Aim: To assess the knowledge, attitude, and practices of caregivers regarding pediatric medicine administration and health literacy allied to this task. Settings and Design: This cross-sectional study was carried out on outpatient and inpatient basis in the pediatrics department of a teaching hospital over 6 months. Subjects and Methods: Data regarding sociodemographic profile of patient and caregiver, idea regarding pediatric dosage forms, dosing of medicines, and medication errors during administration were recorded from 377 caregivers. Reconstitution of dry powder and measurement of 5 mL liquid medicine using measuring cup of the medicine phial was demonstrated by the caregivers. Statistical Analysis: Association assessed by point biserial correlation and Spearman's rank correlation. Results: Majority of the primary caregivers surveyed were young, educated, homemaker mothers. Liquid medicines were used maximally (88.9%). Majority (87.3%) of the caregivers used standardized dosing instruments to measure liquids and reconstitution (85.9%), and teaspoon measurement task (91%) was performed satisfactorily by most. Some potentially wrong practices (e.g., adding medicine to milk, redilution of reconstituted medicine, and storing beyond the recommended period) were recorded. Medication errors were reported by 44.5% caregivers, significantly more in the outpatient setting. Although the statistical correlation was weak, the chance of medication error was less, and the precision of measurement was better with increasing education of the caregiver. Conclusions: Physicians need to be aware of the limitations of knowledge and the possibility of wrong administration practices among caregivers of children. Remedial measures in this regard can reduce the risk of medication errors