The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts

Man was created  with the provision of spiritual awareness of the existence of God. When in the course of his life to find a variety of  problems, which he first headed the Lord. From every human being must  feel that awareness.  If then it is collective  awareness  activities conducted in order to meet the spiritual needs that can be implemented together. That is a God given institution called the Assembly of  dzikir. If then the activity was done with a lot of people, over time some of them  do not  know the exact substance  and virtues of the assembly  itself, but just following everyone else  alone. Moreover, many activities that  involve  mass was boarded by-worldly orientation of  material interests, economic and political. Then the activity will become a kind of wetland that can be exploited in the interests of a handful of people. Key words: majelis dzikir, spiritual awareness, mass cultur

AN EXAMINATION OF THE ABSENCE OF ESTABLISHED MOOSE (ALCES ALCES) POPULATIONS IN SOUTHEASTERN CAPE BRETON ISLAND, NOVA SCOTIA, CANADA

An analysis was performed on habitat-related factors for the southeastern side of Cape Breton Island, Nova Scotia to investigate the continued absence of moose (Alces alces) from the region. Temperature and snow depth, at times, reach levels that could cause thermal stress or impede movement of moose; however, it is unlikely that these factors dictate the absence of moose. No clear relationships were established between environmental concentration levels of the heavy metals molybdenum, cadmium, copper, and lead and moose distribution; however, high concentration levels of molybdenum in the Cape Breton study area warrant further investigation. Road density assessments showed that the study area has a higher level of road density compared to 2 mainland control sites; however, higher road density occurs in other areas in which moose persist. Anthropogenic factors such as poaching were not considered influential enough to exclude moose. A forest habitat comparison analysis was performed to identify habitat features that were statistically correlated with moose presence, and then were applied in a probability model to predict moose presence in the study area. The logistic regression model used to predict the probability of moose presence was composed of positively associated forest inventory variables (softwood average maturity, hardwood average maturity, % mixed hardwood, % non-forested area, total wetland area) that best fit the data. The model identified 43% of the Cape Breton study area as having a high-probability weighting for moose presence. Overall, this study did not reveal a clearly identifiable cause for the continued absence of moose in southeastern Cape Breton Island

Studying learner’s perception of attaining graduate attributes in capstone project units using online flipped classroom

This article describes an empirical study to evaluate how the flipped learning (FL) approach has impacted a learner’s perception in attaining the graduate attributes (GAs) of five capstone project units offered at Melbourne Institute of Technology in Australia, where the authors are affiliated. The subjects include one undergraduate and one postgraduate business unit, and one undergraduate and two postgraduate units in networking. Our study is distinguished from previous research in two novel aspects. First, the subject matter concerns capstone project units which are taken by students in the final year of their degree. In these units, students are expected to apply a variety of knowledge and skills that they have acquired thus far in carrying out an industry-based project of substantial complexity. The learning outcomes (LOs) require students to apply skills and knowledge that they have learned across completed units and connect them with real-world problems. Second, the FL approach has been applied wholly in an online virtual classroom setting due to the social distancing restrictions enforced by local authorities in response to the COVID-19 pandemic. Our hypothesis is that FL has positively influenced the perception of learners in their attaining the GAs. We tested this hypothesis by using data collected by an online survey administered to the student cohorts of the five chosen units at the end of Trimester 1 of 2021. The survey, which comprised 14 questions, assesses a student’s perception of achieving the LOs through developments in three dimensions, including cognitive, affective, and behavioural, acquired in a real-world client setting. Statistical analyses of the survey data reveal that the FL approach resulted in a positive perception by students of their attaining the GAs through achieving the LOs of the capstone project units, which in turn is supported by the responses to the three measured dimensions

Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays

Correction to Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J: Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics 2008, 9: 529

Social Construction of National Reality: Chinese Consciousness versus Hong Kong Consciousness

The struggle to break away from the parent state and claim for independence often results in political unrest, terrorist activities and even ethnic cleansing. In East Asia, the hostilities between people from Hong Kong and mainland China also intensify rapidly in recent years. The late 2000s and early 2010s witness a surge in anti-Mainlander sentiment in Hong Kong and a call for self-determination, resulting in a series of political upheavals. In literatures, irredentist and secessionist advocators generally defend themselves in terms of common blood, race and culture. None of them regards the issue from human agency theory. This paper has two objectives. Firstly, based largely on the works of Max Weber, W.I. Thomas, Alfred Schutz and Peter Berger, this paper constructs a theoretical framework, namely, the social construction of national reality, which allows us to explain the origin of national identity and the reason for people to call for autonomy or secession. It will argue that collective consciousness originates from everyday life experience taken for granted during socialization. Individuals make sense of the external world. Experiences taken for granted become the actor’s stock of knowledge. A common scheme of knowledge shared by the community serves to differentiate in-group (nationals) and out-group (foreigners). Collective consciousness thus defines national identity and hence a nation. Unless people (both in-group and out-group) interact with and learn from each other, different stocks of knowledge taken for granted will create conflict. This theory is applied to explain growing Sinophobia in Hong Kong. The confrontation between traditional Chinese consciousness and emerging Hong Kong consciousness undermines the peaceful coexistence among Hongkongers and Mainlanders, unless both parties redefine their stock of knowledge via dynamic learning. The paper concludes that in order to reduce the conflicts in the regions, understanding the origins of collective consciousness and national identity can help formulate an appropriate policy to resolve growing tensions between Hong Kong and mainland China

Fully-Passive versus Semi-Passive IRS-Enabled Sensing: SNR and CRB Comparison

This paper investigates the sensing performance of two intelligent reflecting surface (IRS)-enabled non-line-of-sight (NLoS) sensing systems with fully-passive and semi-passive IRSs, respectively. In particular, we consider a fundamental setup with one base station (BS), one uniform linear array (ULA) IRS, and one point target in the NLoS region of the BS. Accordingly, we analyze the sensing signal-to-noise ratio (SNR) performance for a target detection scenario and the estimation Cram\'er-Rao bound (CRB) performance for a target's direction-of-arrival (DoA) estimation scenario, in cases where the transmit beamforming at the BS and the reflective beamforming at the IRS are jointly optimized. First, for the target detection scenario, we characterize the maximum sensing SNR when the BS-IRS channels are line-of-sight (LoS) and Rayleigh fading, respectively. It is revealed that when the number of reflecting elements $N$ equipped at the IRS becomes sufficiently large, the maximum sensing SNR increases proportionally to $N^2$ for the semi-passive-IRS sensing system, but proportionally to $N^4$ for the fully-passive-IRS counterpart. Then, for the target's DoA estimation scenario, we analyze the minimum CRB performance when the BS-IRS channel follows Rayleigh fading. Specifically, when $N$ grows, the minimum CRB decreases inversely proportionally to $N^4$ and $N^6$ for the semi-passive and fully-passive-IRS sensing systems, respectively. Finally, numerical results are presented to corroborate our analysis across various transmit and reflective beamforming design schemes under general channel setups. It is shown that the fully-passive-IRS sensing system outperforms the semi-passive counterpart when $N$ exceeds a certain threshold. This advantage is attributed to the additional reflective beamforming gain in the IRS-BS path, which efficiently compensates for the path loss for a large $N$.Comment: 13 pages,7 figure

Hidden genomic MHC disparity between HLA-matched sibling pairs in hematopoietic stem cell transplantation

Matching classical HLA alleles between donor and recipient is an important factor in avoiding adverse immunological effects in HSCT. Siblings with no differences in HLA alleles, either due to identical-by-state or identical-by-descent status, are considered to be optimal donors. We carried out a retrospective genomic sequence and SNP analysis of 336 fully HLA-A, -B, -DRB1 matched and 14 partially HLA-matched sibling HSCT pairs to determine the level of undetected mismatching within the MHC segment as well as to map their recombination sites. The genomic sequence of 34 genes locating in the MHC region revealed allelic mismatching at 1 to 8 additional genes in partially HLA-matched pairs. Also, fully matched pairs were found to have mismatching either at HLA-DPB1 or at non-HLA region within the MHC segment. Altogether, 3.9% of fully HLA-matched HSCT pairs had large genomic mismatching in the MHC segment. Recombination sites mapped to certain restricted locations. The number of mismatched nucleotides correlated with the risk of GvHD supporting the central role of full HLA matching in HSCT. High-density genome analysis revealed that fully HLA-matched siblings may not have identical MHC segments and even single allelic mismatching at any classical HLA gene often implies larger genomic differences along MHC.Peer reviewe

Effect of polymorphisms within probe–target sequences on olignonucleotide microarray experiments

Hybridization-based technologies, such as microarrays, rely on precise probe-target interactions to ensure specific and accurate measurement of RNA expression. Polymorphisms present in the probe–target sequences have been shown to alter probe- hybridization affinities, leading to reduced signal intensity measurements and resulting in false-positive results. Here, we characterize this effect on exon and gene expression estimates derived from the Affymetrix Exon Array. We conducted an association analysis between expression levels of probes, exons and transcripts and the genotypes of neighboring SNPs in 57 CEU HapMap individuals. We quantified the dependence of the effect of genotype on signal intensity with respect to the number of polymorphisms within target sequences, number of affected probes and position of the polymorphism within each probe. The effect of SNPs is quite severe and leads to considerable false-positive rates, particularly when the analysis is performed at the exon level and aimed at detecting alternative splicing events. Finally, we propose simple solutions, based on ‘masking’ probes, which are putatively affected by polymorphisms and show that such strategy results in a large decrease in false-positive rates, with a very modest reduction in coverage of the transcriptome

Personalized and graph genomes reveal missing signal in epigenomic data.

BACKGROUND: Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesize that using a generic reference could lead to incorrectly mapped reads and bias downstream results. RESULTS: We show that accounting for genetic variation using a modified reference genome or a de novo assembled genome can alter histone H3K4me1 and H3K27ac ChIP-seq peak calls either by creating new personal peaks or by the loss of reference peaks. Using permissive cutoffs, modified reference genomes are found to alter approximately 1% of peak calls while de novo assembled genomes alter up to 5% of peaks. We also show statistically significant differences in the amount of reads observed in regions associated with the new, altered, and unchanged peaks. We report that short insertions and deletions (indels), followed by single nucleotide variants (SNVs), have the highest probability of modifying peak calls. We show that using a graph personalized genome represents a reasonable compromise between modified reference genomes and de novo assembled genomes. We demonstrate that altered peaks have a genomic distribution typical of other peaks. CONCLUSIONS: Analyzing epigenomic datasets with personalized and graph genomes allows the recovery of new peaks enriched for indels and SNVs. These altered peaks are more likely to differ between individuals and, as such, could be relevant in the study of various human phenotypes

Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs

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