Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic Regulation of a Murine Retrotransposon by a Dual Histone Modification Mark

Large fractions of eukaryotic genomes contain repetitive sequences of which the vast majority is derived from transposable elements (TEs). In order to inactivate those potentially harmful elements, host organisms silence TEs via methylation of transposon DNA and packaging into chromatin associated with repressive histone marks. The contribution of individual histone modifications in this process is not completely resolved. Therefore, we aimed to define the role of reversible histone acetylation, a modification commonly associated with transcriptional activity, in transcriptional regulation of murine TEs. We surveyed histone acetylation patterns and expression levels of ten different murine TEs in mouse fibroblasts with altered histone acetylation levels, which was achieved via chemical HDAC inhibition with trichostatin A (TSA), or genetic inactivation of the major deacetylase HDAC1. We found that one LTR retrotransposon family encompassing virus-like 30S elements (VL30) showed significant histone H3 hyperacetylation and strong transcriptional activation in response to TSA treatment. Analysis of VL30 transcripts revealed that increased VL30 transcription is due to enhanced expression of a limited number of genomic elements, with one locus being particularly responsive to HDAC inhibition. Importantly, transcriptional induction of VL30 was entirely dependent on the activation of MAP kinase pathways, resulting in serine 10 phosphorylation at histone H3. Stimulation of MAP kinase cascades together with HDAC inhibition led to simultaneous phosphorylation and acetylation (phosphoacetylation) of histone H3 at the VL30 regulatory region. The presence of the phosphoacetylation mark at VL30 LTRs was linked with full transcriptional activation of the mobile element. Our data indicate that the activity of different TEs is controlled by distinct chromatin modifications. We show that activation of a specific mobile element is linked to a dual epigenetic mark and propose a model whereby phosphoacetylation of histone H3 is crucial for full transcriptional activation of VL30 elements.
Digitally controlled point of load converter with very fast transient response

This paper presents a new digital self-oscillating modulator (DiSOM) that allows the duty cycle to be changed instantly. The DiSOM modulator is shown to have variable switching that is a function of the duty cycle. Compared to a more traditional digital PWM modulator based on a counter and comparator the DiSOM modulator allows the sampling frequency of the output voltage control loop to be higher than the switching frequency of the power converter, typically a DC/DC converter. The features of the DiSOM modulator makes it possible to design a digitally controlled DC/DC converter with linear voltage mode control and very fast transient response. The DiSOM modulator is combined with a digital PID compensator algorithm is implemented in a hybrid CPLD/FPGA and is used to control a synchronous Buck converter, which is used in typical Point of Load applications. The computational time is only three clock cycles from the time the A/D converter result is read by the control algorithm to the time the duty cycle command is updated. A typical POL converter has been built and the experimental results show that the transient response of the converter is very fast. The output voltage overshoot is only 2.5% of the nominal output voltage when a load step of 50% - 100% of nominal output current is applied to the converter. The settling time is approximately 8 PWM cycles.
Generalizability of Classroom Behavior Problem and On-Task Scores From the Direct Observation Form

Abstract. The present study used generalizability theory to investigate the dependability of systematic observations of students' problem behavior and on-task behavior in classrooms. The Direct Observation Form (McConaughy & Achenbach, 2009) was used with a sample of 24, 6- to-11-year-old children attending 18 different elementary schools. The participants were referred because of concerns about learning and behavioral problems. All students were observed on eight occasions in the morning and afternoon across four different days. Generalizability analyses revealed important differences in observed variance and the number of observations required to obtain acceptable dependability across different behavioral dimensions. Results are discussed in terms of their implications for future research and practice.
Socio-economic determinants of cooperative societies’ access to the services of the Nigerian Agricultural Cooperative and Rural Development Bank

This paper assesses the extent to which cooperative societies had access to the special intervention fund administered by the Nigerian Agricultural Cooperative And Rural Development Bank (NACRDB) Ltd. The study was carried out between March and September, 2005, on six randomly selected states, one from each of the six geopolitical zones into which Nigeria has been divided. States sampled included Enugu (South-East). Rivers (South-South), Ondo (South West), Benue (North Central), Bauchi (North East) and Kano (North West). Sixty cooperative societies were also randomly selected for the study from each state covered; thirty of them with access and thirty without access to the intervention fund, on the whole 360 cooperative societies were studied. Statistical tools used for data analysis included percentage, means and range. Levene’s test for equality of means was used to determine if the means of the two categories of cooperatives (those with access and those without) were statistically different. Likert scale rating was used to determine cooperative societies’ perception of the effects of agency operational guidelines on access. The Levene’s test for equality of means showed that the difference between the means of the two categories of cooperative societies were statistically significant at 5% probability level. Likert scale rating confirmed that the operational guidelines of NACRDB such as minimum credit requirement, type of crop grown, approved loan size, and insurance cover affected access to the intervention fund. It was recommended that promoters of cooperative societies should pay adequate attention to the socioeconomic characteristics of the cooperative societies so promoted and the credit guidelines of the NACRDB Ltd.
An Intact Action-Perception Coupling Depends on the Integrity of the Cerebellum

It is widely accepted that action and perception in humans functionally interact on multiple levels. Moreover, areas originally suggested to be predominantly motor-related, as the cerebellum, are also involved in action observation. However, as yet, few studies provided unequivocal evidence that the cerebellum is involved in the action perception coupling (APC), specifically in the integration of motor and multisensory information for perception. We addressed this question studying patients with focal cerebellar lesions in a virtual-reality paradigm measuring the effect of action execution on action perception presenting self-generated movements as point lights. We measured the visual sensitivity to the point light stimuli based on signal detection theory. Compared with healthy controls cerebellar patients showed no beneficial influence of action execution on perception indicating deficits in APC. Applying lesion symptom mapping, we identified distinct areas in the dentate nucleus and the lateral cerebellum of both hemispheres that are causally involved in APC. Lesions of the right ventral dentate, the ipsilateral motor representations (lobules V/VI), and most interestingly the contralateral posterior cerebellum (lobule VII) impede the benefits of motor execution on perception. We conclude that the cerebellum establishes time-dependent multisensory representations on different levels, relevant for motor control as well as supporting action perception. Ipsilateral cerebellar motor representations are thought to support the somatosensory state estimate of ongoing movements, whereas the ventral dentate and the contralateral posterior cerebellum likely support sensorimotor integration in the cerebellar-parietal loops. Both the correct somatosensory as well as the multisensory state representations are vital for an intact APC.
Interval Tools for ODEs and DAEs

We overview the current state of interval methods and software for computing bounds on solutions in initial value problems (IVPs)for ordinary differential equations (ODEs). We introduce the VNODE-LP solver for IVP ODEs, a successor of the author's VNODE package. VNODE-LP is implemented entirely using literate programming. A major goal of the VNODE-LP work is to produce an interval solver such that its correctness can be verified by a human expert, similar to how mathematical results are certified for correctness. We also discuss the state in computing bounds on solutions in differential algebraic equations.
2 Object-Oriented Exception Handling : The Object Model

Interface exceptions (explicitly declared exceptions that a method can propagate outside) are an inherent part of the interface describing the behaviour of a particular class of objects. Evolution of system behaviour is thus necessarily accompanied by and reflected in the evolution of interface exceptions. While evolution of normal system behaviour is adequately supported by various language mechanisms, such as subtyping and inheritance, few contemporary object-oriented programming languages offer support for the evolution of interface exceptions. Some languages permit specialising and deleting interface exceptions while subtyping, but none of them provides an adequate support for adding exceptions. In this paper we propose two solutions for dealing with additional exceptions introduced while system evolution. To solve the problem of non-conforming interfaces resulting from the addition of new exceptions in a development step, the first proposal uses rescue handlers and the second one employs the forwarding technique.
Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study

OBJECTIVE Genome-wide association studies (GWAS) require high specificity and large numbers of subjects to identify genotype-phenotype correlations accurately. The aim of this study was to identify type 2 diabetes (T2D) cases and controls for a GWAS, using data captured through routine clinical care across five institutions using different electronic medical record (EMR) systems. MATERIALS AND METHODS An algorithm was developed to identify T2D cases and controls based on a combination of diagnoses, medications, and laboratory results. The performance of the algorithm was validated at three of the five participating institutions compared against clinician review. A GWAS was subsequently performed using cases and controls identified by the algorithm, with samples pooled across all five institutions. RESULTS The algorithm achieved 98% and 100% positive predictive values for the identification of diabetic cases and controls, respectively, as compared against clinician review. By standardizing and applying the algorithm across institutions, 3353 cases and 3352 controls were identified. Subsequent GWAS using data from five institutions replicated the TCF7L2 gene variant (rs7903146) previously associated with T2D. DISCUSSION By applying stringent criteria to EMR data collected through routine clinical care, cases and controls for a GWAS were identified that subsequently replicated a known genetic variant. The use of standard terminologies to define data elements enabled pooling of subjects and data across five different institutions to achieve the robust numbers required for GWAS. CONCLUSIONS An algorithm using commonly available data from five different EMR can accurately identify T2D cases and controls for genetic study across multiple institutions.
Experiment, Modeling, and Analysis of Wireless-Powered Sensor Network for Energy Neutral Power Management

In this paper, we provide a high-level abstract system model of a wireless-powered sensor network (WPSN) based on experimental results on a real-life testbed. In the WPSN, a sensor node is wirelessly powered by the radio frequency (RF) energy transfer from a dedicated RF power source. We define the behavior of each component comprising the WPSN and analyze the interaction between these components to set up a realistic WPSN model from the systematic point of view. Towards this, we implement a real-life and full-fledged testbed for the WPSN and conduct extensive experiments to obtain model parameters and to validate the proposed model. Based on this WPSN model, we propose an energy management scheme for the WPSN, which maximizes RF energy transfer efficiency while guaranteeing energy neutral operation. We implement the proposed energy management scheme in a real testbed and show its operation and performance.
Characterization and short-term culture of cells recovered from human conjunctival epithelium by minimally invasive means

Purpose To characterize conjunctival cells obtained by brush cytology (BC) and establish short-term cultures. Methods Human tarsal and bulbar conjunctival cells were obtained by BC and transported in 3 different media: serum-free medium (DK-SFM) with low [Ca2+], 10% fetal bovine serum (FBS) supplemented medium (FBSm10), and 20% FBS-supplemented medium (FBSm20). Recovered cells were counted and initial viability assessed. Flow cytometry established epithelial or immune lineage, viability, apoptosis, and cell cycle stage. To establish short-term cultures, tarsal conjunctival cells were seeded onto Permanox™ or denuded amniotic membrane (dAM) and cultured in the 3 media. Living adherent cells were assessed on Days 1, 2, and 5 by fluorescence microscopy. Results Initial cell recovery was significantly lower with DK-SFM than in the other two culture media. Flow cytometry showed that 3.8±0.4% of recovered tarsal cells were CD45+ leukocytes and 67.9±1.6% were CK7+ secretory epithelial cells. S-phase cells composed 3.5±0.3% of the recovered tarsal cells and 2.1±0.2% of the bulbar cells (p=0.0006). The percentage of viable, apoptotic, and dead cells was similar for tarsal and bulbar cells. Two different cell populations were observed in both locations. About 24% consisted of smaller, less complex cells with high viability, and the remainder was composed of larger, more complex cells with poor viability. Significantly more living cells were supported by FBSm10 on the dAM substratum (p=0.011) than by the other media on either dAM or Permanox. Conclusions Conjunctival BC recovers proliferating cells that can be maintained on dAM in FBSm10 for up to 5 days.
Array tomography

In array tomography ordered, ribbon‐like assemblies of ultrathin serial sections are deposited on a solid substrate and imaged afterwards. The resulting images are then aligned and reconstructed into a three‐dimensional representation of the object. Depending on the preparation and labelling regime, different imaging modalities can be applied. When using light microscopy, the labelling with fluorescent markers would be the obvious choice, whereas the imaging in a scanning electron microscope would require impregnation with heavy metals. Depending on preparative constraints, the combination of diverse imaging modalities or truly correlative imaging is possible.
Effects of DNA Structure and Homology Length on Vaccinia Virus Recombination

ABSTRACT Replicating poxviruses catalyze high-frequency recombination reactions by a process that is not well understood. Using transfected DNA substrates we show that these viruses probably use a single-strand annealing recombination mechanism. Plasmids carrying overlapping portions of a luciferase gene expression cassette and luciferase assays were first shown to provide an accurate method of assaying recombinant frequencies. We then transfected pairs of DNAs into virus-infected cells and monitored the efficiencies of linear-by-linear, linear-by-circle, and circle-by-circle recombination. These experiments showed that vaccinia virus recombination systems preferentially catalyze linear-by-linear reactions much more efficiently than circle-by-circle reactions and catalyze circle-by-circle reactions more efficiently than linear-by-circle reactions. Reactions involving linear substrates required surprisingly little sequence identity, with only 16-bp overlaps still permitting ∼4% recombinant production. Masking the homologies by adding unrelated DNA sequences to the ends of linear substrates inhibited recombination in a manner dependent upon the number of added sequences. Circular molecules were also recombined by replicating viruses but at frequencies 15- to 50-fold lower than are linear substrates. These results are consistent with mechanisms in which exonuclease or helicase processing of DNA ends permits the forming of recombinants through annealing of complementary single strands. Our data are not consistent with a model involving strand invasion reactions, because such reactions should favor mixtures of linear and circular substrates. We also noted that many of the reaction features seen in vivo were reproduced in a simple in vitro reaction requiring only purified vaccinia virus DNA polymerase, single-strand DNA binding protein, and pairs of linear substrates. The 3′-to-5′ exonuclease activity of poxviral DNA polymerases potentially catalyzes recombination in vivo.
Automated Ulcer Detection Method from CT Images for Computer Aided Diagnosis of Crohn's Disease

Crohn’s disease commonly affects the small and large intestines. Its symptoms include ulcers and intestinal stenosis, and its diagnosis is currently performed using an endoscope. However, because the endoscope cannot pass through the stenosed parts of the intestines, diagnosis of the entire intestines is difficult. A CT image-based method is expected to become an alternative way for the diagnosis of Crohn’s disease because it enables observation of the entire intestine even if stenosis exists. To achieve efficient CT image-based diagnosis, diagnostic-aid by computers is required. This paper presents an automated detection method of the surface of ulcers in the small and large intestines from fecal tagging CT images. Ulcers cause rough surfaces on the intestinal wall and consist of small convex and concave (CC) regions. We detect them by blob and inverse-blob structure enhancement filters. A roughness value is utilized to reduce the false positives of the detection results. Many CC regions are concentrated in ulcers. The roughness value evaluates the concentration ratio of the detected regions. Detected regions with low roughness values are removed by a thresholding process. The thickness of the intestinal lumen and the CT values of the surrounding tissue of the intestinal lumen are also used to reduce false positives. Experimental results using ten cases of CT images showed that our proposed method detects 70.6% of ulcers with 12.7 FPs/case. The proposed method detected most of the ulcers. key words: ulcer, small and large intestines, detection, computer aided diagnosis, CT image
A Two-Dimensional Autoregressive Model for MIMO Wideband Mobile Radio Channels

In this work, we propose the multichannel two- dimensional (2D) autoregressive (AR) model for multiple-input multiple-output (MIMO) wideband mobile wireless channels. The parameters of the proposed model can be estimated from the real- world measurement data. For this purpose, we suggest using a straightforward extension of the prediction error minimization (PEM) algorithm. We also address the problem of possible instability of the multichannel 2D AR model. A model stabilization procedure based on numerical optimization techniques is proposed. The performance of the multichannel 2D AR model has been evaluated based on the synthetic data generated using two different channel simulators.
Placement with symmetry constraints for analog layout design using TCG-S

In order to handle device matching for analog circuits, some pairs of modules need to be placed symmetrically with respect to a common axis. In this paper, we deal with the module placement with symmetry constraints for analog design using the transitive closure graph-sequence (TCG-S) representation. Since the geometric relationships of modules are transparent to TCG-S and its induced operations, TCG-S has better flexibility than previous works in dealing with symmetry constraints. We first propose the necessary and sufficient conditions of TCG-S for symmetry modules. Then, we propose a polynomial-time packing algorithm for a TCG-S with symmetry constraints. Experimental results show that the TCG-S based algorithm results in the best area utilization.
Word naming and memory load: Still searching for an individual differences explanation.

S. E. Bernstein and T. H. Carr (1996) and P. M. Pexman and S. J. Lupker (1995) suggested that classifiable individual differences in word-naming performance can account for the varied findings on the naming and memory load task (NMLT; K. R. Paap & R. W. Noel, 1991). Bernstein and Carr's technique of testing their explanation by using performance on part of the NMLT to classify participants is problematic, however. To remedy this, in the present study participants were classified on the basis of performance on a priori tasks: Participants completed a naming task, a naming task with low memory load, and the NMLT. Performance on the NMLT was not predicted by performance on either a priori task, thus providing no support for either Bernstein and Carr's or Pexman and Lupker's individual differences accounts.
Evaluating the Empowered Curriculum for Adolescents with Visual Impairments

The study reported here evaluated a self-determination intervention using the empowered curriculum for students with visual impairments. The perceptions of students, family members, and teachers of the usefulness of the chosen curriculum were also evaluated. Despite design limitations, the qualitative data suggest that the students enjoyed the empowered curriculum and found it to be useful.
Relationship between BMI and blood pressure in girls and boys

Abstract Aim To investigate the relationship between BMI and blood pressure as this is of crucial interest in evaluating both public health and the clinical impact of the so-called obesity epidemic. Methods Data were gathered from 1899 children aged between 6 and 14 years, analysing and evaluating a possible relationship between BMI and systolic and diastolic blood pressure values for both girls and boys. Each child was classified on the basis of age- and sex-specific BMI percentile as normal weight (<85th percentile), overweight (≥85th and <95th percentile) or obese (≥95th percentile). Results In comparisons among age–sex–BMI percentile groups, systolic and diastolic blood pressure values were higher in obese and overweight groups than in normal weight groups for both sexes. Although BMI among girls was higher than among boys in all three percentile groups, there were no significant differences between sexes with respect to blood pressure values. Conclusion The present findings emphasize the importance of the prevention of obesity in order to prevent future related problems such as hypertension in children and adolescents.