Miracle-dz/UniFAR-FTUs huggingface dataset:
Intronic Parent-of-Origin Dependent Differential Methylation at the Actn1 Gene Is Conserved in Rodents but Is Not Associated with Imprinted Expression

Parent-of-origin differential DNA methylation has been associated with regulation of the preferential expression of paternal or maternal alleles of imprinted genes. Based on this association, recent studies have searched for parent-of-origin dependent differentially methylated regions in order to identify new imprinted genes in their vicinity. In a previous genome-wide analysis of mouse brain DNA methylation, we found a novel differentially methylated region in a CpG island located in the last intron of the alpha 1 Actinin (Actn1) gene. In this region, preferential methylation of the maternal allele was observed; however, there were no reports of imprinted expression of Actn1. Therefore, we have tested if differential methylation of this region is common to other tissues and species and affects the expression of Actn1. We have found that Actn1 differential methylation occurs in diverse mouse tissues. Moreover, it is also present in other murine rodents (rat), but not in the orthologous human region. In contrast, we have found no indication of an imprinted effect on gene expression of Actn1 in mice: expression is always biallelic regardless of sex, tissue type, developmental stage or isoform. Therefore, we have identified a novel parent-of-origin dependent differentially methylated region that has no apparent association with imprinted expression of the closest genes. Our findings sound a cautionary note to genome-wide searches on the use of differentially methylated regions for the identification of imprinted genes and suggest that parent-of-origin dependent differential methylation might be conserved for functions other that the control of imprinted expression.
The Aimms Interface to Constraint Programming

We present an extension of the modeling system Aimms to handle constraint programming problems. Our goal is to provide a more accessible interface to CP technology than current systems offer. We first present basic CP modeling constructs that can be realized with minimum changes to the existing syntax. We then discuss the handling of global constraints. Lastly, we present our extensions to modeling scheduling problems, based on the now-classical representation as activities and resources. An important benefit of the Aimms interface to CP is the ease with which hybrid CP/OR solution methods can be developed.
Connecting Vehicle Scatternets by Internet-Connected Gateways

This paper presents an approach for interconnecting isolated clouds of an ad hoc network that form a scatternet topology using Internet gateways as intermediate nodes. The architecture developed is intended to augment FleetNet, a highly dynamic ad hoc network for inter-vehicle communications. This is achieved by upgrading FleetNet capabilities to establish a communication path between moving vehicles and the Internet via Internet gateways to facilitate direct gateway to gateway communications via the Internet, thus bridging gaps in the network topology and relaying packets closer towards their geographical destination at the same time. After outlining the overall FleetNet approach and its underlying geographical multi-hop routing, we focus on the FleetNet gateway architecture. We describe required modifications to the gateway architecture and to the FleetNet network layer in order to use these gateways as intermediate nodes for FleetNet routing. Finally, we conclude the paper by a short discussion on the prototype gateway implementation and by summarizing first results and ongoing work on inter scatternet communication.
Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain 150, Isolated from Diseased Rainbow Trout

ABSTRACT We present here the draft genome of a pathogenic Yersinia ruckeri strain, isolated from rainbow trout (Oncorhynchus mykiss) affected by enteric redmouth disease. The chromosome has 3,826,775 bp, a GC content of 46.88%, and is predicted to contain 3,538 coding sequences. The data will be useful for comparative pathogenicity studies.
CCR4 Controls the Suppressive Effects of Regulatory T Cells on Early and Late Events during Severe Sepsis

Sepsis is a deadly disease characterized by an overwhelming release of inflammatory mediators and the activation of different types of cells. This altered state of cell activation, termed leukocyte reprogramming, contributes to patient outcome. However, the understanding of the process underlying sepsis and the role of regulatory T cells (Tregs) in sepsis remains to be elucidated. In this study, we investigated the role of CCR4, the CCL17/CCL22 chemokine receptor, in the innate and acquired immune responses during severe sepsis and the role of Tregs in effecting the outcome. In contrast with wild-type (WT) mice subjected to cecal ligation and puncture (CLP) sepsis, CCR4-deficient (CCR4-/-) septic mice presented an increased survival rate, significant neutrophil migration toward the infection site, a low bacterial count in the peritoneum, and reduced lung inflammation and serum cytokine levels. Thus, a better early host response may favor an adequate long-term response. Consequently, the CCR4-/- septic mice were not susceptible to secondary fungal infection, in contrast with the WT septic mice. Furthermore, Tregs cells from the CCR4-/- septic mice showed reduced suppressive effects on neutrophil migration (both in vivo and in vitro), lymphocyte proliferation and ROS production from activated neutrophils, in contrast with what was observed for Tregs from the WT septic mice. These data show that CCR4 is involved in immunosuppression after severe sepsis and suggest that CCR4+ Tregs negatively modulate the short and long-term immune responses.
Comparison of Nasal Epithelial Smoking-Induced Gene Expression on Affymetrix Exon 1.0 and Gene 1.0 ST Arrays

We have previously defined the impact of tobacco smoking on nasal epithelium gene expression using Affymetrix Exon 1.0 ST arrays. In this paper, we compared the performance of the Affymetrix GeneChip Human Gene 1.0 ST array with the Human Exon 1.0 ST array for detecting nasal smoking-related gene expression changes. RNA collected from the nasal epithelium of five current smokers and five never smokers was hybridized to both arrays. While the intersample correlation within each array platform was relatively higher in the Gene array than that in the Exon array, the majority of the genes most changed by smoking were tightly correlated between platforms. Although neither array dataset was powered to detect differentially expressed genes (DEGs) at a false discovery rate (FDR) <0.05, we identified more DEGs than expected by chance using the Gene ST array. These findings suggest that while both platforms show a high degree of correlation for detecting smoking-induced differential gene expression changes, the Gene ST array may be a more cost-effective platform in a clinical setting for gene-level genomewide expression profiling and an effective tool for exploring the host response to cigarette smoking and other inhaled toxins.
Electrochemical Detection with Preconcentration: Nitroenergetic Contaminants

This effort evaluated the potential of two prototype devices for enhanced electrochemical detection of 2,4,6-trinitrotoluene (TNT) and dinitrotoluene (DNT) following preconcentration using an organosilicate sorbent. The bench-scale prototype provides adsorption of the targets from aqueous solution followed by elution in a mixture of methanol and potassium chloride (KCl). Following elution, the eluant is diluted using an aqueous KCl solution to provide sufficient electrolyte for electrochemical analysis. Concentrations of methanol greater than 50% were detrimental to sensor performance and lifetime. Calibration of the electrochemical sensor was completed and results of electrochemical analysis were compared to those of HPLC analysis over a range of concentrations and in varied matrices. TNT detection was found to be consistent and detection limits were improved from 200 ppb to 3 ppb depending on the sample volume utilized. DNT detection showed higher variability and significantly greater false response rates. On the basis of these results, a second, more advanced, prototype was developed and utilized in limited field trials with the intention of moving the technology toward in situ applications.
Clinical significance and effect of AEG-1 on the proliferation, invasion, and migration of NSCLC: a study based on immunohistochemistry, TCGA, bioinformatics, in vitro and in vivo verification

Background Astrocyte elevated gene-1 (AEG-1) is related to the tumorigenesis and deterioration of different cancers, including non-small cell lung cancer (NSCLC). However, the effect of AEG-1 in NSCLC remains unclear. In this study, we aimed to investigate the clinical significance and effect of AEG-1 on biological function of NSCLC. Results AEG-1 was significantly overexpressed in NSCLC tissues and closely correlated to the deterioration of NSCLC based on tissue microarray, TCGA database and meta-analysis. After knock-down of AEG-1, the proliferation, migration and invasion of NSCLC cells were all inhibited, and the tumorigenic and angiogenic ability of NSCLC cells were weakened. Furthermore, the AEG-1 co-expressed genes were significantly related to AMPK signaling pathway based on bioinformatics approaches. Materials and Methods A tissue microarray, the Cancer Genome Atlas (TCGA) database, as well as a meta-analysis were performed to analyze the relationship between AEG-1 and the clinicopathological parameters of NSCLC. Furthermore, immunocytochemistry, Western blot analysis, scratch assay, colony formation assay, Transwell migration and invasion assay and the chick embryo chorioallantoic membrane (CAM) model were conducted to explore the effect of AEG-1 on NSCLC in vitro and in vivo. Additionally, bioinformatics analyses were carried out to assess the potential pathways and networks of the co-expressed genes of AEG-1. Conclusions AEG-1 is positively activated in the tumorigenesis and deterioration of NSCLC. We hypothesize that AEG-1 could play an important role in NSCLC via AMPK signaling pathway. Inhibiting the expression of AEG-1 is expected to become a novel method in the therapeutic strategies of NSCLC.
Design and development of circuit optimizer using TCl and SPECTREMDL(SPICE) interface

Digital and analog designers are always interested in automated optimization of transistor width values for customized requirements. SPICE tools are now embedded with certain options [like L-M algorithm and parametric analysis] by virtue of which automated width optimization can be performed upto a certain extent. Whereas when the optimization requirements are very specific they seem to be helpless. For customization of automation process several research had been done in past, of them the most valuable being the PSPICE and MATLAB interface. Since PSPICE has its own limitation, hence the horizon of the interface is limited. The paper proposes a novel circuit optimizer using TCL and SPECTREMDL interface. Hence, instead of using only the algorithms embedded in SPICE tools, the designer has a flexibility to write new algorithms in TCL and analyze the circuit behavior with the interface, while having the flexibility to re-optimize the circuit again and again by changing the input values with the help of designed algorithm. The interface between TCL and SPECTREMDL has been demonstrated by applying the methodology to standard Flip-Flop circuits.
Queering Counselor Education: Situational Analysis of LGBTQ+ Competent Faculty

ABSTRACT Research demonstrates counselor educators often lack skills and knowledge to train counselors to become lesbian, gay, bisexual, transgender, queer and other sexualities and gender identities (LGBTQ+) competent. This study explores the process of educators integrating LGBTQ+ competencies into their professional work. Using grounded theory and situational analysis methodologies, in-depth interviews with seven LGBTQ+ competent counselor educators were conducted and analyzed. Findings suggest educators infuse personal passion for LGBTQ+ topics into their professional work, experienced discrimination and resistance across multiple domains, infuse advocacy into their work, and have a similar definition of LGBTQ+ competent counseling. Various techniques are presented to help educators infuse LGBTQ+ competency in the classroom.
Topic sentiment trend model: Modeling facets and sentiment dynamics

Mining subtopics and analyzing their sentiment dynamics on weblogs have many applications in multiple domains. Current work pays little attention to the combination of topics and their sentiment evolution simultaneously. In this paper, we study the problem of topic detection and sentiment-topic temporal evolution in weblogs, and propose a novel probabilistic model called topic sentiment trend model (TSTM). With the model, we can integrate the topic with sentiment, and analyze the temporal trend of the sentiment-topic. Experiments on two Chinese weblog datasets show that our approach is effective in modeling the topic facets and extracting their sentiment dynamics.
Altered Persistence of Brain Activity in Schizophrenia during Working Memory Tasks

We studied the dynamic properties of the blood oxygenation level-dependent (BOLD) time series of patients diagnosed with schizophrenia both at resting state and during working memory tasks, by computing a key measure from complexity science, the Hurst exponent (H), using Adaptive Fractal Analysis (AFA). 44 participants meeting the DSM-IV criteria for schizophrenia and 77 healthy controls underwent fMRI scanning at 3.0 T at resting state and during Paired associate Memory Task and Spatial Working Memory Task. Mean H for all the 116 brain regions extracted from Anatomical Automatic Labeling (AAL) template as well as the whole brain were generated and analyzed for each subject based on voxel by voxel time series. At resting state, 103 of 116 brain regions showed significantly reduced H, suggesting overwhelmingly less persistent spontaneous brain activity in patients with schizophrenia at whole brain level and region level. While performing working memory task, only prefrontal cortex (PFC), anterior cingulate cortex (ACC) presented significantly lower H. Either resting state or working memory tasks, H of healthy controls showed wide variation from region to region, while patients with schizophrenia were the opposite. The result provides evidence that brain activity of schizophrenia is associated with weaker persistence and more randomness in signal patterns compared to healthy controls at resting state; PFC and ACC are critical area for working memory; schizophrenia is characterized by limited resource allocation capability.
Pre-existing type 2 diabetes and risk of lung cancer: a report from two prospective cohort studies of 133 024 Chinese adults in urban Shanghai

Objectives Observational studies of type 2 diabetes (T2D) and lung cancer risk are limited and controversial. We thus examined the association between T2D and risk of incident lung cancer using a cohort design. Setting Data from two ongoing population-based cohorts (the Shanghai Men's Health Study, SMHS, 2002–2006 and the Shanghai Women's Health Study, SWHS, 1996–2000) were used. Cox proportional-hazards regression models with T2D as a time-varying exposure were modelled to estimate HRs and 95% CIs. Participants The study population included 61 491 male participants aged 40–74 years from SMHS and 74 941 female participants aged 40–70 years from SWHS. Outcome measure Lung cancer cases were identified through annual record linkage to the Shanghai Cancer Registry and Shanghai Municipal Registry of Vital Statistics, and were further verified through home visits and a review of medical charts by clinical and/or pathological experts. Outcome data until 31 December 2010 for men and women were used for the present analysis. Results After a median follow-up of 6.3 years for SMHS and 12.2 years for SWHS, incident lung cancer cases were detected in 492 men and 525 women. A null association between T2D and lung cancer risk was observed in men (HR=0.87, 95% CI 0.62 to 1.21) and women (HR=0.92, 95% CI 0.69 to 1.24) after adjustments for potential confounders. Similar results were observed among never smokers. Conclusions There is little evidence that pre-existing T2D may influence the incidence of lung cancer.
The Use of Potential Nonrespondents for Studying Nonresponse Bias

Few engaged in survey research ever succeed in avoiding the problem of nonresponse. Yet, its occurrence, as Deming (1960) has warned, can be "devastating and discouraging"; for there is ample evidence to suggest that individuals who do not take part in surveys are likely to differ from those who do on a wide range of variables, including those that are often most germane to the study at hand. In principle, at least, the estimation of nonresponse bias offers no problem. The degree of bias present in any given survey can be shown to be a function of (a) the proportion of nonrespondents in the total sample and (b) the extent o which there is a systematic discrepancy between respondents and nonrespondents on variables relevant o the inquiry (See Cochran, 1953: 292-304; Deming, 1960: 66-67; Kish, 1965: 532-571; Moser, 1959: 127-144, 178-184). 1 In practice, however, the measurement of nonresponse bias proves more difficult. It confronts the researcher with the basic paradox that the variables to be used for analysis require information which the subjects, by not participating, fail to make available.
A dedicated visual for prey detection in larval zebrafish

8 Zebrafish larvae show characteristic prey capture behavior in response to small 9 moving objects. The neural mechanism used to recognize objects as prey remains largely 13 by the optimal prey stimulus. This pretectal region is innervated by two types of retinal 14 ganglion cells, which also send collaterals to the optic tectum. Laser ablation of AF7 15 markedly reduced prey capture behavior. We identified neurons with arbors in AF7 and 16 found that they projected to multiple sensory and premotor areas: the optic tectum, the 17 nucleus of the medial longitudinal fasciculus (nMLF) and the hindbrain. These findings 18 indicate that computations in the retina give rise to a visual stream which transforms 19 sensory information into a directed prey capture response.
Performance evaluation of an efficient counter-based scheme for mobile ad hoc networks based on realistic mobility model

Flooding is the simplest and commonly used mechanism for broadcasting in mobile ad hoc networks (MANETs). Despite its simplicity, it can result in high redundant retransmission, contention and collision in the network, a phenomenon referred to as broadcast storm problem. Several probabilistic broadcast schemes have been proposed to mitigate this problem inherent with flooding. Recently, we have proposed a hybrid-based scheme as one of the probabilistic scheme, which combines the advantages of pure probabilistic and counter-based schemes to yield a significant performance improvement. Despite these considerable numbers of proposed broadcast schemes, majority of these schemespsila performance evaluation was based on random waypoint model. In this paper, we evaluate the performance of our broadcast scheme using a community based mobility model which is based on social network theory and compare it against widely used random waypoint mobility model. Simulation results have shown that using unrealistic movement pattern does not truly reflect on the actual performance of the scheme in terms of saved-rebroadcast, reachability and end to end delay.
A novel hybrid approach to restore historical degraded documents

Old degraded historical documents carry various important information regarding our culture, economics etc. proper restoration of these documents is very necessary. After digitization of these documents there remain noises and other low resolution components. These affect the overall visual appearance of the documents. In this paper a novel approach is proposed to enhance ancient historical documents. To enhance these digital format documents a two way approach is considered. At first Particle Swarm Optimization (PSO) and bilateral filter is applied. At second level Non-Linear Enhancement with bilateral filter is applied. Both the approaches are then tested visually and quantitively to show the effectiveness of the approach.
Mass formulas for stationary Einstein-Yang-Mills black holes and a simple proof of two staticity theorems.

We derive two new integral mass formulas for stationary black holes in Einstein-Yang-Mills theory. From these we derive a formula for JΩ-QV, from which it follows immediately that any stationary, nonrotating, uncharged black hole is static and has a vanishing electric field on the static slices. In the Einstein-Maxwell case, we have, in addition, the «generalized Smarr mass formula,» for which we provide a new, simple derivation. When combined with the other two formulas, we obtain a simple proof that nonrotating Einstein-Maxwell black holes must be static and have a vanishing magnetic field on the static slices
Agent-Based Device Management in RFID Middleware

As an important part of RFID (radio frequency identification) middleware, device management has a direct impact on the stability of RFID system. This paper proposes an agent-based device management approach in RFID middleware. We design two types of agents: control agent and device agent. Control agent manages and maintains the life cycle of each Device Agent, and coordinates the work of multiple device agents. Device agent lies between the RFID middleware and the physical device. It provides a common operating interface for RFID middleware, implements remote configuration and grouping management for RFID devices, monitors the real-time state of RFID devices, deals with unexpected events, and carries out fault-tolerant processing when necessary. Through the collaboration of multiple device agents, we can dynamically schedule jobs for different devices to optimize the allocation of system resources. Applying agent technology in device management reduces the coupling between RFID middleware and physical devices, therefore, increases the flexibility and scalability of RFID system.
A Tutorial on the Optimization of Amplify-and-Forward MIMO Relay Systems

The remarkable promise of multiple-input multiple-output (MIMO) wireless channels has motivated an intense research activity to characterize the theoretical and practical issues associated with the design of transmit (source) and receive (destination) processing matrices under different operating conditions. This activity was primarily focused on point-to-point (single-hop) communications but more recently there has been an extensive work on two-hop or multi-hop settings in which single or multiple relays are used to deliver the information from the source to the destination. The aim of this tutorial is to provide an up-to-date overview of the fundamental results and practical implementation issues in designing amplify-and-forward MIMO relay systems.
L1-norm global localization based on a Differential Evolution Filter

Global localization methods deal with the estimation of a mobile robot's pose assuming no prior state information about it and a complete a priori knowledge of the environment where the mobile robot is going to be localized. Most existent algorithms are based on the minimization of a L2-norm loss function. However, the use of a L1-norm offers some alternative advantages. The present work explores the use of a L1-norm together with an Evolutive Localization Filter to determine its efficiency when applied to the global localization problem. The algorithm has been tested subject to different noise levels to demonstrate the accuracy, effectiveness, robustness and computational efficiency of the L1-norm approach.