Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of the Sigma-1 Receptor Agonist 1-(3,4-Dimethoxyphenethyl)-4-(3-Phenylpropyl)-Piperazine Dihydro-Chloride on Inflammation after Stroke

Activation of the sigma-1 receptor (Sig-1R) improves functional recovery in models of experimental stroke and is known to modulate microglia function. The present study was conducted to investigate if Sig-1R activation after experimental stroke affects mediators of the inflammatory response in the ischemic hemisphere. Male Wistar rats were subjected to transient occlusion of the middle cerebral artery (MCAO) and injected with the specific Sig-1R agonist 1-(3,4-dimethoxyphenethyl)-4-(3-phenylpropyl)piperazine dihydrochloride (SA4503) or saline for 5 days starting on day 2 after MCAO. Treatment did not affect the increased levels of the pro-inflammatory cytokines interleukin 1 beta (IL-1β), tumor necrosis factor alpha (TNF-α), interferon gamma (IFN-γ), interleukin 4 (IL-4), interleukin 5 (IL-5), and interleukin 13 (IL-13) in the infarct core and peri-infarct area after MCAO. In addition, treatment with SA4503 did not affect elevated levels of nitrite, TNF-α and IL-1β observed in primary cultures of microglia exposed to combined Hypoxia/Aglycemia, while the unspecific sigma receptor ligand 1,3-di-o-tolylguanidine (DTG) significantly decreased the production of nitrite and levels of TNF-α. Analysis of the ischemic hemisphere also revealed increased levels of ionized calcium binding adaptor molecule 1 (Iba1) levels in the infarct core of SA4503 treated animals. However, no difference in Iba1 immunoreactivity was detected in the infarct core. Also, levels of the proliferation marker proliferating cell nuclear antigen (PCNA) and OX-42 were not increased in the infarct core in rats treated with SA4503. Together, our results suggest that sigma-1 receptor activation affects Iba1 expression in microglia/macrophages of the ischemic hemisphere after experimental stroke but does not affect post-stroke inflammatory mediators.
VISIR work in progress

The VISIR (Virtual Instrument Systems in Reality) Open Lab Platform is an architecture that enable universities, secondary schools, and other organizations to open instructional laboratories for remote access with preserved context. VISIR emanates from a feasibility study made in 1999 at BTH (Blekinge Institute of Technology) in Sweden. Today, VISIR laboratories are online at seven universities globally where thousands of students can work and conduct most experiments that can be performed on a solderless breadboard remotely without any risk of being harmed. IAOE (International Association of Online Engineering has organized SIG VISIR a Special Interest Group for VISIR. Further development of the platform is carried out in this Community. This paper is about work in progress especially at BTH.
High-Value Design Techniques for Mitigating Random Defect Sensitivities

Today's sophisticated design-for-manufacturability (DFM) methodologies provide a designer with an overwhelming amount of choices, many with significant costs and unclear value. The technology challenges of subwavelength lithography, new materials, device types/sizes, etc., can mask the underlying random defect yield contribution which ultimately dominates mature manufacturing, and the distinction between technology limitations and process excursions must also be understood. The best DFM strategy fully exploits all of the available techniques that mitigate a design's sensitivity to random defects where the value is clearly quantifiable, yet few designers seize this opportunity. This paper provides a roadmap through the entire design flow and gives an overview of the various options.
Cooperative activity of cdk 8 and GCN 5 L within Mediator directs tandem phosphoacetylation of histone

The human Mediator complex is generally required for expression of protein-coding genes. Here, we show that the GCN5L acetyltransferase stably associates with Mediator together with the TRRAP polypeptide. Yet, contrary to expectations, TRRAP/GCN5L does not associate with the transcriptionally active core Mediator but rather with Mediator that contains the cdk8 subcomplex. Consequently, this derivative ‘T/G-Mediator’ complex does not directly activate transcription in a reconstituted human transcription system. However, within T/GMediator, cdk8 phosphorylates serine-10 on histone H3, which in turn stimulates H3K14 acetylation by GCN5L within the complex. Tandem phosphoacetylation of H3 correlates with transcriptional activation, and ChIP assays demonstrate co-occupancy of T/G-Mediator components at several activated genes in vivo. Moreover, cdk8 knockdown causes substantial reduction of global H3 phosphoacetylation, suggesting that T/G-Mediator is a major regulator of this H3 mark. Cooperative H3 modification provides a mechanistic basis for GCN5L association with cdk8-Mediator and also identifies a biochemical means by which cdk8 can indirectly activate gene expression. Indeed our results suggest that T/G-Mediator directs early events—such as modification of chromatin templates—in transcriptional activation. The EMBO Journal (2008) 27, 1447–1457. doi:10.1038/ emboj.2008. 78; Published online 17 April 2008 Subject Categories: chromatin & transcription
Regulatory T cells in health and disease

The healthy host does not normally develop tissue destructive autoimmunity in part because of the presence of natural regulatory T cells. These cells are best identified by their expression of a unique transcription factor forkhead box transcription factor (Foxp3) that controls their regulatory function. Several other types of regulatory T cells also occur most of which are induced in response to antigen stimulation. Some of these express the Foxp3 transcription factor but many do not. The role of natural T‐regulatory cells as well as induceable regulatory cells in autoimmunity, cancer, allergy and infectious disease is described. The current status of therapeutic approaches that modulate regulatory T‐cell responses on the outcome of experimental animal and human disease is also discussed.
High-level geospatial information discovery and fusion for geocoded multimedia

Purpose– Improvements and portability of technologies and smart devices have enabled a rapid growth in the amount of user-generated media such as photographs and videos. Whilst various media generation and management systems exist, it still remains a challenge to discover the right information, for the right purpose. This paper aims to propose an approach to reverse geocoding by cross-referencing multiple geospatial data sources to enable the enrichment of media and therefore enable better organisation and searching of the media to create an overall picture about places.Design/methodology/approach– The paper presents a system architecture that incorporates the proposed approach to aggregate several geospatial databases to enrich geo-tagged media with human readable information, which will further enable the goal of creating an overall picture about places. The approach enables the semantic information relating to point of interest.Findings– Implementation of the proposed approach shows that a single geospatial data source does not contain enough information to accurately describe the high-level geospatial information for geocoded multimedia. However, fusing several geospatial data sources together enables richer, more accurate high-level geospatial information to be tagged to the geocoded multimedia.Originality/value– The contribution in this paper shows that high-level geospatial information can be retrieved from many data sources and fused together to enrich geocoded multimedia which can facilitate better searching and retrieval of the multimedia.
Coordinate signaling by Src and p38 kinases in the induction of cortical cataracts.

PURPOSE The goals of this study were to determine whether MAP kinase signaling pathways play a role in the formation of lens cataracts and to examine the potential signaling relationship between Src and MAP kinases in signaling the induction of lens opacities. METHODS Embryonic day (E)10 chick lenses were cultured in Medium 199 containing 10% fetal bovine serum. The activation state of Src kinases and the MAP kinases extracellular signal-regulated protein kinase (ERK), c-jun N-terminal kinase (JNK), and p38 in the lens epithelium was determined over a time course from 10 minutes to 10 days in culture by immunoblot analysis. Src kinase activation was suppressed by exposure to the Src family kinase-specific inhibitor PP1. To examine the role of specific MAP kinases in the development of lens opacities, lenses were grown for 10 days in the presence or absence of inhibitors of ERK (U0126), JNK (SP600125), and p38 (SB203580). Lenses were observed and photographed daily, and the degree of opacification was quantified by using image-analysis software. RESULTS Within a short time after placing embryonic lenses in culture conditions that induce the formation of cataracts, there occurred a great increase in the activation state of the MAP kinase ERK. Activation of ERK was both rapid and transient. No activation of the MAP kinase JNK was observed in the cataract cultures beyond that which occurred in normal lens epithelium, even though JNK activation is often linked to the cellular response to stress. In contrast, although p38 activation was barely detected in the normal embryonic lens, this stress-activated protein kinase exhibited a robust activation in cataract cultures that was sustained throughout the culture period. Studies conducted to map the cataract signaling pathways indicate that the p38 MAP kinase functions upstream of the Src kinase. To analyze the potential role of ERK, JNK, and p38 in cataract induction, lenses were cultured in the presence of specific MAP kinase inhibitors. Although the inhibitors of ERK and JNK did not interfere with the formation of cataract, p38 inhibitors blocked the development of lens opacities with an efficacy similar to that of the Src kinase inhibitor PP1. CONCLUSIONS Activation of both Src and p38 kinases lead to the induction of cataract.
A Snapshot of the Hepatic Transcriptome: Ad Libitum Alcohol Intake Suppresses Expression of Cholesterol Synthesis Genes in Alcohol-Preferring (P) Rats

Research is uncovering the genetic and biochemical effects of consuming large quantities of alcohol. One prime example is the J- or U-shaped relationship between the levels of alcohol consumption and the risk of atherosclerotic cardiovascular disease. Moderate alcohol consumption in humans (about 30 g ethanol/d) is associated with reduced risk of coronary heart disease, while abstinence and heavier alcohol intake is linked to increased risk. However, the hepatic consequences of moderate alcohol drinking are largely unknown. Previous data from alcohol-preferring (P) rats showed that chronic consumption does not produce significant hepatic steatosis in this well-established model. Therefore, free-choice alcohol drinking in P rats may mimic low risk or nonhazardous drinking in humans, and chronic exposure in P animals can illuminate the molecular underpinnings of free-choice drinking in the liver. To address this gap, we captured the global, steady-state liver transcriptome following a 23 week free-choice, moderate alcohol consumption regimen (∼7.43 g ethanol/kg/day) in inbred alcohol-preferring (iP10a) rats. Chronic consumption led to down-regulation of nine genes in the cholesterol biosynthesis pathway, including HMG-CoA reductase, the rate-limiting step for cholesterol synthesis. These findings corroborate our phenotypic analyses, which indicate that this paradigm produced animals whose hepatic triglyceride levels, cholesterol levels and liver histology were indistinguishable from controls. These findings explain, at least in part, the J- or U-shaped relationship between cardiovascular risk and alcohol intake, and provide outstanding candidates for future studies aimed at understanding the mechanisms that underlie the salutary cardiovascular benefits of chronic low risk and nonhazardous alcohol intake.
Learning generative models of mid-level structure in natural images

Natural images arise from complicated processes involving many factors of variation. They reflect the wealth of shapes and appearances of objects in our three-dimensional world, but they are also affected by factors such as distortions due to perspective, occlusions, and illumination, giving rise to structure with regularities at many different levels. Prior knowledge about these regularities and suitable representations that allow efficient reasoning about the properties of a visual scene are important for many image processing and computer vision tasks. This thesis focuses on models of image structure at intermediate levels of complexity as required, for instance, for image inpainting or segmentation. It aims at developing generative, probabilistic models of this kind of structure, and, in particular, at devising strategies for learning such models in a largely unsupervised manner from data. One hallmark of natural images is that they can often be decomposed into regions with very different visual characteristics. The main approach of this thesis is therefore to represent images in terms of regions that are characterized by their shapes and appearances, and an image is then composed from many such regions. We explore approaches to learn about the appearance of regions, to learn about region shapes, and ways to combine several regions to form a full image. To achieve this goal, we make use of some ideas for unsupervised learning developed in the literature on models of low-level image structure and in the “deep learning” literature. These models are used as building blocks of more structured model formulations that incorporate additional prior knowledge of how images are formed. The thesis makes the following contributions: Firstly, we investigate a popular, MRF based prior of natural image structure, the Field-of Experts, with respect to its ability to model image textures, and propose an extended formulation that is considerably more successful at this task. This formulation gives rise to a fully parametric, translation-invariant probabilistic generative model of image textures. We illustrate how this model can be used as a component of a more comprehensive model of images comprising multiple textured regions. Secondly, we develop a model of region shape. This work is an extension of the “Masked Restricted Boltzmann Machine” proposed by Le Roux et al. (2011) and it allows explicit reasoning about the independent shapes and relative depths of occluding objects. We develop an inference and unsupervised learning scheme and demonstrate how this shape model, in combination with the masked RBM gives rise to a good model of natural image patches. Finally, we demonstrate
Mortality Prediction of ICU patients using Machine Leaning: A survey

Recently health care researchers are working a lot on outcome prediction on Intensive Care Unit (ICU) and trauma. Outcome prediction in intensive care is a difficult process. Accurate synthesis of quality data and application of prior experience to the analysis is required to solve it. In this paper we will review some of the recent advancements in the mortality prediction of ICU patients using machine learning techniques. Mainly the research covered in this survey will be on predicting readmission in Intensive care unit, mortality rate after ICU discharge and life expectancy rate for 5 years. In order to analyse how much a patient will survive in next five years, this expectancy rate is used. These predictions are very useful because using these results doctors can take decision about extending the stay of patient in hospital and also helps in taking decision about the particular treatment needed. An extensive survey of the related research is presented with a stress on the major novelties of their work. At last, the research gaps inferred after analyzing the previous works are highlighted along with the future prospects in the field of research.
Crossing grammar and biology for gender categorisations: investigating the gender congruency effect in generic nouns for animates

ABSTRACT In formal gender languages, all nouns have grammatical gender, regardless of whether their referents have a biological sex. The question of whether the grammatical gender affects how the denoted entities are conceptualised is subject to ongoing debate. Here, we investigate the extent to which a gender congruency effect emerges for three categories of nouns, with a particular focus on generic nouns (or epicenes). In two experiments and two replications with native speakers of German, we used an implicit measure to test possible associations of nouns with biological sex. These experiments revealed a stable gender congruency effect for congruent animates, and a weaker effect for generic animates and non-animates. In a fifth experiment, we combined the implicit measure with an explicit measure and contrasted items that have strong versus weak associations with biological sex. The results indicate that the congruency effect is driven by item-specific associations rather than by grammatical gender.
The Contact Sheet: Combining Evocative and Analytic Modes into Visual Autoethnography of the Moment

This chapter “unpacks” a poster from the CEAD (Contemporary Ethnography Across the Disciplines) conference 2010 and re-situates it within an autoethnographic narrative. The poster presented a project that combined Evocative and Analytic modes in a visual ethnography focused on a collection of tourist photographs taken on Rarotonga in the South Pacific. The framing autoethnography finds in this project evidence of a distinctive tension in contemporary informationalized life between embodied life and data coordinates, plots, or maps of the spaces and times where life takes place. The chapter aligns two sets of terms: on one hand embodied life and the Evocative mode, on the other hand data coordinates/plots and the Analytic mode. With its focus on the photographic image, the chapter also suggests two further terms for both Evocative and Analytic investigation: the image as fantasy and the visual moment. The chapter takes the form of a layered performance text in order to explore these matters.
Molecular and biochemical characterization of a protective 40-kilodalton antigen from Corynebacterium pseudotuberculosis

A 40-kDa protein from Corynebacterium pseudotuberculosis has been previously identified as a protective antigen against ovine caseous lymphadenitis. From genomic DNA libraries of C. pseudotuberculosis, we have cloned and sequenced the 40-kDa protein gene, which was found to contain an open reading frame of 1,137 bp encoding a protein of 379 amino acids. No significant homology with previously published DNA or amino acid sequence data was found in databases, suggesting that this is a novel protein. Recombinant 40-kDa protein was overexpressed as a fusion protein to 15% of total cell proteins in Escherichia coli. Biochemical analysis of native and recombinant 40-kDa proteins has revealed associated proteolytic activity, which was shown to be of the serine protease type through the use of specific inhibitors. We suggest that this novel protective antigen be termed corynebacterial protease 40 (CP40).
Neighborhood Disadvantage, Network Social Capital, and Depressive Symptoms

Research on why neighborhood disadvantage matters for health focuses on the capacity of neighborhoods to regulate residents’ behavior through informal social control. The authors extend this research by conducting a multilevel analysis of data from a 1995 telephone survey of 497 residents of 32 neighborhoods in a U.S. city. The authors find that network social capital mediates the contextual effect of neighborhood disadvantage on depressive symptoms and that health effects of network social capital persist when perceived neighborhood disorder, a standard indicator of low informal social control, is controlled for. The findings demonstrate the value of a conceptualization and measurement of network social capital that (1) considers ties that transcend neighborhood boundaries, (2) investigates health benefits of network social capital in the forms of closure and embedded support resources and range and embedded instrumental resources, and (3) uses network data on specific network members with strong and weak ties to respondents.
An Inverted Repeat Motif Stabilizes Binding of E2F and Enhances Transcription of the Dihydrofolate Reductase Gene (*)

An overlapping inverted repeat sequence that binds the eukaryotic transcription factor E2F is 100% conserved near the major transcription start sites in the promoters of three mammalian genes encoding dihydrofolate reductase, and is also found in the promoters of several other important cellular and viral genes. This element, 5′-TTTCGCGCCAAA-3′, is comprised of two overlapping, oppositely oriented sites which match the consensus E2F site (5′-TTT(C/G)(C/G)CGC-3′). Recent work has shown that E2F binding activity is composed of at least six related cellular polypeptides which are capable of forming DNA-binding homo- and heterodimers. We have investigated the binding of cellular E2F activity and of homo- and heterodimers of cloned E2F proteins to the inverted repeat E2F element. We have demonstrated that mutations in this element that abolish its inverted repeat nature, while preserving a single consensus E2F site, significantly decrease the binding stability of all of the forms of E2F tested. The rate of association of E2F-1/DP-1 heterodimers with the inverted repeat wild type site was not significantly different from those with the two single site mutated probes. Furthermore, the mutations decrease in vitro transcription and transient reporter gene expression 2-5-fold, an effect equivalent to that of abolishing E2F binding altogether. These data suggest a functional role that may explain the conservation of inverted repeat E2F elements among the DHFR promoters and several other cellular and viral promoters.
Mining API protocols based on a balanced probabilistic model

API protocols are important for modern software development. They can be used in program testing, documentation, understanding and validation. Mining API protocols based on probabilistic models is proved to be an effective method to achieve protocols automatically. In this paper, we discuss the unbalanced probability problem caused by loops and recursive functions in application programs and a method based on the suffix tree is proposed to address it. In order to investigate the feasibility and effectiveness of our approach, we implemented it in our previous prototype tool ISpecMiner and performed a comparison test based on several real-world applications. Experimental results show that our approach can achieve protocols with more balanced probabilities than existing approaches, which provides a strong assurance for achieving valid and precise API protocols.