Miracle-dz/UniFAR-FTUs huggingface dataset:
The chemokine SDF-1 differentially regulates axonal elongation and branching in hippocampal neurons

Recent data have shown that the chemokine SDF-1 plays a critical role in several aspects of brain development such as cell migration and axon pathfinding. However, its potential function in the generation of axons and dendrites is poorly characterized. In order to better understand the role of SDF-1 in the development of central neurons, we studied the cellular distribution of the SDF-1 receptor CXCR4 by immunocytochemistry of developing hippocampal neurons and tested the effect of SDF-1 in process patterning at the early stages of neuronal development. We found that CXCR4 immunoreactivity undergoes a striking redistribution during development. At the early stages, from day 2 to day 4 in culture, CXCR4 is particularly concentrated at the leading edge of growing neurites. As the cells mature, staining declines at the tip of the processes and becomes more broadly distributed along axons and, to a lesser extent, dendrites. SDF-1 stimulation of neurons at day 1-2 in culture triggers several effects on neuronal morphogenesis. SDF-1 reduces growth cone number and axonal outgrowth but stimulates axonal branching. These latter two effects are not observed in other neurites. This study unravels a new role for SDF-1/CXCR4 in specifying hippocampal neuron morphology by regulating axonal patterning at an early stage of neuronal development.
Analysis of DNA methylation reveals a partial reprogramming of the Müller glia genome during retina regeneration

Significance Retinal injury in zebrafish stimulates Müller glia (MG) to undergo a reprogramming event that transitions their identity from quiescent supportive cells to multipotent progenitors capable of repairing the damaged retina. Understanding the mechanisms underlying this reprogramming event may provide insights for stimulating retina regeneration in mammals. Here we report an epigenetic analysis of zebrafish MG, monitoring changes in their genomic methylation levels as they reprogram and generate progenitors. Although we find a changing DNA methylation landscape, our data also suggest that a basal methylation program may facilitate this transition. Interestingly, certain aspects of this basal methylation program are shared with mammals, suggesting they too may acquire progenitor properties under appropriate circumstances. Upon retinal injury, zebrafish Müller glia (MG) transition from a quiescent supportive cell to a progenitor cell (MGPC). This event is accompanied by the induction of key transcription and pluripotency factors. Because somatic cell reprogramming during induced pluripotent stem cell generation is accompanied by changes in DNA methylation, especially in pluripotency factor gene promoters, we were interested in determining whether DNA methylation changes also underlie MG reprogramming following retinal injury. Consistent with this idea, we found that genes encoding components of the DNA methylation/demethylation machinery were induced in MGPCs and that manipulating MGPC DNA methylation with 5-aza-2′-deoxycytidine altered their properties. A comprehensive analysis of the DNA methylation landscape as MG reprogram to MGPCs revealed that demethylation predominates at early times, whereas levels of de novo methylation increase at later times. We found that these changes in DNA methylation were largely independent of Apobec2 protein expression. A correlation between promoter DNA demethylation and injury-dependent gene induction was noted. In contrast to induced pluripotent stem cell formation, we found that pluripotency factor gene promoters were already hypomethylated in quiescent MG and remained unchanged in MGPCs. Interestingly, these pluripotency factor promoters were also found to be hypomethylated in mouse MG. Our data identify a dynamic DNA methylation landscape as zebrafish MG transition to an MGPC and suggest that DNA methylation changes will complement other regulatory mechanisms to ensure gene expression programs controlling MG reprogramming are appropriately activated during retina regeneration.
Electromagnetic fields (GSM 1800) do not alter blood–brain barrier permeability to sucrose in models in vitro with high barrier tightness

We previously reported that electromagnetic fields (EMFs) [GSM 1800 standard (Global System for Mobile Communications, 1800 MHz)] increased sucrose permeation across the blood–brain barrier (BBB) in vitro. The cell culture model used in our previous study was comprised of rat astrocytes in coculture with porcine brain microvascular endothelial cells (PBECs). In this study, after optimization of cell culture conditions, distinctly improved barrier tightness was observed, accompanied by a loss of susceptibility to EMF‐related effects on BBB permeability. Cell cultures were exposed for 1–5 days at an average specific absorption rate (SAR) of 0.3 W/kg in the identical exposure system as described before. To quantify barrier tightness, sucrose permeation across exposed PBEC was measured and compared to values of sham exposed cells and to a control group. Additionally, observations in the BBB coculture system were complemented by similar experiments using two other in vitro models, composed of PBEC monocultures with or without serum. These three models display distinctly higher barrier tightness than the previously used system. In all three BBB models, sucrose permeation across the cell layers remained unaffected by exposure to a GSM 1800 field for up to 5 days. We thus could not confirm enhanced permeability of the BBB in vitro after EMF exposure as reported before since the in vitro barrier tightness in these experiments is now more like that of the in vivo situation. Bioelectromagnetics 26:529–535, 2005. © 2005 Wiley‐Liss, Inc.
Characteristics of a pulsating jet through a small modulated orifice, with application to voice production.

A detailed understanding of the aerodynamics of air flow in the larynx and the vocal tract is needed to refine physiological models of human voice production. This understanding can be applied in speech synthesis, voice diagnostics, and voice recognition. To date, most aeroacoustic models of phonation have been based on Bernoulli's orifice theory, i.e., the assumption that flow phenomena within the larynx are "quasi-steady. " This assumption, however, has never been rigorously verified experimentally. In this study, detailed aerodynamic measurements were performed of a pulsating open jet through a modulated orifice with a time-varying area. Orifice geometry and characteristic Reynolds numbers and Strouhal numbers of the pulsating jet flow were representative of speech production. Simple source-filter models based on the quasi-steady flow assumption and an ideal one-dimensional monopole source model were found to yield satisfactory velocity, flow rate, and dynamic pressure predictions for most of the duty cycle. Significant deviations from quasi-steady behavior were observed only during the early part of the duty cycle, where the flow velocity in the center core rapidly reached a peak value immediately after release of the false folds. This acoustic near-field phenomenon did not affect the pressure waves generated by the pulsating jet through the orifice, propagated in the long rigid tube upstream of the orifice. The impact on this phenomenon on actual sound generation within the larynx, and wall pressures on the vocal folds, is not clear.
Interaction of Transcriptional Repressor ArgR with Transcriptional Regulator FarR at the argB Promoter Region in Corynebacterium glutamicum

ABSTRACT In Corynebacterium glutamicum, the ArgR protein, a transcriptional repressor, affects the expression level of the argB gene through binding to its promoter region. The argB promoter region (positions −77 to −25) has been found by in vitro electrophoretic mobility shift assay (EMSA) results and in silico analysis to be important for the DNA binding of ArgR. Proline supplementation prevented the DNA binding of ArgR to the argB promoter region and triggered an increase of the argB mRNA level. Additional mutational analyses of the argB promoter region found nucleotides critical for ArgR binding (G located at position −58, C at position −55, and A at position −41 of the argB promoter) in that region. Another transcriptional repressor, FarR, was also demonstrated to bind to the argB promoter region. This binding was delimited to positions −57 to −77 on the argB promoter. FarR has only one putative binding domain located at positions −57 to −77, but this region exactly overlapped with the binding region located from positions −55 to −77 for the binding of ArgR within the argB promoter; thus, if ArgR bound with the argB promoter first, the binding of FarR was not observed in this region. However, if FarR bound to the binding domain located at positions −57 to −77 first, ArgR could bind other binding sites located at positions −49 to −25 within the argB promoter. Finally, this study suggests that ArgR can affect FarR binding to the argB promoter region, as protein binding is dominated by the protein most able to do so.
Thermally driven magnetization switching of perpendicularly magnetized multilayers

Thermally driven magnetization switching of perpendicularly magnetized [Cu/Ni] multilayer/BaTiO3(100) heterostructures is demonstrated. While the magnetization of the multilayer shows the out-of-plane magnetic anisotropy in the tetragonal phase of BaTiO3 at room temperature, the magnetization orientation is found to switch from the out-of-plane to the in-plane in the rhombohedral phase below 180 K. The magnetization switching is attributed to the interfacial compressive strain transfer from BaTiO3 to [Cu/Ni] due to the structural phase transitions of BaTiO3. Magneto-optical polar Kerr measurement in the rhombohedral phase with and without applying an electric field supports the description that the magnetization switching arises from the compressive strain at the interface induced by the structural phase transition from the orthorhombic to rhombohedral phases.
Macro level analysis of factors contributing to value added: technological changes in European countries

In conditions of globalization and rapidly growing production fragmentation, generation of value added becomes an ultimate goal and a measure of economic performance. The study provides an analysis of factors contributing to value added at macro level in different European countries. The analysis includes a panel framework covering 27 European countries over the period 2006–2015. In order to investigate the differences across regions, three subsamples are considered, namely, developed economies, PIIGS (Portugal, Italy, Ireland, Greece and Spain) and Central-Eastern European Countries (CEEC). Pooled OLS, fixed effects and random effects models are used. The results indicate that increase of value added corresponds to budget discipline, quality of human capital improvement, strong currency and transparent institutions. It could be expected that currency depreciation improves performance of the value added of exported final goods. However, the results show the opposite evidence: currency depreciation causes the value added decrease in all groups. Thus, for transitional countries, it is im¬portant not only to join global production chains, but also to acquire a significant share in generation of value added in these chains based on technological changes.
High Performance Computing Enabled Simulation of the Food-Water-Energy System: Simulation of Intensively Managed Landscapes

Domain science experts are commonly limited by computational efficiency of their code and hardware resources available for execution of desired simulations. Here, we detail a collaboration between domain scientists focused on simulating an ensemble of climate and human management decisions to drive environmental (e.g., water quality) and economic (e.g., crop yield) outcomes. Briefly, the domain scientists developed a message passing interface to execute the formerly serial code across a number of processors, anticipating significant performance improvement by moving to a cluster computing environment from their desktop machines. The code is both too complex to efficiently re-code from scratch and has a shared codebase that must continue to function on desktop machines as well as the parallel implementation. However, inefficiencies in the code caused the LUSTRE filesystem to bottleneck performance for all users. The domain scientists collaborated with Indiana University's Science Applications and Performance Tuning and High Performance File System teams to address the unforeseen performance limitations. The non-linear process of testing software advances and hardware performance is a model of the failures and successes that can be anticipated in similar applications. Ultimately, through a series of iterative software and hardware advances the team worked collaboratively to increase performance of the code, cluster, and file system to enable more than 100-fold increases in performance. As a result, the domain science is able to assess ensembles of climate and human forcing on the model, and sensitivities of ecologically and economically important outcomes of intensively managed agricultural landscapes.
Noninvasive magnetometry based on magnetic rotation spectroscopy of oxygen.

An experimental demonstration of a noninvasive optical probe of magnetic fields is presented. The technique used is magnetic rotation spectroscopy of the b(1)? (g)(+) - X(3)? (g)(-) band of oxygen near 760 nm. Ambient concentrations of oxygen at atmospheric pressure are sufficient to observe substantial signals. In addition, a diode laser is used as the light source, making this a simple and compact measurement possibility.
Fine mapping of autophagy-related proteins during autophagosome formation in Saccharomyces cerevisiae

Summary Autophagy is a bulk degradation system mediated by biogenesis of autophagosomes under starvation conditions. In Saccharomyces cerevisiae, a membrane sac called the isolation membrane (IM) is generated from the pre-autophagosomal structure (PAS); ultimately, the IM expands to become a mature autophagosome. Eighteen autophagy-related (Atg) proteins are engaged in autophagosome formation at the PAS. However, the cup-shaped IM was visualized just as a dot by fluorescence microscopy, posing a challenge to further understanding the detailed functions of Atg proteins during IM expansion. In this study, we visualized expanding IMs as cup-shaped structures using fluorescence microscopy by enlarging a selective cargo of autophagosomes, and finely mapped the localizations of Atg proteins. The PAS scaffold proteins (Atg13 and Atg17) and phosphatidylinositol 3-kinase complex I were localized to a position at the junction between the IM and the vacuolar membrane, termed the vacuole–IM contact site (VICS). By contrast, Atg1, Atg8 and the Atg16–Atg12–Atg5 complex were present at both the VICS and the cup-shaped IM. We designate this localization the ‘IM’ pattern. The Atg2–Atg18 complex and Atg9 localized to the edge of the IM, appearing as two or three dots, in close proximity to the endoplasmic reticulum exit sites. Thus, we designate these dots as the ‘IM edge’ pattern. These data suggest that Atg proteins play individual roles at spatially distinct locations during IM expansion. These findings will facilitate detailed investigations of the function of each Atg protein during autophagosome formation.
User Allocation and Precoder Design for Coordinated Relaying

Relays are used in the current standards to enhance the cell throughput and coverage. Often, the relays are evaluated without considering the overhead involved in providing the relay with the data prior to the transmission. In this paper, we evaluate the system performance by considering the duplexing loss with over- the-air transmission (OTA) for relay with decode and forward as the relaying protocol. We demonstrate that the benefit of relays can be even detrimental if the in-band signaling needs are not properly accounted for. We assume a single-cell system extended with a single multi-antenna relay station serving single-antenna terminals. The system design objective is to allocate the users between the networks nodes and design their precoders such that the total transmit power is minimized while satisfying given user rate constraints.
Heuristic Online Goal Recognition in Continuous Domains

Goal recognition is the problem of inferring the goal of an agent, based on its observed actions. An inspiring approach - plan recognition by planning (PRP) - uses off-the-shelf planners to dynamically generate plans for given goals, eliminating the need for the traditional plan library. However, existing PRP formulation is inherently inefficient in online recognition, and cannot be used with motion planners for continuous spaces. In this paper, we utilize a different PRP formulation which allows for online goal recognition, and for application in continuous spaces. We present an online recognition algorithm, where two heuristic decision points may be used to improve run-time significantly over existing work. We specify heuristics for continuous domains, prove guarantees on their use, and empirically evaluate the algorithm over hundreds of experiments in both a 3D navigational environment and a cooperative robotic team task.
Association between depression and tinnitus in a nationally representative sample of US older adults

Objectives: Few population-based studies examining the association between tinnitus and depression among older adults have been conducted. Therefore, the purpose of this study was to examine the association between tinnitus and depression among a nationally representative sample of US older adults. Methods: Data from the 2005–2006 National Health and Nutrition Examination Survey was used. 696 older adults (70–85 yr) completed questionnaires on tinnitus and depression, with depression assessed using the Patient Health Questionnaire-9. Results: After controlling for firearm use, age, gender, race–ethnicity, cardiovascular/stroke history, diabetes, smoking status, body mass index, physical activity, noise exposure and elevated blood pressure, there was a significant positive association (beta coefficient: 1.28, 95% CI: 0.26–2.29, p = 0.01) between depression and tinnitus being at least a moderate problem, suggesting that those who perceived their tinnitus to be a moderate problem were more likely to be depressed than those perceiving it to be a small or no problem. Additionally, after adjustments, those who were bothered by tinnitus when going to bed were 3.06 times more likely to be depressed than those who were not bothered by tinnitus when going to bed (OR = 2.44, 95% CI: 1.03–5.76, p = 0.04). Conclusion: These findings suggest that individuals who perceive their tinnitus to be a problem or have problems with tinnitus when going to bed may be in need of intervention to prevent or reduce their depression symptoms so as to ensure that other areas of their life are not negatively influenced.
Impact of Governance on Economic Growth

The impacts of governance on economic growth is still only partially understood. The aim of this researh to understand the impact of governance on the economic growth. This study finds that control of corruption is a critical factor for economic growth and one unit increases in control of corruption causes 6.9% increse in the economic growth. However, it is important to manage both corruption control and political stability and absence of violence/ terrorism indicators effectively to achive a higher economic growth. In comparition to the European Union countries and the North American countries, the economic growth rate is significantly lower in all other regions except the Middle East and North Africa. The economic growth rate in high-income countries is 20% higher than the middle income countries. On the other hand, the low-income countries show 23.5% lower economic growth than the middle income countries. This research used data from 145 countries for the period of 2002-2014. The included governance variables are control of corruption, political stability and absence of violence/terrorism, and voice and accountability. foreign direct investments, gross capital formation, government consumption, and trade openness were taken into account the model, to control their effects on economic growth. Dummy variables were included to capture the regional effects and the effects of the income level of the countries. The fixed effects and random effects techniques were applied in a balanced panel. The main data sources are the Worldwide Governance Indicators and the World Development Indicators databases.
The effects of coenzyme Q10 supplementation on gene expression related to insulin, lipid and inflammation in patients with polycystic ovary syndrome

Abstract Objective: This research was conducted to assess the effects of coenzyme Q10 (CoQ10) intake on gene expression related to insulin, lipid and inflammation in subjects with polycystic ovary syndrome (PCOS). Methods: This randomized double-blind, placebo-controlled trial was conducted on 40 subjects diagnosed with PCOS. Subjects were randomly allocated into two groups to intake either 100 mg CoQ10 (n = 20) or placebo (n = 20) per day for 12 weeks. Gene expression related to insulin, lipid and inflammation were quantified in blood samples of PCOS women with RT-PCR method. Results: Results of RT-PCR shown that compared with the placebo, CoQ10 intake downregulated gene expression of oxidized low-density lipoprotein receptor 1 (LDLR) (p < 0.001) and upregulated gene expression of peroxisome proliferator-activated receptor gamma (PPAR-γ) (p = 0.01) in peripheral blood mononuclear cells of subjects with PCOS. In addition, compared to the placebo group, CoQ10 supplementation downregulated gene expression of interleukin-1 (IL-1) (p = 0.03), interleukin-8 (IL-8) (p = 0.001) and tumor necrosis factor alpha (TNF-α) (p < 0.001) in peripheral blood mononuclear cells of subjects with PCOS. Conclusions: Overall, CoQ10 intake for 12 weeks in PCOS women significantly improved gene expression of LDLR, PPAR-γ, IL-1, IL-8 and TNF-α.
Tutorial Proposal : Connecting the Dots – Showing Relationships in Data and Beyond

Relationships are omnipresent in data, views and in how we interact with visualization tools. This tutorial discusses how such relationships can be visually expressed, a process we call linking. The tutorial addresses the three questions, what, how and when to link in three separate parts. The first part – what to link – explains that not only data, but also views and interactions can be linked. The second part – how to link – discusses how relationships can be visually expressed, based on perceptual grouping principles. While we discuss a wide range of methods, we focus on the connectedness grouping principle, specifically on visual links, as the topic is the most powerful in some respects, but also the most difficult to employ. The final part – when to link – will give an introduction to scenarios where linking is beneficial, taking into account issues such as unconventional display devices and collaboration. Again the focus will be on visual links, but other techniques will be discussed where appropriate.
Using ARDUINO development platform in the diagnosis of AC electrical machines

Low cost electronic platforms based on Atmel microcontroller, as Arduino platform, are used in many applications and in several fields. Indeed, their characteristics in terms of inputs, outputs, CPU and RAM make possible to develop rapid smart-systems for measurement avoiding additional components. CPU and RAM performance allows analyzing complex numerical signals. The aim of this paper is to show some boarddevelopments (ARDUINO UNO, M0 and DUE) coupled with specific sensors for electrical rotating machine applications in industrial environment.