Miracle-dz/UniFAR-FTUs huggingface dataset:
Restoring community through traditional neighborhood design: A case study of Diggs town public housing

Abstract This article examines how traditional neighborhood design (TND) can restore a sense of community to distressed neighborhoods. Traditional neighborhoods, such as those found in many cities and inner suburbs, provide their residents numerous opportunities and venues for social interaction. We apply the principles of TND to the redesign of a public housing project. We call our approach an “architecture of engagement. ” Using a case study of Diggs Town, a public housing project in Norfolk, VA, we explore how the application of TND principles transformed a socially alienated and distressed neighborhood into a socially integrated and functional one. We find that TND techniques improve the quality of life by facilitating the social exchanges that create social capital.
Zebrafish, a Novel Model System to Study Uremic Toxins: The Case for the Sulfur Amino Acid Lanthionine

The non-proteinogenic amino acid lanthionine is a byproduct of hydrogen sulfide biosynthesis: the third endogenous vasodilator gas, after nitric oxide and carbon monoxide. While hydrogen sulfide is decreased in uremic patients on hemodialysis, lanthionine is increased and has been proposed as a new uremic toxin, since it is able to impair hydrogen sulfide production in hepatoma cells. To characterize lanthionine as a uremic toxin, we explored its effects during the early development of the zebrafish (Danio rerio), a widely used model to study the organ and tissue alterations induced by xenobiotics. Lanthionine was employed at concentrations reproducing those previously detected in uremia. Light-induced visual motor response was also studied by means of the DanioVision system. Treatment of zebrafish embryos with lanthionine determined acute phenotypical alterations, on heart organogenesis (disproportion in cardiac chambers), increased heart beating, and arrhythmia. Lanthionine also induced locomotor alterations in zebrafish embryos. Some of these effects could be counteracted by glutathione. Lanthionine exerted acute effects on transsulfuration enzymes and the expression of genes involved in inflammation and metabolic regulation, and modified microRNA expression in a way comparable with some alterations detected in uremia. Lanthionine meets the criteria for classification as a uremic toxin. Zebrafish can be successfully used to explore uremic toxin effects.
Bringing Children into Focus on the Social Science Disaster Research Agenda

Significant progress has been made in the social science disaster research field since its inception several decades ago. Despite the advances in knowledge, important areas of research have been seriously understudied, including the impact of hazards and disasters on children and youths. In this paper, it is argued that such knowledge is needed to deepen our understanding of the impacts of disasters on society and to provide a firmer basis for disaster management policy and practice. It is suggested that children should be brought into clearer focus in the disaster research field through studies, particularly those of a comparative nature, that consider (1) children's vulnerability and the outcomes they experience because of their youth, (2) actions taken by the adult society to reduce the vulnerability of children, and (3) actions children and youths undertake for themselves and others to reduce disaster impacts.
MR Imaging of Partially Thrombosed Cerebral Aneurysms: Characteristics and Evolution

Noninvasive imaging of partially thrombosed aneurysm is important because it delineates the true lumen and provides information about the walls. The authors examined 9 patients twice each, separated by 4–22 months, and found thrombus in all MR imaging sequences. Thrombus was better seen on T1-weighted images whereas differentiation between lumen and thrombus was better depicted on the steady-state sequence. Peripheral high T1 signal in the clot was typical and all clots remained stable during the time period between imaging studies. Thus, MR imaging may be used to evaluate aneurysm size, thrombosed portions, and growth and may affect treatment decisions in these patients. BACKGROUND AND PURPOSE: A comprehensive evaluation of aneurysmal morphometry requires appreciation of both the vascular lumen and the intraluminal thrombus. MR imaging methods can both evaluate the lumen and directly image the vessel wall. We investigated the ability of T1-weighted, T2-weighted, and steady-state MR imaging techniques to delineate thrombus morphology and reveal changes with time. MATERIALS AND METHODS: Nine patients with fusiform basilar or intracranial vertebral artery aneurysms that contained intraluminal thrombus were studied with MR imaging. All patients underwent at least 2 imaging sessions, which were separated by 4–22 months. Analysis of signal intensity to determine the mean signal intensity from thrombus, blood, CSF, and brain in matched regions was performed. Aneurysm maximal diameter and cross-sectional area were determined with and without thrombus. RESULTS: Thrombus was identified on all image sequences, and its general appearance was consistent between imaging sessions. Thrombus produced the highest and most consistent signal intensities with T1-weighted and steady-state techniques, though the latter showed superior contrast between luminal blood and thrombus. Heterogeneity within clot was evident in 4/9 of patients, with peripheral hyperintensity being a common feature. CONCLUSIONS: Steady-state imaging was found to be superior to T1- and T2-weighted imaging for delineating and characterizing intraluminal thrombus within aneurysms. The imaging characteristics of intraluminal thrombus proved to be very consistent for long periods. Assessment of overall aneurysm size, including thrombosed portions, permits more accurate evaluation of aneurysm growth and concomitantly may permit more informed clinical decision-making with regard to the timing and need for aneurysm treatment.
A Study of Patent Thickets

This report analyses whether entry of UK enterprises into patenting in a technology area is affected by patent thickets in the technology area. The aim is to contribute to our understanding of the role of patent thickets as a barrier to entry into patenting for UK enterprises, in particular small and medium sized enterprises (SMEs). To do this we review the literature on patent thickets, discuss factors contributing to thicket formation and growth, and evaluate to what extent patent thickets might be considered to be barriers to entry in some technology areas. We also summarize the limited existing empirical evidence regarding effects of patent thickets on R&D investments and competition. We find overwhelming evidence in the literature that patent thickets arise in specific technology areas. This conclusion is based on a comprehensive review of the empirical literature on patent thickets of the last 15 years. This literature consists of surveys of firm representatives as well as of econometric analyses of firm level data. The literature on thickets contains more than 100 peer reviewed papers and a number of extensive studies undertaken by competition regulators. Our main contribution in this study consists of an empirical analysis of the effects of patent thickets at the European Patent Office on entry into patenting by UK firms. Using a new measure of patent thickets developed by Graevenitz et al. (2012), the report provides a descriptive analysis of the growth of patent thickets in the European patent system and an analysis of the exposure to these thickets of UK entrants into patenting. Econometric analysis of the probability of entry into patenting by technology area shows that the density of a patent thicket is associated with reduced entry into patenting in the technology area in the data set used for this study. We discuss limitations of the data used and suggest how further work might test the reliability of our findings.
Formation of Globular Clusters in Hierarchical Cosmology

We study the formation of globular clusters in a Milky Way-size galaxy using a high-resolution cosmological simulation. The clusters in our model form in the strongly baryon-dominated cores of supergiant molecular clouds in the gaseous disks of high-redshift galaxies. The properties of clusters are estimated using a physically motivated subgrid model of the isothermal cloud collapse. The first clusters in the simulation form at z ≈ 12, while we conjecture that the best conditions for globular cluster formation appear to be at z ~ 3-5. Most clusters form in the progenitor galaxies of the virial mass Mh > 109 M☉, and the total mass of the cluster population is strongly correlated with the mass of its host galaxy: MGC = 3 × 106 M☉(Mh/1011 M☉)1.1. This corresponds to a fraction ~2 × 10-4 of the galactic baryons being in the form of globular clusters. In addition, the mass of the globular cluster population and the maximum cluster mass in a given region strongly correlate with the local average star formation rate. We find that the mass, size, and metallicity distributions of the globular cluster population identified in the simulation are remarkably similar to the corresponding distributions of the Milky Way globular clusters. We find no clear mass-metallicity or age-metallicity correlations for the old clusters. The zero-age mass function of globular clusters can be approximated by a power law dN/dM ∝ M-α with α ≈ 2, in agreement with the mass function of young stellar clusters in starbursting galaxies. We discuss in detail the origin and universality of the globular cluster mass function. Our results indicate that globular clusters with properties similar to those of observed clusters can form naturally within dense gaseous disks at z ≳ 3 in the concordance ΛCDM cosmology.
Partial Least Squares with Structured Output for Modelling the Metabolomics Data Obtained from Complex Experimental Designs: A Study into the Y-Block Coding

Partial least squares (PLS) is one of the most commonly used supervised modelling approaches for analysing multivariate metabolomics data. PLS is typically employed as either a regression model (PLS-R) or a classification model (PLS-DA). However, in metabolomics studies it is common to investigate multiple, potentially interacting, factors simultaneously following a specific experimental design. Such data often cannot be considered as a “pure” regression or a classification problem. Nevertheless, these data have often still been treated as a regression or classification problem and this could lead to ambiguous results. In this study, we investigated the feasibility of designing a hybrid target matrix Y that better reflects the experimental design than simple regression or binary class membership coding commonly used in PLS modelling. The new design of Y coding was based on the same principle used by structural modelling in machine learning techniques. Two real metabolomics datasets were used as examples to illustrate how the new Y coding can improve the interpretability of the PLS model compared to classic regression/classification coding.
Understanding Social Factors in the Context of Trauma: Implications for Measurement and Intervention

ABSTRACT One of the most important factors predicting the presence of posttraumatic stress disorder (PTSD) after trauma exposure is social support, yet the construct is theoretically complex and remains variably defined. To better inform the trauma literature on the impact of social factors, a theoretical review of social support and PTSD was conducted, and implications for measurement and intervention are outlined. Type of trauma, sex of participant, timing of social support, and support providers are described as significant moderators of the association between social factors and PTSD. The developmental trajectory of the association between social factors and PTSD occurrence is outlined, emphasizing the positive influence of social support initially following trauma, and the deterioration effect of PTSD symptoms on social support over the longer term. Possibilities for future research and intervention at multiple levels and at different time points are described.
Superior Temporal SulcusIt's My Area: Or Is It?

The superior temporal sulcus (STS) is the chameleon of the human brain. Several research areas claim the STS as the host brain region for their particular behavior of interest. Some see it as one of the core structures for theory of mind. For others, it is the main region for audiovisual integration. It plays an important role in biological motion perception, but is also claimed to be essential for speech processing and processing of faces. We review the foci of activations in the STS from multiple functional magnetic resonance imaging studies, focusing on theory of mind, audiovisual integration, motion processing, speech processing, and face processing. The results indicate a differentiation of the STS region in an anterior portion, mainly involved in speech processing, and a posterior portion recruited by cognitive demands of all these different research areas. The latter finding argues against a strict functional subdivision of the STS. In line with anatomical evidence from tracer studies, we propose that the function of the STS varies depending on the nature of network coactivations with different regions in the frontal cortex and medial-temporal lobe. This view is more in keeping with the notion that the same brain region can support different cognitive operations depending on task-dependent network connections, emphasizing the role of network connectivity analysis in neuroimaging.
Understanding the gut–kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers

Objectives The involvement of the gut microbiota in the pathogenesis of calcium nephrolithiasis has been hypothesised since the discovery of the oxalate-degrading activity of Oxalobacter formigenes, but never comprehensively studied with metagenomics. The aim of this case–control study was to compare the faecal microbiota composition and functionality between recurrent idiopathic calcium stone formers (SFs) and controls. Design Faecal samples were collected from 52 SFs and 48 controls (mean age 48±11). The microbiota composition was analysed through 16S rRNA microbial profiling approach. Ten samples (five SFs, five controls) were also analysed with deep shotgun metagenomics sequencing, with focus on oxalate-degrading microbial metabolic pathways. Dietary habits, assessed through a food-frequency questionnaire, and 24-hour urinary excretion of prolithogenic and antilithogenic factors, including calcium and oxalate, were compared between SFs and controls, and considered as covariates in the comparison of microbiota profiles. Results SFs exhibited lower faecal microbial diversity than controls (Chao1 index 1460±363vs 1658±297, fully adjusted p=0.02 with stepwise backward regression analysis). At multivariate analyses, three taxa (Faecalibacterium, Enterobacter, Dorea) were significantly less represented in faecal samples of SFs. The Oxalobacter abundance was not different between groups. Faecal samples from SFs exhibited a significantly lower bacterial representation of genes involved in oxalate degradation, with inverse correlation with 24-hour oxalate excretion (r=−0.87, p=0.002). The oxalate-degrading genes were represented in several bacterial species, whose cumulative abundance was inversely correlated with oxaluria (r=−0.85, p=0.02). Conclusions Idiopathic calcium SFs exhibited altered gut microbiota composition and functionality that could contribute to nephrolithiasis physiopathology.
Conn: A Functional Connectivity Toolbox for Correlated and Anticorrelated Brain Networks

Resting state functional connectivity reveals intrinsic, spontaneous networks that elucidate the functional architecture of the human brain. However, valid statistical analysis used to identify such networks must address sources of noise in order to avoid possible confounds such as spurious correlations based on non-neuronal sources. We have developed a functional connectivity toolbox Conn ( www.nitrc.org/projects/conn ) that implements the component-based noise correction method (CompCor) strategy for physiological and other noise source reduction, additional removal of movement, and temporal covariates, temporal filtering and windowing of the residual blood oxygen level-dependent (BOLD) contrast signal, first-level estimation of multiple standard functional connectivity magnetic resonance imaging (fcMRI) measures, and second-level random-effect analysis for resting state as well as task-related data. Compared to methods that rely on global signal regression, the CompCor noise reduction method allows for interpretation of anticorrelations as there is no regression of the global signal. The toolbox implements fcMRI measures, such as estimation of seed-to-voxel and region of interest (ROI)-to-ROI functional correlations, as well as semipartial correlation and bivariate/multivariate regression analysis for multiple ROI sources, graph theoretical analysis, and novel voxel-to-voxel analysis of functional connectivity. We describe the methods implemented in the Conn toolbox for the analysis of fcMRI data, together with examples of use and interscan reliability estimates of all the implemented fcMRI measures. The results indicate that the CompCor method increases the sensitivity and selectivity of fcMRI analysis, and show a high degree of interscan reliability for many fcMRI measures.
Modeling and Synthesis of Aperture Effects in Cameras

In this paper we describe the capture, analysis, and synthesis of optical vignetting in conventional cameras. We analyze the spatially-varying point spread function (PSF) to accurately model the vignetting for any given focus or aperture setting. In contrast to existing "flat-field" calibration procedures, we propose a simple calibration pattern consisting of a two-dimensional array of point light sources - allowing simultaneous estimation of vignetting correction tables and spatially-varying blur kernels. We demonstrate the accuracy of our model by deblurring images with focus and aperture settings not sampled during calibration. We also introduce the Bokeh Brush: a novel, post-capture method for full-resolution control of the shape of out-of-focus points. This effect is achieved by collecting a small set of images with varying basis aperture shapes. We demonstrate the effectiveness of this approach for a variety of scenes and aperture sets.
The RAVE Survey: Constraining the Local Galactic Escape Speed

Abstract We report new constraints on the local escape speed of our Galaxy. Our analysis is based on a sample of high velocity stars from the RAVE survey and two previously published datasets (the Geneva-Copenhagen survey and the Beers et al. catalogue of metal-poor stars). We use cosmological simulations of disk galaxy formation to motivate our assumptions on the shape of the velocity distribution, allowing for a significantly more precise measurement of the escape velocity compared to previous studies. We find that the escape velocity lies within the range 492 km s−1 < vesc <594 kms (90% confidence), with a median likelihood of 536 kms. The fact that v2esc is significantly greater than 2v2circ implies that there must be a significant amount of mass exterior to the Solar circle, i.e. this convincingly demonstrates the presence of a dark halo in the Galaxy. For a simple isothermal halo, one can calculate that the minimum radial extent is ~54 kpc. We use our constraints on vesc to determine the mass of the Milky Way halo for three halo profiles. For example, an adiabatically contracted NFW halo model results in a virial mass of 1.31+0.97−0.49 × 1012M⊙ and virial radius of 297+60−44 kpc (90% confidence). For this model the circular velocity at the virial radius is 141+27−19kms. Although our halo masses are model dependent, we find that they are in good agreement with each other.
The Influence of Quality of Information on the McGurk Effect

Quality of information in the McGurk effect was manipulated by using auditory stimuli that spanned a wide range of intelligibility, and by adding auditory and/or visual noise. Questions were whether responses are affected by subjects' awareness of the variation in stimulus quality, and whether quality of information affects type as well as number of McGurk responses. Expt 1 established the auditory intelligibility of 8 tokens of /DJD/ from 4 speakers. In Expt 2 each /DJD/ was presented simultaneously with a videod face saying /DED/ with and without visual and/or auditory noise. There were fewer McGurk responses with more visual noise; and more McGurk responses with more auditory noise, including more responses of /E/ alone rather than e.g. /EJ/. Less intelligible auditory stimuli increased the number of McGurk responses when the second syllable was stressed. The data suggest that what the subject perceives depends on both the physical and relative quality of the stimuli, and the perceiver’s judgement of their quality.
Temporally coherent completion of dynamic video

We present an automatic video completion algorithm that synthesizes missing regions in videos in a temporally coherent fashion. Our algorithm can handle dynamic scenes captured using a moving camera. State-of-the-art approaches have difficulties handling such videos because viewpoint changes cause image-space motion vectors in the missing and known regions to be inconsistent. We address this problem by jointly estimating optical flow and color in the missing regions. Using pixel-wise forward/backward flow fields enables us to synthesize temporally coherent colors. We formulate the problem as a non-parametric patch-based optimization. We demonstrate our technique on numerous challenging videos.
Transforming Growth Factor-α Improves Memory Impairment and Neurogenesis Following Ischemia Reperfusion

Objective Stroke is most important cause of death and disability in adults. The hippocampal CA1 and sub-ventricular zone neurons are vulnerable to ischemia that can impair memory and learning functions. Although neurogenesis normally occurs in the dentate gyrus (DG) of the hippocampus and sub-ventricular zone (SVZ) following brain damage, this response is unable to compensate for severely damaged areas. This study aims to assess both neurogenesis and the neuroprotective effects of transforming growth factor-alpha (TGF-α) on the hippocampus and SVZ following ischemia-reperfusion. Materials and Methods In this experimental study, a total of 48 male Wistar rats were divided into the following groups: surgical (n=12), phosphate buffered saline (PBS) treated vehicle shams (n=12), ischemia (n=12) and treatment (n=12) groups. Ischemia was induced by common carotid occlusion for 30 minutes followed by reperfusion, and TGF-α was then injected into the right lateral ventricle. Spatial memory was assessed using Morris water maze (MWM). Nestin and Bcl-2 family protein expressions were studied by immunohistochemistry (IHC) and Western blot methods, respectively. Finally, data were analyzed using Statistical Package for the Social Sciences (SPSS, SPSS Inc., Chicago, USA) version 16 and one-way analysis of variance (ANOVA). Results TGF-α injection significantly increased nestin expression in both the hippocampal DG and SVZ areas. TGF-α treatment caused a significant decrease in Bax expression and an increase in Bcl-2 anti-apoptotic protein expression in the hippocampus. Our results showed a significant increase in the number of pyramidal neurons. Memory also improved significantly following TGF-α treatment. Conclusion Our findings proved that TGF-α reduced ischemic injury and played a neuroprotective role in the pathogenesis of ischemic injury.