Miracle-dz/UniFAR-FTUs huggingface dataset:
The Indirect Neuron-astrocyte Coculture Assay: An In Vitro Set-up for the Detailed Investigation of Neuron-glia Interactions.

Proper neuronal development and function is the prerequisite of the developing and the adult brain. However, the mechanisms underlying the highly controlled formation and maintenance of complex neuronal networks are not completely understood thus far. The open questions concerning neurons in health and disease are diverse and reaching from understanding the basic development to investigating human related pathologies, e.g., Alzheimer's disease and Schizophrenia. The most detailed analysis of neurons can be performed in vitro. However, neurons are demanding cells and need the additional support of astrocytes for their long-term survival. This cellular heterogeneity is in conflict with the aim to dissect the analysis of neurons and astrocytes. We present here a cell-culture assay that allows for the long-term cocultivation of pure primary neurons and astrocytes, which share the same chemically defined medium, while being physically separated. In this setup, the cultures survive for up to four weeks and the assay is suitable for a diversity of investigations concerning neuron-glia interaction.
Temporal Regulation of GABAA Receptor Subunit Expression: Role in Synaptic and Extrasynaptic Communication in the Suprachiasmatic Nucleus

Visual Abstract Abstract Recent molecular studies suggest that the expression levels of δ and γ2 GABAA receptor (GABAAR) subunits regulate the balance between synaptic and extrasynaptic GABA neurotransmission in multiple brain regions. We investigated the expression of GABAAδ and GABAAγ2 and the functional significance of a change in balance between these subunits in a robust local GABA network contained within the suprachiasmatic nucleus of the hypothalamus (SCN). Muscimol, which can activate both synaptic and extrasynaptic GABAARs, injected into the SCN during the day phase advanced the circadian pacemaker, whereas injection of the extrasynaptic GABAA superagonist 4,5,6,7-tetrahydroisoxazolo(5,4-c)pyridin-3-ol (THIP) had no effect on circadian phase. In contrast, injection of either THIP or muscimol during the night was sufficient to block the phase shifting effects of light. Gene expression analysis of the whole SCN revealed different temporal patterns in GABAAδ and GABAAγ2 mRNA expression. When examined across all subregions of the SCN, quantitative immunohistochemical analysis found no significant variations in GABAAδ protein immunoreactivity (IR) but did find significant variations in GABAAγ2 protein-IR in hamsters housed in either LD cycles or in constant darkness. Remarkably, significant interactions in the ratio of GABAAδ:GABAAγ2 subunits between lighting condition and circadian phase occurred only within one highly discrete anatomical area of the SCN; a region that functions as the input for lighting information from the retina. Taken together, these data support the hypothesis that the balance between synaptic and extrasynaptic GABAARs determines the functional response to GABA, and that this balance is differentially regulated in a region-specific manner.
Rational discovery and development of a mitochondria-targeted antioxidant based on cinnamic acid scaffold

Abstract A novel mitochondria-targeted antioxidant (TPP-OH) was synthesized by attaching the natural hydrophilic antioxidant caffeic acid to an aliphatic lipophilic carbon chain containing a triphenylphosphonium (TPP) cation. This compound has similar antioxidant activity to caffeic acid as demonstrated by measurement of DPPH/ABTS radical quenching and redox potentials, but is significantly more hydrophobic than its precursor as indicated by the relative partition coefficients. The antioxidant activity of both compounds was intrinsic related to the ortho-catechol system, as the methoxylation of the phenolic functions, namely in TPP-OCH3 and dimethoxycinnamic acid, gave compounds with negligible antioxidant action. The incorporation of the lipophilic TPP cation to form TTP-OH and TPP-OCH3 allowed the cinnamic derivatives to accumulate within mitochondria in a process driven by the membrane potential. However, only TPP-OH was an effective antioxidant: TPP-OH protected cells against H2O2 and linoleic acid hydroperoxide-induced oxidative stress. As mitochondrial oxidative damage is associated with a number of clinical disorders, TPP-OH may be a useful lead that could be added to the family of mitochondria-targeted antioxidants that can decrease mitochondrial oxidative damage.
Predictors of anxiety and depression among parents of children with cancer in Jordan

The number of Jordanians diagnosed with cancer increased by 46% over the last decade, from 3362 new cases in 2000 to 5013 in 2012. Of these cases, 6.2% occurred in patients who were younger than 19 years. Cancer diagnoses affect not only the children themselves but also their families, forcing them to face up to several life challenges. Caring for a child with cancer and its consequences may lead to loss of family interest in the surrounding environment, worry, loss of hope, and other emotional disturbances. For instance, a study conducted to assess the psychological distress among parents of pediatric oncology patients included 215 participants who were mostly mothers (88%). The results show that the parents reported mid‐range scores of depression and anxiety. However, 16% of them had moderate to severe depression, and 21% had moderate to severe anxiety levels. Parents' responsibilities have been broadening with the shift of more care from hospital to the home. There is a need to investigate the predictors of these symptoms for more efficient use of the limited resources, especially in developing countries such as Jordan.
Optimization of MCM-48 synthesis using factorial design

MCM-48 mesoporous materials were hydrothermally synthesized according to the 22 factorial design by varying the crystallization time and temperature of the synthesis gel, and characterized by means of X-ray diffraction analysis and adsorption of N2. In the crystallization temperature and time conditions used, specific areas between 924 to 1102 m 2.g-1, pore volumes between 0.015 to 0.087 cm3.g-1 and pore diameters between 3.2 to 4.0 nm were obtained. It was observed that for the syntheses performed at high temperature, the crystallization time should be reduced so that the material structure is formed.
Contemporary Demographic, Treatment, and Geographic Distribution Patterns for Disorders of Sex Development

This study aimed to describe the demographic characteristics, hospital utilizations, patterns of inpatient surgical management, and the overall state/regional variation in surgery rate among patients with disorders of sex development (DSD). We analyzed the Nationwide Inpatient Sample from 2001 to 2012 for patients younger than 21 years. DSD-related diagnoses and procedures were identified via International Classification of Diseases, Ninth Revision (ICD-9) codes. We identified a total of 43,968 DSD-related admissions. Of these, 73.4% of the admissions were designated as female and 642 (1.9%) were inpatient surgical admissions. Among neonates, less than 1% underwent any type of genital surgery. Nonsurgical admissions were associated with longer length of stay and higher cost. There was no significant regional variation in the rate of DSD surgeries, but we observed higher concentrations of DSD surgeries in states associated with tertiary referral centers.
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com
Evaluating the diagnostic utility of applying a machine learning algorithm to diffusion tensor MRI measures in individuals with major depressive disorder

Using MRI to diagnose mental disorders has been a long-term goal. Despite this, the vast majority of prior neuroimaging work has been descriptive rather than predictive. The current study applies support vector machine (SVM) learning to MRI measures of brain white matter to classify adults with Major Depressive Disorder (MDD) and healthy controls. In a precisely matched group of individuals with MDD (n = 25) and healthy controls (n = 25), SVM learning accurately (70%) classified patients and controls across a brain map of white matter fractional anisotropy values (FA). The study revealed three main findings: 1) SVM applied to DTI derived FA maps can accurately classify MDD vs. healthy controls; 2) prediction is strongest when only right hemisphere white matter is examined; and 3) removing FA values from a region identified by univariate contrast as significantly different between MDD and healthy controls does not change the SVM accuracy. These results indicate that SVM learning applied to neuroimaging data can classify the presence versus absence of MDD and that predictive information is distributed across brain networks rather than being highly localized. Finally, MDD group differences revealed through typical univariate contrasts do not necessarily reveal patterns that provide accurate predictive information.
Neural Font Style Transfer

In this paper, we chose an approach to generate fonts by using neural style transfer. Neural style transfer uses Convolution Neural Networks(CNN) to transfer the style of one image to another. By modifying neural style transfer, we can achieve neural font style transfer. We also demonstrate the effects of using different weighted factors, character placements, and orientations. In addition, we show the results of using non-Latin alphabets, non-text patterns, and non-text images as style images. Finally, we provide insight into the characteristics of style transfer with fonts.
A Case for Memory Frequency Sensitivity

Service optimization and energy conservation requires a thorough understanding of the performance impact of different hardware configurations. In this paper we focus on the configuration of memory and investigate the impact of memory dynamic voltage and frequency scaling (DVFS) on the performance of services/applications. We propose a quantitative metric called frequency sensitivity (FS) and study memory FS of various benchmarks. Our experiments yield several insights for memory DVFS based performance tuning.
Towards a poststructural understanding of abortion and social class in England

ABSTRACT Despite previous research suggesting that social class influences experiences of and attitudes to abortion, there is a dearth of research which studies the intersection of abortion and social class in England. Across the UK, abortion rates and experiences differ by region and socio-economic status, reflecting broader health inequalities. Contemporary austerity in the UK creates an imperative for new research which contextualises the experience of abortion within this socio-historical moment, and the worsening inequalities which have accompanied it. Whilst work on abortion and social inequality exists, it has often approached class as an a priori category. I argue that contemporary post-structural work on class provides a framework to go beyond this approach by examining how these social classifications occur; who has the power to classify; and how these classifications might be resisted. This framework is demonstrated with emerging findings from a life history study of abortion experiences in England. The applications of this to the work on abortion are potentially rich, because the act of ending a pregnancy invites classification from many quarters, from the legal (legal/illegal) to the medical (early/late) to the moral (deserved/undeserved). This work, therefore, speaks to public health concerns about access to and stigma around abortion and social inequalities.
DNA-Repair Gene Mutations in Metastatic Prostate Cancer.

TO THE EDITOR: The study by Pritchard et al. (Aug. 4 issue)1 has major implications for translational science, and it provides support for germ-line genetic testing to determine the risk of aggressive prostate cancer. In our sequencing analysis involving a large population of men who died of prostate cancer (unpublished data), we observed similar findings regarding germline mutations, with one interesting exception: CHEK2.
Requirement of a Functional Flavin Mononucleotide Prenyltransferase for the Activity of a Bacterial Decarboxylase in a Heterologous Muconic Acid Pathway in Saccharomyces cerevisiae

ABSTRACT Biotechnological production of cis,cis-muconic acid from renewable feedstocks is an environmentally sustainable alternative to conventional, petroleum-based methods. Even though a heterologous production pathway for cis,cis-muconic acid has already been established in the host organism Saccharomyces cerevisiae, the generation of industrially relevant amounts of cis,cis-muconic acid is hampered by the low activity of the bacterial protocatechuic acid (PCA) decarboxylase AroY isomeric subunit Ciso (AroY-Ciso), leading to secretion of large amounts of the intermediate PCA into the medium. In the present study, we show that the activity of AroY-Ciso in S. cerevisiae strongly depends on the strain background. We could demonstrate that the strain dependency is caused by the presence or absence of an intact genomic copy of PAD1, which encodes a mitochondrial enzyme responsible for the biosynthesis of a prenylated form of the cofactor flavin mononucleotide (prFMN). The inactivity of AroY-Ciso in strain CEN.PK2-1 could be overcome by plasmid-borne expression of Pad1 or its bacterial homologue AroY subunit B (AroY-B). Our data reveal that the two enzymes perform the same function in decarboxylation of PCA by AroY-Ciso, although coexpression of Pad1 led to higher decarboxylase activity. Conversely, AroY-B can replace Pad1 in its function in decarboxylation of phenylacrylic acids by ferulic acid decarboxylase Fdc1. Targeting of the majority of AroY-B to mitochondria by fusion to a heterologous mitochondrial targeting signal did not improve decarboxylase activity of AroY-Ciso, suggesting that mitochondrial localization has no major impact on cofactor biosynthesis. IMPORTANCE In Saccharomyces cerevisiae, the decarboxylation of protocatechuic acid (PCA) to catechol is the bottleneck reaction in the heterologous biosynthetic pathway for production of cis,cis-muconic acid, a valuable precursor for the production of bulk chemicals. In our work, we demonstrate the importance of the strain background for the activity of a bacterial PCA decarboxylase in S. cerevisiae. Inactivity of the decarboxylase is due to a nonsense mutation in a gene encoding a mitochondrial enzyme involved in the biosynthesis of a cofactor required for decarboxylase function. Our study reveals functional interchangeability of Pad1 and a bacterial homologue, irrespective of their intracellular localization. Our results open up new possibilities to improve muconic acid production by engineering cofactor supply. Furthermore, the results have important implications for the choice of the production strain.
Exploring Old Maps by Finger Tracing of Characters

In this paper, we propose a system that supports its users to explore old maps by showing extracted areas having similar images with the character region traced by the user's fingers. Since Japanese old maps do not have a predetermined character orientation, characters of the various orientation are drawn. Tracing gives a clue to extract region and orientation of characters. The system cuts out connected components existing on the user's traced line as characters. We describe two usage scenarios for better reading historical maps: revealing historical background by highlighting specific keywords; and comparison of multiple maps clued by highly specific queries.
Clonal Lineages of Erysipelothrix rhusiopathiae Responsible for Acute Swine Erysipelas in Japan Identified by Using Genome-Wide Single-Nucleotide Polymorphism Analysis

ABSTRACT Erysipelothrix rhusiopathiae causes swine erysipelas, an important infectious disease in the swine industry. In Japan, the incidence of acute swine erysipelas due to E. rhusiopathiae serovar 1a has recently increased markedly. To study the genetic relatedness of the strains from the recent cases, we analyzed 34 E. rhusiopathiae serovar 1a swine isolates collected between 1990 and 2011 and further investigated the possible association of the live Koganei 65-0.15 vaccine strain (serovar 1a) with the increase in cases. Pulsed-field gel electrophoresis analysis revealed no marked variation among the isolates; however, sequencing analysis of a hypervariable region in the surface-protective antigen A gene (spaA) revealed that the strains isolated after 2007 exhibited the same spaA genotype and could be differentiated from older strains. Phylogenetic analysis based on genome-wide single-nucleotide polymorphisms (SNPs) revealed that the Japanese strains examined were closely related, showing a relatively small number of SNPs among them. The strains were classified into four major lineages, with Koganei 65-0.15 (lineage III) being phylogenetically separated from the other three lineages. The strains isolated after 2007 and the two older strains constituted one major lineage (lineage IV) with a specific spaA genotype (M203/I257-SpaA), while the recent isolates were further divided into two geographic groups. The remaining older isolates belonged to either lineage I, with the I203/L257-SpaA type, or lineage II, with the I203/I257-SpaA type. These results indicate that the recent increased incidence of acute swine erysipelas in Japan is associated with two sublineages of lineage IV, which have independently evolved in two different geographic regions. IMPORTANCE Using large-scale whole-genome sequence data from Erysipelothrix rhusiopathiae isolates from a wide range of hosts and geographic origins, a recent study clarified the existence of three distinct clades (clades 1, 2, and 3) that are found across multiple continents and host species, representing both livestock and wildlife, and an “intermediate” clade between clade 2 and the dominant clade 3 within the species. In this study, we found that the E. rhusiopathiae Japanese strains examined exhibited remarkably low levels of genetic diversity and confirmed that all of the Japanese and Chinese swine isolates examined in this study belong to clonal lineages within the intermediate clade. We report that spaA genotyping of E. rhusiopathiae strains is a practical alternative to whole-genome sequencing analysis of the E. rhusiopathiae isolates from eastern Asian countries.
Hydraulic Conductivity of a Biopolymer Treated Sand

This paper presents results of laboratory assessment of creating seepage barriers in a sandy soil using biopolymer additives (bio substance), which consist of polysaccharides and water. Polysaccharides strongly interact with water to produce a viscous suspension. The aim of conducted work was to investigate the influence of a biosubstance employed in a highly permeable sandy soil. Amount of the biopolymer used in a sample fall between 0.1 and 1.5%, by dry weight. Tests were carried out on two different specimens, which were coarse sand (1.18 - 2.00 mm) and medium sand (0.075 - 1.00 mm). The test results indicate that the hydraulic conductivity values change significantly based on the amount of bio substance, gradation of the sand and curing time. It is concluded that such application, which is a relatively new soil improvement technique, could be used as a seepage barrier installation, required to protect some geotechnical works including foundation, underground structures and waste disposals.
Preparation and In Vitro Evaluation of a MRI Contrast Agent Based on Aptamer-Modified Gadolinium-Loaded Liposomes for Tumor Targeting

The aim of this study was to prepare aptamer-modified liposomes loaded with gadolinium (Gd) to enhance the effective diagnosis for tumor by MRI. A modified GBI-10 (GBI-10m) was used to prepare targeted liposomes (GmLs). Liposomes with GBI-10 aptamer (GLs) and without aptamer (non-targeted liposomes (NLs)) were also prepared as controls. The particle size and zeta potential of GmLs, GLs, and NLs were all assayed. A clinical 3.0 T MR scanner was employed to assess the imaging efficiency and measure the longitudinal relaxivity (r1) of the above liposomes. Confocal laser scanning microscopy and flow cytometry were used to analyze and compare the targeting effects of GmLs, GLs, and NLs to MDA-MB-435s cells at 37°C. The particle size of the prepared liposomes was scattered at 100–200 nm, and their values of r1 were ∼4 mM−1 s−1. The images of confocal laser scanning microscopy showed that GmLs in the cytoplasm were significantly more than GLs and both GmLs and GLs were more than NLs. The fluorescence intensity of GmLs was increased by about two times than that of GLs and three times than that of NLs by flow cytometry. Therefore, the GmLs in this initial study were suggested to be a potential MRI contrast agent at 37°C for diagnosing tumors with the protein of tenascin-C over-expressed.
A Noise-Resilient Sparse Subspace Clustering Algorithm for Image Sequences

With the rapid development of digital technology, videos are playing an increasingly important role in social networks. Automatically detecting scenes from a video, viewed as an image sequence, is an important task in video analysis. This is usually done via image sequence clustering, the first task of which is representation. Image sequences are very high dimensional and noisy in their form, even though they are intrinsically low dimensional in their content. It is however a challenge to represent image sequences in its intrinsically low dimensional space in a noise-robust way. In this paper, a novel sparse subspace clustering method is proposed for clustering image sequences, which extends the state of the art sparse subspace clustering method by simultaneously performing wavelet multi-scale transform on images and block-diagonal prior spectral clustering based denoising on image sequences. It applies the wavelet multi-scale transform on images based on the spatial similarity of images to reveal the within-image structure, it adds a penalty term in the formulation of the problem to enhance the correlation between neighboring images in the time domain, and it uses denoising to maximize the within-class correlation and minimize the between-class correlation. Experiments using various public datasets, including the ordered face dataset and video scene segmentation dataset, have shown that the proposed method has lower error rate, and is more resilient to noise than other representative sparse subspace clustering methods.