Miracle-dz/UniFAR-FTUs huggingface dataset:
Barriers in the brain: resolving dendritic spine morphology and compartmentalization

Dendritic spines are micron-sized protrusions that harbor the majority of excitatory synapses in the central nervous system. The head of the spine is connected to the dendritic shaft by a 50–400 nm thin membrane tube, called the spine neck, which has been hypothesized to confine biochemical and electric signals within the spine compartment. Such compartmentalization could minimize interspinal crosstalk and thereby support spine-specific synapse plasticity. However, to what extent compartmentalization is governed by spine morphology, and in particular the diameter of the spine neck, has remained unresolved. Here, we review recent advances in tool development – both experimental and theoretical – that facilitate studying the role of the spine neck in compartmentalization. Special emphasis is given to recent advances in microscopy methods and quantitative modeling applications as we discuss compartmentalization of biochemical signals, membrane receptors and electrical signals in spines. Multidisciplinary approaches should help to answer how dendritic spine architecture affects the cellular and molecular processes required for synapse maintenance and modulation.
The Case for Considering Quality of Life in Addiction Research and Clinical Practice

Substance use disorders are increasingly viewed as chronic conditions, and addiction treatment services are beginning to adopt models that were developed to address other chronic conditions. These models address the impact of disease and services on the patient’s overall well-being. From this perspective, treatment for addiction aims for the broad goal of recovery, which is defined as abstinence plus improved quality of life. However, the addiction field has come late to the chronic disease perspective, and the concept of quality of life in addiction is relatively undeveloped. This article reviews the evidence for the relevance of quality of life in substance use disorder treatment and recovery and discusses the importance of incorporating quality-of-life indices into research and services.
Natural nano soy proteins for improvement of beef burgers quality

Beef burgers produced using 100% meat as the primary source present are of lower quality than burgers produced with soy proteins. The growing field of nanotechnology presents the potential for further improvement in the cooking properties of beef burgers. This study was conducted to improve the quality characteristics of the beef burger through the usage of nano soy protein particles and nano glycinin protein. Ultrasonic cavitation was used to synthesize the nano proteins. The obtained nano proteins were characterized to evaluate zeta potential, particle size distribution, crystallite and polydispersity index, as well as functional properties such as water holding capacity, oil holding capacity, hydrophobicity, solubility and emulsion properties. Beef burger quality was evaluated by comparing cooking loss, cooking yield, shrinkage, and pH with control negative. The results showed the shrinkage and cooking loss of nano beef burgers decreased in nano soy protein and nano glycinin samples compared with soy protein isolate and glycinin burgers during storage period. The nano glycinin protein exhibited the highest cooking yield among all proteins and was significantly higher (𝑃 ≤ 0.05) than control negative. After storage, percent shrinkage was significantly lower (𝑃 ≤ 0.05) for nano soy protein and nano glycinin (18 and 17.8 %, respectively) than control negative (30%). Plasticity for nano soy protein and nano glycinin (4.42 and 4.23, respectively) increase compared with control negative burger (3.7) after 3 months. The addition of nano formulated proteins to beef burger improved the cooking quality of the meat product.
SAFEWAPI: web API misuse detector for web applications

The evolution of Web 2.0 technologies makes web applications prevalent in various platforms including mobile devices and smart TVs. While one of the driving technologies of web applications is JavaScript, the extremely dynamic features of JavaScript make it very difficult to define and detect errors in JavaScript applications. The problem becomes more important and complicated for JavaScript web applications which may lead to severe security vulnerabilities. To help developers write safe JavaScript web applications using vendor-specific Web APIs, vendors specify their APIs often in Web IDL, which enables both API writers and users to communicate better by understanding the expected behaviors of the Web APIs. In this paper, we present SAFEWAPI, a tool to analyze Web APIs and JavaScript web applications that use the Web APIs and to detect possible misuses of Web APIs by the web applications. Even though the JavaScript language semantics allows to call a function defined with some parameters without any arguments, platform developers may require application writers to provide the exact number of arguments. Because the library functions in Web APIs expose their intended semantics clearly to web application developers unlike pure JavaScript functions, we can detect wrong uses of Web APIs precisely. For representative misuses of Web APIs defined by software quality assurance engineers, our SAFEWAPI detects such misuses in real-world JavaScript web applications.
Real-time analytics for urban road transport

Urban road traffic congestion has been a constant problem both in UK and worldwide. Urban road transport authorities collect data from different sources. These data can be effectively utilised with an objective to minimize congestion and its impact. One of the ways for the same can be to find possible congestion in different routes beforehand and then plan accordingly either to reduce the effect or to avoid it entirely. So this project aims to make effective use of existing data to predict journey time for near future e.g. 15/30/60 minutes ahead for different routes within the urban road traffic network. It also produced a working prototype for the journey time prediction with necessary data visualisations. A complete data centric approach has been adopted to solve the problem of prediction by building a predictive model using machine learning algorithms with traffic volumes at different points as predictor and journey time for near future as the target. Given the nature and volume of the data, a big data platform (Apache Spark) was chosen as the analytics platform and the work also proposes a high level technical architecture for the end to end solution. The results for journey time prediction for near future are quite encouraging with a consistency for different routes under the area of consideration.
Can Radiative Cooling and Nongravitational Heating Explain Simultaneously the Global X-Ray Properties of Clusters and the Unresolved Cosmic X-Ray Background?

Using a simple analytic approach we address the question of whether radiative cooling, nongravitational heating, and cooling plus heating models can simultaneously explain the observed global X-ray properties (entropy and X-ray luminosity distributions) of groups and clusters and the residual soft X-ray background (XRB) after discrete sources are removed. Within the framework of typical cold dark matter structure formation characterized by an amplitude of matter power spectrum σ8 = 0.9, it is argued that while radiative cooling alone is able to marginally reproduce the entropy floor detected in the central regions of groups and clusters, it is insufficient to account for the steepening of the X-ray luminosity-temperature relation for groups and the unresolved soft XRB. A phenomenological preheating model, in which either an extra specific energy budget or an entropy floor is added to the hot gas in groups and clusters, fails in the recovery of at least one of the X-ray observed features. Finally, the soft XRB predicted by our combined model of cooling plus heating exceeds the observational upper limits by a factor of ~2, if the model is required to reproduce the observed entropy and X-ray luminosity-temperature relationships of groups and clusters. Inclusion of the cosmic variation of metallicity and the self-absorption of the cooled gas as a result of radiative cooling in groups and clusters, or exclusion of the contribution of nearby massive clusters to the XRB, does not significantly alter the situation. If the discrepancy is not a result of the oversimplification of our analytic models, this implies that either our current understanding of the physical processes of the hot gas is still incomplete, or the normalization of the present power spectrum has been systematically overestimated. For the latter, both the X-ray properties of groups and clusters and the XRB predicted by the preheating model and the cooling plus heating model can be reconciled with the X-ray observations if a lower value of the normalization parameter σ8 ≈ 0.7 is assumed.
Influence of Selected Polymorphisms of the Renin-Angiotensin System on the Regulation of Blood Pressure during Pregnancy

Hypertension during pregnancy is a heterogeneous group of disorders with elevated blood pressure with or without proteinuria. The blood pressure regulation is a complex issue, and research on this issue have been present in the world literature for many years. The study was designed to evaluate the impact of the ACE I/D, AGT-235, AGT-174 polymorphisms on the regulation of blood pressure. It is a case-control study. The study included 104 women with uncomplicated pregnancies in the control group and 75 pregnant women with hypertension disorders in the study group, hospitalized in the Perinatology and Obstetrics Department of the University Hospital in Cracow. Genomic DNA was extracted from peripheral blood leukocytes and polymorphisms were genotyped from all the patients. We analyzed the genotypes distribution and its association to blood pressure values, the time of hypertension occurrence, the medications needed to control it and the time postpartum till the blood pressure normalization in all the groups. A p-value <0.05 was considered as significant. Clinical evaluation included many standard anthropometric measures like weight and height for the calculation of the BMI in the beginning of the pregnancy and blood pressure values. It may be concluded that there is no influence of studied polymorphisms not only on the regulation of blood pressure during pregnancy, but also on the time of the onset or pharmacological treatment of hypertension during pregnancy and the time after delivery needed to normalization of blood pressure values. Further studies on larger groups are needed.
Development of a Measuring Instrument to Understand the Impact of Mobile Product Information Systems on Consumers' Food Choice

Consumers’ Food Choice has been researched in the past, but with the rise of mobile technologies such as barcode scanning, new possibilities of obtaining additional information at the Point of Sale (PoS) emerged. This raises the question about the impact of Mobile Product Information Systems (MPIS) on consumers’ perceived food quality and thus their food choices. Since most MPIS are not provided by producers of the food product, there is a risk that consumers no longer base their decisions on information provided on the product packaging, but instead on mobile information of third party service providers. As a first step this study provides a conceptual model to identify relevant influencing factors of MPIS. Thereafter, an instrument measuring the impact of MPIS on consumers’ food choice is developed
Genetic and phenotypic analysis of Borrelia valaisiana sp. nov. (Borrelia genomic groups VS116 and M19).

To clarify the taxonomic status of two recently described Borrelia genomic groups, groups VS116 and M19, three group VS116 strains and eight group M19 strains isolated from Ixodes ricinus ticks in Switzerland, The Netherlands, and the United Kingdom were characterized. PCR-restriction fragment length polymorphism (RFLP) analysis of the 5S-23S intergenic spacer amplicon, rRNA gene restriction analysis, 16S rRNA gene sequence analysis, randomly amplified polymorphic DNA (RAPD) fingerprinting, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and immunoblotting with monoclonal antibodies were used for genetic and phenotypic analysis. The PCR-RFLP and RAPD patterns of three group VS116 strains and eight group M19 strains were identical but differed from those of Borrelia burgdorferi sensu stricto, Borrelia garinii, Borrelia afzelii, and Borrelia japonica. DNAs from all group VS116 and M19 strains yielded three fragments (6.9, 3.2, and 1.4 kb) and four fragments (2.1, 1.2, 0.8, and 0.6 kb) after digestion with EcoRV and HindIII, respectively, hybridizing with an Escherichia coli 16S + 23S cDNA probe. The SDS-PAGE protein profiles of group VS116 and M19 strains were heterogeneous. Phylogenetic analysis of the partial 16S rRNA gene sequences showed that group VS116 and M19 spirochetes were members of a Borrelia species distinct from previously characterized members of the genus Borrelia. Based on our present study and data from previous DNA-DNA hybridizations, a new Borrelia species, Borrelia valaisiana sp.nov., in the B. burgdorferi complex, is proposed. Strain VS116 is the type strain of this new species.
Beneficial Effects of Heme Oxygenase-1 Up-Regulation in the Development of Experimental Inflammation Induced by Zymosan

Heme oxygenase-1 (HO-1) is part of the integrated response to oxidative stress. This enzyme may exert anti-inflammatory effects in some animal models, although the precise mechanisms are not fully understood. We have examined the role of HO-1 in the inflammatory response induced by zymosan in the mouse air pouch. Zymosan administration induced HO-1 protein expression in leukocytes migrating to exudates, with maximal levels in the late phase of this response (24–48 h). This was accompanied by ferritin induction and bilirubin accumulation, indicating that this enzyme is active in our model. HO-1 expression by zymosan treatment was partly reduced by aminoguanidine, suggesting the participation of endogenous nitric oxide in the mechanisms leading to HO-1 synthesis in the zymosan-injected mouse air pouch. Up-regulation of HO-1 by hemin administration resulted in inhibition of nitric-oxide synthase-2 activity, cellular infiltration into the air pouch exudate, and plasmatic exudation. Leukotriene B4 levels in exudates were significantly decreased in the early phase of this response (4 h), whereas interleukin-1β and tumor necrosis factor-α were inhibited at all time points. Inhibition of HO-1 activity by zinc protoporphyrin IX prevented most of the effects caused by hemin administration. Our results indicate that HO-1 exerts anti-inflammatory effects on the response to zymosan in the mouse air pouch and support a role for this enzyme in the modulation of inflammatory processes.
Influence of sulfated carbohydrates on the accessibility of CD4 and other CD molecules on the cell surface and implications for human immunodeficiency virus infection

The modulatory activity of dextran sulfate with a relative molecular mass of 8 and 500 kDa and pentosan polysulfate with a relative molecular mass of 6 kDa on human T cell surface molecules CD2, CD3, CD4, CD8 and HLA‐DR was investigated by analytical flow cytometry. The 500‐kDa dextran sulfate induces a complete disappearance of the CD4 and a 50% diminuition of CD2 immune reactivity on peripheral blood lymphocytes after a 4‐h incubation while the low molecular mass polyanions do not. This modulation of the CD4 immune reactivity includes all CD4 epitopes investigated. It does not correlate with the antiviral effect of polyanions against human immunodeficiency virus infection. The interaction of polyanions with the CD4 presentation is temperature dependent and differs between fresh lymphocytes and immortal cell lines. From our data it can be concluded that mechanisms other than cell surface effects are responsible for the antiviral potency of these drugs. Implications for the modes of antiviral action of sulfated carbohydrates are discussed.
SPT10 and SPT21 are required for transcription of particular histone genes in Saccharomyces cerevisiae

The Saccharomyces cerevisiae genome contains four loci that encode histone proteins. Two of these loci, HTA1-HTB1 and HTA2-HTB2, each encode histones H2A and H2B. The other two loci, HHT1-HHF1 and HHT2-HHF2, each encode histones H3 and H4. Because of their redundancy, deletion of any one histone locus does not cause lethality. Previous experiments demonstrated that mutations at one histone locus, HTA1-HTB1, do cause lethality when in conjunction with mutations in the SPT10 gene. SPT10 has been shown to be required for normal levels of transcription of several genes in S. cerevisiae. Motivated by this double-mutant lethality, we have now investigated the interactions of mutations in SPT10 and in a functionally related gene, SPT21, with mutations at each of the four histone loci. These experiments have demonstrated that both SPT10 and SPT21 are required for transcription at two particular histone loci, HTA2-HTB2 and HHF2-HHT2, but not at the other two histone loci. These results suggest that under some conditions, S. cerevisiae may control the level of histone proteins by differential expression of its histone genes.
Study the Effect of Electrodeposition Parameters on Ni/SiC Composite Coating

In this research, we successfully obtained Ni/SiC micro-composite coatings with various contents of SiC particles of particle size(10 μm), by using electrodeposition method from nickel watts bath in which the SiC particles suspend. The effects of the current density, temperature, and particle loading(PL) of SiC particles in the electrolyte on the morphology, texture, and vol% of SiC in deposit were investigated. The morphological and structural analysis show uniform distribution of SiC particles within the composite coatings. It was found that the depositing conditions affect the microstructure of deposited nickel and the SiC vol% in deposit. Furthermore, the vol% of SiC increases in deposit by increasing the particle loading(PL) in the bath, while decreased by increasing the current density. Also the higher values of SiC vol% were obtained at temperature (50°C).
Almost tight upper bounds for vertical decompositions in four dimensions

We show that the complexity of the vertical decomposition of an arrangement of n fixed-degree algebraic surfaces or surface patches in four dimensions is O(n/sup 4+/spl epsi//) for any /spl epsi/ > 0. This improves the best previously known upper bound for this problem by a near-linear factor, and settles a major problem in the theory of arrangements of surfaces, open since 1989. The new bound can be extended to higher dimensions, yielding the bound O (n/sup 2d-4+/spl epsi//), for any /spl epsi/ > 0, on the complexity of vertical decompositions in dimensions d /spl ges/ 4. We also describe the immediate algorithmic applications of these results, which include improved algorithms for point location, range searching, ray shooting, robot motion planning, and some geometric optimization problems.
Endocrinological studies in patients with Klinefelter's syndrome treated with clomiphene.

The effect of clomiphene citrate on excretion values for fsh, lh, testosterone and epitestosterone has been investigated in four patients with Klinefelter's syndrome. During the pretreatment period, levels of fsh and lh were above the normal range for male subjects, while readings of testosterone and epitestosterone were generally low. Clomiphene produced a significant increase in fsh output in one subject and in lh excretion in another. In the remaining patients, pituitary gonadotrophic function was not affected by the administration of the compound. The effect ofclomiphene on excretion values for C-19 steroids was inconsistent. The study did not provide definite evidence regarding the site of of action of clomiphene in patients with Klinefelter's syndrome.
Allele specific expression and methylation in the bumblebee, Bombus terrestris

The social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the role of methylation on allele specific expression in social insects. The aim of this paper is to investigate allele specific expression and monoallelic methylation in the bumblebee, Bombus terrestris. We found nineteen genes that were both monoallelically methylated and monoallelically expressed in a single bee. Fourteen of these genes express the hypermethylated allele, while the other five express the hypomethylated allele. We also searched for allele specific expression in twenty-nine published RNA-seq libraries. We found 555 loci with allele-specific expression. We discuss our results with reference to the functional role of methylation in gene expression in insects and in the, as yet unquantified, role of genetic cis effects in insect allele specific methylation and expression.
Melting during steady-state transcription of the rrnB P1 promoter in vivo and in vitro

The rRNA rrnB P1 promoter was probed with the single-strand-selective reagent potassium permanganate during steady-state transcription in vitro and in vivo. In both cases, a weak but significant level of permanganate sensitivity was observed, which was not changed by treatment with rifampin. In contrast, static studies showed that rifampin strongly affects the very high level signal associated with polymerases that have used ATP and CTP as initiating nucleotides. We infer that the permanganate sensitivity associated with steady-state transcription is due to polymerases that have not yet used ATP and CTP. The slow and regulated step during rrnB P1 transcription may be the use of the initiating nucleotides to catalyze stable opening of the promoter DNA.
Atomic-Level Models of the Bacterial Carboxysome Shell

The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.