Miracle-dz/UniFAR-FTUs huggingface dataset:
Astrophysical gas dynamics of structure formation

Several problems concerning the behaviour of gas during structure formation in the Universe are investigated. The beta problem concerns the relative distributions of gas and gravitating matter in clusters of galaxies. One-dimensional self-similar simulations of clus­ ter collapse are used to investigate whether the different collisional properties of the gas and gravitating matter in clusters can significantly affect their relative distributions. These models can produce beta values similar to those observed. Data for the beta problem are considered next. Beta is found to correlate with cluster temperature. This trend can be explained by a fixed specific energy excess in the gas, but simple modelling shows that the range of excesses required by the data is large. The energy excess can be a significant fraction of the total specific energy of the gas. Possible mechanisms for the excess are considered in the light of these results. A new axisymmetric iV-body/hydrodynamic code is outlined. The axisymmetric code gives better resolution than 3-dimensional codes using the same num­ ber of particles. The axisymmetric code is adapted to study the collapse and formation of disk galaxies. This code includes the effects of shock heating, radiative cooling, shear viscosity and mass deposition. Radiative cooling within shocks is shown to be a severe problem in numerical simulations of galaxy collapse. The collapse code is used to simulate galaxy formation following the model of Nulsen & Fabian (1995). The disk galaxies formed during these simulations resemble observed spirals, with flat rotation curves and exponential surface den­ sities, but the disk masses are low. The disks are formed from radiatively cooled hot gets and so form later than in previous models. The low disk masses are, at least in part, due to problems of simulating radiative cooling.
A qRT-PCR RFLP Method for Monitoring Highly Conserved Transgene Expression during Gene Therapy

, Abstract Evaluation of the transfer efficiency of a rat heme oxygenase-1 (HO-1) transgene into mice requires differentiation of rat and mouse HO-1. However, rat and mouse HO-1 have 94% homology; antibodies and enzyme activity cannot adequately distinguish HO-1. We designed a qRT-PCR method to monitor HO-1 transcription relative to a housekeeping gene, GAPDH. The ratio of rat and mouse HO-1 mRNA could be estimated through restriction fragment length polymorphism (RFLP) analysis of the PCR products. In vitro , murine AML12 hepatocytes were transfected with rat HO-1. After 40 h, total HO-1 mRNA was enriched 2-fold relative to control cells and rat HO-1 comprised 84% of HO-1 cDNA. In vivo , the rat HO-1 transgene was cloned into a Sleeping Beauty transposase ( SB -Tn) construct and injected hydrodynamically into a mouse model of sickle cell disease (SCD). After 21 days, there was a 32% enrichment of HO-1 mRNA relative to control mice and the rat transgene comprised 88% of HO-1 cDNA. After 21 days, HO-1 protein expression in liver was increased 2.5-fold. In summary, qRT-PCR RFLP is a useful and reliable method to differentiate transgene from host gene transcription, especially when the host and transgene protein are identical or highly homologous. This method has translational applications to the design, delivery and monitoring of gene therapy vectors. and 93% identity at the nucleic acid level. The high degree of amino acid similarity makes it difficult to differentiate rat and mouse HO-1 using primary antibodies. As an alternative to measuring protein expression and enzyme activity, mRNA can be measured by qRT-PCR and coupled with RFLP analysis to differentiate host and transgene transcription. This method is more sensitive and accurate than antibody or activity assay methods for distinguishing endogenous and transgene expression in host tissues. RFLP can accurately distinguish single nucleotide differences at restriction endonuclease sites between target DNA sequences. The method developed in this study is applicable to all stages of gene transfer studies and provides a general tool for the detection of transgenes.
Function and regulation of large conductance Ca 21 -activated K 1 channel in vascular smooth muscle cells

Large conductance Ca 21 -activated K 1 (BK Ca ) channels are abundantly expressed in vascular smooth muscle cells. Activation of BK Ca channels leads to hyperpolarization of cell membrane, which in turn counteracts vasoconstriction. Therefore, BK Ca channels have an important role in regulation of vascular tone and blood pressure. The activity of BK Ca channels is subject to modulation by various factors. Furthermore, the function of BK Ca channels are altered in both physiological and pathophysiological conditions, such as pregnancy, hypertension and diabetes, which has dramatic impacts on vascular tone and hemodynamics. Consequently, compounds and genetic manipulation that alter activity and expression of the channel might be of therapeutic interest. Teaser Sentence : BKCa channels in VSMCs are key players in both cardiovascular adaption and dysfunctions during physiological and pathophysiological conditions and constitutes a potential therapeutic target for cardiovascular disorders associated with altered BKCa channel activity. The major cause for activation of BK Ca channels in VSMCs is an increase in intracellular Ca 21 concentrations in the vicinity of BK Ca channel (Ca 21 microdomain). Such a localized increase in Ca 21 could be achieved by spontaneous or agonist-stimulated Ca 21 release from intracellular stores through RyR or IP 3 R on SR and Ca 21 influx through L-type Ca V 1.2. Activation of BK Ca channels enables K 1 efflux due to the K 1 electrochemical gradient, resulting in hyperpolarization of the myocyte membrane and subsequent closure of Ca V 1.2. BK and and/or of NO, CO, H 1 , BK Ca channel activity, an increase production of 20-HETE and ROS and a decrease in pO2 BK Ca channel myocyte vasodilation, Ca BK Ca channels in VSMCs could form macromolecular complexes with other signaling components including GPCRs, ion channels, enzyems, G proteins, and anchor proteins. The association of Ca 21 -permeable channels (Ca V 1.2 and RyR) and BK Ca channel enables creation of a high concentration of Ca 21 in the vicinity of BK Ca channels (Ca 21 microdomain). The formation of GPCR-BK Ca channel complex permits direct modulation of the channel by thromboxane A2 receptor (TP) or indirect modulation by β 2AR-associated PKA or AT1R-associated c-Src. The inclusion of nonpnagocytic NAD(P)H oxidases (NOX-1) in the AT1R-BK Ca complex provide addition modulation of BK Ca channels by ROS, which might have a role in the pathophysiology of cardiovascular dysfunction in patients with diabetes.
Prognostic value of normal positron emission tomography myocardial perfusion imaging in patients with known or suspected coronary artery disease: a meta-analysis

and this article. Objective: Several studies have confirmed high diagnostic performance of positron emission tomography (PET) myocardial perfusion imaging (MPI) in patients with known or suspected coronary artery disease. However, whether the superior diagnostic accuracy could translate into improved mortality outcomes remains unknown. The aim of this study was to define the prognostic value of normal PET MPI. Methods: PubMed and EMBASE were searched to identify related studies up to June 2016. All studies using PET MPI to evaluate subjects with known or suspected coronary artery disease and providing absolute number of patients with a negative test and primary data on clinical outcomes with a follow-up time $ 3 months were included for analysis. Results: The search yielded 11 studies comprising 20,471 patients for final analysis. The negative-predictive value (NPV) for cardiac death, all-cause death and major adverse cardiovascular events (MACE) were 98.80% [95% confidence interval (CI), 97.64% – 99.39%], 94.89% (95% CI: 92.99 – 96.30%) and 90.26% (95% CI: 78.01 – 96.03%), over 36.9 months of follow-up for cardiac death, over 26.8 months for all-cause death and 35.7 months for MACE. The corresponding annualized event rates were 0.39%, 2.29% and 3.27%, respectively. In subgroup analyses of different imaging analysis methods for PET MPI, studies using perfusion abnormity had a similar NPV as compared with those using coronary flow reserve (98.46% vs 98.86%, p -value 5 NS), with a corresponding annualized event rate after negative tests (equal to 1 2 NPV) as 0.45% and 0.42%, respectively. Conclusion: Normal PET has a high NPV for cardiac death, MACE and all-cause mortality. Different indexes used for PET imaging analysis have a comparable prognostic value. Advances in knowledge: A normal PET MPI conferred a very low risk of cardiac death of 0.39% per year, which is close to that of a normal aged-matched population. coronary artery bypass grafting; coronary artery
Improving Noninvasive Methods of Assessing Liver Fibrosis Using an Ordinal Regression Index

Background & Aims— Liver fibrosis is a significant concern for patients with hepatitis C virus (HCV)/HIV co-infection. Fibrosis staging by biopsy is accurate but costly and invasive. Several fibrosis prediction models utilizing non-invasive biomarkers have been developed but are suboptimal in co-infected patients. We compared results from different staging models and ordinal regression with biopsy data. Methods— Data from the Adult AIDS Clinical Trials Group protocol A5178 were used to evaluate 5 models of fibrosis staging; areas under receiver-operator characteristic curves (AUROC) were assessed. Individual covariates were assessed with univariable regression then entered into an ordinal logistic regression model from which a stage-wise index was developed. Results— Data from 173 patients were evaluated; 85% were on anti-retroviral therapy, 31.2% had severe fibrosis (F3/F4) and 14% had cirrhosis (F4). Differences in CD4+ cell and platelets counts and international normalized ratio values were observed between those with and without F3/F4. Among existing models, the FIB-4 index performed best, with 88% specificity for F4 and >86% negative predictive values for F3/F4, although AUROC values were low (0.56±0.03 for F3/ invasive fibrosis prediction models. Longitudinal studies with paired biopsies will assist in refining the ordinal regression index.
Genetic analyses of Rce1 function in Ras membrane association and function

Proteins terminating with a CAAX motif, such as the nuclear lamins and the Ras family of proteins, undergo posttranslational modification of a carboxyl-terminal cysteine with an isoprenyl lipid—a process called protein prenylation. After prenylation, the last three residues of CAAX proteins are clipped off by an endoprotease of the endoplasmic reticulum. Rce1 is responsible for the endoproteolytic processing of the Ras proteins and is likely responsible for endoproteolytic processing of the vast majority of CAAX proteins. Prenylation has been shown to be essential for the proper intracellular targeting and function of several CAAX proteins, but the physiologic importance of the endoprotease step has remained less certain. Here, we will review methods that have been used to define the physiologic importance of the endoproteolytic processing step of CAAX protein processing.
A Parthood Approach for the conceptual modelling of Tangible Objects Composition (TOC) - an application on Cultural Heritage (CH)

Several semantic web approaches tend to address and solve the problem of integrating multidisciplinary rich content using Linked Open Data. Cultural heritage (CH) is a multidisciplinary domain that contains a massive heterogeneous content that varies distinctly by types and properties and is managed by diﬀerent organizations. Various semantic web approaches have been proposed in the context of CH, and at multiple integration levels (local, national, international). These approaches focus on metadata schemata integration but give no signiﬁcant importance to the representation of a tangible cultural heritage object, as an entity and the diﬀerent parts that compose it. Knowing that the preservation and restoration of CH artifacts is an important goal in the CH ﬁeld, we aim at modeling the content of this domain by representing the composition of a cultural heritage object and studying its evolution with time and space. In our present work, we illustrate the ﬁrst part of the approach which is a parthood approach for the conceptual modeling of the composition of a tangible object in general, with the application on CH objects in particular. To do this, we introduce some parthood concepts and properties that are used for representing the composition mechanism. We limit the possible cases of part-whole relations in tangible objects to 7 cases and choose a corresponding logical/ontological part-whole relation(s) for it. This resulted in introducing also a hierarchy of tangible object types. We plan to build and implement our approach using OWL2 as the ontological language for our linked open data approach.
Change in waist circumference with longer time in the US among Hispanic and Chinese immigrants: the modifying role of the neighborhood built environment

Purpose— We examined whether living in neighborhoods supportive of healthier diets and more active lifestyles may buffer immigrants against the unhealthy weight gain that is purported to occur with longer length of US residence. Methods— Neighborhood data referring to a 1-mile buffer around participants’ baseline home addresses were linked to longitudinal data from 877 Hispanic and 684 Chinese immigrants aged 45-84 years in the Multi-Ethnic Study of Atherosclerosis. We used ethnicity-stratified linear mixed models to examine whether food and activity-based neighborhood measures (healthy food Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Conflict of interest: None declared. stores, walkability, and recreational facilities) were associated with change in waist circumference (WC) over a 9-year follow-up. Results— Among Hispanics, living in neighborhoods with more resources for healthy food and recreational activity was related to lower baseline WC. However, there was no association with change in WC over time. Among Chinese, living in more walkable neighborhoods was associated with lower baseline WC and with slower increases in WC over time, especially among the most recent immigrant arrivals. Conclusions— Where immigrants reside may have implications for health patterns that emerge with longer time in the US.
Calculation of organ doses for a large number of patients undergoing computed tomography examinations

Purpose— To develop and demonstrate an automated calculation method to provide organ dose assessment for a large cohort of pediatric and adult patients undergoing CT examinations. Methods— We adopted two dose libraries that were previously published: the CTDI vol normalized organ dose library and the mAs-normalized CTDI w library. We developed an algorithm to calculate organ doses using the two dose libraries and CT scan parameters available from DICOM data. To demonstrate the established method, we calculated organ doses for pediatric (n=2499) and adult (n=2043) CT scans randomly selected from four health care systems in the United States, and compared the adult organ doses with the values calculated from the ImPACT calculator. Results— Median brain dose was 20 mGy (pediatric) and 24 mGy (adult), and brain dose was greater than 40 mGy for 11% (pediatric) and 18% (adult) of head scans. Both the NCI and the ImPACT methods provided similar organ doses (median discrepancy < 20%) for all organs except for the organs located close to scan boundaries. The visual comparisons of scan coverage and phantom anatomies revealed that the NCI method based realistic computational phantoms provides more realistic organ doses compared to the ImPACT method. Conclusion— The automated organ dose calculation method developed in this study reduces the time needed to calculate doses on a large number of patients. We have successfully utilized this method for a variety of CT-related studies including retrospective epidemiological study and CT dose trend analysis studies.
Structures of the rare-cutting restriction endonuclease NotI reveal a novel metal binding fold involved in DNA recognition

The structure of the rare-cutting restriction endonuclease NotI, which recognizes the 8 basepair target 5 ′ -GCGGCCGC-3 ′ , has been solved with and without bound DNA. Because of its specificity (recognizing a site that occurs once per 65kb), NotI is used to generate large genomic fragments and to map DNA methylation status. NotI contains a unique metal-binding fold, found in a variety of putative endonucleases, occupied by an iron atom coordinated within a tetrahedral Cys 4 motif. This domain positions nearby structural elements for DNA recognition, and serves a structural role. While recognition of the central six basepairs of the target is accomplished via a saturated hydrogen bond network typical of restriction enzymes, the most peripheral basepairs are engaged in a single direct contact in the major groove, reflecting reduced pressure to recognize those positions. NotI may represent an evolutionary intermediate between mobile endonucleases (which recognize longer target sites) and canonical restriction endonucleases.
Real-time detection of abandoned bags using CNN

The problem of automatic abandoned bag detection is of the great importance for ensuring security in the public areas. At the same time emergency situations occur rarely in the large-scale video surveillance systems. Therefore it is important to keep false alarms low maintaining high accuracy of detection. The approach that satisfies mentioned requirements for abandoned bag detection in complex environments is proposed. It consists of two blocks. The first block does the preliminary detection of abandoned bags on pixel level by background modelling via Gaussian mixture model. It ensures high speed and precise positioning of the bounding boxes on the objects of interest. The second part performs the bag recognition on a region level via a compact convolutional neural network. Using of the convolutional neural network is a key component to success. All processing happens on a central processing unit. The proposed approach is suitable for systems (microcomputers), which do not have powerful graphical subsystems. The experiments have been conducted on the real-world scenes. Obtained results indicate that the proposed approach is efficient and provides acceptable quality characteristics.
Sequence of the El a Subunit of Branched-Chain a-Ketoacid Dehydrogenase in Two Patients with Thiamine-responsive Maple Syrup Urine Disease

Summary Some patients with maple syrup urine disease respond to thiamine administration with a reduction in ketoaciduria and increase in activity of branched-chain a-ketoacid dehydrogenase. The biochemical mecha-nism underlying this effect is unknown but may result from decreased affinity of the mutant enzyme for thiamine or from stabilization of the abnormal enzyme by thiamine. The Ela subunit of the complex par-ticipates in the thiamine-dependent decarboxylation of branched-chain a-ketoacids. We sequenced the Ela subunit by using reverse transcription of RNA followed by enzymatic amplification of cDNA in two patients with thiamine-responsive maple syrup urine disease. The deduced amino acid sequence of this subunit in the patients was identical to that in normal controls, suggesting that in the patients the thia-mine-binding site is abnormal because of a mutation in the ElB subunit. Other possible explanations are (a) that a mutation in the E1p or E2 subunits either alters thiamine binding by Ela because of allosteric interactions or causes the complex to be unstable and (b) that thiamine stabilizes the complex.
ARMS/Kidins220 regulates dendritic branching and spine stability in vivo

The development of nervous system connectivity depends upon the arborization of dendritic fields and the stabilization of dendritic spine synapses. It is well established that neuronal activity and the neurotrophin BDNF modulate these correlated processes. However, the downstream mechanisms by which these extrinsic signals regulate dendritic development and spine stabilization are less well known. Here we report that a substrate of BDNF signaling, the Ankyrin Repeat-rich Membrane Spanning protein (ARMS) or Kidins220, plays a critical role in the branching of cortical and hippocampal dendrites and in the turnover of cortical spines. In the barrel somatosensory cortex and the dentate gyrus, regions where ARMS/Kidins220 is highly expressed, no difference in the complexity of dendritic arbors was observed in 1-month-old adolescent ARMS/Kidins220 +/− mice compared to wild-type littermates. However, at 3 months of age, young adult ARMS/Kidins220 +/− mice exhibited decreased dendritic complexity. This suggests that ARMS/Kidins220 does not play a significant role in the initial formation of dendrites but, rather, is involved in the refinement or stabilization of the arbors later in development. In addition, at 1 month of age the rate of spine elimination was higher in ARMS/Kidins220 +/− mice than in wild-type mice, suggesting that adolescent ARMS/Kidins220 +/− mice exhibit reduced spine stability. Taken together, these data suggest that ARMS/Kidins220 is important for the growth of dendritic arbors and spine stability during an activity- and BDNF-dependent period of development.
Racial/Ethnic Disparities in Disease Burden and Costs Related to Exposure to Endocrine Disrupting Chemicals in the US: an Exploratory Analysis

Objective: Studies have documented disparities in exposure to endocrine disrupting chemicals (EDC), but no studies have investigated potential implications for racial/ethnic disparities in chronic disease and associated costs. Our objective was to examine EDC levels in the US population according to race/ethnicity and to quantify disease burden and associated costs. Study Design and Setting: EDC exposure levels in 2007-2010 were obtained from the National Health and Nutrition Examination Surveys. The associated disease burden and costs for twelve exposure-response relationships were determined for Non-Hispanic Whites, Non-Hispanic Blacks, Mexican-Americans, Other Hispanics, and Other/Multicultural. Results: EDC exposure levels and associated burden of disease and costs were higher in Non-Hispanic Blacks ($56.8 billion; 16.5% of total costs) and Mexican-Americans ($50.1 billion; 14.6%) compared to their proportion of the total population (12.6% and 13.5%, respectively). Associated costs among Non-Hispanic Whites comprised 52.3% of total costs ($179.8 billion), though they comprise 66.1% of the US population. These disparities are driven by generally higher exposure to persistent pesticides and flame retardants among Non-Hispanic Blacks and Mexican-Americans. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Potential Conflicts of Interests: The authors have no conflicts of interest relevant to this article to disclose. Conclusion: Our estimates suggest that racial/ethnic disparities in chronic diseases in the US may be due to chemical exposures, and are an important tool to inform policies that address such disparities.