Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant flavone apigenin inhibits HDAC and remodels chromatin to induce growth arrest and apoptosis in human prostate cancer cells: In vitro and in vivo study

Apigenin (4′,5,7,‐trihydroxyflavone), an anticancer agent, selectively toxic to cancer cells induces cell cycle arrest and apoptosis through mechanisms that have not been fully elucidated. Our studies indicate that apigenin‐mediated growth inhibitory responses are due to inhibition of class I histone deacetylases (HDACs) in prostate cancer cells. Treatment of PC‐3 and 22Rv1 cells with apigenin (20–40 µM) resulted in the inhibition of HDAC enzyme activity, specifically HDAC1 and HDAC3 at the protein and message level. Apigenin‐mediated HDAC inhibition resulted in global histone H3 and H4 acetylation, as well as localized hyperacetylation of histone H3 on the p21/waf1 promoter. A corresponding increase was observed in p21/waf1 and bax protein and mRNA expression after apigenin exposure, consistent with the use of HDAC inhibitor, trichostatin A. The downstream events demonstrated cell cycle arrest and induction of apoptosis in both cancer cells. Studies of PC‐3 xenografts in athymic nude mice further demonstrated that oral intake of apigenin at doses of 20 and 50 µg/mouse/d over an 8‐wk period resulted in a marked reduction in tumor growth, HDAC activity, and HDAC1 and HDAC3 protein expression at both doses of apigenin. An increase in p21/waf1 expression was observed in apigenin‐fed mice, compared to the control group. Furthermore, apigenin intake caused a significant decrease in bcl2 expression with concomitant increase in bax, shifting the bax/bcl2 ratio in favor of apoptosis. Our findings confirm for the first time that apigenin inhibits class I HDACs, particularly HDAC1 and HDAC3 and its exposure results in reversal of aberrant epigenetic events that promote malignancy. © 2011 Wiley Periodicals, Inc.
Concatenated space-time block coding with trellis coded modulation over fading channels in the absence of channel state information

A concatenating space-time block code (STBC) with trellis coded modulation (TCM) system over fading channels in the absence of channel state information (CSI) is proposed. Analytical expressions for the error event probability are derived based on which certain corresponding designing rules are proposed. Analytical results demonstrate that the achievable temporal diversity for such a system is half of the achievable temporal diversity for CSI aware system. Moreover, simulation results show that the performance of the proposed system with no CSI at the receiver is at least 3 dB worse than the system in which CSI is known to the receiver.
Spectroscopic response and charge transport properties of CdZnTe detectors grown by the vertical Bridgman technique

In this work, we present the results of spectroscopic investigations on CdZnTe (CZT) detectors grown by the boron oxide encapsulated vertical Bridgman technique (IMEM-CNR, Parma, Italy). The detectors, with different thicknesses (1 and 2.5 mm), are characterized by the same electrode layout (gold electroless contacts): the anode is a central electrode (2 × 2 mm2) surrounded by a guard-ring electrode, while the cathode is a planar electrode covering the detector surface (4.1 × 4.1 mm2). The results of electrical investigations point out the low leakage currents of these detectors even at high bias voltages: 38 nA/cm2 (T = 25°C) at 10000 V/cm. The time-stability and the spectroscopic response of the detectors, at different temperatures and fluxes, were investigated. 241Am spectra were measured up to 1 Mcps. The detectors were compared with the traveling heater method (THM) CZT grown detectors (Redlen), fabricated with the same electrode layout. These activities are in the framework of an Italian research project on the development of energy-resolved photon counting (ERPC) systems for high flux energy-resolved X-ray imaging.
Purification of multisubunit membrane protein complexes: isolation of chloroplast FoF1-ATP synthase, CFo and CF1 by blue native electrophoresis.

The proton-ATP synthase of thylakoid membranes from chloroplasts (CFoF1) is composed of two parts with different structural and functional properties: the membrane-integral, proton-conducting complex CFo and the hydrophilic part, CF1 which catalyze the formation of adenosine-5'-triphosphate (ATP). To date it is difficult to isolate functional CFoF1 from thylakoids in high purity and yield. Blue native polyacrylamide gel electrophoresis (BN-PAGE) was therefore successfully employed to isolate CFoF1 in a one-step procedure from thylakoid membranes. Using a cathode buffer with low Coomassie Blue G-250 (CBG) concentration (0.002%), CFoF1 remains intact and can be obtained in high purity from solubilized, prepurified ATP synthase. Using BN-PAGE and a cathode buffer with 0.02% CBG, the ATP synthase bifurcates, and we were able to isolate both parts, CFo and CF1, separately. CFoF1, CFo, and CF1, respectively, were electroeluted nearly quantitatively electroeluted from the gel. BN-PAGE is a generally applicable method for the isolation and characterization of multisubunit membrane protein complexes in their native structure. However, the combination of neutral detergents and the negatively charged dye CBG seems to mimic properties of mild ionic detergents. This effect can lead to dissociation of labile subunits and subcomplexes, especially when delipidated membrane protein complexes are applied to BN-PAGE. By variation of the initial electrophoresis conditions, i.e., dye concentration in the cathode buffer, amount of lipid and detergent, BN-PAGE can be used for the isolation of either intact complexes or of subcomplexes.
Plant stanol ester spreads as components of a balanced diet for pregnant and breast-feeding women: evaluation of clinical safety

Clinical safety of consuming plant stanol ester spreads during pregnancy and lactation, the impact on maternal and infant serum and breast-milk cholesterol and the ratios (μmol/mmol of cholesterol) of synthesis and absorption markers were evaluated. Pregnant women (n 21) were randomised to control and dietary intervention groups, the intervention including advice to follow a balanced diet and to consume spreads enriched with plant stanol esters. Participants were followed during and after pregnancy and their infants up to 1 year of age. A mean 1·1 (sd 0·4) g consumption of plant stanols during pregnancy and 1·4 (sd 0·9) g 1 month post-partum increased sitostanol and the markers for cholesterol synthesis, lathosterol, lathosterol/campesterol and lathosterol/sitosterol, and reduced a marker for cholesterol absorption, campesterol, in maternal serum. In breast milk, desmosterol was lower in the intervention group, while no differences were detected between the groups in infants' serum. Plant stanol ester spread consumption had no impact on the length of gestation, infants' growth or serum β-carotene concentration at 1 and 6 months of age, but the cholesterol-adjusted serum β-carotene concentration was lowered at 1 month in the intervention group. Plant stanol ester spread consumption appeared safe in the clinical setting, except for potential lowering of infants' serum β-carotene concentration, and was reflected in the markers of cholesterol synthesis and absorption in mothers' serum, encouraging further studies in larger settings.
Up-grading the physical topology of transparent optical networks using a multiobjective evolutionary algorithm considering quality of service and capital cost

In this paper we propose a methodology based on an evolutionary multiobjective optimization algorithm for the problem of up-grading (expansion) the physical topology of transparent optical networks. The aim is to define the new topology layout and the specification of the new optical devices that should be deployed in an existing network in order to improve its performance, considering simultaneously the total installation cost (capital cost) and the total network blocking probability (performance criteria). To accomplish that, we propose a capital cost model for the network. We considered the following physical layer impairments: losses in optical devices, amplified spontaneous emission in optical amplifier and homodyne crosstalk in optical cross connect. The multiobjective optimization evolutionary algorithm used in the optimization process is the NSGA-II. Our proposed methodology can solve the expand physical topology design problem taking into account the physical layer impairments and the capital costs simultaneously. We also present a case study to show the effectiveness of our methodology.
Levels of microparticle tissue factor activity correlate with coagulation activation in endotoxemic mice

Summary. Background: Tissue factor (TF) is present in blood in various forms, including small membrane vesicles called microparticles (MPs). Elevated levels of these MPs appear to play a role in the pathogenesis of thrombosis in a variety of diseases, including sepsis. Objective: Measure levels of MP TF activity and activation of coagulation in control and endotoxemic mice. Materials and methods: MPs were prepared from plasma by centrifugation. The procoagulant activity (PCA) of MPs was measured using a two‐stage chromogenic assay. We also measured levels of thrombin‐antithrombin and the number of MPs. Results: Lipopolysaccharide (LPS) increased MP PCA in wild‐type mice; this PCA was significantly reduced by an anti‐mouse TF antibody (1H1) but not with an anti‐human TF antibody (HTF‐1). Conversely, in mice expressing only human TF, MP PCA was inhibited by HTF‐1 but not 1H1. MPs from wild‐type mice had 6‐fold higher levels of PCA using mouse factor (F)VIIa compared with human FVIIa, which is consistent with reported species‐specific differences in FVIIa. Mice expressing low levels of human TF had significantly lower levels of MP TF activity and TAT than mice expressing high levels of human TF; however, there were similar levels of phosphatidylserine (PS)‐positive MPs. Importantly, levels of MP TF activity in wild‐type mice correlated with levels of TAT but not with PS‐positive MPs in endotoxemic mice. Conclusion: These results suggest that the levels of TF‐positive MPs can be used as a biomarker for evaluating the risk of disseminated intravascular coagulation in endotoxemia.
Gene‐Edited Human Kidney Organoids Reveal Mechanisms of Disease in Podocyte Development

A critical event during kidney organogenesis is the differentiation of podocytes, specialized epithelial cells that filter blood plasma to form urine. Podocytes derived from human pluripotent stem cells (hPSC‐podocytes) have recently been generated in nephron‐like kidney organoids, but the developmental stage of these cells and their capacity to reveal disease mechanisms remains unclear. Here, we show that hPSC‐podocytes phenocopy mammalian podocytes at the capillary loop stage (CLS), recapitulating key features of ultrastructure, gene expression, and mutant phenotype. hPSC‐podocytes in vitro progressively establish junction‐rich basal membranes (nephrin+podocin+ZO‐1+) and microvillus‐rich apical membranes (podocalyxin+), similar to CLS podocytes in vivo. Ultrastructural, biophysical, and transcriptomic analysis of podocalyxin‐knockout hPSCs and derived podocytes, generated using CRISPR/Cas9, reveals defects in the assembly of microvilli and lateral spaces between developing podocytes, resulting in failed junctional migration. These defects are phenocopied in CLS glomeruli of podocalyxin‐deficient mice, which cannot produce urine, thereby demonstrating that podocalyxin has a conserved and essential role in mammalian podocyte maturation. Defining the maturity of hPSC‐podocytes and their capacity to reveal and recapitulate pathophysiological mechanisms establishes a powerful framework for studying human kidney disease and regeneration. Stem Cells 2017;35:2366–2378
Long Memory, Realized Volatility and HAR Models

The presence of long memory in Realized Volatility (RV) is a widespread stylized fact. The origins of long memory in RV have been attributed to jumps, structural breaks, non-linearities, or pure long memory. An important development has been the Heterogeneous Autoregressive (HAR) model and its extensions. This paper assesses the separate roles of fractionally integrated long memory models, extended HAR models and time varying parameter HAR models. We find that the presence of the long memory parameter is often important in addition to the HAR models.
Report on the Carcinogenesis Bioassay of Chloroform (CAS No. 67-66-3).

UNLABELLED Chloroform, also known as trichloromethane, is primarily used (93%) in the manufacture of fluorocarbons for refrigerants, propellants, and plastics. The remainder is used for many purposes including extracting and purifying antibiotics, as an industrial solvent, in preparation of dyes, drugs and pesticides, as a component of some toothpastes, cough medicines, liniments, salves, in photographic processing and in industrial drycleaning. A carcinogenesis bioassay of USP grade chloroform was conducted using Osborne-Mendel rats and B6C3F1 mice. Chloroform was administered orally (by gavage) in corn oil to 50 animals of each sex and at two dose levels five times per week for 78 weeks. Rats were started on test at 52 days of age and sacrificed after 111 weeks. The dose levels for males were 90 and 180 mg/kg body weight. Female rats were started at 125 and 250 mg/kg, reduced to 90 and 180 mg/kg after 22 weeks, with an average level of 100 and 200 mg/kg for the study. A decrease in survival rate and weight gain was evident for all treated groups. The most significant observation (P=.0016) was kidney epithelial tumors in male rats with incidences of: 0% in controls, 8% in the low dose and 24% in the high dose groups. Although an increase in thyroid tumors was also observed in treated female rats, this finding was not considered biologically significant. Mice were started on test at 35 days and sacrificed after 92-93 weeks. Initial dose levels were 100 and 200 mg/kg for males and 200 and 400 mg/kg or female mice. These levels were increased after 18 weeks to 150/300 and 250/500 mg/kg respectively so that the average levels were 138 and 277 mg/kg for males and 238 and 477 mg/kg for female mice. Survival rates and weight gains were comparable for all groups except high dose females which had a decreased survival. Highly significant increases (P<.001) in hepatocellular carcinoma were observed in both sexes of mice with incidences of: 98% and 95% for males and females at the high dose; 36% and 80% for males and females at the low dose as compared with 6% in both matched and colony control males, 0% in matched control females and 1% in colony control females. Nodular hyperplasia of the liver was observed in many low dose male mice that had not developed hepatocellular carcinoma. SYNONYMS trichloromethane LEVELS OF EVIDENCE OF CARCINOGENICITY: Male Rats: Positive; Female Rats: Negative; Male Mice: Positive; Female Mice: Positive.
Oxygen Deficiency Responsive Gene Expression inChlamydomonas reinhardtii through a Copper-Sensing Signal Transduction Pathway1

Chlamydomonas reinhardtii activatesCpx1, Cyc6, and Crd1, encoding, respectively, coproporphyrinogen oxidase, cytochromec 6, and a novel di-iron enzyme when transferred to oxygen-deficient growth conditions. This response is physiologically relevant because C. reinhardtiiexperiences these growth conditions routinely, and furthermore, one of the target genes, Crd1, is functionally required for normal growth under oxygen-depleted conditions. The same genes are activated also in response to copper-deficiency through copper-response elements that function as target sites for a transcriptional activator. The core of the copper-response element, GTAC, is required also for the hypoxic response, as is a trans-acting locus, CRR1. Mercuric ions, which antagonize the copper-deficiency response, also antagonize the oxygen-deficiency response of these target genes. Taken together, these observations suggest that the oxygen- and copper-deficiency responses share signal transduction components. Nevertheless, whereas the copper-response element is sufficient for the nutritional copper response, the oxygen-deficiency response requires, in addition, a second cis-element, indicating that the response to oxygen depletion is not identical to the nutritional copper response. The distinction between the two responses is also supported by comparative analysis of the response of the target genes,Cyc6, Cpx1, and Crd1, to copper versus oxygen deficiency. A Crr1-independent pathway forHyd1 expression in oxygen-depleted C. reinhardtii demonstrates the existence of multiple oxygen/redox-responsive circuits in this model organism.
Morphology and Histochemistry of Juvenile American Alligator (Alligator mississippiensis) Nephrons

Here we present a detailed morphological description of the alligator (Alligator mississippiensis) kidney and nephron. We present a series of histological, histochemical, and immunohistochemical markers that clearly define the seven regions of the alligator nephron. The alligator kidney is composed of many paired (mirrored) lobules on each kidney (lobe). Single nephrons span the width of lobules three times. The fine structure of glomeruli, lying in rows spanning the height of the lobule, is resolved by periodic acid methionine silver (PAMS) and periodic acid Schiff's (PAS) histochemistry. Glomeruli are connected to the proximal tubule (PT) via a neck segment. The PT is alcian blue‐negative, making it distinct from the distal tubule (DT), connecting segment (CS), and collecting duct (CD). The PT is clearly identifiable by a PAS‐positive brush border membrane. The PT is connected to the DT via an intermediate segment (IS) that makes a 180° turn to connect these tubules. PAMS‐positive material is found in the lumens of the PT, IS, and DT. Also, PAMS‐positive granules are found in the DT, CS, and CD. Immunolocalization of the Na+, K+‐ATPase to the basolateral membrane of the DT, CS, and CD suggests a role of this enzyme in driving primary and secondary transport processes in these segments, including bicarbonate transport into the lumen of the DT (leading to an alkaline urine). Through the techniques described here, we have identified a series of distinct markers to be used by pathologists, veterinarians, and researchers to easily identify alligator nephron segments. Anat Rec, 2009. © 2009 Wiley‐Liss, Inc.
Relationships Between Propulsion and Anthropometry in Paralympic Swimmers.

PURPOSE To characterize relationships between propulsion, anthropometry, and performance in Paralympic swimming. METHODS A cross-sectional study of swimmers (13 male, 15 female) age 20.5 ± 4.4 y was conducted. Subject locomotor categorizations were no physical disability (n = 8, classes S13-S14) and low-severity (n = 11, classes S9-S10) or midseverity disability (n = 9, classes S6-S8). Full anthropometric profiles estimated muscle mass and body fat, a bilateral swim-bench ergometer quantified upper-body power production, and 100-m time trials quantified swimming performance. RESULTS Correlations between ergometer mean power and swimming performance increased with degree of physical disability (low-severity male r = .65, ± 0.56, and female r = .68, ± 0.64; midseverity, r = .87, ± 0.41, and r = .79, ± 0.75). The female midseverity group showed nearperfect (positive) relationships for taller swimmers' (with a greater muscle mass and longer arm span) swimming faster, while for female no- and low-severity-disability groups, greater muscle mass was associated with slower velocity (r = .78, ± 0.43, and r = .65, ± 0.66). This was supported with lighter females (with less frontal surface area) in the low-severity group being faster (r = .94, ± 0.24). In a gender contrast, low-severity males with less muscle mass (r = -.64, ± 0.56), high skinfolds (r = .78, ± 0.43), a longer arm span (r = .58, ± 0.60) or smaller frontal surface area (r = -.93, ± 0.19) were detrimental to swimming-velocity production. CONCLUSION Low-severity male and midseverity female Paralympic swimmers should be encouraged to develop muscle mass and upper-body power to enhance swimming performance. The generalized anthropometric measures appear to be a secondary consideration for coaches.
Photothermal multispectral image cytometry for quantitative histology of nanoparticles and micrometastasis in intact, stained and selectively burned tissues

There is a rapidly growing interest in the advanced analysis of histological data and the development of appropriate detection technologies in particular for mapping of nanoparticle distributions in tissue in nanomedicine applications. We evaluated photothermal (PT) scanning cytometry for color‐coded imaging, spectral identification, and quantitative detection of individual nanoparticles and abnormal cells in histological samples with and without staining. Using this tool, individual carbon nanotubes, gold nanorods, and melanoma cells with intrinsic melanin markers were identified in unstained (e.g. sentinel lymph nodes) and conventionally‐stained tissues. In addition, we introduced a spectral burning technique for histology through selective laser bleaching areas with nondesired absorption background and nanobubble‐based PT signal amplification. The obtained data demonstrated the promise of PT cytometry in the analysis of low‐absorption samples and mapping of various individual nanoparticles' distribution that would be impossible with existing assays. Comparison of PT cytometry and photoacoustic (PA) cytometry previously developed by us, revealed that these methods supplement each other with a sensitivity advantage (up to 10‐fold) of contactless PT technique in assessment of thin (≤100 μm) histological samples, while PA imaging provides characterization of thicker samples which, however, requires an acoustic contact with transducers. A potential of high‐speed integrated PT–PA cytometry for express histology and immunohistochemistry of both intact and stained heterogeneous tissues with high sensitivity at the zepromolar concentration level is further highlighted. © 2010 International Society for Advancement of Cytometry.
Powder pattern indexing using the weighted crosscorrelation and genetic algorithms

X‐ray diffraction is a powerful technique for investigating the structure of crystals and crystalline powders. Unfortunately, for powders, the first step in the structure elucidation process, retrieving the unit cell parameters (indexing), is still very critical. In the present article, an improved approach to powder pattern indexing is presented. The proposed method matches peak positions from experimental X‐ray powder patterns with peak positions from trial cells using a recently published method for pattern comparison (weighted crosscorrelation). Trial cells are optimized with Genetic Algorithms. Patterns are not pretreated to remove any existing zero point shift, as this is determined during optimization. Another improvement is the peak assignment procedure. This assignment is needed for determining the similarity between lines from trial cells and experiment. It no longer allows calculated peaks to be assigned twice to different experimental peaks, which is beneficial for the indexing process. The procedure proves to be robust with respect to false peaks and accidental or systematic absensences of reflections, and is successfully applied to powder patterns originating from orthorhombic, monoclinic, and triclinic compounds measured with synchrotron as well as with conventional laboratory X‐ray diffractometers. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1043–1051, 2003