Miracle-dz/UniFAR-FTUs huggingface dataset:
Progress in characterizing submonolayer island growth: Capture-zone distributions, growth exponents, & hot precursors

In studies of epitaxial growth, analysis of the distribution of the areas of capture zones (i.e. proximity polygons or Voronoi tessellations with respect to island centers) is often the best way to extract the critical nucleus size i. For non-random nucleation the normalized areas s of these Voronoi cells are well described by the generalized Wigner distribution (GWD) Pβ(s) = asβ exp(-bs2), particularly in the central region 0.5 < s < 2 where data are least noisy. Extensive Monte Carlo simulations reveal inadequacies of our earlier mean field analysis, suggesting β = i + 2 for diffusion-limited aggregation (DLA). Since simulations generate orders of magnitude more data than experiments, they permit close examination of the tails of the distribution, which differ from the simple GWD form. One refinement is based on a fragmentation model. We also compare island-size distributions. We compare analysis by island-size distribution and by scaling of island density with flux. Modifications appear for attach-limited aggregation (ALA). We focus on the experimental system para-hexaphenyl on amorphous mica, comparing the results of the three analysis techniques and reconciling their results via a novel model of hot precursors based on rate equations, pointing out the existence of intermediate scaling regimes between DLA and ALA.
A Novel Bioassay for the Activity Determination of Therapeutic Human Brain Natriuretic Peptide (BNP)

Background Recombinant human brain natriuretic peptide (rhBNP) is an important peptide-based therapeutic drug indicated for the treatment of acute heart failure. Accurate determination of the potency of therapeutic rhBNP is crucial for the safety and efficacy of the drug. The current bioassay involves use of rabbit aortic strips, with experiments being complicated and time-consuming and markedly variable in results. Animal-less methods with better precision and accuracy should be explored. We have therefore developed an alternative cell-based assay, which relies on the ability of BNP to induce cGMP production in HEK293 cells expressing BNP receptor guanylyl cyclase-A. Methodology/Principal Findings An alternative assay based on the measurement of BNP-induced cGMP production was developed. Specifically, the bioassay employs cells engineered to express BNP receptor guanylyl cyclase-A (GCA). Upon rhBNP stimulation, the levels of the second messager cGMP in these cells drastically increased and subsequently secreted into culture supernatants. The quantity of cGMP, which corresponds to the rhBNP activity, was determined using a competitive ELISA developed by us. Compared with the traditional assay, the novel cell-based assay demonstrated better reproducibility and precision. Conclusion/Significance The optimized cell-based assay is much simpler, more rapid and precise compared with the traditional assay using animal tissues. To our knowledge, this is the first report on a novel and viable alternative assay for rhBNP potency analysis.
Registration method for multispectral skin images

A feature-based image registration method is presented for the use on the multispectral skin images. The proposed method allows the use and combination of different kinds of feature points, so it can be adjusted to different applications. The local minima and maxima are used as features for the skin images. By analyzing all possible shifts among feature points in the reference and sensed images, the proposed method efficiently finds translation among these images. The method is expanded to also determine rotation and scale. The proposed method is compared with other area-based and feature-based methods (proposed in the literature specifically for skin images) by testing those methods on a set of multispectral skin images.
Fulminant parvovirus B19‐associated pancarditis with haemophagocytic lympho‐histiocytosis in an immunocompetent adult

Myocarditis is a common cardiac disease that is identified on routine postmortem examinations. Initially, coxsackie viruses, other enteroviruses and adenoviruses were thought to be more common causes of myocarditis; however, recently, parvovirus B19 (PVB19) as well as human herpesvirus 6 (HHV6) have entered the arena. We describe autopsy findings of a patient who had a lethal myocarditis with haemophagocytic lympho‐histiocytosis in a course of systemic PVB19 infection. The present case illustrates the unusually severe and rapid course of PVB19 myocarditis with associated haemophagocytic lympho‐histiocytosis leading to death.
Amino Acid Changes at Positions 173 and 187 in the Human T-Cell Leukemia Virus Type 1 Surface Glycoprotein Induce Specific Neutralizing Antibodies

ABSTRACT The nucleotide sequence of human T-cell leukemia virus type 1 (HTLV-1) is highly conserved, most strains sharing at least 95% sequence identity. This sequence conservation is also found in the viral env gene, which codes for the two envelope glycoproteins that play a major role in the induction of a protective immune response against the virus. However, recent reports have indicated that some variations in env sequences may induce incomplete cross-reactivity between HTLV-1 strains. To identify the amino acid changes that might be involved in the antigenicity of neutralizable epitopes, we constructed expression vectors coding for the envelope glycoproteins of two HTLV-1 isolates (2060 and 2072) which induced human antibodies with different neutralization patterns. The amino acid sequences of the envelope glycoproteins differed at four positions. Vectors coding for chimeric or point-mutated envelope proteins were derived from 2060 and 2072 HTLV-1 env genes. Syncytium formation induced by the wild-type or mutated envelope proteins was inhibited by human sera with different neutralizing specificities. We thus identified two amino acid changes, I173→V and A187→T, that play an important role in the antigenicity of neutralizable epitopes located in this region of the surface envelope glycoprotein.
Social Interactions and Subjective Well-Being: Evidence from Latin America

In this paper, we seek to examine the effect of comparisons and social capital on subjective well-being. Furthermore, we test if, through social influence and exposure, social capital is either an enhancer or appeaser of the comparison effect. Using the Latinobarometro Survey (2007) we find that in contrast to most previous studies, the comparison effect on well-being is positive; that is, the better others perform, the happier the individual is. We also find that social capital is among the strongest correlates of individuals’ subjective well-being in Latin American countries. Furthermore, our findings suggest that social contacts may enhance the comparison effect on individual’s happiness, which is more intense for those who perform worse in their reference group.
NAD(P)H oxidase isoform Nox2 plays a prosurvival role in human leukaemia cells

The mechanism involved in the prosurvival effect of interleukin-3 on the human acute myeloid leukaemia cell line M07e is investigated. A decrease in intracellular reactive oxygen species (ROS) content, glucose transport activity and cell survival was observed in the presence of inhibitors of plasma membrane ROS sources, such as diphenylene iodonium and apocynin, and by small interference RNA for Nox2. Moreover, IL-3 incubation stimulated the synthesis of Nox2 cytosolic sub-unit p47phox and glucose transporter Glut1. Thus, the inhibition of ROS generation by Nox inhibitors stimulated apoptosis showing that ROS production, induced by IL-3 via Nox2, protects leukaemic cells from cell death. Also incubation with receptor tyrosine kinase inhibitors, such as anti-leukaemic drugs blocking the stem cell factor receptor (c-kit), showed similar effects, hinting that IL-3 transmodulates c-kit phosphorylation. These mechanisms may play an important role in acute myeloid leukaemia treatment, representing a novel therapeutic target.
Nitrate Reduction Functional Genes and Nitrate Reduction Potentials Persist in Deeper Estuarine Sediments. Why?

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases.
Proteomic exploration of pancreatic islets in mice null for the α2A adrenergic receptor

The present studies extend recent findings that mice null for the 2A adrenergic receptor (2A AR KO mice) lack suppression of exogenous secretagogue-stimulated insulin secretion in response to 2 AR agonists by evaluating the endogenous secretagogue, glucose, ex vivo, and providing in vivo data that baseline insulin levels are elevated and baseline glucose levels are decreased in 2A AR KO mice. These latter findings reveal that the 2A AR subtype regulates glucose-stimulated insulin release in response to endogenous catecholamines in vivo. The changes in 2A AR responsiveness and resultant changes in insulin/glucose homeostasis encouraged us to utilize proteomics strategies to identify possible 2A AR downstream signaling molecules or other resultant changes due to perturbation of 2A AR expression. Although agonist stimulation of islets from wild type (WT) mice did not significantly alter islet protein profiles, several proteins were enriched in islets from 2A AR KO mice when compared with those from WT mice, including an enzyme participating in insulin protein processing. The present studies document the important role of the 2A AR subtype in tonic suppression of insulin release in response to endogenous catecholamines as well as exogenous 2 agonists and provide insights into pleiotropic changes that result from loss of 2A AR expression and tonic suppression of insulin release.
No Effect of Added Sugar Consumed at Median American Intake Level on Glucose Tolerance or Insulin Resistance

Excess sugar consumption may promote adverse changes in hepatic and total body insulin resistance. Debate continues over the effects of sugars at more typically consumed levels and whether the identity of the sugar consumed is important. In the present study participants (20–60 years old) were randomly assigned to one of five groups, three that consumed low fat milk with added fructose containing sugars in amounts equivalent to the 50th percentile of fructose consumption (US), one which consumed low-fat milk sweetened with glucose, and one unsweetened low-fat milk control group. The intervention lasted ten weeks. In the entire study population there was less than 1 kg increase in weight (73.6 ± 13.0 vs. 74.5 ± 13.3 kg, p < 0.001), but the change in weight was comparable among groups (p > 0.05). There were no changes in fasting glucose (49 ± 0.4 vs. 5.0 ± 0.5 mmol/L), insulin (56.9 ± 38.9 vs. 61.8 ± 50.0 pmol/L), or insulin resistance, as measured by the Homeostasis Model Assessment method (1.8 ± 1.3 vs. 2.0 ± 1.5, all p > 0.05). These data suggest that added sugar consumed at the median American intake level does not produce changes in measures of insulin sensitivity or glucose tolerance and that no sugar has more deleterious effects than others.
Learning skeletons for shape and pose

In this paper a method for estimating a rigid skeleton, including skinning weights, skeleton connectivity, and joint positions, given a sparse set of example poses is presented. In contrast to other methods, we are able to simultaneously take examples of different subjects into account, which improves the robustness of the estimation. It is additionally possible to generate a skeleton that primarily describes variations in body shape instead of pose. The shape skeleton can then be combined with a regular pose varying skeleton. That way pose and body shape can be controlled simultaneously but separately. As this skeleton is technically still just a skinned rigid skeleton, compatibility with major modelling packages and game engines is retained. We further present an approach for synthesizing a suitable bind shape that additionally improves the accuracy of the generated model.
Defragmenting DHT-based Distributed File Systems

Existing DHT-based file systems use consistent hashing to assign file blocks to random machines. As a result, a user task accessing an entire file or multiple files needs to retrieve blocks from many different machines. This paper demonstrates that significant availability and performance gains can be achieved if instead, users are able to retrieve all the data needed for a given task from only a few DHT nodes. We explore the design and implications of such a "defragmented" DHT-based distributed file system, called D2, that also maintains important DHT properties like storage load balance. We show using real-world file system traces that a simple key encoding scheme is sufficient to maintain good defragmentation for most user tasks. Using both simulation and an actual 1,000 node deployment, we show that D2 increases availability by over an order of magnitude and improves user-perceived latency by 30- 100% compared to a traditional design.
Impact by an orthogonal metal grid upon differential- and common-mode characteristics of coupled lines in PCB technology structures

This paper deals with a rigorous study of the impact by perpendicular metal grids on the characteristics of microstrip and coplanar coupled transmission lines. An electromagnetic analysis shows the variations of the propagation parameters in common and differential modes for each type of lines, in the presence of a metal grid. As transmission zeroes are liable to occur at certain frequencies, in particular in the common mode, we investigated the part played by the most influential grid parameters on these disturbances.
Absolute configuration of 3β-acetoxyolean-11,12-aziridin-28,13-β-olide

The title compound, C32H49NO4, has been isolated from the dichloromethane extract of the stem bark of Garcinia atroviridis Griff. ex T. Anders. Rings A and B, B and C, and C and D are trans-fused, whereas rings D and E are cis-fused. Rings A, B, C and E have slightly distorted chair conformations, while ring D is most heavily distorted towards a half-chair conformation owing to the strain induced by the lactonization. The ester group attached to ring A is in an equatorial position.
Effect of long-term monitoring of glycosylated hemoglobin levels in insulin-dependent diabetes mellitus.

BACKGROUND The value of routine measurements of glycosylated hemoglobin (hemoglobin A1c) in the care of patients with diabetes mellitus is uncertain. We undertook this study to determine whether knowledge of hemoglobin A1c values would result in improved metabolic control in a group of patients with insulin-dependent diabetes mellitus (IDDM). METHODS We randomly assigned 240 patients with IDDM to one of two groups that were comparable in age, sex, duration of diabetes, and initial hemoglobin A1c levels. The patients were followed for a year, and the hemoglobin A1c concentration was measured at three-month intervals. The hemoglobin A1c values were used in assessing glycemic control and modifying therapy in one of the two groups. In the other, care givers were not aware of the hemoglobin A1c levels and relied on blood or urine glucose measurements to monitor treatment. RESULTS Among the 222 patients still being followed after one year, the mean hemoglobin A1c value decreased significantly--from 10.1 to 9.5 percent (P less than 0.005)--in the group whose hemoglobin A1c level was monitored (n = 115), whereas the initial and one-year values in the control group (n = 107) were 10.0 and 10.1 percent, respectively. The proportion of patients with poor control, defined as those having a hemoglobin A1c value above 10.0 percent, decreased from 46 to 30 percent (P less than 0.01) in the group whose hemoglobin A1c level was monitored but did not change significantly (45 to 50 percent) in the control group. The patients in the group whose hemoglobin A1c level was monitored were seen and their insulin regimens changed more often, but they were hospitalized for acute care of their diabetes less often than those in the control group. A similar decrease in hemoglobin A1c values occurred in the control group in the following year, when their care givers knew their hemoglobin A1c values. CONCLUSIONS Regular measurements of hemoglobin A1c lead to changes in diabetes treatment and improvement of metabolic control, indicated by a lowering of hemoglobin A1c values.
New vaccinia virus recombination plasmids incorporating a synthetic late promoter for high level expression of foreign proteins.

(1990) New vaccinia virus recombination plasmids incorporating a synthetic late promoter for high level expression of foreign proteins. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge The content must not be changed in any way or reproduced in any format or medium without the formal permission of the copyright holder(s) When referring to this work, full bibliographic details must be given Vaccinia virus has found considerable utility as a vector for expressing foreign genes in eukaryotic cells. Foreign genes may be regulated by early or late vaccinia promoters, but much higher levels of expression may be achieved with the latter (1,2). Based on a detailed analysis of vaccinia late promoters, we designed a synthetic promoter that is at least half as strong again as the most active poxvirus natural late promoters presently used in expression systems (3). We describe here a pair of recombination plasmids incorporating this powerful late promoter. The plasmids, pMJ601 and pMJ602, are 7.2 kbp in size, and comprise a cassette inserted into the EcoRI site of the vaccinia virus thymidine kinase (TK) gene, which is carried on a portion of pBR328 that includes the betalactamase gene. They were made by insertion of synthetic oligonucleotide duplexes into a parental plasmid, pMJ7 (4). The cassette consists of the powerful late promoter immediately upstream from a multiple cloning site (MCS) containing 11 unique restriction endonuclease sites and lacking ATG codons, followed by lacZ under the control of the vaccinia 7.5-kD early promoter. The two plasmids differ only in the orientation of the MCS. Features of pMJ601 and the sequence upstream oflacZ are shown in Fig. 1. The mRNA starts within the indicated AAA sequence, and contains a poly(A) leader. A DNA fragment containing a continuous ATG-initiated open reading frame may be inserted into the MCS, and the resulting cassette recombined into the vaccinia virus genome at the TK locus (4). Recombinant virus may be isolated by selecting for lack of TK expression and by screening for expression of betagalactosidase from lacZ (4). We have used pMJ601 and pMJ602 to construct several recombinant viruses that express herpesvirus proteins. As an example, Fig. 2 shows the proteins expressed by two recombinant viruses. The virus made using the parental plasmid pMJ601 expressed betagalactosidase at a high level (lane 1) because, in the absence of an insert, lacZ is regulated by both the powerful late …
How to Build a System that Manages Bioinformatics Content

We discuss how to build systems with sophisticated features based on a core set of bioinformatics tool s. Beside from being the front-end server to the core analyses, such a system can manage users, bioinform atics content and shared data. Using tools available in the open-source community, we show how to build a syste m with such sophisticated features with a relatively minimal effort, especially in comparison to building such a system from scratch. We discuss the notion of Model-Conte nt Management-View, under whose framework similar applications with such desirable features beyond th e field Bioinformatics can be built. Our system can be vi ewed at http://cetus.cs. memphis.edu/rnamotif
Inhibition of Hepatitis C Virus Replication by Arsenic Trioxide

ABSTRACT Hepatitis C virus (HCV) is a serious global problem, and present therapeutics are inadequate to cure HCV infection. In the present study, various antiviral assays show that As2O3 at submicromolar concentrations is capable of inhibiting HCV replication. The 50% effective concentration (EC50) of As2O3 required to inhibit HCV replication was 0.35 μM when it was determined by a reporter-based HCV replication assay, and the EC50 was below 0.2 μM when it was determined by quantitative reverse transcription-PCR analysis. As2O3 did not cause cellular toxicity at this concentration, as revealed by an MTS [3-(4,5-dimethylthiozol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt] assay. A combination of As2O3 and alpha interferon exerted synergistic effects against HCV, as revealed by a multiple linear logistic model and isobologram analysis. Furthermore, in an alternative HCV antiviral system that may recapitulate additional steps involved in HCV infection and replication, As2O3 at 0.3 μM totally abolished the HCV signal, whereas alpha interferon at a high dose (5,000 IU/ml) only partially suppressed the HCV signal. The study highlights the indications for use of a novel class of anti-HCV agent. Further elucidation of the exact antiviral mechanism of As2O3 may lead to the development of agents with potent activities against HCV or related viruses.