Miracle-dz/UniFAR-FTUs huggingface dataset:
Armored Long RNA Controls or Standards for Branched DNA Assay for Detection of Human Immunodeficiency Virus Type 1

ABSTRACT The branched DNA (bDNA) assay is a reliable method for quantifying the RNA of human immunodeficiency virus type 1 (HIV-1). The positive controls and standards for this assay for the detection of HIV-1 consist of naked RNA, which is susceptible to degradation by RNase. Armored RNA is a good candidate for an RNase-resistant positive control or standard. However, its use has been limited by the maximal length of the exogenous RNA packaged into virus-like particles by routine armored RNA technology. In the present study, we produced armored long RNA (armored L-RNA) controls or standards (AR-HIV-pol-3034b) for a bDNA assay of HIV-1 by increasing the amount and affinity of the pac sites (the pac site is a specific 19-nucleotide stem-loop region located at the 5′ terminus of the MS2 bacteriophage replicase gene) by a one-plasmid double-expression system. AR-HIV-pol-3034b was completely resistant to DNase and RNase, was stable in normal human EDTA-preserved plasma at 4°C for at least 6 months, and produced reproducible, linear results in the Versant HIV-1 RNA 3.0 assay. In conclusion, AR-HIV-pol-3034b could act as a positive control or standard in a bDNA assay for the detection of HIV-1. In addition, the one-plasmid double-expression system can be used as a better platform than the one-plasmid expression system and the two-plasmid coexpression system for expressing armored L-RNA.
Phase 2 randomized safety and efficacy trial of nebulized denufosol tetrasodium in cystic fibrosis.

RATIONALE Denufosol tetrasodium is a selective P2Y(2) agonist that enhances mucosal hydration and mucus clearance by activating Cl(-) secretion and inhibiting epithelial Na(+) transport through a non-cystic fibrosis transmembrane conductance regulator mechanism in the lung. OBJECTIVES To examine the safety and efficacy of 28 days of treatment with denufosol compared with placebo in patients with mild cystic fibrosis. METHODS The study was a randomized, double-blind, multi-center, 28-day, phase 2 clinical trial of denufosol tetrasodium inhalation solution (20, 40, or 60 mg) versus placebo (normal saline). Patients with screening FEV(1) >or= 75% of predicted normal value and not treated with inhaled antibiotics for the past 30 days were randomized to receive one of three doses of denufosol or placebo administered three times daily. MEASUREMENTS AND MAIN RESULTS Eighty-nine patients were randomized and received the study drug, 94% completed the study, and 98% were compliant with dosing. All treatments were generally well tolerated, with no dose-response trends observed with respect to safety parameters. The most common adverse event was cough (52% of placebo patients and 47% of denufosol patients). Five patients discontinued early due to adverse events, two on placebo and three on denufosol. Denufosol patients (pooling active doses) had significantly higher changes from baseline in FEV(1) (P = 0.006), FEF(25%-75%) (P = 0.008), FVC (P = 0.022), and FEV(1)/FVC (P = 0.047) than placebo patients at the end of the study. CONCLUSIONS Denufosol administered three times daily for 28 days appeared to be safe and well tolerated in this population with mild cystic fibrosis and provided preliminary evidence of potential benefit in lung function.
An Opsonizing Monoclonal Antibody That Recognizes a Noncapsular Epitope Expressed on Cryptococcus neoformans

ABSTRACT A mouse hybridoma secreting a monoclonal antibody (MAb) that bound a noncapsular epitope expressed on C. neoformans was developed by immunizing BALB/c mice with formalin-killed serotype A yeasts. The hybridoma, designated CSFi, secreted an immunoglobulin G2b MAb that reacted with all C. neoformans serotypes tested, including the acapsular mutant ATCC 52817 (Cap67). Postsectioned immune electron microscopy revealed extensive binding of the MAb to the cell walls of both encapsulated and acapsular yeasts. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis of secreted antigens recovered from concentrated culture supernatants from both encapsulated and acapsular strains was conducted. The results showed that this MAb bound predominantly to antigens with molecular masses of approximately 75 and 100 kDa. A competitive enzyme-linked immunosorbent assay was used to demonstrate that the MAb was not cross-reactive with purified glucuronoxylomannan derived from either serotypes A or D. Experiments conducted with mouse peritoneal phagocytes and the mouse phagocyte-like cell line, J774A.1, demonstrated that the CSFi MAb opsonized the yeasts and increased their adherence to both types of phagocytic cells. We conclude, therefore, that antibodies directed at noncapsular epitopes can serve as opsonins and may have a role in modulating cryptococcal infection.
Effects of Nonresponse on the Mean Squared Error of Estimates from a Longitudinal Study

and Background Research in this study focuses on two related aspects of unit nonresponse (nonresponse by sampled members of study populations) in the rounds of the National Longitudinal Study of Adolescent Health (Add Health) (Chantala and Tabor, 1999): (i) round-specific nonresponse bias and its component contributions, and (ii) the statistical utility of alternative approaches to adjusting sample weights for nonresponse. This work is part of four research studies funded by CDC-NCHS, at the UNC Center for Health Statistics Research. Nonrespondents in surveys can be classified according to the reason for nonresponse (Lessler and Kalsbeek, 1992): 1) Not Solicited (NS): Sample members are not solicited as perhaps their address is unknown, or they are out of the country; 2) Solicited but Unable (SUA): Sample members are contacted but decline to participate based on inability. Reasons include physical or language limitations; 3) Solicited but Unwilling (SUW): Sample members are contacted but refuse to participate for reasons such as lack of time or, apathy; and 4) Other Nonrespondents (OTH): Sample nonrespondents give a reason that does not fit in any of the previous categories. Examples are lost schedules and partial respondents Response outcome information and data to obtain 13 different measures of health risk from Add Health are used to accomplish two main tasks in this study. First, we estimate the round-specific nonresponse bias and its component contributions corresponding to the four nonresponse categories described. The sign (negative or positive) of these components and the offsetting effects of some components on the overall bias is of particular interest. Second, we compare the statistical effects of alternate sample adjustments for nonresponse on the bias and variance of study estimates. It is important to note here that we are examining the effects of nonresponse in IH1 and IH2 separately, and not the cumulative effects of nonresponse through these rounds.
Volume Shrinkage of Bone, Brain and Muscle Tissue in Sample Preparation for Micro-CT and Light Sheet Fluorescence Microscopy (LSFM)

Abstract Two methods are especially suited for tomographic imaging with histological detail of macroscopic samples that consist of multiple tissue types (bone, muscle, nerve or fat): Light sheet (based) fluorescence microscopy (LSFM) and micro-computed tomography (micro-CT). Micro-CT requires staining with heavy chemical elements (and thus fixation and sometimes dehydration) in order to make soft tissue imageable when measured alongside denser structures. LSMF requires fixation, decalcification, dehydration, clearing and staining with a fluorescent dye. The specimen preparation of both imaging methods is prone to shrinkage, which is often not mentioned, let alone quantified. In this paper the presence and degree of shrinkage are quantitatively identified for the selected preparation methods/stains. LSFM delivers a volume shrinkage of 17% for bone, 56% for muscle and 62% for brain tissue. The three most popular micro-CT stains (phosphotungstic acid, iodine with potassium iodide, and iodine in absolute ethanol) deliver a volume shrinkage ranging from 10 to 56% for muscle and 27–66% for brain, while bone does not shrink in micro-CT preparation.
Homologous recombination between single-stranded DNA and chromosomal genes in Saccharomyces cerevisiae

Transformation of Saccharomyces cerevisiae strains was examined by using the URA3 and TRP1 genes cloned into M13 vectors in the absence of sequences capable of promoting autonomous replication. These constructs transform S. cerevisiae cells to prototrophy by homologous recombination with the resident mutant gene. Single-stranded DNA was found to transform S. cerevisiae cells at efficiencies greater than that of double-stranded DNA. No conversion of single-stranded transforming DNA into duplex forms could be detected during the transformation process, and we conclude that single-stranded DNA may participate directly in recombination with chromosomal sequences. Transformation with single-stranded DNA gave rise to both gene conversion and reciprocal exchange events. Cotransformation with competing heterologous single-stranded DNA specifically inhibited transformation by single-stranded DNA, suggesting that one of the components in the transformation-recombination process has a preferential affinity for single-stranded DNA.
Managing Blame: An Experimental Test of the Effects of Political Accounts

Public officials are not passive bystanders in the electoral process. Rather, they actively try to shape or manage citizens' perceptions of events (particularly those involving negative outcomes) through explanations or accounts. I argue that consideration of citizens' understandings of political accountability and how these are shaped by public officials represent critical missing components of models of electoral behavior. The distinction between excuses and justifications provides a valuable conceptual framework for understanding the impact of political accounts on a variety of judgments and psychological processes. I examine satisfaction with various excuses and justifications and their impact on subsequent evaluations of the official.
Enhanced decomposition based evolutionary algorithm for solving unit commitment problem in uncertain environment

In this paper, a modified decomposition based evolutionary algorithm (DBEA) has been proposed to solve the unit commitment (UC) problem in uncertain environment as a multi-objective optimization problem considering cost, emission, and reliability as the multiple objectives. The uncertainties occurring due to thermal generator outage and load forecast error are incorporated using expected energy not served (EENS) reliability index. Further, a neighborhood based recombination approach has been incorporated to enhance the performance of DBEA. Experimental results are presented on two different test systems to demonstrate the effectiveness of the proposed approach.
A Multi-criteria Decision-making Approach for Prioritizing Reverse Logistics Adoption Barriers under Fuzzy Environment: Case of Indian Electronics Industry

Reverse logistics (RL) practices are gaining attention due to environmental and waste disposal issues, enforced law, rapidly changing technologies and corporate social concern. Reverse logistics has been seen as a part of sustainable development due to reduction in pollution by using a product again after the end of its life. The goal of this article is to evaluate and rank the barriers of RL implementation so that companies can design strategies to tackle them on a priority basis. This article proposes multi-criteria decision-making (MCDM) model based on fuzzy analytic hierarchy process (FAHP) to prioritize the barriers of RL adoption. The proposed approach is revealed by empirical case of Indian electronics industry. This proposed method considered fuzzy framework that can handle impreciseness and uncertainty easily. Totally, 38 barriers were identified through literature review and experts’ opinions. These barriers were classified into seven major criteria. The result of the study indicates that customer acuity about RL, lack of coordination/collaboration with third-party logistics (3PL) providers and uncertain quality and timing of return are the three most important barriers of RL adoption. Organizations should overcome these barriers on a priority basis for effective RL adoption. Finally, the robustness of the model is checked by sensitivity analysis.
The influence of amplifier, interface and biological noise on signal quality in high-resolution EEG recordings

First, the intrinsic random noise sources of a biopotential measurement in general are reviewed. For the special case of an electroencephalographic (EEG) measurement we have extended the commonly used amplifier noise model by biological generated background noise. As the strongest of all noise sources involved will dominate the resulting signal to noise ratio (S/N), we have investigated under which conditions this will be the case. We illustrate experimentally that up to 100 Hz S/N practically depends only on cortical generated background noise, while at a few hundred Hz or more amplifier and thermal noise of interelectrode resistance are the major sources.
Reusing OE-Scheduler in Aperiodic Environments

OEA-scheduler is a scheduler that generates a schedule of aperiodic tasks and periodic tasks by the principle of eliminating unnecessary context switches under the rate monotonic algorithm. This new scheduler will minimize the average response time of aperiodic tasks and also guarantee the hard deadlines of an arbitrary number of periodic tasks in hard real-time environments. In previous research, the OE-scheduler was developed to schedule periodic tasks only, and later improved to use object-oriented methods. Due to the object-oriented approach, the authors have been able to reuse the OE-scheduler algorithm and extend it to work with both periodic tasks and aperiodic tasks. An object oriented design of the scheduler will be presented, along with an implementation result
Characterization of a new lipopeptide surfactant produced by thermotolerant and halotolerant subsurface Bacillus licheniformis BAS50

Strain BAS50, isolated from a petroleum reservoir at a depth of 1,500 m and identified as Bacillus licheniformis, grew and produced a lipopeptide surfactant when cultured on a variety of substrates at salinities of up to 13% NaCl. Surfactant production occurred both aerobically and anaerobically and was optimal at 5% NaCl and temperatures between 35 and 45 degrees C. The biosurfactant, termed lichenysin A, was purified and chemically characterized. A tentative structure and composition for the surfactant are described. Lichenysin A is a mixture of lipopeptides, with the major components ranging in size from 1,006 to 1,034 Da. The lipid moiety contains a mixture of 14 linear and branched beta-hydroxy fatty acids ranging in size from C12 to C17. There are seven amino acids per molecule. The peptide moiety is composed of the following amino acids: glutamic acid as the N-terminal amino acid, asparagine, valine, leucine, and isoleucine as the C-terminal amino acid, at a ratio of 1.1:1.1:1.0:2.8:1.0, respectively. Purified lichenysin A decreases the surface tension of water from 72 mN/m to 28 mN/m and achieves the critical micelle concentration with as little as 12 mg/liter, characterizing the product as a powerful surface-active agent that compares favorably to others surfactants. The antibacterial activity of lichenysin A has been demonstrated.
The Binding of Receptor-recognized α2-Macroglobulin to the Low Density Lipoprotein Receptor-related Protein and the α2M Signaling Receptor Is Decoupled by Oxidation*

Receptor-recognized forms of α2-macroglobulin (α2M*) bind to two classes of cellular receptors, a high affinity site comprising approximately 1500 sites/cell and a lower affinity site comprising about 60,000 sites/cell. The latter class has been identified as the so-called low density lipoprotein receptor-related protein (LRP). Ligation of receptors distinct from LRP activates cell signaling pathways. Strong circumstantial evidence suggests that the high affinity binding sites are responsible for cell signaling induced by α2M*. Using sodium hypochlorite, a powerful oxidant produced by the H2O2-myeloperoxidase-Cl− system, we now demonstrate that binding to the high affinity sites correlates directly with activation of the signaling cascade. Oxidation of α2M* using 200 μm hypochlorite completely abolishes its binding to LRP without affecting its ability to activate the macrophage signaling cascade. Scatchard analysis shows binding to a single class of high affinity sites (K d − 71 ± 12 pm). Surprisingly, oxidation of native α2-macroglobulin (α2M) with 125 μm hypochlorite results in the exposure of its receptor-binding site to LRP, but the ligand is unable to induce cell signaling. Scatchard analysis shows binding to a single class of lower affinity sites (K d − 0.7 ± 0.15 nm). Oxidation of a cloned and expressed carboxyl-terminal 20-kDa fragment of α2M (RBF), which is capable of binding to both LRP and the signaling receptor, results in no significant change in its binding K d , supporting our earlier finding that the oxidation-sensitive site is predominantly outside of RBF. Attempts to understand the mechanism responsible for the selective exposure of LRP-binding sites in oxidized native α2M suggest that partial protein unfolding may be the most likely mechanism. These studies provide strong evidence that the high affinity sites (K d − 71 pm) are the α2M* signaling receptor.
Recommandation contextuelle d'utilisateurs pour les plateformes de micro-blogging

Les services de micro-blogging sont devenus recemment une source d’information importante. Cependant, victimes de leur succes, ils doivent actuellement gerer une quantite sans precedent d’informations generees par les utilisateurs. Il devient par consequent difﬁcile pour les utilisateurs de trouver dans ces services des contenus proches de leurs interets. Aﬁn de recommander des utilisateurs a suivre sur un sujet donne, nous proposons dans cet article des scores bases sur la topologie du graphe social ainsi que sur le contenu textuel des microblogs. Pour permettre le passage a l’echelle, nous presentons une approche qui s’appuie sur l’utilisation de landmarks pour pre-calculer des recommandations pour certains comptes choisis dans le graphe. Nos experiences conﬁrment la pertinence de notre score de recommandation par rapport a des approches existantes ainsi que le passage a l’echelle de notre algorithme base sur l’utilisation des landmarks.
Modular Multilevel Converter Machine Drive using current source H-bridges

This paper proposes a Machine Drive based on a Modular Multilevel Converter. The proposed converter uses current source cells with asymmetrical IGCTs as switching devices. A control scheme to manage the input and output current and, additionally, reduce the oscillations in the inductors currents is also proposed. The resulting machine drive will exhibit high power and high dynamical performance as shown in the simulation results.
Amino Acid Signatures to Evaluate the Beneficial Effects of Weight Loss

Aims. We investigated the relationship between circulating amino acid levels and obesity; to what extent weight loss followed by weight maintenance can correct amino acid abnormalities; and whether amino acids are related to weight loss. Methods. Amino acids associated with waist circumference (WC) and BMI were studied in 804 participants from the Malmö Diet and Cancer Cardiovascular Cohort (MDC-CC). Changes in amino acid levels were analyzed after weight loss and weight maintenance in 12 obese subjects and evaluated in a replication cohort (n = 83). Results. Out of the eight identified BMI-associated amino acids from the MDC-CC, alanine, isoleucine, tyrosine, phenylalanine, and glutamate decreased after weight loss, while asparagine increased after weight maintenance. These changes were validated in the replication cohort. Scores that were constructed based on obesity-associated amino acids and known risk factors decreased in the ≥10% weight loss group with an associated change in BMI (R2 = 0.16–0.22, p < 0.002), whereas the scores increased in the <10% weight loss group (p < 0.0004). Conclusions. Weight loss followed by weight maintenance leads to differential changes in amino acid levels associated with obesity. Treatment modifiable scores based on epidemiological and interventional data may be used to evaluate the potential metabolic benefit of weight loss.
Childhood adversity, adult stress, and the risk of major depression or generalized anxiety disorder in US soldiers: a test of the stress sensitization hypothesis

Background The stress sensitization theory hypothesizes that individuals exposed to childhood adversity will be more vulnerable to mental disorders from proximal stressors. We aimed to test this theory with respect to risk of 30-day major depressive episode (MDE) and generalized anxiety disorder (GAD) among new US Army soldiers. Methods The sample consisted of 30 436 new soldier recruits in the Army Study to Assess Risk and Resilience (Army STARRS). Generalized linear models were constructed, and additive interactions between childhood maltreatment profiles and level of 12-month stressful experiences on the risk of 30-day MDE and GAD were analyzed. Results Stress sensitization was observed in models of past 30-day MDE (χ2 8 = 17.6, p = 0.025) and GAD (χ2 8 = 26.8, p = 0.001). This sensitization only occurred at high (3+) levels of reported 12-month stressful experiences. In pairwise comparisons for the risk of 30-day MDE, the risk difference between 3+ stressful experiences and no stressful experiences was significantly greater for all maltreatment profiles relative to No Maltreatment. Similar results were found with the risk for 30-day GAD with the exception of the risk difference for Episodic Emotional and Sexual Abuse, which did not differ statistically from No Maltreatment. Conclusions New soldiers are at an increased risk of 30-day MDE or GAD following recent stressful experiences if they were exposed to childhood maltreatment. Particularly in the military with an abundance of unique stressors, attempts to identify this population and improve stress management may be useful in the effort to reduce the risk of mental disorders.
Differential Roles of ASK1 and TAK1 in Helicobacter pylori-Induced Cellular Responses

ABSTRACT The mitogen-activated protein kinase (MAPK) signaling pathway regulates various cellular functions, including those induced by Helicobacter pylori. TAK1 is an upstream MAPK kinase kinase (MAP3K) required for H. pylori-induced MAPK and NF-κB activation, but it remains unclear whether other MAP3Ks are involved in H. pylori-induced cellular responses. In this study, we focused on the MAP3K ASK1, which plays a critical role in gastric tumorigenesis. In gastric epithelial cells, H. pylori activates ASK1 in a reactive oxygen species (ROS)- and cag pathogenicity island-dependent manner, and ASK1 regulates sustained JNK activation and apoptosis induced by H. pylori. In contrast, TAK1 regulates H. pylori-mediated early JNK activation and cytokine production. We also found reciprocal regulation between ASK1 and TAK1 in H. pylori-related responses, whereby inhibition of TAK1 or downstream p38 MAPK activates ASK1 through ROS production, and ASK1 suppresses TAK1 and downstream NF-κB activation. We identified ROS/ASK1/JNK as a new signaling pathway induced by H. pylori, which regulates apoptotic cell death. The balance of ASK1-induced apoptosis and TAK1-induced antiapoptotic or inflammatory responses may determine the fate of epithelial cells infected with H. pylori and thus be involved in the pathogenesis of gastritis and gastric cancer.