Miracle-dz/UniFAR-FTUs huggingface dataset:
Addition of a Missense Mutation Present in the L Gene of Respiratory Syncytial Virus (RSV) cpts530/1030 to RSV Vaccine Candidate cpts248/404 Increases Its Attenuation and Temperature Sensitivity

ABSTRACT Respiratory syncytial virus (RSV) cpts530/1030 is an attenuated, temperature-sensitive subgroup A vaccine candidate derived previously from cold-passaged RSV (cpRSV) by two sequential rounds of chemical mutagenesis and biological selection. Here,cpts530/1030 was shown to be highly attenuated in the upper and lower respiratory tracts of seronegative chimpanzees. However, evaluation in seropositive children showed that it retains sufficient replicative capacity and virulence to preclude its direct use as a live attenuated vaccine. Nucleotide sequence analysis of the genome of cpts530/1030 showed that it had acquired two nucleotide substitutions (compared to its cpts530 parent), both of which were in the L gene: a silent mutation at nucleotide position 8821 (amino acid 108) and a missense mutation at nucleotide position 12458 resulting in a tyrosine-to-asparagine change at amino acid 1321, herein referred to as the 1030 mutation. It also contained the previously identified 530 missense mutation at nucleotide 10060 in the L gene. The genetic basis of attenuation ofcpts530/1030 was defined by the introduction of the 530 and 1030 mutations into a cDNA clone of cpRSV, from which recombinant RSV was derived and analyzed to determine the contribution of each mutation to the temperature sensitivity (ts) and attenuation (att) phenotypes of cpts530/1030. The 530 mutation, derived from cpts530, was previously shown to be responsible for the ts and attphenotypes of that virus. In the present study, the 1030 mutation was shown to be responsible for the increased temperature sensitivity ofcpts530/1030. In addition, the 1030 mutation was shown to be responsible for the increased level of attenuation ofcpts530/1030 in the upper and lower respiratory tracts of mice. The 530 and 1030 mutations were additive in their effects on thets and att phenotypes. It was possible to introduce the 1030 mutation, but not the 530 mutation, into an attenuated vaccine candidate with residual reactogenicity in very young infants, namely, cpts248/404, by use of reverse genetics. The inability to introduce the 530 mutation into thecpts248/404 virus was shown to be due to its incompatibility with the 248 missense mutation at the level of L protein function. The resulting rA2cp248/404/1030 mutant virus was more temperature sensitive and more attenuated than thecpts248/404 parent virus, making it a promising new RSV vaccine candidate created by use of reverse genetics to improve upon an existing vaccine virus.
Evaluating SQL-on-Hadoop for Big Data Warehousing on Not-So-Good Hardware

Big Data is currently conceptualized as data whose volume, variety or velocity impose significant difficulties in traditional techniques and technologies. Big Data Warehousing is emerging as a new concept for Big Data analytics. In this context, SQL-on-Hadoop systems increased notoriety, providing Structured Query Language (SQL) interfaces and interactive queries on Hadoop. A benchmark based on a denormalized version of the TPC-H is used to compare the performance of Hive on Tez, Spark, Presto and Drill. Some key contributions of this work include: the direct comparison of a vast set of technologies; unlike previous scientific works, SQL-on-Hadoop systems were connected to Hive tables instead of raw files; allow to understand the behaviour of these systems in scenarios with ever-increasing requirements, but not-so-good hardware. Besides these benchmark results, this paper also makes available interesting findings regarding an architecture and infrastructure in SQL-on-Hadoop for Big Data Warehousing, helping practitioners and fostering future research.
Exploded View Diagrams of 3D Grids

We present a system for creating interactive exploded view diagrams in generalized 3D grids. The primary difference between our approach and existing ones is that our technique neither requires geometrical information of the whole model nor any information regarding the relationship among model parts, instead our implementation depends on which grid cells are considered as object of interest, and which view angle to use. To achieve this, we introduce the Explosion Tree, a data structure closely related to a BSP tree, which supports the explosion view diagrams technique based on the relationship between disjoint convex polygons. In this paper we discuss the application of this technique to Corner-Point Grid which has been extensively used for geological modeling and flow simulation. All the data presented in this work consists of real data currently used in the industry.
Quadriceps Inhibition Induced by an Experimental Knee Joint Effusion Affects Knee Joint Mechanics during a Single-Legged Drop Landing

Background Arthrogenic quadriceps muscle inhibition accompanies knee joint effusion and impedes rehabilitation after knee joint injury. Hypothesis We hypothesized that an experimentally induced knee joint effusion would cause arthrogenic quadriceps muscle inhibition and lead to increased ground reaction forces, as well as sagittal plane knee angles and moments, during a single-legged drop landing. Study Design Controlled laboratory study. Methods Nine subjects (4 women and 5 men) underwent 4 conditions (no effusion, lidocaine injection, “low” effusion [30 mL], and “high” effusion [60 mL]) and then performed a single-legged drop landing. Lower extremity muscle activity, peak sagittal plane knee flexion angles, net sagittal plane knee moments, and peak ground reaction forces were measured. Results Vastus medialis and lateralis activity were decreased during the low and high effusion conditions (P < .05). However, increases in peak ground reaction forces and decreases in peak knee flexion angle and net knee extension moments occurred only during the high effusion condition (P < .05). Conclusions Knee joint effusion induced quadriceps inhibition and altered knee joint mechanics during a landing task. Subjects landed with larger ground reaction forces and in greater knee extension, thereby suggesting that more force will be transferred to the knee joint and its passive restraints when quadriceps inhibition is present. Clinical Relevance Knee joint effusion results in arthrogenic quadriceps muscle inhibition, increasing loading about the knee that may potentially increase the risk of future knee joint trauma or degeneration.
Biosynthesis, Post-translation Modification, and Functional Characterization of Drm/Gremlin*

Down-regulated bymos (Drm)/Gremlin is a highly conserved protein whose properties and expression pattern suggest a role in early development, tissue-specific differentiation, and cell transformation. We have investigated the biosynthesis and processing of Drm expressed endogenously in rat fibroblasts or overexpressed following transient or stable transfection. Analysis of metabolically labeled cells revealed that Drm exists in secreted and cell-associated forms that exhibit similar mobilities in SDS-polyacrylamide gel electrophoresis. Protein analysis indicated that Drm is present in two major species: a slow migrating glycosylated form and a nonglycosylated form. Both forms of Drm are able to undergo phosphorylation. Drm is released into the media within 30 min of synthesis and is detectable for up to 4–5 h, whereas the cell-associated form has a half-life of about 1 h. Confocal immunofluorescent microscopy indicates that Drm is present both on the external surface of expressing cells, as well as within the endoplasmic reticulum and the Golgi. Both glycosylated and nonglycosylated forms of Drm exhibit identical distributions and are able to antagonize bone morphogenetic protein signaling. Like the soluble form, the cell-associated forms are capable of binding125I-bone morphogenetic protein-4. These properties are consistent with a role for Drm in interfering with signaling and indicate that Drm may act at the cell surface during tissue development and transformation.
Optical forces: Some fundamentals and some surprises

We address the general problem of evaluating optical forces on general dielectric and magneto-dielectric materials. Our starting point is the familiar Lorentz force law and we exploit symmetries and physical reasoning to build up a complete theory. At the quantum level, this allows us to identify the mechanical properties of photons propagating through such media.
Cytosolic Proteins Regulate α-Synuclein Dissociation from Presynaptic Membranes*

Intracellular accumulation of insoluble α-synuclein in Lewy bodies is a key neuropathological trait of Parkinson disease (PD). Neither the normal function of α-synuclein nor the biochemical mechanisms that cause its deposition are understood, although both are likely influenced by the interaction of α-synuclein with vesicular membranes, either for a physiological role in vesicular trafficking or as a pathological seeding mechanism that exacerbates the propensity of α-synuclein to self-assemble into fibrils. In addition to the α-helical form that is peripherally-attached to vesicles, a substantial portion of α-synuclein is freely diffusible in the cytoplasm. The mechanisms controlling α-synuclein exchange between these compartments are unknown and the possibility that chronic dysregulation of membrane-bound and soluble α-synuclein pools may contribute to Lewy body pathology led us to search for cellular factors that can regulate α-synuclein membrane interactions. Here we reveal that dissociation of membrane-bound α-synuclein is dependent on brain-specific cytosolic proteins and insensitive to calcium or metabolic energy. Two PD-linked mutations (A30P and A53T) significantly increase the cytosol-dependent α-synuclein off-rate but have no effect on cytosol-independent dissociation. These results reveal a novel mechanism by which cytosolic brain proteins modulate α-synuclein interactions with intracellular membranes. Importantly, our finding that α-synuclein dissociation is up-regulated by both familial PD mutations implicates cytosolic cofactors in disease pathogenesis and as molecular targets to influence α-synuclein aggregation.
The close homologue of the neural adhesion molecule L1 (CHL1): patterns of expression and promotion of neurite outgrowth by heterophilic interactions

The close homologue of L1 (CHL1), a member of the L1 family of neural adhesion molecules, is first expressed at times of neurite outgrowth during brain development, and is detectable in subpopulations of neurons, astrocytes, oligodendrocyte precursors and Schwann cells of the mouse and rat. Aggregation assays with CHL1‐transfected cells show that CHL1 does not promote homophilic adhesion or does it mediate heterophilic adhesion with L1. CHL1 promotes neurite outgrowth by hippocampal and small cerebellar neurons in substrate‐bound and soluble form. The observation that CHL1 and L1 show overlapping, but also distinct patterns of synthesis in neurons and glia, suggests differential effects of L1‐like molecules on neurite outgrowth.
Structure of keyhole limpet hemocyanin type 1 (KLH1) at 15 A resolution by electron cryomicroscopy and angular reconstitution.

A three-dimensional reconstruction of keyhole limpet hemocyanin type 1 (KLH1) has been obtained using electron cryomicroscopy at liquid helium temperatures and single particle image processing. The use of a high-contrast embedding medium, 1% (w/v) glucose and 2% (w/v) ammonium molybdate (pH 7.0), enables high-resolution electron micrographs to be recorded close to focus, i.e. with excellent transfer of high-resolution information, while maintaining enough image contrast to localise the individual macromolecules in the images. When low-pass filtered to approximately 45 A resolution, the new 15 A resolution reconstruction is very similar to the earlier reconstructions of gastropodan hemocyanins of specimens embedded in vitreous ice. The map shows much detail and reveals many new symmetry elements in this very large cylindrical molluscan hemocyanin. The full KLH1 didecamer has D5 pointgroup symmetry, yet within the KLH1 decameric half-molecules local 2-fold axes have emerged that make the wall of the KLH1 decamer, in spite of its having an exact C5 symmetry only, resemble the D5-symmetric wall of the decameric cephalopod hemocyanins. In fact, the outside of each tier of this six-tiered gastropodan hemocyanin was found to have an approximate D5 symmetry. Local 2-fold axes also relate the "functional units" within the dimeric "morphological units" of the wall and the collar areas of the 8 MDa KLH1 molecule. Certain local-symmetry-related surface motifs may be present up to 60 times on the outside wall of this highly symmetric cylindrical hemocyanin. Keyhole limpet hemocyanin is used clinically as an immunostimulant. The very strong immune reaction elicited by this hemocyanin may be associated with its intricate hierarchy of local-symmetry components.
An LMI-Based Stabilization Criterion of Sliding Mode Control for a Class of Bilinear State-Delay Systems

This paper focuses on the problem of sliding mode control for delay-dependent stabilization criterion of bilinear state-delay systems. Based on the linear matrix inequality (LMI) method and a parameterized model transformation technique, we provide a sufficient condition for the existence of sliding surface and we give an explicit formula of sliding surface guaranteeing the asymptotic stability of the reduced-order equivalent system dynamics restricted to the sliding surface. The proposed stabilization criterion can also be applied to control the bilinear systems with time-varying delay. Finally, a simulation study shows that our method is effective and useful. Keywords—sliding mode control, delay-dependent stabilization criterion, bilinear state-delay systems, parameterized model transformation, sliding surface.
C-REACTIVE PROTEIN: SCREENING OF CORONARY ARTERY DISEASE

Coronary artery disease (CAD), the leading cause of death in the United States, resulted in 459,841 deaths in 1998 and accounted for one of every five deaths. CAD is the leading cause of premature and permanent disability in the United States and in 1997, $10.8 billion was paid by Medicare for CAD. Numerous studies suggest that inflammatory changes in the vessel walls initiate atherosclerosis. As the disease progresses, the atherosclerotic plaques erode, become unstable, and eventually rupture. Plaque rupture causes thrombosis and the acute coronary syndromes, unstable angina (UA) and acute myocardial infarction (MI). Due to this link between chronic, low-grade inflammation and CAD, researchers have investigated serum inflammatory markers, particularly, acute-phase reactants, to determine if their appearance correlates with the presence or extent of CAD.
Lithium Therapy Improves Neurological Function and Hippocampal Dendritic Arborization in a Spinocerebellar Ataxia Type 1 Mouse Model

Background Spinocerebellar ataxia type 1 (SCA1) is a dominantly inherited neurodegenerative disorder characterized by progressive motor and cognitive dysfunction. Caused by an expanded polyglutamine tract in ataxin 1 (ATXN1), SCA1 pathogenesis involves a multifactorial process that likely begins with misfolding of ATXN1, which has functional consequences on its interactions, leading to transcriptional dysregulation. Because lithium has been shown to exert neuroprotective effects in a variety of conditions, possibly by affecting gene expression, we tested the efficacy of lithium treatment in a knock-in mouse model of SCA1 (Sca1154Q/2Q mice) that replicates many features of the human disease. Methods and Findings Sca1154Q/2Q mice and their wild-type littermates were fed either regular chow or chow that contained 0.2% lithium carbonate. Dietary lithium carbonate supplementation resulted in improvement of motor coordination, learning, and memory in Sca1154Q/2Q mice. Importantly, motor improvement was seen when treatment was initiated both presymptomatically and after symptom onset. Neuropathologically, lithium treatment attenuated the reduction of dendritic branching in mutant hippocampal pyramidal neurons. We also report that lithium treatment restored the levels of isoprenylcysteine carboxyl methyltransferase (Icmt; alternatively, Pccmt), down-regulation of which is an early marker of mutant ATXN1 toxicity. Conclusions The effect of lithium on a marker altered early in the course of SCA1 pathogenesis, coupled with its positive effect on multiple behavioral measures and hippocampal neuropathology in an authentic disease model, make it an excellent candidate treatment for human SCA1 patients.
Using the Framework for Health Promotion Action to address staff perceptions of occupational health and safety at a fly-in/fly-out mine in north-west Queensland.

ISSUE ADDRESSED An exploratory descriptive study was undertaken to identify staff perceptions of the types and sources of occupational health and safety hazards at a remote fly-in-fly-out minerals extraction and processing plant in northwest Queensland. METHODS Ongoing focus groups with all sectors of the operation were conducted concurrently with quantitative research studies from 2001 to 2005. Action research processes were used with management and staff to develop responses to identified issues. RESULTS Staff identified and generated solutions to the core themes of: health and safety policies and procedures; chemical exposures; hydration and fatigue. The Framework for Health Promotion Action was applied to ensure a comprehensive and holistic response to identified issues. CONCLUSIONS Participatory processes using an action research framework enabled a deep understanding of staff perceptions of occupational health and safety hazards in this setting. The Framework for Health Promotion provided a relevant and useful tool to engage with staff and develop solutions to perceived occupational health and safety issues in the workplace.
Self-Efficacy as a Mediator of Children's Achievement Motivation and in-Class Physical Activity

The present study was designed to examine the mediating effect of self-efficacy on relations of middle school students' four achievement goals with their perceptions of two motivational climates and in-class physical activity in physical education. The four achievement goals (mastery-approach, mastery-avoidance, performance-approach, and performance-avoidance), perceptions of the motivational climate (mastery- and performance-involving climates), and self-efficacy were measured in a sample of 194 students (93 boys, 101 girls) in a public school. Students' in-class physical activity was assessed using Actical Accelerometers. A series of multiple-regression analyses supported the mediating effect of self-efficacy on the relationships among students' mastery-approach goal, perceived mastery-involving climate, and physical activity.
CELL RECONSTRUCTION UNDER VORONOI AND ENCLOSING ELLIPSES FROM 3 D MICROSCOPY

Cell occlusion, staining variation, particulate forms and diversity of cervical cells are some of the challenges in automating cervical cytology. This paper tackles some of these issues, including the detection of nucleus and cytoplasm from a new standardization for specimen preparation through mono/thin-layer technology. Our approach consists of three main steps: (a) rough segmentation of subcellular compartments using super pixel combined to Voronoi diagrams, (b) structural refinement of the cytoplasm boundary through calculus of variations, and (c) morphological reconstruction combined to optimization methods to determine minimum enclosing ellipse. We test our implementation on real 3D cervical cell images, containing several cells at different occlusion levels and variable contrast. Our results show both qualitative and quantitative assessment of the datasets, using a completely automated computer program. The quantitative performance presents average Dice Coefficient higher than 87%.
Physicians’ Attitude and Practices in Sickle Cell Disease Pain Management

Many physicians believe that patients with sickle cell disease (SCD) are more likely to become addicted to pain medication than are other patient populations. This study hypothesizes that physicians’ attitudes towards addiction in patients with SCD affects pain management practices. The Physician Attitudes Survey was sent to 286 physicians at seven National Institutes of Health-funded university-based comprehensive sickle cell centres. The survey assessed demographic information; and physician's attitudes toward and knowledge of pain, pain treatment, and drug addiction and abuse. Significant Pearson product-moment correlations were found between attitudes towards pain and beliefs regarding addiction to prescribed opioids. Physicians reported varied pain management strategies, however, many believe that attitudes toward addiction and to patients in pain crises may result in undertreatment of pain. These results indicate that physicians might benefit from additional education regarding sickle cell disease, addiction to pain medication, the pharmacology of opioids, and the assessment and treatment of pain.
Effects of the home environment on school-aged children's sleep.

STUDY OBJECTIVE Examine the relationship between the sleep behavior of elementary school-aged children and characteristics of the home environment. DESIGN Cross-sectional analysis of children participating in a cohort study. SETTING Cleveland Children's Sleep and Health Study, an ethnically mixed, urban, community-based cohort. PARTICIPANTS Four hundred forty-nine children (50% girls, 46% African-American) aged 8 to 11 years. MEASUREMENTS AND RESULTS Sleep and health data were obtained from a child-completed 7-day sleep journal and caregiver-completed health and sleep questionnaire. Home-environment predictors were Middle-Childhood Home Observation for Measurement of the Environment (MC-HOME) total score and Encouragement of Maturity and Physical Environment subscale scores. Sleep outcomes were mean nightly sleep duration, night-to-night variation in sleep duration, and bedtime of 11 PM or later. Adjusted analyses showed that higher Encouragement of Maturity subscale scores were associated with longer sleep duration (P < .05) and decreased odds of a bedtime at 11 PM or later (odds ratio = .74, 95% confidence interval, .58-.95). In girls, higher Encouragement of Maturity scores were also associated with decreased nightly variation in mean sleep duration (P < .001). Increases in total MC-HOME score were associated with increased mean sleep duration among African-American children only (P < .05). CONCLUSION Collectively, results indicate that a parenting style encouraging social maturity in children is linked to healthier sleep patterns.
Design of a Real-Time Security Assessment Tool for Situational Awareness Enhancement in Modern Power Systems

Detailed security analysis for N-k contingencies (k = 1, 2, 3, .) in a real-time setting is still a great challenge due to the significant computational burden. This paper takes advantage of phasor measurement units (PMUs) and decision trees (DTs) to develop a real-time security assessment tool to assess four important post-contingency security issues, including voltage magnitude violation (VMV), thermal limit violation (TV), voltage stability (VS) and transient stability (TS). The proposed scheme is tested on the Salt River Project (SRP) power system represented by a series of operating conditions (OCs) during a representative day. The properly trained DTs demonstrate excellent prediction performance. Robustness tests for the offline trained DTs are performed on a group of changed OCs that were not included for training the DTs and the idea of tuning critical system attributes for preventive controls is also presented to improve system security.