Miracle-dz/UniFAR-FTUs huggingface dataset:
From molecules to living systems: historical and contemporary issues in oxidative stress and antioxidant ecology

Summary 1. Initial work on oxidative stress and antioxidant defences described basic chemical and biochemical properties and processes and applied this information to issues of animal health and husbandry. Seminal experimental investigations on the damaging effects of oxidative stress and the mitigating effects of antioxidant defences were conducted primarily in domesticated organisms. 2. In recent years, ecologists have taken to studying antioxidants and oxidative stress in free-ranging organisms and have integrated principles of oxidative stress into several core evolutionary concepts, such as life-history trade-offs (e.g. survival vs. reproduction), senescence and sexual selection. This initial flurry of studies has provided major advances in our understanding of how antioxidant defences evolve and function. 3. In this overview, it is our goal to provide ecologists with an accessible summary of (i) the biochemical basis and conceptual frameworks behind oxidative stress and antioxidants, (ii) the research questions and hypotheses that are generated by incorporating antioxidants and oxidative stress into models of life-history theory, ageing, mate selection, and honest signalling, and (iii) the trends in the evidence that have emerged from initial studies in these areas. 4. Though much progress has been made on the ecological and evolutionary relevance of antioxidant and oxidative stress physiology, no consensus has emerged regarding the primacy of how oxidative stress challenges or antioxidant limits or values shape organismal life-histories. However, there are many taxonomic biases in studies to date and several ideal environmental systems that are as-of-yet untapped.
Stimulating the In Situ Activity of Geobacter Species To Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer

ABSTRACT The potential for removing uranium from contaminated groundwater by stimulating the in situ activity of dissimilatory metal-reducing microorganisms was evaluated in a uranium-contaminated aquifer located in Rifle, Colo. Acetate (1 to 3 mM) was injected into the subsurface over a 3-month period via an injection gallery composed of 20 injection wells, which was installed upgradient from a series of 15 monitoring wells. U(VI) concentrations decreased in as little as 9 days after acetate injection was initiated, and within 50 days uranium had declined below the prescribed treatment level of 0.18 μM in some of the monitoring wells. Analysis of 16S ribosomal DNA (rDNA) sequences and phospholipid fatty acid profiles demonstrated that the initial loss of uranium from the groundwater was associated with an enrichment of Geobacter species in the treatment zone. Fe(II) in the groundwater also increased during this period, suggesting that U(VI) reduction was coincident with Fe(III) reduction. As the acetate injection continued over 50 days there was a loss of sulfate from the groundwater and an accumulation of sulfide and the composition of the microbial community changed. Organisms with 16S rDNA sequences most closely related to those of sulfate reducers became predominant, and Geobacter species became a minor component of the community. This apparent switch from Fe(III) reduction to sulfate reduction as the terminal electron accepting process for the oxidation of the injected acetate was associated with an increase in uranium concentration in the groundwater. These results demonstrate that in situ bioremediation of uranium-contaminated groundwater is feasible but suggest that the strategy should be optimized to better maintain long-term activity of Geobacter species.
Two-point discrimination threshold as a function of frequency and polarity at fingertip by electrical stimulation

The effect of frequencies and current polarity of electrical stimulation to fingertip was investigated toward realizing electrocutaneous display. We measured the two-point discrimination threshold of electrical stimulation with 1.0 mm diameter electrodes spaced by 2.0 mm. The waveform pattern with the smallest two-point discrimination threshold was anode at frequencies from 200 to 400 Hz; most subjects could clearly discriminate the physical separation of 4 mm, some of them could discriminate 2 mm with optimized electrical stimulation.
Direct N-body Simulations of Rubble Pile Collisions in Strong Tidal Fields: Applied to Saturn's F Ring

There is increasing evidence that many kilometer-sized bodies in the Solar System are piles of rubble bound together by gravity. We present results from a project to map the parameter space of collisions between kilometer-sized spherical rubble piles. The results will assist in parameterization of collision outcomes for Solar System formation models and give insight into disruption scaling laws. We use a direct numerical method to evolve the positions and velocities of the rubble pile particles under the constraints of gravity and physical collisions. We test the dependence of the collision outcomes on impact parameter and speed, impactor spin, mass ratio, and coefficient of restitution. Speeds are kept low (<10 m s−1, appropriate for dynamically cool systems such as the primordial disk during early planet formation) so that the maximum strain on the component material does not exceed the crushing strength, assuming sufficient granularity. We compare our results with analytic estimates and hydrocode simulations. We find that net accretion dominates the outcome in slow head-on collisions while net erosion dominates for fast off-axis collisions. The dependence on impact parameter is almost equally as important as the dependence on impact speed. Off-axis collisions can result in fast-spinning elongated remnants or contact binaries while fast collisions result in smaller fragments overall. Clumping of debris escaping from the remnant can occur, leading to the formation of smaller rubble piles. In the cases we tested, less than 2% of the system mass ends up orbiting the remnant. Initial spin can reduce or enhance collision outcomes, depending on the relative orientation of the spin and orbital angular momenta. We derive a relationship between impact speed and angle for critical dispersal of mass in the system. We find that our rubble piles are relatively easy to disperse, even at low impact speed. This may provide a way of constraining the energy dissipation parameter and related properties of the initial planetesimal population.
Learning Language Games through Interaction

We introduce a new language learning setting relevant to building adaptive natural language interfaces. It is inspired by Wittgenstein's language games: a human wishes to accomplish some task (e.g., achieving a certain configuration of blocks), but can only communicate with a computer, who performs the actual actions (e.g., removing all red blocks). The computer initially knows nothing about language and therefore must learn it from scratch through interaction, while the human adapts to the computer's capabilities. We created a game in a blocks world and collected interactions from 100 people playing it. First, we analyze the humans' strategies, showing that using compositionality and avoiding synonyms correlates positively with task performance. Second, we compare computer strategies, showing how to quickly learn a semantic parsing model from scratch, and that modeling pragmatics further accelerates learning for successful players.
A preliminary psychometric evaluation of Music in Dementia Assessment Scales (MiDAS)

ABSTRACT Background: Music in Dementia Assessment Scales (MiDAS), an observational outcome measure for music therapy with people with moderate to severe dementia, was developed from qualitative data of focus groups and interviews. Expert and peer consultations were conducted at each stage of the scale development to maximize its content validity. This study aimed to evaluate the psychometric properties of MiDAS. Methods: Care home residents with dementia attended weekly group music therapy for up to ten sessions. Music therapists and care home staff were requested to complete weekly MiDAS ratings. The Quality of Life Scale (QoL-AD) was completed at three time-points. Results: A total of 629 (staff = 306, therapist = 323) MiDAS forms were completed. The statistical analysis revealed that MiDAS has high therapist inter-rater reliability, low staff inter-rater reliability, adequate staff test-retest reliability, adequate concurrent validity, and good construct validity. High factor loadings between the five MiDAS Visual Analogue Scale (VAS) items, levels of Interest, Response, Initiation, Involvement, and Enjoyment, were found. Conclusions: This study indicates that MiDAS has good psychometric properties despite the small sample size. Future research with a larger sample size could provide a more in-depth psychometric evaluation, including further exploration of the underlying factors. MiDAS provides a measure of engagement with musical experience and offers insight into who is likely to benefit on other outcomes such as quality of life or reduction in psychiatric symptoms.
Unsupervised feature selection for ensemble of classifiers

In this paper we discuss a strategy to create ensemble of classifiers based on unsupervised features selection. It takes into account a hierarchical multi-objective genetic algorithm that generates a set of classifiers by performing feature selection and then combines them to provide a set of powerful ensembles. The proposed method is evaluated in the context of handwritten month word recognition, using three different feature sets and hidden Markov models as classifiers. Comprehensive experiments demonstrate the effectiveness of the proposed strategy.
Structural and biochemical characterization of gentisate 1,2‐dioxygenase from Escherichia coli O157:H7

Gentisic acid (2,5‐dihydroxybenzoic acid) is a key intermediate in aerobic bacterial pathways that are responsible for the metabolism of a large number of aromatic compounds. The critical step of these pathways is the oxygen‐dependent reaction catalysed by gentisate 1,2‐dioxygenase which opens the aromatic ring of gentisate to form maleylpyruvate. From gentisic acid, the cell derives carbon and energy through the conversion of maleylpyruvate to central metabolites. We have confirmed the annotation of a gentisate 1,2‐dioygenase from the pathogenic O157:H7 Escherichia coli strain and present the first structural characterization of this family of enzymes. The identity of the reaction product was revealed using tandem mass spectroscopy. The operon responsible for the degradation of gentisate in this organism exhibits a high degree of conservation with the gentisate‐degrading operons of other pathogenic bacteria, including the Shiga toxin‐producing E. coli O103:H2, but does not appear to be present in non‐pathogenic strains. The acquisition of the gentisate operon may represent a special adaptation to meet carbon source requirements under conditions of environmental stress and may provide a selective advantage for enterohaemorrhagic E. coli relative to their non‐pathogenic counterparts.
Strengthening of Unreinforced Masonry Walls Using FRPs

An experimental program conducted at the University of Alberta showed that externally applied fiber reinforced polymers (FRPs) are effective in increasing the load-carrying capacity of unreinforced masonry walls that are subjected to out-of-plane flexural loads. Ten walls with a height of 4 m were used to conduct 13 tests in two series. Both undamaged and slightly damaged walls were tested. The following experimental parameters were investigated: (1) type of fiber reinforcement; (2) amount of fiber reinforcement; (3) layout of fiber reinforcement; (4) effects of moderate compressive axial load; and (5) cyclic behavior. This paper briefly reviews the existing rehabilitation methods available and explains why the use of FRPs as external reinforcement is a possible alternative. The test setup and instrumentation of the specimens are described followed by a discussion of the results. The general behavior of the specimens is discussed with emphasis on the load deflection and strain characteristics. The modes of failure are identified and categorized. Finally, a simple analytical model is proposed and compared with the test results followed by a summary of the major results.
Sliding window adaptive Constant Modulus Algorithm based on complex Hyperbolic Givens rotations

This paper proposes a new adaptive Constant Modulus Algorithm (CMA) for the blind separation of communication signals. Although many existing CMA-like algorithms have been proposed in the literature, their efficiency in terms of convergence rate and separation quality is still relatively low. We introduce herein a new adaptive technique based on the use of complex Hyperbolic Givens rotations which shows very good performance as illustrated by the simulation results and comparative study provided at the end of the paper.
Patterns Of Asthma Exacerbation Related To Climate And Weather In The Northeast Kingdom Of Vermont

Asthma is a chronic respiratory disease characterized by longand short-term inflammation and bronchospasm susceptible to multiple triggers that affects patients across the lifespan. Asthma management is a primary care priority in Vermont, where there continues to be an above-average prevalence of asthma among both children and adults as compared to other states. However, many of Vermont’s children and especially adults with asthma are not participating in regular check-ups for asthma management that would best prevent exacerbation of asthma symptoms. Several climate and weather elements including, but not limited to, extreme temperatures and particulate matter are known asthma triggers. Vermont’s high per capita use of old woodstoves, pockets of poverty and cold winters are all factors that might collide to adversely impact residents’ asthma. Insights into how climate and weather might be related to peak periods of acute asthma exacerbation (AAE) among individuals living in the rural Northeast Kingdom of Vermont (NEK) could provide valuable, regionally focused public health information to primary care providers on the front lines of asthma management. The objective of this research was to examine the potential relationship between the climate and weather of the NEK and visits for asthma exacerbation in the primary care setting. The research began with a retrospective chart review including visits to five different clinic sites in the NEK between 2009-2014 with the ICD-9 code for asthma exacerbation (493.xx) as the primary diagnosis. When visits were individually validated as an AAE, the clinic site, date of visit, and the patients’ age and sex were documented. These validated visits were then analyzed against weather and climate data including temperature and air quality. Results suggest that while diurnal shifts and air quality do not show a strong relationship with AAEs in this area, colder days do appear to correlate to when patients visit primary care clinics in the NEK for AAEs.
Proteoglycans in primate arteries. II. Synthesis and secretion of glycosaminoglycans by arterial smooth muscle cells in culture

Glycosaminoglycan synthesis and secretion by primate arterial smooth muscle have been examined in cell culture. Mass cultures of diploid primate arterial smooth muscle cells were either double labeled with [35S]sulfate and [3H]acetate or single labeled with [3H]glucosamine for 24 h and glycosaminoglycans were extracted and isolated from the culture medium. Incorporation of labeled precursors into glycosaminoglycan was maximal during stationary phase of smooth muscle cell growth in culture and reduced, but not eliminated during logarithmic growth. The glycosaminoglycans synthesized and secreted into the culture medium were characterized by differential susceptibility to glycosaminoglycan-degradative enzymes and by cellulose acetate electrophoresis. Both assay procedures indicate that cultured primate arterial smooth muscle cells synthesize principally dermatan sulfate (60%-80% of total), chondroitin sulfate A and/or C (10%-20%of total) and little or no hyaluronic acid (0%-5% of total). This pattern of glycosaminoglycan formation differed significantly from that exhibited by isologous skin fibroblasts cultured under identical conditions. Dermal fibroblasts synthesize and secrete primarily hyaluronic acid (50%-60% of total) with lesser amounts of dermatan sulfate (10%-20% of total) and chondroitin sulfate A and/or C (10%-20% of total). These results indicate that differences exist in proteoglycan metabolism between these two connective tissue-producing cells in vitro, and suggest that the observed pattern of in vitro glycosaminoglycan synthesis by primate arterial smooth muscle cells may be characteristic for this cell type and not a general response to conditions of cell culture.
Improved coronary artery definition with T2-weighted, free-breathing, three-dimensional coronary MRA.

BACKGROUND Three-dimensional (3D) navigator-gated and prospectively corrected free-breathing coronary magnetic resonance angiography (MRA) allows for submillimeter image resolution but suffers from poor contrast between coronary blood and myocardium. Data collected over >100 ms/heart beat are also susceptible to bulk cardiac and respiratory motion. To address these problems, we examined the effect of a T2 preparation prepulse (T2prep) for myocardial suppression and a shortened acquisition window on coronary definition. METHODS AND RESULTS Eight healthy adult subjects and 5 patients with confirmed coronary artery disease (CAD) underwent free-breathing 3D MRA with and without T2prep and with 120- and 60-ms data-acquisition windows. The T2prep resulted in a 123% (P<0. 001) increase in contrast-to-noise ratio (CNR). Coronary edge definition was improved by 33% (P<0.001). Acquisition window shortening from 120 to 60 ms resulted in better vessel definition (11%; P<0.001). Among patients with CAD, there was a good correspondence with disease. CONCLUSIONS Free-breathing, T2prep, 3D coronary MRA with a shorter acquisition window resulted in improved CNR and better coronary artery definition, allowing the assessment of coronary disease. This approach offers the potential for free-breathing, noninvasive assessment of the major coronary arteries.
Live migration of virtual machines

Migrating operating system instances across distinct physical hosts is a useful tool for administrators of data centers and clusters: It allows a clean separation between hard-ware and software, and facilitates fault management, load balancing, and low-level system maintenance. By carrying out the majority of migration while OSes continue to run, we achieve impressive performance with minimal service downtimes; we demonstrate the migration of entire OS instances on a commodity cluster, recording service downtimes as low as 60ms. We show that that our performance is sufficient to make live migration a practical tool even for servers running interactive loads. In this paper we consider the design options for migrating OSes running services with liveness constraints, focusing on data center and cluster environments. We introduce and analyze the concept of writable working set, and present the design, implementation and evaluation of high-performance OS migration built on top of the Xen VMM.
Effects of Probiotics on the Recurrence of Bacterial Vaginosis: A Review

Objective Bacterial vaginosis (BV) is a common cause of genital discomfort in women in reproductive ages, which causes many complications. Bacterial vaginosis is usually treated by metronidazole and clindamycin. However, this protocol does not prevent its recurrence, which is a main complaint of the patients. The number of lactobacilli in the vagina of women with BV is significantly lower than that in healthy women. Hence, efforts have been made to normalize vaginal flora by oral or vaginal administration of lactobacilli. The objective of the present study was to review clinical evidences available regarding the efficacy of probiotics in the prevention and treatment of BV. Materials and Methods Published randomized controlled trials were searched in PubMed, Science Direct, and the Cochrane Database between 1990 and 2011. Search terms included bacterial vaginosis, urinary tract infection, lactobacillus, and probiotics. Results Orally consumed probiotics are believed to ascend to the vaginal tract after they are excreted from the rectum; vaginal administration allows for direct replacement of the probiotics for unhealthy vaginal microbiota and occupation of specific adhesion sites at the epithelial surface of the urinary tract, which consequently results in maintenance of a low pH and production of antimicrobial substances like acids and hydrogen peroxide. Receiving Lactobacillus acidophilus, Lactobacillus rhamnosus GR-1, and Lactobacillus fermentum RC-14 at a dose of at least 108 CFU/day for 2 months has been shown to present the patients with better results. Conclusions Although the results of different studies are controversial, most studies have been in favor of the probiotics in the prevention or treatment of BV, and no adverse effects have been reported. Therefore, it may be helpful to recommend daily consumption of probiotic products to improve public health among women.
Identification of S-nitroso-CoA reductases that regulate protein S-nitrosylation

Significance Coenzyme A (CoA) is a small-molecular-weight thiol that plays a central role in cellular metabolism. We have discovered a novel, phylogenetically conserved class of enzymes that reduce S-nitroso-CoA (SNO-CoA) and thereby regulate protein S-nitrosylation. These denitrosylases, identified as alcohol dehydrogenase 6 (Adh6) in yeast and aldo-keto reductase 1A1 in mammals, may be analogized to deacetylases, which regulate CoA-mediated protein acetylation. In yeast, Adh6 (previously without ascribed cellular function) regulates endogenous protein S-nitrosylation (heretofore unknown) including function-altering S-nitrosylation that impacts CoA-related metabolism. Thus, our findings establish a novel role for CoA in protein S-nitrosylation (operating through SNO-CoA), which is governed by specific enzymes. This mechanism may regulate the influence of nitric oxide on cellular metabolism in health and disease. Coenzyme A (CoA) mediates thiol-based acyl-group transfer (acetylation and palmitoylation). However, a role for CoA in the thiol-based transfer of NO groups (S-nitrosylation) has not been considered. Here we describe protein S-nitrosylation in yeast (heretofore unknown) that is mediated by S-nitroso-CoA (SNO-CoA). We identify a specific SNO-CoA reductase encoded by the alcohol dehydrogenase 6 (ADH6) gene and show that deletion of ADH6 increases cellular S-nitrosylation and alters CoA metabolism. Further, we report that Adh6, acting as a selective SNO-CoA reductase, protects acetoacetyl–CoA thiolase from inhibitory S-nitrosylation and thereby affects sterol biosynthesis. Thus, Adh6-regulated, SNO-CoA–mediated protein S-nitrosylation provides a regulatory mechanism paralleling protein acetylation. We also find that SNO-CoA reductases are present from bacteria to mammals, and we identify aldo-keto reductase 1A1 as the mammalian functional analog of Adh6. Our studies reveal a novel functional class of enzymes that regulate protein S-nitrosylation from yeast to mammals and suggest that SNO-CoA–mediated S-nitrosylation may subserve metabolic regulation.