Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuroimage: Clinical Understanding Disease Processes in Multiple Sclerosis through Magnetic Resonance Imaging Studies in Animal Models

Experimental autoimmune encephalomyelitis Theiler's murine encephalomyelitis virus Lysolecithin Cuprizone a b s t r a c t There are exciting new advances in multiple sclerosis (MS) resulting in a growing understanding of both the complexity of the disorder and the relative involvement of grey matter, white matter and inflammation. Increasing need for preclinical imaging is anticipated, as animal models provide insights into the pathophysi-ology of the disease. Magnetic resonance (MR) is the key imaging tool used to diagnose and to monitor disease progression in MS, and thus will be a cornerstone for future research. Although gadolinium-enhancing and T 2 lesions on MRI have been useful for detecting MS pathology, they are not correlative of disability. Therefore, new MRI methods are needed. Such methods require validation in animal models. The increasing necessity for MRI of animal models makes it critical and timely to understand what research has been conducted in this area and what potential there is for use of MRI in preclinical models of MS. Here, we provide a review of MRI and magnetic resonance spectroscopy (MRS) studies that have been carried out in animal models of MS that focus on pathology. We compare the MRI phenotypes of animals and patients and provide advice on how best to use animal MR studies to increase our understanding of the linkages between MR and pathology in patients. This review describes how MRI studies of animal models have been, and will continue to be, used in the ongoing effort to understand MS.
Particle Swarm Optimization for Constrained Instruction Scheduling

Instruction scheduling is an optimization phase aimed at balancing the performance-cost tradeoffs of the design of digital systems. In this paper, a formal framework is tailored in particular to find an optimal solution to the resource-constrained instruction scheduling problem in high-level synthesis. The scheduling problem is formulated as a discrete optimization problem and an efficient population-based search technique; particle swarm optimization (PSO) is incorporated for efficient pruning of the solution space. As PSO has proven to be successful in many applications in continuous optimization problems, the main contribution of this paper is to propose a new hybrid algorithm that combines PSO with the traditional list scheduling algorithm to solve the discrete problem of instruction scheduling. The performance of the proposed algorithms is evaluated on a set of HLS benchmarks, and the experimental results demonstrate that the proposed algorithm outperforms other scheduling metaheuristics and is a promising alternative for obtaining near optimal solutions to NP-complete scheduling problem instances.
Genetic selection reveals the role of a buried, conserved polar residue

The burial of nonpolar surface area is known to enhance markedly the conformational stability of proteins. The contribution from the burial of polar surface area is less clear. Here, we report on the tolerance to substitution of Ser75 of bovine pancreatic ribonuclease (RNase A), a residue that has the unusual attributes of being buried, conserved, and polar. To identify variants that retain biological function, we used a genetic selection based on the intrinsic cytotoxicity of ribonucleolytic activity. Cell growth at 30°C, 37°C, and 44°C correlated with residue size, indicating that the primary attribute of Ser75 is its small size. The side‐chain hydroxyl group of Ser75 forms a hydrogen bond with a main‐chain nitrogen. The conformational stability of the S75A variant, which lacks this hydrogen bond, was diminished by ΔΔG = 2.5 kcal/mol. Threonine, which can reinstate this hydrogen bond, provided a catalytically active RNase A variant at higher temperatures than did some smaller residues (including aspartate), indicating that a secondary attribute of Ser75 is the ability of its uncharged side chain to accept a hydrogen bond. These results provide insight on the imperatives for the conservation of a buried polar residue.
THE HOST GALAXIES OF SWIFT DARK GAMMA-RAY BURSTS: OBSERVATIONAL CONSTRAINTS ON HIGHLY OBSCURED AND VERY HIGH REDSHIFT GRBs

In this work, we present the first results of our imaging campaign at Keck Observatory to identify the host galaxies of “dark” gamma-ray bursts (GRBs), events with no detected optical afterglow or with detected optical flux significantly fainter than expected from the observed X-ray afterglow. We find that out of a uniform sample of 29 Swift bursts rapidly observed by the Palomar 60 inch telescope through 2008 March (14 of which we classify as dark), all events have either a detected optical afterglow, a probable optical host-galaxy detection, or both. Our results constrain the fraction of Swift GRBs coming from very high redshift (z>7), such as the recent GRB 090423, to between 0.2% and 7% at 80% confidence. In contrast, a significant fraction of the sample requires large extinction columns (host-frame AV ≳ 1 mag, with several events showing AV> 2–6 mag), identifying dust extinction as the dominant cause of the dark GRB phenomenon. We infer that a significant fraction of GRBs (and, by association, of high-mass star formation) occurs in highly obscured regions. However, the host galaxies of dark GRBs seem to have normal optical colors, suggesting that the source of obscuring dust is local to the vicinity of the GRB progenitor or highly unevenly distributed within the host galaxy.
Coping with Risks Through Mismatches: Domestic and International Financial Contracts for Emerging Economies

The authors argue that short termism, dollarization, and the use of foreign jurisdictions are endogenous ways of coping with systemic risks prevalent in emerging markets. They represent a symptom at least as much as a problem. These coping mechanisms are jointly determined and the choice of one of them involves risk tradeoffs. Various conclusions can be derived from the analysis. First, because of the dominance of dollar contracts over short-duration contracts, dedollarization might be much more difficult to achieve than often believed. Second, one-dimensional policies aimed at reducing currency and duration mismatches might just displace risk and not diminish it. Third, as systemic risks rise, the market equilibrium settles in favor of investor protection against price risk (through dollar and short-duration contracts) at the expense of exposure to credit risk. Finally, the option value to litigate in the event of default might explain this equilibrium outcome.
Genome-Wide Transcriptional Profiling of the Response of Staphylococcus aureus to Cryptotanshinone

Staphylococcus aureus (S. aureus) strains with multiple antibiotic resistances are increasingly widespread, and new agents are required for the treatment of S. aureus. Cryptotanshinone (CT), a major tanshinone of medicinal plant Salvia miltiorrhiza Bunge, demonstrated effective in vitro antibacterial activity against all 21 S. aureus strains tested in this experiment. Affymetrix GeneChips were utilized to determine the global transcriptional response of S. aureus ATCC 25923 to treatment with subinhibitory concentrations of CT. Transcriptome profiling indicated that the antibacterial action of CT may be associated with its action as active oxygen radical generator; S. aureus undergoes an oxygen-limiting state upon exposure to CT.
Testing Three Species Distribution Modelling Strategies to Define Fish Assemblage Reference Conditions for Stream Bioassessment and Related Applications

Species distribution models are widely used for stream bioassessment, estimating changes in habitat suitability and identifying conservation priorities. We tested the accuracy of three modelling strategies (single species ensemble, multi-species response and community classification models) to predict fish assemblages at reference stream segments in coastal subtropical Australia. We aimed to evaluate each modelling strategy for consistency of predictor variable selection; determine which strategy is most suitable for stream bioassessment using fish indicators; and appraise which strategies best match other stream management applications. Five models, one single species ensemble, two multi-species response and two community classification models, were calibrated using fish species presence-absence data from 103 reference sites. Models were evaluated for generality and transferability through space and time using four external reference site datasets. Elevation and catchment slope were consistently identified as key correlates of fish assemblage composition among models. The community classification models had high omission error rates and contributed fewer taxa to the ‘expected’ component of the taxonomic completeness (O/E50) index than the other strategies. This potentially decreases the model sensitivity for site impact assessment. The ensemble model accurately and precisely modelled O/E50 for the training data, but produced biased predictions for the external datasets. The multi-species response models afforded relatively high accuracy and precision coupled with low bias across external datasets and had lower taxa omission rates than the community classification models. They inherently included rare, but predictable species while excluding species that were poorly modelled among all strategies. We suggest that the multi-species response modelling strategy is most suited to bioassessment using freshwater fish assemblages in our study area. At the species level, the ensemble model exhibited high sensitivity without reductions in specificity, relative to the other models. We suggest that this strategy is well suited to other non-bioassessment stream management applications, e.g., identifying priority areas for species conservation.
Effect of climate on interannual variability of terrestrial CO2 fluxes

We evaluated how climate influences interannual variability in the terrestrial Net Ecosystem Exchange (NEE) of CO2 using the Simple Biosphere Model, Version 2 (SiB2) for 1983 to 1993 on a global, 1° by 1° latitude/longitude grid with a 10‐min time step. We quantified climate influences on NEE, explained regional differences, and related NEE variability to the Arctic Oscillation (AO) and the El Niño‐Southern Oscillation (ENSO). The simulated NEE reproduces the salient features and magnitude of the measured global CO2 growth rate. The Northern Hemisphere shows a pattern of alternating positive and negative NEE anomalies that cancel such that the tropics dominate the global simulated NEE interannual variability. Climate influences have strong regional differences with precipitation dominating in the tropics and temperature in the extratropics. In tropical regions with drier soils, precipitation control of photosynthesis (i.e., drought stress) dominates; in nearly saturated soils, precipitation control of respiration dominates. Because of cancellation and competing effects, no single climate variable controls global or regional NEE interannual variability. Globally, precipitation accounts for 44% of NEE variability; followed by Leaf Area Index (23%), soil carbon (12%), and temperature (16%). The influence of ENSO on NEE variability is consistent with that expected for shifting precipitation patterns in the tropics. Except in northern Europe, temperature advection by the AO does not significantly influence NEE variability. Neither the AO nor ENSO fully explain the temperature influence on respiration or the simulated NEE anomaly pattern in the Northern Hemisphere.
The association between maternal hyperglycemia and perinatal outcomes in gestational diabetes mellitus patients

AbstractPregnancies complicated by gestational diabetes mellitus (GDM) are associated with increased risks of adverse maternal and fetal outcomes. The risks of adverse pregnancy outcomes differ depending on the glucose values among GDM patients. For accurate and effective prenatal counseling, it is necessary to understand the relationship between different maternal hyperglycemia values and the severity of adverse outcomes. With this objective, this study reexamines the relationship between maternal hyperglycemia versus maternal and perinatal outcomes in GDM patients. For this study, maternal hyperglycemia was diagnosed using the 2-step diagnostic approach.Medical records of 3434 pregnant women, who received the 50-g glucose challenge test (GCT) between March 2001 and April 2013, were reviewed. As a result, 307 patients were diagnosed with GDM, and they were divided into 2 groups according to their fasting glucose levels. A total of 171 patients had normal fasting glucose level (<95 mg/dL), and 136 patients had abnormal fasting glucose level (≥95 mg/dL). The 50-g GCT results were subdivided by 20-unit increments (140–159, n = 123; 160–179, n = 84; 180–199, n = 50; and ≥200, n = 50), and the maternal and perinatal outcomes were compared against the normal 50-g GCT group (n = 307). Maternal fasting blood glucose (FBG) level showed clear association with adverse perinatal outcomes. The odds ratio (OR) of macrosomia was 6.72 (95% CI: 2.59–17.49, P < 0.001) between the 2 groups. The ORs of large for gestational age (LGA) and neonatal hypoglycemia were 3.75 (95% CI: 1.97–7.12, P < 0.001) and 1.65 (95% CI: 0.79–3.43, P = 0.183), respectively. Also, the results of the 50-g GCT for each category showed strong association with increased risks of adverse perinatal outcomes compared to the normal 50-g GCT group. The OR of macrosomia (up to 20.31-fold), LGA (up to 6.15-fold), and neonatal hypoglycemia (up to 84.00-fold) increased with increasing 50-g GCT result.
Genetic variants within microRNA‐binding site of RAD51B are associated with risk of cervical cancer in Chinese women

RAD51B plays a central role in homologous recombinational repair (HRR) of DNA double‐strand breaks (DSBs), which is important to prevent genomic instability, a hallmark of cancer. Recent studies suggested that common genetic variants of RAD51B may contribute to cancer susceptibility. In this study, we aimed to investigate whether potentially functional variants within miRNA‐binding sites of RAD51B are associated with risk of cervical cancer. A total of 1486 cervical cancer patients and 1536 cancer‐free controls were enrolled, and two genetic variants, rs963917 (A > G) and rs963918 (T > C), were genotyped in all participants. Using multivariate logistic regression analyses, we found that G allele of rs963917 conferred lower risk of cervical cancer compared to A allele (adjusted OR = 0.89, 95% CI = 0.80–0.99, P = 0.039). Similarly, rs963918 allele C was associated with a decreased risk for cervical cancer compared with allele T (adjusted OR = 0.84, 95% CI = 0.74–0.94, P = 0.004). Haplotype analyses showed that haplotype GC was also correlated with lower risk (OR = 0.83, 95% CI = 0.73–0.95, P = 0.005) compared with the most common haplotype AT. In summary, our study suggested that miRNA‐binding site genetic variants of RAD51B may modify the susceptibility to cervical cancer, which is important to identify individuals with differential risk for this malignancy and to improve the effectiveness of preventive intervention.
Perception of Words and Pitch Patterns in Song and Speech

This functional magnetic resonance imaging study examines shared and distinct cortical areas involved in the auditory perception of song and speech at the level of their underlying constituents: words and pitch patterns. Univariate and multivariate analyses were performed to isolate the neural correlates of the word- and pitch-based discrimination between song and speech, corrected for rhythmic differences in both. Therefore, six conditions, arranged in a subtractive hierarchy were created: sung sentences including words, pitch and rhythm; hummed speech prosody and song melody containing only pitch patterns and rhythm; and as a control the pure musical or speech rhythm. Systematic contrasts between these balanced conditions following their hierarchical organization showed a great overlap between song and speech at all levels in the bilateral temporal lobe, but suggested a differential role of the inferior frontal gyrus (IFG) and intraparietal sulcus (IPS) in processing song and speech. While the left IFG coded for spoken words and showed predominance over the right IFG in prosodic pitch processing, an opposite lateralization was found for pitch in song. The IPS showed sensitivity to discrete pitch relations in song as opposed to the gliding pitch in speech. Finally, the superior temporal gyrus and premotor cortex coded for general differences between words and pitch patterns, irrespective of whether they were sung or spoken. Thus, song and speech share many features which are reflected in a fundamental similarity of brain areas involved in their perception. However, fine-grained acoustic differences on word and pitch level are reflected in the IPS and the lateralized activity of the IFG.
Analysis of Plant Growth-Promoting Effects of Fluorescent Pseudomonas Strains Isolated from Mentha piperita Rhizosphere and Effects of Their Volatile Organic Compounds on Essential Oil Composition

Many species or strains of the genus Pseudomonas have been characterized as plant growth promoting rhizobacteria (PGPR). We used a combination of phenotypic and genotypic techniques to analyze the community of fluorescent Pseudomonas strains in the rhizosphere of commercially grown Mentha piperita (peppermint). Biochemical techniques, Amplified rDNA Restriction Analysis (ARDRA), and 16S rRNA gene sequence analysis revealed that the majority of the isolated native fluorescent strains were P. putida. Use of two Repetitive Sequence-based PCR (rep-PCR) techniques, BOX-PCR and ERIC-PCR, allowed us to evaluate diversity among the native strains and to more effectively distinguish among them. PGPR activity was tested for the native strains and reference strain P. fluorescens WCS417r. Micropropagated M. piperita plantlets were exposed to microbial volatile organic compounds (mVOCs) emitted by the bacterial strains, and plant biomass parameters and production of essential oils (EOs) were measured. mVOCs from 11 of the native strains caused an increase in shoot fresh weight. mVOCs from three native strains (SJ04, SJ25, SJ48) induced changes in M. pierita EO composition. The mVOCs caused a reduction of metabolites in the monoterpene pathway, for example menthofuran, and an increase in menthol production. Menthol production is the primary indicator of EO quality. The mVOCs produced by native strains SJ04, SJ25, SJ48, and strain WCS417r were analyzed. The obtained mVOC chromatographic profiles were unique for each of the three native strains analyzed, containing varying hydrocarbon, aromatic, and alogenic compounds. The differential effects of the strains were most likely due to the specific mixtures of mVOCs emitted by each strain, suggesting a synergistic effect occurs among the compounds present.
Effective Bandwidths for Stationary Sources

At a buffered switch in an ATM (asynchronous transfer mode) network it is important to know what combinations of different types of traffic can be carried simultaneously without risking more than a very small probability of overflowing the buffer. We show that a simple and serviceable measure of effective bandwidths may be computed for stationary traffic sources. For large buffers the effective bandwidth of a source is a function only of its mean rate, index of dispersion, and the size of the buffer.
Submillimetre detection of a high-redshift type 2 QSO

We report on the first SCUBA detection of a type 2 QSO at z = 3.660 in the Chandra Deep Field South. This source is X-ray-absorbed, shows only narrow emission lines in the optical spectrum and is detected in the submillimetre: it is the ideal candidate in an evolution scheme for active galactic nuclei (AGN) (e.g. Fabian 1999; Page et al. 2004) of an early phase corresponding to the main growth of the host galaxy and formation of the central black hole. The overall photometry (from the radio to the X-ray energy band) of this source is well reproduced by the spectral energy distribution (SED) of NGC 6240, while it is incompatible with the spectrum of a type 1 QSO (3C 273) or a starburst galaxy (Arp 220). Its submillimetre (850 μm) to X-ray (2 keV) spectral slope (α SX ) is close to the predicted value for a Compton-thick AGN in which only 1 per cent of the nuclear emission emerges through scattering. Using the observed flux at 850 μm we have derived a star formation rate of 550-680 M ○. yr -1 and an estimate of the dust mass M dust = 4.2 x 10 8 M ○.
Effects of physical training in asthma: a systematic review

Objectives—To assess the evidence for the effects of physical training on pulmonary function, symptoms, cardiopulmonary fitness, and quality of life in subjects with asthma. Methods—A search was conducted for randomised controlled trials of subjects with asthma undertaking physical training using the Cochrane Airways Group register of controlled clinical trials, Medline, Embase, Sportdiscus, Science citation index, and Current contents index. Studies were included in the review if the subjects had asthma, were 8 years of age or older, and had undertaken physical training for at least 20 minutes per session, twice a week, for a minimum of four weeks. The eligibility of trials for inclusion in the review and the quality of the trials were independently assessed by two reviewers. Results—Eight studies with a total of 226 subjects met the inclusion criteria for this review. Physical training had no effect on resting lung function but led to an improvement in cardiopulmonary fitness as measured by an increase in maximum oxygen uptake of 5.6 ml/kg/min (95% confidence interval 3.9 to 7.2). None of the studies measured quality of life. Conclusions—Physical training improves cardiopulmonary fitness without changing lung function. It is not clear if the improvement in fitness translates into a reduction in symptoms or an improvement in the quality of life. There is a need for further randomised controlled trials of the effects of physical training in the management of asthma.
Hot off the wiki: dynamics, practices, and structures in Wikipedia's coverage of the Tōhoku catastrophes

Wikipedia editors are uniquely motivated to collaborate around current and breaking news events. However, the speed, urgency, and intensity with which these collaborations unfold also impose a substantial burden on editors' abilities to effectively coordinate tasks and process information. We analyze the patterns of activity on Wikipedia following the 2011 Tōhoku earthquake and tsunami to understand the dynamics of editor attention and participation, novel practices employed to collaborate on these articles, and the resulting coauthorship structures which emerge between editors and articles. Our findings have implications for supporting future coverage of breaking news articles, theorizing about motivations to participate in online community, and illuminating Wikipedia's potential role in storing cultural memories of catastrophe.