Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of signature files as set access facilities in OODBs

Object-oriented database systems (OODBs) need efficient support for manipulation of complex objects. In particular, support of queries involving evaluations of set predicates is often required in handling complex objects. In this paper, we propose a scheme to apply signature file techniques, which were originally invented for text retrieval, to the support of set value accesses, and quantitatively evaluate their potential capabilities. Two signature file organizations, the sequential signature file and the bit-sliced signature file, are considered and their performance is compared with that of the nested index for queries involving the set inclusion operator (⊆). We develop a detailed cost model and present analytical results clarifying their retrieval, storage, and update costs. Our analysis shows that the bit-sliced signature file is a very promising set access facility in OODBs.
Oxidative stress and respiratory muscle dysfunction in severe chronic obstructive pulmonary disease.

RATIONALE Oxidative stress is involved in the skeletal muscle dysfunction observed in patients with severe chronic obstructive pulmonary disease (COPD). We hypothesized that the diaphragms of such patients might generate greater levels of oxidants than those neutralized by antioxidants. OBJECTIVES To assess the levels of both oxidative and nitrosative stress and different antioxidants in the diaphragms of those patients, and to analyze potential relationships with lung and respiratory muscle dysfunctions. METHODS AND MEASUREMENTS We conducted a case-control study in which reactive carbonyl groups, hydroxynonenal-protein adducts, antioxidant enzyme levels, nitric oxide synthases, and 3-nitrotyrosine formation were detected using immunoblotting and immunhistochemistry in diaphragm specimens (thoracotomy) obtained from six patients with severe COPD, six patients with moderate COPD, and seven control subjects. MAIN RESULTS Diaphragms of patients with severe COPD showed both higher protein carbonyl groups and hydroxynonenal-protein adducts than control subjects. When only considering patients with COPD, negative correlations were found between carbonyl groups and airway obstruction, and between hydroxynonenal-protein adducts and respiratory muscle strength. Although diaphragmatic neuronal nitric oxide synthase did not differ among the three groups and no inducible nitric oxide synthase was detected in any muscle, muscle endothelial nitric oxide synthase was lower in patients with severe COPD than in control subjects. Muscle nitrotyrosine levels were similar in both patients with severe COPD and control subjects. CONCLUSIONS This study shows that oxidative stress rather than nitric oxide is likely to be involved in the respiratory muscle dysfunction in severe COPD.
Arabidopsis MYB24 Regulates Jasmonate-Mediated Stamen Development

The phytohormone jasmonates (JAs) regulate various defense responses and diverse developmental processes including stamen development and fertility. Previous studies showed that JA induces CORONATINE INSENSITIVE 1-mediated degradation of JA ZIM-domain (JAZ) proteins, and activates the MYB transcription factors (such as MYB21 and MYB24) to regulate stamen development. In this study, we further uncover the mechanism underlying how MYB24 interacts with JAZs to control JA-regulated stamen development. We show that N-terminus of MYB21/24 interacts with 10 out of 12 JAZ proteins while both N-terminus and C-terminus of MYB24 are involved in dimerization of MYB21 and MYB24. Interestingly, male sterility of the JA-deficient mutant opr3 can be rescued by suitable level of the MYB24 overexpression but not by excessive high level of MYB24. Surprisingly, overexpression of MYB24NT, but not MYB24CT, could cause male sterility. These results provide new insights on MYB factors in JA-regulated stamen development.
Effects of N-acetylcysteine on liver remote injury after skeletal muscle ischemia reperfusion in rats.

BACKGROUND/AIMS This study evaluated the effects of N-acetylcysteine as a scavenger of radical oxygen species on liver injury as a remote organ after skeletal muscle ischemia reperfusion. MATERIALS AND METHODS Twenty male Wistar rats were allocated randomly into two experimental groups: ischemia reperfusion (I/R) and ischemia reperfusion + N-acetylcysteine (I/R+NAC). All animals were undergone 2h of ischemia by occlusion femoral artery and 24h of reperfusion. Rats that were treated with N-acetylcysteine given intravenously at a dose of 150 mg/kg, immediately before reperfusion. Serum levels of aspartate aminotransferase (AST), and alanine aminotransferase (ALT) were measured. Livers were harvested for histopathological and biochemical studies. Liver tissue malondialdehyde (MDA), glutathione (GSH) and myeloperoxidase (MPO) activity were assayed. RESULTS The ALT and AST values were significantly lower in I/R+NAC group. Hepatic MDA level and MPO activity were significantly increased in I/R group. The levels of GSH in liver tissue were significantly depressed by ischemia reperfusion. Liver histopathologic study in I/R group showed enlarged sinusoids, sinusoidal congestion, cytoplasmic vacuolation, cellular degenerative changes and necrosis. Histopathologically, there was a significant difference between two groups. CONCLUSION Histopatological and biochemical results have shown that N-acetylcysteine was able to protect liver from skeletal muscle ischemia reperfusion injury.
Persistent elevation of aminotransferases in liver transplant in association with chronic norovirus infection

Corresponding author : Ammar Abdulaziz Khayat Department of Pediatric Gastroenterology, Medical College of Wisconsin, 8701 W Watertown Plank Road, Milwaukee, WI 53226, USA Tel: +1-414-955-8296, Fax: +1-414-266-3676 E-mail: Ammarkhayat307@hotmail.com https://orcid.org/0000-0002-4819-9552 Abbreviations: ALT, alanine aminotransferase; AST, aspartate aminotransferase; CMV, cytomegalovirus; C. diff, Clostridium difficile; EBV, Epstein-Barr virus; HHV, human herpes virus; IVIG, intravenous immunoglobulin
Air quality monitoring in Mega city

Particulate matter (PM) including PM10 and PM2.5 is sampled widely in many areas of the world because high concentrations can degrade air quality. Our group monitors PM2.5 in Osaka, which is the second largest metropolitan area in Japan. Industrial plants and highways are located near our observation site. A clear atmosphere is rare in this area, and the air is usually polluted with suspended particles emitted from vehicles and industries. We have various ground measurement devices on the campus of Kinki University in Osaka. These devices include the AERONET (aerosol robotics network) radiometer, a PM sampler, and LIDAR (light detection and ranging) equipment. In this work, we investigate the seasonal variation of air quality in Osaka using observation data.
Social media’s enduring effect on adolescent life satisfaction

In this study, we used large-scale representative panel data to disentangle the between-person and within-person relations linking adolescent social media use and well-being. We found that social media use is not, in and of itself, a strong predictor of life satisfaction across the adolescent population. Instead, social media effects are nuanced, small at best, reciprocal over time, gender specific, and contingent on analytic methods.
Beyond PD-1/PD-L1 Inhibition: What the Future Holds for Breast Cancer Immunotherapy

Cancer immunotherapy has altered the management of human malignancies, improving outcomes in an expanding list of diseases. Breast cancer - presumably due to its perceived low immunogenicity - is a late addition to this list. Furthermore, most of the focus has been on the triple negative subtype because of its higher tumor mutational load and lymphocyte-enriched stroma, although emerging data show promise on the other breast cancer subtypes as well. To this point the clinical use of immunotherapy is limited to the inhibition of two immune checkpoints, Programmed Cell Death Protein 1 (PD-1) and Cytotoxic T-lymphocyte-associated Protein 4 (CTLA-4). Consistent with the complexity of the regulation of the tumor – host interactions and their lack of reliance on a single regulatory pathway, combinatory approaches have shown improved efficacy albeit at the cost of increased toxicity. Beyond those two checkpoints though, a large number of co-stimulatory or co-inhibitory molecules play major roles on tumor evasion from immunosurveillance. These molecules likely represent future targets of immunotherapy provided that the promise shown in early data is translated into improved patient survival in randomized trials. The biological role, prognostic and predictive implications regarding breast cancer and early clinical efforts on exploiting these immune-related therapeutic targets are herein reviewed.
Health Claims: Let Science Prevail

levels at or above 0.3% of total fatty acids and visual function at 12 months in formula-fed infants, and also in breastfed infants receiving such formulae after weaning [3] . EFSA concluded that the wording ‘DHA contributes to the visual development of infants’ reflects the scientific evidence but should be restricted to formulae that contain at least 0.3% of the total fatty acids as DHA. While this seemed like a straightforward case based on adequate scientific data, an activist group in the United Kingdom embarked on active lobbying against the adoption of this health claim, apparently driven by the conviction that no infant food should bear health claims. The activist group convinced some members of the European Parliament to support its cause and to propose the cited resolution, which has adopted a number of pseudoscientific arguments of the activists, unfortunately without critical evaluation of their validity. The adopted resolution reports that scientific evidence shows a benefit of DHA in breast milk for the visual development of infants, whereas such effects of DHA in formula had not been demonstrated. To support this conclusion, one single systematic review is cited which states that there would be no conclusive evidence for benefits of adding the -3 fatty acid DHA to infant formulae, although the authors acknowledged that some studies found benefits on visual function [4] . However, in contrast to the EFSA analysis, these authors did not consider the amount of DHA added to formula as a predictor of outcome. On March 16, 2011, a slight majority of members of the European Parliament’s Committee on Environment, Public Health and Food Safety adopted a resolution aiming at the refusal of authorising a health claim on infant foods (30 votes in favour, 28 against, 1 abstention) [1] . This resolution opposes the adoption of the health claim ‘Docosahexaenoic acid (DHA) intake contributes to the normal visual development of infants up to 12 months of age’, which had been recommended for adoption by both the European Commission and the Standing Committee on Food of the European Member States. Following this committee vote, the European Parliament’s plenary will now have to take a decision in the near future as to whether it supports or rejects the adoption of this health claim. How did this amazing controversy evolve? The European regulation on health claims for foods stipulates that these should be truthful and based on generally accepted scientific evidence of the relationship between diet and health [2] . Scientific substantiation should be the main aspect to be taken into account for the use of nutrition and health claims, and it should be based on the totality of available scientific data [2] . The European Food Safety Authority (EFSA) has been charged to perform this scientific evaluation, with the help of qualified scientists. In the current case, EFSA has reviewed the available evidence. It concluded that a cause and effect relationship is established between the intake of infant and follow-on formulae supplemented with docosahexaenoic acid (DHA) at Published online: March 31, 2011
Population Studies of Methicillin-Resistant and -Sensitive Staphylococcus aureus Strains Reveal a Lack of Variability in the agrD Gene, Encoding a Staphylococcal Autoinducer Peptide

ABSTRACT The virulence of Staphylococcus aureus is controlled by the accessory gene regulator (agr) system, including an extracellular inducer encoded by agrD. Variableagr PCR restriction fragment length polymorphism (RFLP) patterns of unique S. aureus strains (n = 192) were determined for a region comprising agrD and parts of the neighboring agrC and agrB genes. Twelve unique RFLP patterns were identified among S. aureusstrains in general; these patterns were further specified by sequencing. All sequences could be catalogued in the three currentagr groups. A major proportion of the S. aureusstrains belong to agr group 1, whereas only 6% of the methicillin-susceptible S. aureus strains and 5% of the methicillin-resistant S. aureus strains belong toagr groups 2 and 3, respectively. The homology between groups varied from 75 to 80%, and within groups it varied from 96 to 100%. Different levels of sequence variability were observed in the different agr genes. agr-related bacterial interference among colonizing S. aureus strains in the noses of persistent and intermittent human carriers was studied.S. aureus strains belonging to different agr groups were encountered in the same individual. This may suggest that the activity of the agrD gene product does not define colonization dynamics, which is further substantiated by the rarity ofagr group 2 and 3 strains.
Evolution of corticosteroid specificity for human, chicken, alligator and frog glucocorticoid receptors

We investigated the evolution of the response of human, chicken, alligator and frog glucocorticoid receptors (GRs) to dexamethasone, cortisol, corticosterone, 11-deoxycorticosterone, 11-deoxycortisol and aldosterone. We find significant differences among these vertebrates in the transcriptional activation of their full length GRs by these steroids, indicating that there were changes in the specificity of the GR for steroids during the evolution of terrestrial vertebrates. To begin to study the role of interactions between different domains on the GR in steroid sensitivity and specificity for terrestrial GRs, we investigated transcriptional activation of truncated GRs containing their hinge domain and ligand binding domain (LBD) fused to a GAL4 DNA binding domain (GAL4 DBD). Compared to corresponding full length GRs, transcriptional activation of GAL4 DBD-GR hinge/LBD constructs required higher steroid concentrations and displayed altered steroid specificity, indicating that interactions between the hinge/LBD and other domains are important in glucocorticoid activation of these terrestrial GRs.
Non-selective inhibition of inappropriate motor-tendencies during response-conflict by a fronto-subthalamic mechanism

To effectively interact with their environment, humans must often select actions from multiple incompatible options. Existing theories propose that during motoric response-conflict, inappropriate motor activity is actively (and perhaps non-selectively) suppressed by an inhibitory fronto-basal ganglia mechanism. We here tested this theory across three experiments. First, using scalp-EEG, we found that both outright action-stopping and response-conflict during action-selection invoke low-frequency activity of a common fronto-central source, whose activity relates to trial-by-trial behavioral indices of inhibition in both tasks. Second, using simultaneous intracranial recordings from the basal ganglia and motor cortex, we found that response-conflict increases the influence of the subthalamic nucleus on M1-representations of incorrect response-tendencies. Finally, using transcranial magnetic stimulation, we found that during the same time period when conflict-related STN-to-M1 communication is increased, cortico-spinal excitability is broadly suppressed. Together, these findings demonstrate that fronto-basal ganglia networks buttress action-selection under response-conflict by rapidly and non-selectively net-inhibiting inappropriate motor tendencies.
Modelling pitch accents for concept-to-speech synthesis.

This paper addresses the problem of generating a full range of appropriate intonation contours for concept-to-speech synthesis systems where there is a specific requirement to produce different semantic meanings and contrasts through intonation. We show improvements through the appropriate use of prosodic structure and by improving the way in which individual accent shapes are modelled.
Metalloproteinases, inflammation, and rheumatoid arthritis

Ideally, the inflammatory response occurs rapidly to terminate infection. It also must halt in a timely manner to stop this reaction from inflicting self damage. Such a highly regulated process results from altering balances in pro- and anti-inflammatory signals orchestrated by multiple cell types and factors within the tissue microenvironment. The discovery of new substrates of metalloproteinases within this microenvironment has disclosed a new function in inflammation. The role of these proteases now extends beyond extracellular matrix remodelling enzymes to that of mediators of inflammatory signals involving various chemokines and cytokines. As natural inhibitors of these metalloproteinases, TIMPs have the potential of regulating the inflammatory response and affecting diseases such as rheumatoid arthritis. TIMP-3, in particular, stands out as an important regulator of inflammation with its ability to specifically inhibit proinflammatory cytokines and tissue destruction in the joint.
Requirements for effective malaria control with homing endonuclease genes

Malaria continues to impose a substantial burden on human health. We have previously proposed that biological approaches to control the mosquito vector of disease could be developed using homing endonuclease genes (HEGs), a class of selfish or parasitic gene that exists naturally in many microbes. Recent lab studies have demonstrated that HEGs can function in mosquitoes. We constructed and analyzed a model of mosquito population genetics and malaria epidemiology to determine how well HEGs need to function in order to have a significant effect on the burden of disease. Our model, combined with currently available data, indicates that populations of Anopheles gambiae could be eliminated by releasing 2–3 HEGs targeting female fertility genes, or a driving-Y chromosome that is transmitted to 75–96% of progeny. Combinations of fertility-targeting HEGs and Y drive may also be effective. It is possible to eliminate the disease without eliminating the vector, but the parameter space producing this outcome appears to be small. HEGs causing a quantitative reduction in adult survival can be more effective than those targeting female fertility, but the selection coefficients that need to be imposed are still large, unless many HEGs are to be released. Simulations show that HEG-based strategies can be effective over socially relevant time frames. Important limiting assumptions of the models are that there is only a single vector species, and we model a homogeneous population, not a landscape. Nevertheless, we conclude that HEG-based approaches could have a transformational effect on malaria control efforts.
Genetic and Environmental Influences on Serum Lipid Tracking: A Population-Based, Longitudinal Chinese Twin Study

We conducted cross-sectional and longitudinal twin analysis to explore genetic and environmental contribution to serum lipid tracking during childhood and adolescence. The study sample was part of a population-based twin cohort that was recruited in the rural areas of the Anhui Province of China. The baseline recruitment of twins was carried out from 1998 through 2000 and the follow-up from 2005 through 2007. Serum lipids showed significant tracking during childhood and adolescence. Participants with lipids at the highest tertile at the baseline tended to remain high at follow-up across ages and Tanner stages, whereas subjects with lipids at the lowest tertile at the baseline tended to remain low at follow-up. Using twin modeling, we showed that genetic and environmental factors contributed to individual variations in lipid levels and tracking from the baseline to the follow-up visit. The estimated tracking correlations for total cholesterol, triglyceride, and LDL cholesterol were in the range of 0.25–0.53 and were predominantly influenced by genetic factors. In contrast, the phenotypic tracking of HDL cholesterol was influenced by both genetic and environmental factors. Our study underscores the importance of considering both environmental and genetic factors in studying the etiology of dyslipidemia.
New Insights into the Cyp51 Contribution to Azole Resistance in Aspergillus Section Nigri

Invasive aspergillosis (IA) is a severe condition mainly caused by Aspergillus fumigatus, although other species of the genus, such as section Nigri members, can also be involved. Voriconazole (VRC) is the recommended treatment for IA; however, the prevalence of azole-resistant Aspergillus isolates has alarmingly increased in recent years, and the underlying resistance mechanisms in non-fumigatus species remain unclear. ABSTRACT Invasive aspergillosis (IA) is a severe condition mainly caused by Aspergillus fumigatus, although other species of the genus, such as section Nigri members, can also be involved. Voriconazole (VRC) is the recommended treatment for IA; however, the prevalence of azole-resistant Aspergillus isolates has alarmingly increased in recent years, and the underlying resistance mechanisms in non-fumigatus species remain unclear. We have determined the in vitro susceptibility of 36 strains from section Nigri to VRC, posaconazole (POS), and itraconazole (ITC), and we have explored the role of Cyp51A and Cyp51B, both targets of azoles, in azole resistance. The three drugs were highly active; POS displayed the best in vitro activity, while ITC and VRC showed MICs above the established epidemiological cutoff values in 9 and 16% of the strains, respectively. Furthermore, expression studies of cyp51A and cyp51B in control condition and after VRC exposure were performed in 14 strains with different VRC susceptibility. We found higher transcription of cyp51A, which was upregulated upon VRC exposure, but no correlation between MICs and cyp51 transcription levels was observed. In addition, cyp51A sequence analyses revealed nonsynonymous mutations present in both, wild-type and non-wild-type strains of A. niger and A. tubingensis. Nevertheless, a few mutations were exclusively present in non-wild-type A. tubingensis strains. Altogether, our results suggest that azole resistance in section Nigri is not clearly explained by Cyp51A protein alteration or by cyp51 gene upregulation, which indicates that other mechanisms might be involved.