Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic coupling and finite element discretization of the Navier–Stokes and heat equations

We consider the finite element discretization of the Navier–Stokes equations coupled with the heat equation where the viscosity depends on the temperature. We prove a posteriori error estimates which allow us to automatically determine the zone where the temperature-dependent viscosity must be inserted into the Navier–Stokes equations and also to perform mesh adaptivity in order to optimize the discretization of these equations. Résumé: Nous considérons une discrétisation par éléments finis des équations de Navier– Stokes couplées avec l’équation de la chaleur là où la viscosité dépend de la température. Nous prouvons des estimations d’erreur a posteriori qui permettent de déterminer automatiquement la zône où cette viscosité doit être insérée dans les équations de Navier–Stokes et simultanément d’adapter le maillage pour optimiser la discrétisation de ces équations. ∗ Laboratoire Jacques-Louis Lions, C.N. R.S. & Université Pierre et Marie Curie Paris 6, bôıte 187, 4 place Jussieu, 75252 Paris Cedex 05, France. † Present address: C.M.A.P. (U.M.R. 7641 du C.N.R.S.), École Polytechnique, Route de Saclay, 91128 Palaiseau Cedex, France. bernardi@ann.jussieu. fr, coquel@ann.jussieu. fr, raviart@ann.jussieu. fr
Synthesis and characterization of eggshell-derived hydroxyapatite via mechanochemical method: A comparative study

The focus of bone graft properties has developed through generations, from the ability to withstand mechanical stress to the ability to integrate with the biological structure. In recent years, the use of hydroxyapatite (HA) as bone graft material in orthopedic and dental applications has been increasing. HA is a natural occuring mineral with excellent bioactivity but relatively poor mechanical properties. It constitutes 96% portion of enamel in teeth and 67% portion of bone. HA can be extracted from animal bones or fabricated from synthetic or biologic sources. In this study, eggshells were used as raw material to synthesize eggshell-derived HA (EHA) via mechanochemical method. The synthesis of EHA involved CaO, which was obtained from the calcination of eggshells, and reaction with dicalcium hydrogen phosphate dihydrous (DCPD) or phosphoric acid (H3PO4). The effects of rotational speed and heat treatment temperature on EHA’s characteristics were investigated. The characterization studies were carried ou.
Below and beyond the recognition of emotional facial expressions in alcohol dependence: from basic perception to social cognition

Studies that have carried out experimental evaluation of emotional skills in alcohol-dependence have, up to now, been mainly focused on the exploration of emotional facial expressions (EFE) decoding. In the present paper, we provide some complements to the recent systematic literature review published by Donadon and de Lima Osório on this crucial topic. We also suggest research avenues that must be, in our opinion, considered in the coming years. More precisely, we propose, first, that a battery integrating a set of emotional tasks relating to different processes should be developed to better systemize EFE decoding measures in alcohol-dependence. Second, we propose to go below EFE recognition deficits and to seek for the roots of those alterations, particularly by investigating the putative role played by early visual processing and vision–emotion interactions in the emotional impairment observed in alcohol-dependence. Third, we insist on the need to go beyond EFE recognition deficits by suggesting that they only constitute a part of wider emotional deficits in alcohol-dependence. Importantly, since the efficient decoding of emotions is a crucial ability for the development and maintenance of satisfactory interpersonal relationships, we suggest that disruption of this ability in alcohol-dependent individuals may have adverse consequences for their social integration. One way to achieve this research agenda would be to develop the field of affective and social neuroscience of alcohol-dependence, which could ultimately lead to major advances at both theoretical and therapeutic levels.
Differential Response of Oyster Shell Powder on Enzyme Profile and Nutritional Value of Oyster Mushroom Pleurotus florida PF05

Oyster mushroom Pleurotus florida was cultivated on different combinations of wheat straw (WS) as basal substrate and oyster shell powder (OSP) supplement. The OSP supplementation considerably responded to different cultivation phases. The mycelium grew fast and showed rapid growth rate (8.91 mmd−1) in WS + OSP (97 + 3) combination while WS + OSP (92 + 8) showed maximum laccase (3.133 U/g) and Mn peroxidase (MnP) activities (0.091 U/g). The climax level of laccase (5.433 U/g) and MnP (0.097 U/g) was recorded during fruit body initiation in WS + OSP (97 + 3) and WS + OSP (98 + 2) combinations, respectively. The WS + OSP (97 + 3) combination represented the best condition for mushroom cultivation and produced the highest biological efficiency (147%). In addition, protein and lipid contents in fruit bodies were slightly improved in response to OSP. The carbohydrate was significantly increased by raising concentration of OSP. The highest values of protein, carbohydrate, and lipid noted were 31.3 μg/g, 0.0639 (g/g), and 0.373 (g/g) correspondingly. Conclusively it was evident that lower concentrations of OSP acted positively and relatively to higher concentrations and improved nutritional content which may suitably be used to enhance both yield and nutritional values of mushroom.
Metabolic crisis occurs with seizures and periodic discharges after brain trauma

Traumatic brain injury (TBI) results in persistent disruption of brain metabolism that has yet to be mechanistically defined. Early post‐traumatic seizures are one potential mechanism for metabolic crisis and hence could be a therapeutic target. We hypothesized that seizures and pseudoperiodic discharges (PDs) may be mechanistically linked to metabolic crisis as measured by cerebral microdialysis.
A hybrid phonotactic language identification system with an SVM back-end for simultaneous lecture translation

In this paper we describe our work in constructing a language identification system for use in our simultaneous lecture translation system. We first built PPR and PPRLM baseline systems that produce score-fusing language cue feature vectors for language discrimination and utilize an SVM back-end classifier for the actual language identification. On our bi-lingual lecture tasks the PPRLM system clearly outperforms the PPR system in various segment length conditions, however at the cost of slower run-time. By using lexical information in the form of keyword spotting, and additional language models we show ways to improve the performance of both baseline systems. In order to combine the faster run-time of the PPR system with the better performance of the PPRLM system we finally built a hybrid of both approaches that clearly outperforms the PPR system while not adding any additional computing time. This hybrid system is therefore our choice for the use in the lecture translation system due to its faster run-time and good performance.
Social Network Effects on the Transmission of Sexually Transmitted Diseases

Background Only a limited number of studies have examined the effects of social networks on sexually transmitted diseases (STDs), although the findings of such studies would be helpful in designing more effective prevention strategies. Goal This study attempts (1) to determine whether there are any social network effects on STD transmission after controlling for other risk factors and (2) to explore the possible mechanisms by which social networks exert their effects. Study Design Logistic regressions examine the effects of friendship networks on STD transmission using data drawn from the Chicago Health and Social Life Survey (CHSLS). Additional logistic regressions probe the possible mechanisms (social control versus information and dyadic versus third party) that account for how the observed effects of networks might arise. Results and Conclusion Among people who had fewer than 13 lifetime sex partners, those with no social friends were only 0.4 times as likely to be infected as those with one or more social friends. Among people who had 13 or more lifetime partners, those with many friends (5 or 6) but weak ties to them (talking less than once a day with them) were only 0.2 times as likely to be infected as those with either fewer friends or stronger ties to their friends. Additional regressions suggest that network effects resting on dyadic control prevail among those with fewer than 13 lifetime sex partners. In contrast, network effects resting on information exchange among third parties prevail among those with 13 or more lifetime partners.
Gemcitabine, a broad-spectrum antiviral drug, suppresses enterovirus infections through innate immunity induced by the inhibition of pyrimidine biosynthesis and nucleotide depletion

Gemcitabine, an anti-cancer chemotherapy drug, has additionally shown the antiviral activity against a broad range of viruses and we also have previously reported its synergistic antiviral activity with ribavirin against enteroviruses. As a cytidine analog, gemcitabine has been reported to have an inhibitory activity on the pyrimidine biosynthesis. In addition, a few inhibitors of the pyrimidine biosynthesis have shown to induce the innate immunity in a yet-to-be-determined manner and inhibit the virus infection. Thus, we also investigated whether the anti-enteroviral activity of gemcitabine is mediated by innate immunity, induction of which is related with the inhibition of the pyrimidine synthesis. In this study, we found that the addition of exogenous cytidine, uridine and uridine mono-phosphate (UMP) effectively reversed the antiviral activity of gemcitabine in enterovirus-infected as well as enteroviral replicon-harboring cells, demonstrating gemcitabine’s targeting of the salvage pathway. Moreover, the expression of several interferon (IFN)-stimulated genes (ISGs) was significantly induced by the treatment of gemcitabine, which was also suppressed by the co-treatment with cytidine. These results suggest that the antiviral activity of gemcitabine involves ISGs induced by the inhibition of the pyrimidine biosynthesis.
Difference-Huffman Coding of Multidimensional Databases

A new compression method called difference-Huffman coding (DHC) is introduced in this paper. It is verified empirically that DHC results in a smaller multidimensional physical representation than those for other previously published techniques (single count header compression, logical position compression, base-offset compression and difference sequence compression). The article examines how caching influences the expected retrieval time of the multidimensional and table representations of relations. A model is proposed for this, which is then verified with empirical data. Conclusions are drawn, based on the model and the experiment, about when one physical representation outperforms another in terms of retrieval time. Over the tested range of available memory, the performance for the multidimensional representation was always much quicker than for the table representation.
Low-Dose Physical Activity Attenuates Cardiovascular Disease Mortality in Men and Women With Clustered Metabolic Risk Factors

Background— Physical activity may ameliorate the health hazards of metabolic disorders but evidence is inconclusive, and estimates of the minimal threshold for protection remain unknown. Methods and Results— The sample comprised 23 747 men and women (aged 54.1 ± 12.7 years [mean±SD], 45.2% men) without a known history of cardiovascular disease at baseline who were drawn from the Health Survey for England and the Scottish Health Survey. Based on blood pressure, high-density lipoprotein cholesterol, diabetes, waist circumference, and low-grade inflammation (C-reactive protein ≥ 3 mg/L), participants were classified as metabolically healthy (zero or one metabolic abnormality) or unhealthy (≥ 2 metabolic abnormalities). Self-reported physical activity was assessed at baseline. Cox proportional hazards models were used to examine the association of clustered metabolic risk and physical activity with mortality, controlling for age, sex, smoking, socioeconomic group, cardiovascular disease medication, and self-rated health. Over 7.0 ± 3.0 years follow-up, there were 2264 all-cause and 717 cardiovascular disease deaths, respectively. A physical activity threshold of at least one to 2 sessions per week was found to provide protection against mortality. Compared with active/metabolically healthy, the active with clustered metabolic abnormalities were not at elevated risk of cardiovascular disease (hazard ratio, 0.82; 95% CI, 0.54 –1.26) or all-cause mortality (hazard ratio, 1.11; 95% CI, 0.89 –1.39), although their inactive counterparts were at elevated risk of cardiovascular disease (hazard ratio, 1.41; 95% CI, 1.05 –1.91) and all-cause mortality (hazard ratio, 1.50; 95% CI, 1.27–1.78). Conclusions— The risk of cardiovascular disease associated with poor metabolic health is substantially lower among those who are physically active. At minimum, a weekly bout of moderate to vigorous physical activity is protective in men and women with clustered metabolic abnormalities.
The therapeutic design of environments for people with dementia: further reflections and recent findings from the National Institute on Aging Collaborative studies of Dementia special care units.

The article by Day, Carreon, and Stump (2000) in the current issue provides an excellent, comprehensive review of findings related to environments for individuals with cognitive impairment. It is timely in that the environment was an area identified by experts as critical to specialized dementia care and was one focus of the ten National Institute on Aging (NIA) collaborative studies of Dementia Special Care Units (DSCUs). In addition to reflecting on the major conclusions in the article by Day and colleagues (2000), this commentary elaborates on the conceptualization and measurement of physical and social environments in long-term care settings, drawing heavily on the experiences and recent findings of the NIA DSCU studies.
Challenges of ligand identification for the second wave of orphan riboswitch candidates

ABSTRACT Orphan riboswitch candidates are noncoding RNA motifs whose representatives are believed to function as genetic regulatory elements, but whose target ligands have yet to be identified. The study of certain orphans, particularly classes that have resisted experimental validation for many years, has led to the discovery of important biological pathways and processes once their ligands were identified. Previously, we highlighted details for four of the most common and intriguing orphan riboswitch candidates. This facilitated the validation of riboswitches for the signaling molecules c-di-AMP, ZTP, and ppGpp, the metal ion Mn2+, and the metabolites guanidine and PRPP. Such studies also yield useful linkages between the ligands sensed by the riboswitches and numerous biochemical pathways. In the current report, we describe the known characteristics of 30 distinct classes of orphan riboswitch candidates – some of which have remained unsolved for over a decade. We also discuss the prospects for uncovering novel biological insights via focused studies on these RNAs. Lastly, we make recommendations for experimental objectives along the path to finding ligands for these mysterious RNAs.
Activity Dynamics and Signal Representation in a Striatal Network Model with Distance-Dependent Connectivity

Visual Abstract The striatum is the main input nucleus of the basal ganglia. Characterizing striatal activity dynamics is crucial to understanding mechanisms underlying action selection, initiation, and execution. Here, we studied the effects of spatial network connectivity on the spatiotemporal structure of striatal activity. We show that a striatal network with nonmonotonically changing distance-dependent connectivity (according to a gamma distribution) can exhibit a wide repertoire of spatiotemporal dynamics, ranging from spatially homogeneous, asynchronous-irregular (AI) activity to a state with stable, spatially localized activity bumps, as in “winner-take-all” (WTA) dynamics. Among these regimes, the unstable activity bumps [transition activity (TA)] regime closely resembles the experimentally observed spatiotemporal activity dynamics and neuronal assemblies in the striatum. In contrast, striatal networks with monotonically decreasing distance-dependent connectivity (in a Gaussian fashion) can exhibit only an AI state. Thus, given the observation of spatially compact neuronal clusters in the striatum, our model suggests that recurrent connectivity among striatal projection neurons should vary nonmonotonically. In brain disorders such as Parkinson’s disease, increased cortical inputs and high striatal firing rates are associated with a reduction in stimulus sensitivity. Consistent with this, our model suggests that strong cortical inputs drive the striatum to a WTA state, leading to low stimulus sensitivity and high variability. In contrast, the AI and TA states show high stimulus sensitivity and reliability. Thus, based on these results, we propose that in a healthy state the striatum operates in a AI/TA state and that lack of dopamine pushes it into a WTA state.
Clinical Utility of Insulin-Like Growth Factor 1 and 2; Determination by High Resolution Mass Spectrometry

Measurement of insulin-like growth factor-1 (IGF-I) has utility for the diagnosis and management of growth disorders, but inter-assay comparison of results has been complicated by a multitude of reference standards, antibodies, detection methods, and pre-analytical preparation strategies. We developed a quantitative LC-MS method for intact IGF-I, which has advantages in throughput and complexity when compared to mass spectrometric approaches that rely on stable isotope dilution analysis of tryptic peptides. Since the method makes use of full-scan data, the assay was easily extended to provide quantitative measurement of IGF-II using the same assay protocol. The validated LC-MS assay for IGF-I and IGF-II provides accurate results across the pediatric and adult reference range and is suitable for clinical use.
Diabetic Retinopathy in Native and Nonnative Canadians

High prevalence rates of type 2 diabetes are being observed in native Canadian communities. It is believed that native populations have a higher prevalence rate of vascular complications than nonnatives. The Southern Alberta Study of Diabetic Retinopathy (DR) examined the prevalence and incidence of DR and associated metabolic abnormalities in native and nonnative subjects. Prevalence rates of DR in type 2 diabetic native and nonnative subjects were identical, with a prevalence rate of 40%. Native subjects with retinopathy, however, tended to have more advanced changes of retinopathy compared to the nonnative subjects. Key factors such as A1c, blood pressure, duration of diabetes, and lipid values were not significantly different between the two cohorts. These data indicate that ethnicity does play a role in the development and severity of DR but potential risk factors that may affect the development of retinopathy are not significantly different between native and nonnative groups.
Computerized temporal handwriting characteristics of proficient and non-proficient handwriters.

OBJECTIVE The purpose of this study was to use computerized temporal measures to examine and compare the writing process of proficient and non-proficient third-grade handwriters. METHOD A computerized digitizer system was used to compare the temporal handwriting measures of two groups of 8-9-year-old students. Classroom teachers used a questionnaire to identify 50 students who were non-proficient handwriters and 50 students who were proficient handwriters. Multivariate analysis of variance (MANOVA) analyses were used to test for the group differences across tasks for each dependent variable. Total time, "on paper" time, "in air" time, speed, and number of characters per minute were recorded as the participants performed graded writing tasks. RESULTS Non-proficient handwriters required significantly more time to perform handwriting tasks [F(4,91) = 14.83, p < . 0001]; their "in air" time, was especially longer as compared to the proficient handwriters [F(4,91) = 13.63, p < . 0001]. Their handwriting speed was slower [F(4,91) = 5.99, p < . 0002], and they wrote fewer characters per minute (F(4,91) = 14.63, p < . 0001). CONCLUSION The use of a computerized handwriting system provides objective temporal measures of handwriting performance, and may lead to the development of additional tools for the evaluation and treatment of handwriting difficulties.
Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome.

CTD kinase I (CTDK-I) of Saccharomyces cerevisiae is required for normal phosphorylation of the C-terminal repeat domain (CTD) on elongating RNA polymerase II. To elucidate cellular roles played by this kinase and the hyperphosphorylated CTD (phosphoCTD) it generates, we systematically searched yeast extracts for proteins that bound to the phosphoCTD made by CTDK-I in vitro. Initially, using a combination of far-western blotting and phosphoCTD affinity chromatography, we discovered a set of novel phosphoCTD-associating proteins (PCAPs) implicated in a variety of nuclear functions. We identified the phosphoCTD-interacting domains of a number of these PCAPs, and in several test cases (namely, Set2, Ssd1, and Hrr25) adduced evidence that phosphoCTD binding is functionally important in vivo. Employing surface plasmon resonance (BIACORE) analysis, we found that recombinant versions of these and other PCAPs bind preferentially to CTD repeat peptides carrying SerPO(4) residues at positions 2 and 5 of each seven amino acid repeat, consistent with the positional specificity of CTDK-I in vitro [Jones, J. C. , et al. (2004) J. Biol. Chem. 279, 24957-24964]. Subsequently, we used a synthetic CTD peptide with three doubly phosphorylated repeats (2,5P) as an affinity matrix, greatly expanding our search for PCAPs. This resulted in identification of approximately 100 PCAPs and associated proteins representing a wide range of functions (e.g., transcription, RNA processing, chromatin structure, DNA metabolism, protein synthesis and turnover, RNA degradation, snRNA modification, and snoRNP biogenesis). The varied nature of these PCAPs and associated proteins points to an unexpectedly diverse set of connections between Pol II elongation and other processes, conceptually expanding the role played by CTD phosphorylation in functional organization of the nucleus.