Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimizing the Definition of a Sudden Stratospheric Warming

AbstractVarious criteria exist for determining the occurrence of a major sudden stratospheric warming (SSW), but the most common is based on the reversal of the climatological westerly zonal-mean zonal winds at 60° latitude and 10 hPa in the winter stratosphere. This definition was established at a time when observations of the stratosphere were sparse. Given greater access to data in the satellite era, a systematic analysis of the optimal parameters of latitude, altitude, and threshold for the wind reversal is now possible. Here, the frequency of SSWs, the strength of the wave forcing associated with the events, changes in stratospheric temperature and zonal winds, and surface impacts are examined as a function of the stratospheric wind reversal parameters. The results provide a methodical assessment of how to best define a standard metric for major SSWs. While the continuum nature of stratospheric variability makes it difficult to identify a decisively optimal threshold, there is a relatively narrow env.
Factors Associated with Suicide in Four Age Groups: A Population Based Study

Life events and circumstances leading to death change throughout the life course. In this study, 4 age groups within those who have died by suicide are compared in terms method of suicide, sex, occupation, mental disorders, prior suicide attempts, and life events prior to death. Analyses were based on a database of deaths by suicide and undetermined intent based on data in the Northern Ireland (NI) coronial files from 2005–2011 (N = 1667). Research determined that hanging is very prominent as a method of death within the under-20 age group. Women who die by suicide are more likely to have a known mental disorder than men, and the proportions increase with age group. Relationship difficulties are associated with many of these deaths and particularly for males aged under 40 years. Physical health and life events were more relevant than mental illness per se, in males aged over 61 years. For a sizeable proportion of the cases included in the current database there was no information on the life events prior to death. Understanding the factors associated with suicide across age groups is essential to informing suicide prevention strategy and programs and the development of more nuanced and effective interventions.
Quercetin promotes the apoptosis of fibroblast-like synoviocytes in rheumatoid arthritis by upregulating lncRNA MALAT1.

Rheumatoid arthritis (RA) is a chronic autoimmune joint disease and fibroblast-like synoviocytes (FLS) are the resident mesenchymal cells of synovial joints. Quercetin is a dietary antioxidant. In this study, we aimed to explore the mechanisms responsible for the quercetin-induced apoptosis of FLS from patients with RA (termed RAFLS). RAFLS viability was determined following treatent of the cells with or without quercetin using the Cell Counting kit-8 (CCK-8) assay. The apoptosis of the RAFLS was analyzed using the Annexin V-fluorescein isothiocyanate (FITC) apoptosis detection kit I. The results revealed that RAFLS viability decreased and apoptosis increased in following treatment with quercetin. The differentially expressed long non-coding RNAs (lncRNAs) were screened and marked by PCR array following treatment with quercetin. The expression levels of the screened lncRNAs were then determined and compared in the cells treated with or without quercetin by quantitative PCR. The lncRNA metastasis associated lung adenocarcinoma transcript 1 (MALAT1) was finally selected. Small interfering RNA (siRNA) was then used to knock down the expression of MALAT1 in order to determine the role of MALAT1 in the quercetin-induced apoptosis of RAFLS. The results revealed that the knockdown of MALAT1 inhibited RAFLS apoptosis. At the same time, the expression of caspase-3 and caspase-9 was significantly decreased in the cells in which MALAT1 was knocked down. The phosphoinositide 3-kinase (PI3K)/AKT signaling pathway was activated; this activation is known to be associated with enhanced cell proliferation and decreased apoptosis. The findings of our study indicate that quercetin promotes RAFLS apoptosis by upregulating lncRNA MALAT1, and that MALAT1 induces apoptosis by inhibiting the activation of the PI3K/AKT pathway.
Social Mediation of Persuasive Media in Adolescent Substance Prevention

Social commentary about prevention messages may affect their likelihood of acceptance. To investigate this possibility, student participants (N = 663) viewed 3 antimarijuana advertisements, each followed immediately by videotaped discussions involving 4 adults or 4 adolescents using either extreme or moderate language in their positive commentaries. The commentaries were expected to affect participants’ perceptions of the extent to which the ads were designed to control their behavior (perceived control), which was hypothesized to inhibit persuasion. Two indirect effects analyses were conducted. Marijuana attitudes and usage intentions were the outcome variables. Both analyses revealed statistically significant source by language interactions on participants’ perceived control (both p < .02). Further analyses revealed significant indirect effects of language extremity on attitudes and intentions through perceived control with adult, but not peer sources (both p < .05). These perceptions were associated with more negative marijuana attitudes and diminished usage intentions when adults used moderate (vs. extreme) language in their favorable ad commentaries (both p < .05). The findings may facilitate development of more effective prevention methods that emphasize the importance of the role of perceived control in persuasion, and the impact of interpersonal communication variations on acceptance of media-transmitted prevention messages.
Owls, larks, swifts, woodcocks and they are not alone: A historical review of methodology for multidimensional self-assessment of individual differences in sleep-wake pattern

ABSTRACT Differences between the so-called larks and owls representing the opposite poles of morningness-eveningness dimension are widely known. However, scientific consensus has not yet been reached on the methodology for ranking and typing people along other dimensions of individual variation in their sleep-wake pattern. This review focused on the history and state-of-the-art of the methodology for self-assessment of individual differences in more than one trait or adaptability of the human sleep-wake cycle. The differences between this and other methodologies for the self-assessment of trait- and state-like variation in the perceived characteristics of daily rhythms were discussed and the critical issues that remained to be addressed in future studies were highlighted. These issues include a) a failure to develop a unidimensional scale for scoring chronotypological differences, b) the inconclusive results of the long-lasting search for objective markers of chronotype, c) a disagreement on both number and content of scales required for multidimensional self-assessment of chronobiological differences, d) a lack of evidence for the reliability and/or external validity of most of the proposed scales and e) an insufficient development of conceptualizations, models and model-based quantitative simulations linking the differences between people in their sleep-wake pattern with the differences in the basic parameters of underlying chronoregulatory processes. It seems that, in the nearest future, the wide implementation of portable actigraphic and somnographic devices might lead to the development of objective methodologies for multidimensional assessment and classification of sleep-wake traits and adaptabilities.
Wander Join and XDB: Online Aggregation via Random Walks

Joins are expensive, and online aggregation is an effective approach to explore the tradeoff between query efficiency and accuracy in a continuous, online fashion. However, the stateof- the-art approach, in both internal and external memory, is based on ripple join, which is still very expensive and needs strong assumptions (e.g., the tuples in a table are stored in random order). This paper proposes a new approach, the wander join algorithm, to the online aggregation problem by performing random walks over the underlying join graph. We also design an optimizer that chooses the optimal plan for conducting the random walks without having to collect any statistics a priori. Selection predicates and group-by clauses can be handled as well. We have developed an online engine called XDB by integrating wander join in the latest version of PostgreSQL. Extensive experiments using the TPC-H benchmark have shown the superior performance of wander join. The XDB implementation has demonstrated its practicality in a full-fledged database system.
Author ’ s Accepted Manuscript Variability in functional brain networks predicts expertise during action observation

Observing an action performed by another individual activates, in the observer, similar circuits as those involved in the actual execution of that action. This activation is modulated by prior experience; indeed, sustained training in a particular motor domain leads to structural and functional changes in critical brain areas. Here, we capitalized on a novel graph-theory approach to electroencephalographic data [1] to test whether variability in functional brain networks implicated in Tango observation can discriminate between groups differing in their level of expertise. We found that experts and beginners significantly differed in the functional organization of task-relevant networks. Specifically, networks in expert Tango dancers exhibited less variability and a more robust functional architecture. Notably, these expertise-dependent effects were captured within networks derived from electrophysiological brain activity recorded in a very short time window (2 s). In brief, variability in the organization of task-related networks seems to be a highly sensitive indicator of long-lasting training effects. This finding opens new methodological and theoretical windows to explore the impact of domain-specific expertise on brain plasticity, while highlighting variability as a fruitful measure in neuroimaging research.
Intelligible enhancement of 3D articulation animation by incorporating airflow information

The 3D talking head has been developed fast, in which both external and internal articulators were demonstrated. For Mandarin pronunciation, the aspiration airflow is crucial to discriminate confusable Mandarin consonants. In this paper, we present a 3D talking head system for articulatory and aspiration animation with the use of EMA articulation data and airflow data simultaneously. The quantitative analyses of airflow data indicated confusable Mandarin consonants could be distinguished from each other by the mean airflow during voicing, peak expiratory airflow, and airflow duration. An airflow model was then incorporated into the 3D articulatory model to produce the airflow in accordance with articulator movements of Mandarin pronunciation. An audio-visual test was designed to evaluate the current 3D articulation and aspiration system, where minimal pairs were used to recognize the animation. The identification accuracy was significantly improved from 43.9% without airflow to 84.8% with airflow-incorporated information.
Robust, Causal, and Incremental Approaches to Investigating Linguistic Adaptation

This paper discusses the maximum robustness approach for studying cases of adaptation in language. We live in an age where we have more data on more languages than ever before, and more data to link it with from other domains. This should make it easier to test hypotheses involving adaptation, and also to spot new patterns that might be explained by adaptation. However, there is not much discussion of the overall approach to research in this area. There are outstanding questions about how to formalize theories, what the criteria are for directing research and how to integrate results from different methods into a clear assessment of a hypothesis. This paper addresses some of those issues by suggesting an approach which is causal, incremental and robust. It illustrates the approach with reference to a recent claim that dry environments select against the use of precise contrasts in pitch. Study 1 replicates a previous analysis of the link between humidity and lexical tone with an alternative dataset and finds that it is not robust. Study 2 performs an analysis with a continuous measure of tone and finds no significant correlation. Study 3 addresses a more recent analysis of the link between humidity and vowel use and finds that it is robust, though the effect size is small and the robustness of the measurement of vowel use is low. Methodological robustness of the general theory is addressed by suggesting additional approaches including iterated learning, a historical case study, corpus studies, and studying individual speech.
First Report on Chitin in a Non-Verongiid Marine Demosponge: The Mycale euplectellioides Case

Sponges (Porifera) are recognized as aquatic multicellular organisms which developed an effective biochemical pathway over millions of years of evolution to produce both biologically active secondary metabolites and biopolymer-based skeletal structures. Among marine demosponges, only representatives of the Verongiida order are known to synthetize biologically active substances as well as skeletons made of structural polysaccharide chitin. The unique three-dimensional (3D) architecture of such chitinous skeletons opens the widow for their recent applications as adsorbents, as well as scaffolds for tissue engineering and biomimetics. This study has the ambitious goal of monitoring other orders beyond Verongiida demosponges and finding alternative sources of naturally prestructured chitinous scaffolds; especially in those demosponge species which can be cultivated at large scales using marine farming conditions. Special attention has been paid to the demosponge Mycale euplectellioides (Heteroscleromorpha: Poecilosclerida: Mycalidae) collected in the Red Sea. For the first time, we present here a detailed study of the isolation of chitin from the skeleton of this sponge, as well as its identification using diverse bioanalytical tools. Calcofluor white staining, Fourier-transform Infrared Spcetcroscopy (FTIR), electrospray ionization mass spectrometry (ESI-MS), scanning electron microscopy (SEM), and fluorescence microscopy, as well as a chitinase digestion assay were applied in order to confirm with strong evidence the finding of a-chitin in the skeleton of M. euplectellioides. We suggest that the discovery of chitin within representatives of the Mycale genus is a promising step in their evaluation of these globally distributed sponges as new renewable sources for both biologically active metabolites and chitin, which are of prospective use for pharmacology and biomaterials oriented biomedicine, respectively.
Na+ channel function, regulation, structure, trafficking and sequestration

This paper is the second of a series of three reviews published in this issue resulting from the University of California Davis Cardiovascular Symposium 2014: Systems approach to understanding cardiac excitation–contraction coupling and arrhythmias: Na+ channel and Na+ transport. The goal of the symposium was to bring together experts in the field to discuss points of consensus and controversy on the topic of sodium in the heart. The present review focuses on Na+ channel function and regulation, Na+ channel structure and function, and Na+ channel trafficking, sequestration and complexing.
Prevalence of sexually transmitted infections among Tanzanian migrants: a cross-sectional study

For the many millions of migrants, mobility creates vulnerabilities and elevates risk for sexually transmitted infections (STIs). We document, among Tanzanian agricultural plantation residents, migrant characteristics and test associations between migrant status and prevalent STI (HSV-2, syphilis, and HIV). From 623 plantation resident participants, we limit this analysis to participants about whom we know migration status (migrants n = 242, non-migrants n = 291). We collected behavioral data via audio-computer assisted self-interview survey, and clinical data via STI testing. We used multivariate Poisson regression models, stratified by gender and controlling for behavioral risk factors, to measure associations between migrant status and STI. In men, HIV prevalence was 9% for migrants, and 6% for non-migrants. HSV-2 prevalence was 57% for migrants, and 32% for non-migrants. Syphilis prevalence was 12% for migrants, and 3% for non-migrants. Among women, there were few differences in STI prevalence by migrant status: prevalence of HIV was 6% vs. 5% (migrants vs. non-migrants); HSV-2 prevalence was 68% vs. 65%; and syphilis prevalence was 11% vs. 8%. Being a male migrant was significantly associated with increased prevalence of any STI after controlling for sociodemographic and behavioral characteristics (APR = 1.53, 95% CI 1.23–5.25). Migrant women did not have increased prevalence of STI as compared to non-migrant women (APR = 1.03, 95% CI 0.85–1.24). Amongst Tanzanian agricultural workers, male migrants experienced elevated risk for prevalent STI as compared to male non-migrants. We suggest structural interventions to reduce risks associated with migration, especially in male migrants, including workplace-based STI prevention programs, and connecting migrants to resources and support within new communities. The key messages are: migrant men experience significantly elevated risk for prevalent STI, above and beyond sociodemographic and behavioral risk factors, as compared to their non-migrant peers; women in this Tanzanian agricultural plantation community overall had higher prevalence of some STIs than men, migrant women had similar STI risk as non-migrant women; and migration for work, an economic strategy for millions, also creates vulnerabilities, so workplace-based STI prevention programs and connecting migrants to community resources are essential.
Double somatic mutations in mismatch repair genes are frequent in colorectal cancer after Hodgkin's lymphoma treatment

Objective Hodgkin's lymphoma survivors who were treated with infradiaphragmatic radiotherapy or procarbazine-containing chemotherapy have a fivefold increased risk of developing colorectal cancer (CRC). This study aims to provide insight into the development of therapy-related CRC (t-CRC) by evaluating histopathological and molecular characteristics. Design 54 t-CRCs diagnosed in a Hodgkin's lymphoma survivor cohort were analysed for mismatch repair (MMR) proteins by immunohistochemistry, microsatellite instability (MSI) and KRAS/BRAF mutations. MSI t-CRCs were evaluated for promoter methylation and mutations in MMR genes. Pathogenicity of MMR gene mutations was evaluated by in silico predictions and functional analyses. Frequencies were compared with a general population cohort of CRC (n=1111). Results KRAS and BRAF mutations were present in 41% and 15% t-CRCs, respectively. Compared with CRCs in the general population, t-CRCs had a higher MSI frequency (24% vs 11%, p=0.003) and more frequent loss of MSH2/MSH6 staining (13% vs 1%, p<0.001). Loss of MLH1/PMS2 staining and MLH1 promoter methylation were equally common in t-CRCs and the general population. In MSI CRCs without MLH1 promoter methylation, double somatic MMR gene mutations (or loss of heterozygosity as second hit) were detected in 7/10 (70%) t-CRCs and 8/36 (22%) CRCs in the general population (p=0.008). These MMR gene mutations in t-CRCs were classified as pathogenic. MSI t-CRC cases could not be ascribed to Lynch syndrome. Conclusions We have demonstrated a higher frequency of MSI among t-CRCs, which results from somatic MMR gene mutations. This suggests a novel association of somatic MMR gene mutations with prior anticancer treatment.
Methods for estimation of model accuracy in CASP12

Methods for reliably estimating the quality of 3D models of proteins are essential drivers for the wide adoption and serious acceptance of protein structure predictions by life scientists. In this paper, the most successful groups in CASP12 describe their latest methods for Estimates of Model Accuracy (EMA). We show that pure single model accuracy estimation methods has shown clear progress since CASP11; the three top methods (MESHI, ProQ3, SVMQA) all perform better than the top method of CASP11 (ProQ2). The pure single model accuracy estimation methods outperform quasi-single (ModFOLD6 variations) and consensus methods (Pcons, ModFOLDclust2, Pcomb-domain and Wallner) in model selection, but are still not as good as those methods in absolute model quality estimation and predictions of local quality. Finally, we show that when using contact based model quality measures (CAD, 1DDT) the single model quality methods perform relatively better.
Decoupled Response of Ocean Acidification to Variations in Climate Sensitivity

AbstractIt is now well understood that the global surface ocean, whose pH has been reduced by ~0.1 in response to rising atmospheric CO2 since industrialization, will continue to become more acidic as fossil fuel CO2 emissions escalate. However, it is unclear how uncertainties in climate sensitivity to future CO2 emissions will alter the manifestation of ocean acidification. Using an earth system model of intermediate complexity, this study performs a set of simulations that varies equilibrium climate sensitivity by 1.0°–4.5°C for a given CO2 emissions scenario and finds two unexpected and decoupled responses. First, the greater the climate sensitivity, the larger the surface mixed layer acidification signal but the smaller the subsurface acidification. However, taken throughout the ocean, the highest climate sensitivity will paradoxically cause greater global warming while buffering whole-ocean pH by up to 24% on centennial time scales. Second, this study finds a large decoupling between pH and carbonate.
Compressive image recovery using recurrent generative model

Reconstruction of signals from compressively sensed measurements is an ill-posed problem. In this paper, we leverage the recurrent generative model, RIDE, as an image prior for compressive image reconstruction. Recurrent networks can model long-range dependencies in images and hence can handle global multiplexing in compressive imaging. We perform MAP inference with RIDE using back-propagation to the inputs and projected gradient method. We propose an entropy thresholding based approach for preserving texture in images well. Our approach shows superior reconstructions compared to recent global reconstruction approaches like D-AMP and TVAL3 on both simulated and real data.