Miracle-dz/UniFAR-FTUs huggingface dataset:
COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features

Recent genomic studies suggest that novel long non-coding RNAs (lncRNAs) are specifically expressed and far outnumber annotated lncRNA sequences. To identify and characterize novel lncRNAs in RNA sequencing data from new samples, we have developed COME, a coding potential calculation tool based on multiple features. It integrates multiple sequence-derived and experiment-based features using a decompose–compose method, which makes it more accurate and robust than other well-known tools. We also showed that COME was able to substantially improve the consistency of predication results from other coding potential calculators. Moreover, COME annotates and characterizes each predicted lncRNA transcript with multiple lines of supporting evidence, which are not provided by other tools. Remarkably, we found that one subgroup of lncRNAs classified by such supporting features (i.e. conserved local RNA secondary structure) was highly enriched in a well-validated database (lncRNAdb). We further found that the conserved structural domains on lncRNAs had better chance than other RNA regions to interact with RNA binding proteins, based on the recent eCLIP-seq data in human, indicating their potential regulatory roles. Overall, we present COME as an accurate, robust and multiple-feature supported method for the identification and characterization of novel lncRNAs. The software implementation is available at https://github.com/lulab/COME.
The Dictionary of Feminist Theory

The Dictionary. Additional Theorists in the Revised Edition Include: Anzaldua, Butler, Castellanos, Chow, Cixous, de Lauretis, Fetterley, Fox Keller, Friedan, Gilbert and Gubar, Haraway, Harding, Irigary, Jacobus, Jardine, Kaplan, Kristeva, Lakoff, Le Doeuff, Minh-ha, Modleski, Mohanty, Morris, Mulvey, Olsen, Ruddick, Sedgwick, Spillers, Spivak, Stimpson, Walker, and Zimmerman. Additional Entries in the Revised Edition Include: Autobiography, Backlash, Black Criticism, Censorship, Citizenship, Critical Theory, Cultural Theory, Deconstruction, Discourse Analysis, Ecofeminism, Empowerment, Essentialism, First Wave, Gender Studies, Gynesis, Logocentrism, Materialist Feminist Criticism, Modernism, Networking, Pedagogy, Post-colonialism, Post-feminism, Postmodernism, Post-structuralism, Preservative Love, Queer Theory, Reader Response Criticism, Reproductive Technology, Second Sex, Second Wave, Semiotic, Sexual Harassment, Women of Colour, Writing, the Body.
Baseline Levels of Rapid Eye Movement Sleep May Protect Against Excessive Activity in Fear-Related Neural Circuitry

Sleep, and particularly rapid eye movement sleep (REM), has been implicated in the modulation of neural activity following fear conditioning and extinction in both human and animal studies. It has long been presumed that such effects play a role in the formation and persistence of posttraumatic stress disorder, of which sleep impairments are a core feature. However, to date, few studies have thoroughly examined the potential effects of sleep prior to conditioning on subsequent acquisition of fear learning in humans. Furthermore, these studies have been restricted to analyzing the effects of a single night of sleep—thus assuming a state-like relationship between the two. In the current study, we used long-term mobile sleep monitoring and functional neuroimaging (fMRI) to explore whether trait-like variations in sleep patterns, measured in advance in both male and female participants, predict subsequent patterns of neural activity during fear learning. Our results indicate that higher baseline levels of REM sleep predict reduced fear-related activity in, and connectivity between, the hippocampus, amygdala and ventromedial PFC during conditioning. Additionally, skin conductance responses (SCRs) were weakly correlated to the activity in the amygdala. Conversely, there was no direct correlation between REM sleep and SCRs, indicating that REM may only modulate fear acquisition indirectly. In a follow-up experiment, we show that these results are replicable, though to a lesser extent, when measuring sleep over a single night just before conditioning. As such, baseline sleep parameters may be able to serve as biomarkers for resilience, or lack thereof, to trauma. SIGNIFICANCE STATEMENT Numerous studies over the past two decades have established a clear role of sleep in fear-learning processes. However, previous work has focused on the effects of sleep following fear acquisition, thus neglecting the potential effects of baseline sleep levels on the acquisition itself. The current study provides the first evidence in humans of such an effect. Specifically, the results of this study suggest that baseline rapid eye movement (REM) sleep may serve a protective function against enhanced fear encoding through the modulation of connectivity between the hippocampus, amygdala, and the ventromedial PFC. Building on this finding, baseline REM measurements may serve as a noninvasive biomarker for resilience to trauma or, conversely, to the potential development of posttraumatic stress disorder following trauma.
No use for waist-for-height ratio in addition to body mass index to identify children with elevated blood pressure

Abstract Background. In children, waist-for-height ratio (WHtR) has been proposed to identify subjects at higher risk of cardiovascular diseases. The utility of WHtR to identify children with elevated blood pressure (BP) is unclear. Design. Cross-sectional population-based study of schoolchildren. Methods. Weight, height, waist circumference and BP were measured in all sixth-grade schoolchildren of the canton de Vaud (Switzerland) in 2005/06. WHtR was computed as waist [cm]/height [cm]. Elevated BP was defined according to sex-, age- and height-specific US reference data. The area under the receiver operating characteristic curve (AUC) statistic was computed to compare the ability of body mass index (BMI) z-score and WHtR, alone or in combination, to identify children with elevated BP. Results. 5207 children participated (76% response) [2621 boys, 2586 girls; mean (± SD) age, 12.3 ± 0.5 years; range: 10.1–14.9]. The prevalence of elevated BP was 11%. Mean WHtR was 0.44 ± 0.05 (range: 0.29– 0.77) and 11% had high WHtR (> 0.5). BMI z-score and WHtR were strongly correlated (Spearman correlation coefficient r = 0.76). Both indices were positively associated with elevated BP. AUCs for elevated BP was relatively low for BMI z-score (0.62) or for WHtR (0.62), and was not substantially improved when both indices were considered together (0.63). Conclusions. The ability of BMI z-score or WHtR to identify children aged 10–14 with elevated BP was weak. Adding WHtR did not confer additional discriminative power to BMI alone. These findings do not support the measurement of WHtR in addition to BMI to identify children with elevated BP.
Fundamental bounds on the accuracy of network performance measurements

This paper considers the basic problem of "how accurate can we make Internet performance measurements". The answer is somewhat counter-intuitive in that there are bounds on the accuracy of such measurements, no matter how many probes we can use in a given time interval, and thus arises a type of Heisenberg inequality describing the bounds in our knowledge of the performance of a network. The results stem from the fact that we cannot make independent measurements of a system's performance: all such measures are correlated, and these correlations reduce the efficacy of measurements. The degree of correlation is also strongly dependent on system load. The result has important practical implications that reach beyond the design of Internet measurement experiments, into the design of network protocols.
Research on marketing in emerging firms: key issues and open questions

In many industries, emerging firms derive their initial strength from R&D activities. Though technological capabilities are important for building technologically sound products, they are not sufficient for turning an emerging firm into a viable economic actor, as numerous examples illustrate. Based on a discussion of the specific challenges of marketing in new ventures and a brief overview on past and current research studies, this article focuses on reviewing research findings on four key topics: establishing a market orientation, building credibility and trust with stakeholders, establishing marketing alliances and low-cost marketing. Though previous research has produced important insights into each of these topics, there are still plenty of issues that offer promising opportunities for future studies.
Predictability of STRFs in auditory cortex neurons depends on stimulus class

The goal of this study was to predict neuronal responses based on STRF-estimates for different stimulus sets of primary auditory cortex neurons of Mongolian gerbils. Here we review results from STRF estimations after stimulation with frequency modulated (FM) tones, Dynamic Moving Ripples (DMR), as well as, prediction of responses to logatomes stemming from the Oldenburg Logatome Corpus (OLLO) data set [1]. Our results suggest that it is not merely the similarity of the presented power spectrum of stimuli that leads to better STRF predictions. We will suggest new STRF-approaches to categorize neuronal responses to more natural stimuli.
Leaving Prostitution: Getting Out and Staying Out of Sex Work

Acknowledgments 1. Introduction: Leaving the Tricks and the Trade 2. All in a Day's Work: The Good, Bad, and Ugly 3. Getting In: From the Streets to the Program 4. Getting On: Role Distancing 5. Still Getting On: Embracing a New Role and Identity 6. Getting Out: Remaining Out of Sex Work Methodological Appendix Notes References IndexAbout the Author
Relationship between the pedagogical variables of coaching a mini-basketball team

This study arises from the importance of analyzing the coaching process and knowing how to coach in the first stages of sports initiation. The purpose of this study was to analyze how a basketball coach establishes teaching the game phases in youth categories, through the relationship between the pedagogical variables that define each of the coaching tasks. A total of 452 tasks, organized in 80 training sessions that were planned by a coach of mini-basketball (10-11 yearolds) from the 2004-2005 season were analyzed. After a descriptive analysis of the game phase variable, a non-parametric inferential analysis (chi-square and contingency coefficient) was carried out to study the relationships between the variables of the study (game phase, game situation, type of content, and content). The results make clear that for the coach that was analyzed, there is a disproportionate amount of work done on phases of offense to the detriment of defensive work. The aspects of the attack that are developed most are those without opposition, 1-on-0 (RAS=9.7) and to a lesser degree 1-on-1 (RAS=-10.7), although the opposite happens in the case of defensive fundamentals, 1-on-0 (RAS=-5.4) and 1-on-1 (RAS=12.3). A higher proportion of tasks without opposition, 1- on-0, were planned to work on individual offense technique (RAS=15.7), such as shooting. The analysis of the coaching process provides much information when generating sport teaching principles. The results have an important practical application, and they facilitate the process of continuing education and reflection on coaches' actions.
Anti-heart and anti-intercalated disk autoantibodies: evidence for autoimmunity in idiopathic recurrent acute pericarditis

Background Idiopathic recurrent acute pericarditis (IRAP) is a rare disease of suspected, yet unproved, immune-mediated origin. The finding of serum heart-specific autoantibodies in IRAP would strengthen the autoimmune hypothesis and provide aetiology-specific non-invasive biomarkers. Objective To assess frequency of serum anti-heart (AHA), anti-intercalated-disk (AIDA) and non-cardiac-specific autoantibodies and their clinical and instrumental correlates in patients with IRAP. Patients 40 consecutive patients with IRAP, 25 male, aged 37±16 years, representing a large single-centre cohort collected at a referral centre over a long time period (median 5 years, range 1–22 years). Control groups included patients with non-inflammatory cardiac disease (NICD) (n=160), ischaemic heart failure (n=141) and normal subjects (n=270). Methods AHA (organ-specific, cross-reactive 1 and 2 types) and AIDA were detected in serum samples from patients, at last follow-up, and control subjects by indirect immunofluorescence (IIF) on human myocardium and skeletal muscle. Non-cardiac-specific autoantibodies were detected by IIF, and anti-Ro/SSA, anti-La/SSB by ELISA. Results The frequencies of cross-reactive 1 AHA and of AIDA were higher (50%; 25%) in IRAP than in NICD (4%; 4%), ischaemic (1%; 2%) or normal subjects (3%; 0%) (p=0.0001). AHA and/or AIDA were found in 67.5% patients with IRAP. Of the non-cardiac-specific antibodies, only antinuclear autoantibodies at titre ≥1/160 were more common in IRAP (5%) versus normal (0.5%, p<0.04). AIDA in IRAP were associated with a higher number of recurrences (p=0.01) and hospitalisations (p=0.0001), high titre (1/80 or higher) AHA with a higher number of recurrences (p=0.02). Conclusions The detection of AHA and of AIDA supports the involvement of autoimmunity in the majority of patients with IRAP.
Evaluación del estrés infantil: Inventario Infantil de Estresores Cotidianos (IIEC)

El presente estudio ofrece una nueva medida para la evaluacion del estres cotidiano en poblacion escolar mediante el desarrollo del Inventario Infantil de Estresores Cotidianos (IIEC). La administracion del instrumento se realizo en una muestra de 1.094 alumnos de Educacion Primaria. La version final del inventario se compone de 25 items dicotomicos referentes a los ambitos de salud, escuela/iguales y familia. Su puntuacion se obtiene sumando el numero de respuestas afirmativas. Se presenta un analisis de sus propiedades psicometricas, incluyendo analisis de items, consistencia interna, fiabilidad test-retest y diversas evidencias externas de validez basadas en sus relaciones con otras variables. Los resultados muestran propiedades psicometricas adecuadas para la evaluacion del estres cotidiano en la poblacion infantil. Assessment of stress in childhood: Children’s Daily Stress Inventory (Inventario Infantil de Estresores Cotidiano, IIEC). The present study introduces the Children’s Daily Stress Inventory (Inventario Infantil de Estresores Cotidianos, IIEC) as a measure that assesses daily stress in primary school children. The inventory was applied to a sample of 1094 primary school students. The final version includes 25 dichotomic items covering the areas of health, school/peers, and family. The score is obtained by adding the total of positive answers. Analyses of items, reliability and several external pieces of evidence of validity based on relations with other variables are presented. The results show adequate psychometric properties for the assessment of daily stress in children.
Increasing self-esteem and empathy to prevent violent radicalization: a longitudinal quantitative evaluation of a resilience training focused on adolescents with a dual identity

Quantitative results are reported of a longitudinal evaluation of a resilience training as a possible method to prevent violent radicalization (Diamant; SIPI, 2010). A total of 46 male and female Muslim adolescents and young adults with a migrant background participated. Results show that the training significantly increased participants' reports of agency and a marginal increase was found in reported self-esteem, empathy and perspective taking but also narcissism. Attitudes toward ideology-based violence and own violent intentions were significantly lower after the training than before. Higher reports of empathy were related to less positive attitudes toward ideology-based violence. These results suggest that an intervention aimed at empowering individuals in combination with strengthening empathy is successful in countering violent radicalization.
Making Inclusion Work

Autism spectrum disorders (ASD) are a group of interrelated disorders includ- ing autistic disorder, Asperger's syn- drome, and Pervasive Developmental Disorder-Not Otherwise Specified (PDD-NOS). Aspect's "working model" (see box, "Aspect Satellite Classroom Working Model Elements") in operation for 14 years, meets Batten et al . 's recommendations that children with ASD have access to a diverse range of mainstream and specialist educational provision, teachers in general education schools are provided with resources, ASD consultants and specialist teachers receive ASD-specific training, and students receive ASD-specific skills-based programs.
Medication Adherence in Outpatients With Severe Mental Disorders: Relation Between Self-Reports and Serum Level

Medication nonadherence in severe mental disorders is an important clinical issue, but estimates vary between studies. There is a need for valid self-reports for both research and clinical practice. This study examined the level of adherence to prescribed medication in outpatients with severe mental disorders and evaluated the validity of a simple self-report rating of adherence. From an ongoing study of severe mental disorders, 280 patients with schizophrenia and bipolar disorder who were prescribed psychopharmacological agents were included. We assessed adherence with serum concentration of medicines and tested the sensitivity and specificity of a simple self-report questionnaire for patients and compared with a report from health personnel. Adherence rate defined by serum concentrations within reference level was 61.6% in the total sample, 58.4% for schizophrenia and 66.3% for bipolar disorder. The patients' self-report scores overestimated adherence, but correlated significantly to health personnel scores (r = 0.50) and to serum concentration of medication (r = 0.52); the positive predictive value was 70%, and the negative predictive value was 91%. In this naturalistic sample, outpatients with severe mental disorders showed relatively good adherence to prescribed medication, and self-report questionnaires seem to be a valid method for measuring adherence.
Cellular Cardiomyoplasty Improves Survival After Myocardial Injury

Background—Cellular cardiomyoplasty is discussed as an alternative therapeutic approach to heart failure. To date, however, the functional characteristics of the transplanted cells, their contribution to heart function, and most importantly, the potential therapeutic benefit of this treatment remain unclear. Methods and Results—Murine ventricular cardiomyocytes (E12.5–E15.5) labeled with enhanced green fluorescent protein (EGFP) were transplanted into the cryoinjured left ventricular walls of 2-month-old male mice. Ultrastructural analysis of the cryoinfarction showed a complete loss of cardiomyocytes within 2 days and fibrotic healing within 7 days after injury. Two weeks after operation, EGFP-positive cardiomyocytes were engrafted throughout the wall of the lesioned myocardium. Morphological studies showed differentiation and formation of intercellular contacts. Furthermore, electrophysiological experiments on isolated EGFP-positive cardiomyocytes showed time-dependent differentiation with postnatal ventricular action potentials and intact &bgr;-adrenergic modulation. These findings were corroborated by Western blotting, in which accelerated differentiation of the transplanted cells was detected on the basis of a switch in troponin I isoforms. When contractility was tested in muscle strips and heart function was assessed by use of echocardiography, a significant improvement of force generation and heart function was seen. These findings were supported by a clear improvement of survival of mice in the cardiomyoplasty group when a large group of animals was analyzed (n=153). Conclusions—Transplanted embryonic cardiomyocytes engraft and display accelerated differentiation and intact cellular excitability. The present study demonstrates, as a proof of principle, that cellular cardiomyoplasty improves heart function and increases survival on myocardial injury.
Sergliflozin, a Novel Selective Inhibitor of Low-Affinity Sodium Glucose Cotransporter (SGLT2), Validates the Critical Role of SGLT2 in Renal Glucose Reabsorption and Modulates Plasma Glucose Level

The low-affinity sodium glucose cotransporter (SGLT2), which is expressed specifically in the kidney, plays a major role in renal glucose reabsorption in the proximal tubule. We have discovered sergliflozin, a prodrug of a novel selective SGLT2 inhibitor, based on benzylphenol glucoside. In structure, it belongs to a new category of SGLT2 inhibitors and its skeleton differs from that of phlorizin, a nonselective SGLT inhibitor. We investigated its pharmacological properties and potencies in vitro and in vivo. By examining a Chinese hamster ovary-K1 cell line stably expressing either human SGLT2 or human high-affinity sodium glucose cotransporter (SGLT1), we found sergliflozin-A (active form) to be a highly selective and potent inhibitor of human SGLT2. At pharmacological doses, sergliflozin, sergliflozin-A, and its aglycon had no effects on facilitative glucose transporter 1 activity, which was inhibited by phloretin (the aglycon of phlorizin). The transport maximum for glucose in the kidney was reduced by sergliflozin-A in normal rats. As a result of this effect, orally administered sergliflozin increased urinary glucose excretion in mice, rats, and dogs in a dose-dependent manner. In an oral glucose tolerance test in diabetic rats, sergliflozin exhibited glucose-lowering effects independently of insulin secretion. Any glucose excretion induced by sergliflozin did not affect normoglycemia or electrolyte balance. These data indicate that selective inhibition of SGLT2 increases urinary glucose excretion by inhibiting renal glucose reabsorption. As a representative of a new category of antidiabetic drugs, sergliflozin may provide a new and unique approach to the treatment of diabetes mellitus.
Characterizing the Materials-Based Bias Effect: A Robust yet Mysterious Conservative Response Bias in Recognition Memory for Paintings

Supervisory Committee Dr. D. Stephen Lindsay, Department of Psychology Supervisor Dr. Michael E. J. Masson, Department of Psychology Co-Supervisor A series of recognition memory experiments using masterwork paintings and words are reported in which participants were reliably conservative in endorsing images of paintings as “studied”. The current paper establishes the historical context of this materials-based bias effect (MBBE) and presents two new experiments aimed at characterizing the underlying mechanisms. Nine previous experiments are reviewed to illustrate the MBBE’s robustness to various encoding and test manipulations and the insufficiency of two prior hypotheses in accounting for its origins. Meta-analyses of response bias and sensitivity and analysis of these measures by test quartile are presented and discussed along with receiver operating characteristics and response time data for all of these experiments. In one new experiment, the response scale on the recognition test was modified to allow participants to choose from not only “studied” or “not studied” options, but also options indicating uncertainty due to the similarity among test items. The hypothesis that these similarity/confusability-related responses would be chosen more for paintings was not supported. A second new experiment aimed to better characterize the time course of the MBBE by implementing a 1-s respond deadline, which was hypothesized to reduce the effect, but this hypothesis was also not supported. Results of all experiments are discussed in the context of unequal variance and dual process models of recognition memory.