Miracle-dz/UniFAR-FTUs huggingface dataset:
A computational system to select candidate genes for complex human traits

MOTIVATION Identification of the genetic variation underlying complex traits is challenging. The wealth of information publicly available about the biology of complex traits and the function of individual genes permits the development of informatics-assisted methods for the selection of candidate genes for these traits. RESULTS We have developed a computational system named CAESAR that ranks all annotated human genes as candidates for a complex trait by using ontologies to semantically map natural language descriptions of the trait with a variety of gene-centric information sources. In a test of its effectiveness, CAESAR successfully selected 7 out of 18 (39%) complex human trait susceptibility genes within the top 2% of ranked candidates genome-wide, a subset that represents roughly 1% of genes in the human genome and provides sufficient enrichment for an association study of several hundred human genes. This approach can be applied to any well-documented mono- or multi-factorial trait in any organism for which an annotated gene set exists. AVAILABILITY CAESAR scripts and test data can be downloaded from http://visionlab.bio. unc.edu/caesar/
Length of Acupuncture Training and Structural Plastic Brain Changes in Professional Acupuncturists

Background The research on brain plasticity has fascinated researchers for decades. Use/training serves as an instrumental factor to influence brain neuroplasticity. Parallel to acquisition of behavioral expertise, extensive use/training is concomitant with substantial changes of cortical structure. Acupuncturists, serving as a model par excellence to study tactile-motor and emotional regulation plasticity, receive intensive training in national medical schools following standardized training protocol. Moreover, their behavioral expertise is corroborated during long-term clinical practice. Although our previous study reported functional plastic brain changes in the acupuncturists, whether or not structural plastic changes occurred in acupuncturists is yet elusive. Methodology/Principal Findings Cohorts of acupuncturists (N = 22) and non-acupuncturists (N = 22) were recruited. Behavioral tests were delivered to assess the acupuncturists’ behavioral expertise. The results confirmed acupuncturists’ tactile-motor skills and emotion regulation proficiency compared to non-acupuncturists. Using the voxel-based morphometry technique, we revealed larger grey matter volumes in acupuncturists in the hand representation of the contralateral primary somatosensory cortex (SI), the right lobule V/VI and the bilateral ventral anterior cingulate cortex/ventral medial prefrontal cortex. Grey matter volumes of the SI and Lobule V/VI positively correlated with the duration of acupuncture practice. Conclusions To our best knowledge, this study provides first evidence for the anatomical alterations in acupuncturists, which would possibly be the neural correlates underlying acupuncturists’ exceptional skills. On one hand, we suggest our findings may have ramifications for tactile-motor rehabilitation. On the other hand, our results in emotion regulation domain may serve as a target for our future studies, from which we can understand how modulations of aversive emotions elicited by empathic pain develop in the context of expertise. Future longitudinal study is necessary to establish the presence and direction of a causal link between practice/use and brain anatomy.
Gendering Fiction: A Mixed Methods Examination Of The Influence Of The "boy" Book/ "girl" Book Phenomenon On The Willingness To Read Of Young Adolescents

Well-meaning educators often recommend more “boy” books to increase reading motivation amongst boys. This experimental mixed-methods study investigated the influence of the “boy” book/ “girl” book phenomenon on willingness to read using a researcher-designed instrument called the Textual Features Sort (TFS). The TFS measured two attitudinal constructs—gendered beliefs about texts and willingness to read—in relation to individual textual features of selected young adult novels. Data came from 50 sixth and seventh grade students at a mid-sized public school in a rural New England state. Mean scores, frequencies, and percentages were analyzed using independent samples t-tests, paired t-tests, and Fisher’s exact test. Qualitative data was used to explain quantitative results. Findings indicate that boys were not more willing to read “boy” books than other books, nor less willing to read books with female protagonists. Boys were significantly less willing to read “girl” books, though individual textual features of a single novel elicited different gendered beliefs along with varying degrees of willingness to read. Girls were significantly less willing to read a novel if it was first sorted as a “boy” book. Research revealed a widespread belief in social consequences for a boy carrying a “girl” book down the hallway, that did not hold for girls. Findings suggest that sociocultural constructions of gender inhibit both boys and girls as readers, though to varying degrees, and challenge the notion that highly gendered and heteronormative assumptions about books and reading practices will increase willingness to read among young adolescent boys.
Inhomogeneous Helium Reionization and the Equation of State of the Intergalactic Medium

The temperature of the intergalactic medium (IGM) is set by the competition between photoheating and adiabatic cooling, which are usually assumed to define a tight equation of state in which the temperature increases monotonically with density. We use a semianalytic model, accurate at low to moderate IGM densities (≲5 times the mean), to show that inhomogeneous reionization can substantially modify these expectations. Because reionization is driven by biased sources, dense pockets of the IGM are likely to be ionized first. As a result, voids initially remain cool while dense regions are heated substantially. However, near the end of reionization, dense regions have already cooled from their initially large temperature while voids have only just been heated. Thus, near the end of helium reionization the equation of state can invert itself, with the hottest gas inside voids. The degree to which this happens depends on the magnitude of the density bias during reionization: if rare, bright sources dominate reionization, so that each ionized region contains a typical volume of the IGM, the equation of state will remain monotonic. We also show that the distribution of temperatures at a fixed density has significant scatter and evolves rapidly throughout and even after reionization. Finally, we show that the observed temperature jump at z ∼ 3.2 is consistent with the behavior at the end of helium reionization, although it requires a somewhat larger temperature increase than expected.
Development of the Teacher Attitudes Towards Self-Regulated Learning Scale

We describe the development and validation of an instrument for measuring the affective component of primary school teachers’ attitudes towards self-regulated learning. The questionnaire assesses the affective component towards those cognitive and metacognitive strategies that are especially effective in primary school. In a first study (n = 230), the factor structure was verified via an exploratory factor analysis. A confirmatory factor analysis with data from a second study (n = 400) indicated that the theoretical factor structure is appropriate. A comparison with four alternative models identified the theoretically derived factor structure as the most appropriate. Concurrent validity was demonstrated by correlations with a scale that measures the degree to which teachers create learning environments that enable students to self-regulate their learning. Retrospective validity was demonstrated by correlations with a scale that measures teachers’ experiences with self-regulated learning. In a third study (n = 47), the scale’s concurrent validity was tested with scales measuring teachers’ evaluation of the desirability of different aspects of self-regulated learning in class. Additionally, predictive validity was demonstrated via a binary logistic regression, with teachers attitudes as predictor on their registration for a workshop on self-regulated learning and their willingness to implement a seven-week training program on self-regulated learning.
Gender Differences in Psychosocial and Medical Outcomes Stemming From Testing Positive for the BRCA1/2 Genetic Mutation for Breast Cancer: An Explanatory Sequential Mixed Methods Study

This quantitatively driven sequential mixed methods study articulates the role of theory in mixed methods research and assesses the contribution of a mixed methods design to examining gender differences in men and women’s genetic testing decisions and the psychosocial factors impacting health-seeking behaviors post-testing. A quantitative online survey of BRCA-positive mutation men and women was followed by a qualitative component consisting of semi-structured telephone interviews regarding genetic testing and post-testing decision making. Findings reveal gender differences in testing motivations: women focus on health; men focus on their family’s needs. Gender differences also appeared in psychological states and surgical decisions, revealing women’s more negative psychosocial reactions to a positive BRCA test result and higher rate of selecting preventative surgery.
Blood Pressure Variations Real-Time Reflect the Conditioned Fear Learning and Memory

The conditioned fear learning and memory occurs when a neutral conditioned stimulus (CS) is paired with an aversive unconditioned stimulus (US). This process is critically dependent on the amygdala and inevitably involves blood pressure (BP) alterations. We hypothesized that BP variations could instantaneously reveal individual steps during conditioned fear learning and memory. An implanted telemetric probe was used to monitor the BP real-time in rats during training and testing sessions of the fear-potentiated startle. Our results showed that (i) the conditioned fear learning during the training sessions was reflected by light (CS)-induced rapid BP elevations and by electric shock (US)-evoked sympathetic tone elevations; (ii) these two BP-related parameters were not only negatively correlated with each other but also coupled to each other in the training session trials; (iii) both parameters closely predicted the performance of fear-potentiated startle on the next day; and (iv) although local blocking of one of the two fear-conditioned pathways in the training session partially inhibited fear learning, the fear memory retrieval still used both pathways. Altogether, real-time blood pressure variations faithfully revealed the critical steps involved in conditioned fear learning and memory, and our results supported a coupling between the cued learning and the post-shock calmness.
Role of Cardiovascular Magnetic Resonance as a Gatekeeper to Invasive Coronary Angiography in Patients Presenting With Heart Failure of Unknown Etiology

Background— In patients presenting with new-onset heart failure of uncertain etiology, the role of coronary angiography (CA) is unclear. Although conventionally performed to differentiate underlying coronary artery disease from dilated cardiomyopathy, CA is associated with a risk of complications and may not detect an ischemic cause resulting from arterial recanalization or an embolic episode. In this study, we assessed the diagnostic accuracy of a cardiovascular magnetic resonance (CMR) protocol incorporating late gadolinium enhancement (LGE) and magnetic resonance CA as a noninvasive gatekeeper to CA in determining the etiology of heart failure in this subset of patients. Methods and Results— One hundred twenty consecutive patients underwent CMR and CA. The etiology was ascribed by a consensus panel that used the results of the CMR scans. Similarly, a separate consensus group ascribed an underlying cause by using the results of CA. The diagnostic accuracy of both strategies was compared against a gold-standard panel that made a definitive judgment by reviewing all clinical data. The study was powered to show noninferiority between the 2 techniques. The sensitivity of 100%, specificity of 96%, and diagnostic accuracy of 97% for LGE-CMR were equivalent to CA (sensitivity, 93%; specificity, 96%; and diagnostic accuracy, 95%). As a gatekeeper to CA, LGE-CMR was also found to be a cheaper diagnostic strategy in a decision tree model when United Kingdom–based costs were assumed. The economic merits of this model would change, depending on the relative costs of LGE-CMR and CA in any specific healthcare system. Conclusion— This study showed that LGE-CMR is a safe, clinically effective, and potentially economical gatekeeper to CA in patients presenting with heart failure of uncertain etiology.
Learning Crosslingual Word Embeddings without Bilingual Corpora

Crosslingual word embeddings represent lexical items from different languages in the same vector space, enabling transfer of NLP tools. However, previous attempts had expensive resource requirements, difficulty incorporating monolingual data or were unable to handle polysemy. We address these drawbacks in our method which takes advantage of a high coverage dictionary in an EM style training algorithm over monolingual corpora in two languages. Our model achieves state-of-the-art performance on bilingual lexicon induction task exceeding models using large bilingual corpora, and competitive results on the monolingual word similarity and cross-lingual document classification task.
A New Look at the Empirical Initial--Final Mass Relation

We examine new methods of producing and analyzing the empirical initial-final mass relation for open cluster white dwarfs (WDs). We re-determine initial and final masses for the complete sample of published cluster WDs and then pare this sample using stringent criteria. We create an empirical initial-final mass relation by binning all WDs in individual clusters to a single point. Despite potentially significant systematics arising from this approach, we are comfortable concluding that, to within current observational constraints, the initial-final mass relation is linear, any intrinsic scatter in the relation is <~0.05 solar masses, and there is no metallicity dependence. More exploration of these issues is clearly warranted.
The effect of an aerobic exercise on serum level of liver enzymes and liver echogenicity in patients with non alcoholic fatty liver disease

Aim The aim of this study was to evaluate the effect of an aerobic exercise on serum level of liver enzymes and liver echogenicity in patients with non alcoholic fatty liver disease. Background Non alcoholic fatty liver disease (NAFLD) has different prevalence in various parts of the world. Obesity and low physical activity are main risk factors for the development of NAFLD. Patients and methods Ninety patients diagnosed by ultrasound as NAFLD was evaluated in a clinical trial as case (A) and control groups (B). The effect of aerobic exercise on changing in liver enzymes and liver echogenicity was assessed in cases compared with control group which were only on medical therapy. Results The mean age in the sample group was 37.6±8.3 in the 17-56 yrs age range. In group A, fatty liver was in stage I in 26 (57.8%) cases, stage II in 17 (37.8%), and stage III in 2 (4.4%). In group B, fatty liver was in stage I in 30 (66.7%) patients, in stage II in 14 (31.1%) and stage III in 1 (2.2%). After an aerobic exercise, serum level of liver enzymes and liver echogenicity in patients with non alcoholic fatty liver disease was significant improved in case group (ALT (P= 0.0001), AST (P = 0.01). Conclusion Considering the present study, we can suggest that a controlled aerobic exercise schedule can be helpful in the association of medical therapy in the treatment of NAFLD.
Methanol Masers: Reliable Tracers of the Early Stages of High-Mass Star Formation

The GLIMPSE and MSX surveys have been used to examine the mid-infrared properties of a statistically complete sample of 6.7 GHz methanol masers. The GLIMPSE point sources associated with methanol masers are clearly distinguished from the majority, typically having extremely red mid-infrared colors similar to those expected of low-mass Class 0 young stellar objects. The intensity of the GLIMPSE sources associated with methanol masers is typically 4 mag brighter at 8.0 μm than at 3.6 μm. Targeted searches toward GLIMPSE point sources with [3.6] - [4.5] > 1.3 and an 8.0 μm magnitude less than 10 will detect more than 80% of Class II methanol masers. Many of the methanol masers are associated with sources within infrared dark clouds (IRDCs), which are believed to mark regions where high-mass star formation is in its very early stages. The presence of Class II methanol masers in a significant fraction of IRDC suggests that high-mass star formation is common in these regions. Different maser species are thought to trace different evolutionary phases of the high-mass star formation process. Comparison of the properties of the GLIMPSE sources associated with Class II methanol masers and other maser species shows interesting trends, consistent with Class I methanol masers tracing a generally earlier evolutionary phase and OH masers tracing a later evolutionary phase.
Formation of Early-Type Galaxies from Cosmological Initial Conditions

We describe high-resolution smoothed particle hydrodynamics (SPH) simulations of three approximately M* field galaxies starting from ΛCDM initial conditions. The simulations are made intentionally simple, and include photoionization, cooling of the intergalactic medium, and star formation, but not feedback from AGNs or supernovae. All of the galaxies undergo an initial burst of star formation at z ≈ 5, accompanied by the formation of a bubble of heated gas. Two out of three galaxies show early-type properties at present, whereas only one of them experienced a major merger. Heating from shocks and PdV work dominates over cooling so that for most of the gas the temperature is an increasing function of time. By z ≈ 1 a significant fraction of the final stellar system is in place and the spectral energy distribution resembles those of observed massive red galaxies. The galaxies have grown from z = 1 → 0 on average by 25% in mass and in size by gas-poor (dry) stellar mergers. By the present day the simulated galaxies are old (≈10 Gyr), kinematically hot stellar systems surrounded by hot gaseous haloes. Stars dominate the mass of the galaxies up to ≈4 effective radii (≈10 kpc). Kinematic and most photometric properties are in good agreement with those of observed elliptical galaxies. The galaxy with a major merger develops a counter-rotating core. Our simulations show that realistic intermediate-mass giant elliptical galaxies with plausible formation histories can be formed from ΛCDM initial conditions even without requiring recent major mergers or feedback from supernovae or AGNs.
The effect of thin-ideals on body satisfaction and body appreciation across different age groups

Previous research has shown that exposure to thin images has a negative impact on the body image states of women (Grabe, Ward & Hyde, 2008). The present study aimed to investigate if the negative effects associated with exposure to thin-ideals differ according to age. Participants were 80 women, categorised as young (N=40) or older (N=40). Participants were required to complete a questionnaire comprised of a body satisfaction scale and a body appreciation scale before and after viewing thin images or neutral images. Differences between pre and post image scores were calculated. Results show there was a significant main effect for image on scores of both body satisfaction and appreciation (p <.001), indicating that thin images negatively affect the body image state of women irrespective of age. There was also a significant interaction effect between age and image on scores of body appreciation (p <.01). This indicates that there was less of a negative impact on the body appreciation scores of older women compared to the young women following exposure to thin-ideals, suggesting that body appreciation increases with age and body appreciation remains in older women even after exposure to thin-ideals.
Effect of dental restorative materials on total antioxidant capacity and calcium concentration of unstimulated saliva

Background To evaluate the effect of dental amalgam and composite restorations on total antioxidant capacity (TAC) and calcium (Ca) ion concentration of unstimulated saliva. Material and Methods Forty-eight children aged 6-10 years selected and divided into three groups of sixteen (8 males, 8 females). In group A and B, samples consisted of two class II dental composite or amalgam restorations, while in group C samples were caries-free (control group). Unstimulated saliva from all samples was collected and TAC was measured by spectrophotometry using an adaptation of 2, 2’-azino-di-(3-ethylbenzthiazoline-6-sulphonate) (ABTS) assay. The Ca ion level was estimated by an auto- analyzer. Data were analyzed with one- and two-way ANOVA test, at a p<. 05 level of significance. Results Composite samples showed significantly higher TAC and lower Ca ion levels compared to amalgam and caries-free samples (p<.05). The TAC values showed only significant difference between groups (p<.05), while the Ca ion results showed significant differences within and between groups (p<.05). Conclusions Dental composite restorations increased TAC and decreased Ca ion levels more than amalgam restorations in saliva. Gender is an effective factor in changes induced in oral cavity as females showed more emphatic reaction to dental filling materials than males. Statement of Clinical Relevance Patients who have dental restorations, especially dental composites, should pay more attention to their dental hygiene, because dental restorations can increase oxidative stress and decrease Ca ion level in saliva, which might jeopardize remineralization process of tooth structures after demineralization. Key words:Amalgam, caries, composite, saliva, total antioxidant capacity.
Realist evaluation and randomised controlled trials for testing program theory in complex social systems

Scientific evaluation seeks to develop and test theories that describe and explain the value of interventions into the world. Realist approaches to scientific evaluation tend to be strong on theory and explanation, but lack adequate tests or means of validating theory. The focus of this article is the potential for randomisation and experimentation to provide evidence for transfactual (i.e. reusable or portable) context–mechanism–outcome configurations (CMOs) in complex adaptive systems. The article is not concerned with attribution of outcomes to past programs but for developing scientific knowledge that can be used for future interventions. It seeks to elucidate the warrant that underpins the randomised controlled trial (RCT) and why it is useful in some fields of science but less so in complex social systems. Realist RCTs are considered but rejected; instead a form of propensity score matching is proposed for testing realist program theory, estimating the effect size of a purported CMO, and generating scientific knowledge for developing more effective interventions into complex social systems.