Miracle-dz/UniFAR-FTUs huggingface dataset:
DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition

Transposable elements (TEs) are selfish DNA sequences that multiply within host genomes. They are present in most species investigated so far at varying degrees of abundance and sequence diversity. The TE composition may not only vary between but also within species and could have important biological implications. Variation in prevalence among populations may for example indicate a recent TE invasion, whereas sequence variation could indicate the presence of hyperactive or inactive forms. Gaining unbiased estimates of TE composition is thus vital for understanding the evolutionary dynamics of transposons. To this end, we developed DeviaTE, a tool to analyse and visualize TE abundance using Illumina or Sanger sequencing reads. Our tool requires sequencing reads of one or more samples (tissue, individual or population) and consensus sequences of TEs. It generates a table and a visual representation of TE composition. This allows for an intuitive assessment of coverage, sequence divergence, segregating SNPs and indels, as well as the presence of internal and terminal deletions. By contrasting the coverage between TEs and single copy genes, DeviaTE derives unbiased estimates of TE abundance. We show that naive approaches, which do not consider regions spanned by internal deletions, may substantially underestimate TE abundance. Using published data we demonstrate that DeviaTE can be used to study the TE composition within samples, identify clinal variation in TEs, compare TE diversity among species, and monitor TE invasions. Finally we present careful validations with publicly available and simulated data. DeviaTE is implemented in Python and distributed under the GPLv3 (https://github.com/W-L/deviaTE).
The effect of body size on countermovement jump kinetics in children aged 7–11 years

Abstract The purpose this study was to examine the effect of body size on countermovement jump (CMJ) kinetics in children. Participants (n = 160) aged 7–11 years, divided equally by sex and into primary school year groups (years 3, 4, 5 and 6), each performed one CMJ on a force platform. The variables bodyweight (BW), peak force (Fmax), in-jump minimum force (IMF), in-jump vertical force range (IFR) and basic rate of force development (BRFD) were attained from the force-time history and then subsequently scaled to account for body size. A significant age, sex and interaction effect were found for the absolute variables BW, IMF, Fmax and IFR (P < 0.05) between school year groups 3 and 4 against year’s 5 and 6. Simple main effects highlighted no significant sex differences between the boys and girls for all variables (P > 0.05). No significant age or sex differences were observed for normalised or allometrically scaled values (P > 0.05). The results indicate that girls and boys can be grouped together but that body size must be accounted for to enable accurate conclusions to be drawn independent of growth. Body size significantly effects the representation of CMJ kinetic results and therefore, future studies should report both absolute and scaled values. Future research should develop an age-appropriate criterion method for children in order to determine processed CMJ variables to further investigate the neuromuscular performance of children.
Physical Activity, Screen Time, and Sleep in Children With ADHD.

Background: Children with attention deficit hyperactivity disorder (ADHD) are at increased risk for poor health and obesity. The authors describe obesity-related movement behaviors in children with ADHD, determine higher risk groups, and compare with children with other disorders. Methods: Physical activity (PA), sleep, and screen time of children with ADHD (aged 6-18 y) were compared with recommendations and with behaviors of children with autism, asthma, and a normative group using 2011 National Survey of Child Health data. Results: Approximately one-third of children with ADHD participated in daily PA and half in sports in the past year. Older children with ADHD were less likely to get daily PA, get enough sleep, and limit screen time to <2 hours per day. Obese children had lower odds of daily PA. Children who had lower socioeconomic status, or severe ADHD, had lower odds of sports participation. Children with ADHD had 50% lower odds of sports participation than children with asthma. Conclusions: Children with ADHD did not engage in recommended amounts of PA, sleep, and screen time. Children with ADHD who are older, poor, obese, and/or with more severe symptoms are at higher risk for suboptimal movement behaviors. These domains represent novel treatment targets in ADHD youth.
De novo expression of endothelial sialyl Lewis(a) and sialyl Lewis(x) during cardiac transplant rejection: superior capacity of a tetravalent sialyl Lewis(x) oligosaccharide in inhibiting L-selectin-dependent lymphocyte adhesion

Acute organ transplant rejection is characterized by a heavy lymphocyte infiltration. We have previously shown that alterations in the graft endothelium lead to increased lymphocyte traffic into the graft. Here, we demonstrate that lymphocytes adhere to the endothelium of rejecting cardiac transplants, but not to the endothelium of syngeneic grafts or normal hearts analyzed with the in vitro Stamper-Woodruff binding assay. Concomitant with the enhanced lymphocyte adhesion, the cardiac endothelium begins to de novo express sialyl Lewis(a) and sialyl Lewis(x) (sLea and sLex) epitopes, which have been shown to be sequences of L-selectin counterreceptors. The endothelium of allografts, but not that of syngeneic grafts or normal controls, also reacted with the L-selectin-immunoglobulin G fusion protein, giving further proof of inducible L-selectin counterreceptors. The lymphocyte adhesion to endothelium could be significantly decreased either by treating the lymphocytes with anti-L-selectin antibody HRL-1, or by treating the tissue sections with sialidase or anti-sLea or anti-sLex monoclonal antibodies. Finally, we synthetized enzymatically several members of the sLex family oligosaccharides and analyzed their ability to block lymphocyte adhesion to cardiac endothelium. The monovalent sLex (a tetramer), divalent sLex (a decamer), and tetravalent sLex (a 22-mer) could all significantly reduce lymphocyte binding, but the inhibition by the tetravalent sLex-construct was clearly superior to other members of the sLex family. The crucial control oligosaccharides, sialyl lactosamines lacking fucose but being otherwise similar to the members of sLex family, had no effect on lymphocyte binding.
Consumption of Ready-to-Eat Cereal in Canada and Its Contribution to Nutrient Intake and Nutrient Density among Canadians

In recent years, ready-to-eat cereal (RTEC) has become a common breakfast option in Canada and worldwide. This study used the nationally representative cross-sectional data from the Canadian Community Health Survey (CCHS) 2015-Nutrition to determine patterns of RTEC consumption in Canada and the contribution to nutrient intake among Canadians who were ≥2 years, of whom 22 ± 0.6% consumed RTEC on any given day. The prevalence of RTEC consumption was highest in children aged two to 12 years (37.6 ± 1.2%), followed by adolescents aged 13 to 18 years (28.8 ± 1.4%), and then by adults ≥19 years (18.9 ± 0.6%). RTEC consumers had higher intakes of “nutrients to encourage” compared to the RTEC non-consumers. More than 15% of the daily intake of some nutrients, such as folic acid, iron, thiamin, and vitamin B6, were contributed by RTEC. It was noted that nearly 66% of milk consumption was co-consumed with RTEC among RTEC consumers. The nutrient density of the diet, as defined by Nutrient-Rich Food Index (NRF 9.3), was significantly higher among RTEC consumers compared to non-consumers. RTEC consumption was not associated with overweight/obesity. RTEC consumption considerably contributed to the intake of some key nutrients among all age groups in Canada.
Global Chromatin Domain Organization of the Drosophila Genome

In eukaryotes, neighboring genes can be packaged together in specific chromatin structures that ensure their coordinated expression. Examples of such multi-gene chromatin domains are well-documented, but a global view of the chromatin organization of eukaryotic genomes is lacking. To systematically identify multi-gene chromatin domains, we constructed a compendium of genome-scale binding maps for a broad panel of chromatin-associated proteins in Drosophila melanogaster. Next, we computationally analyzed this compendium for evidence of multi-gene chromatin domains using a novel statistical segmentation algorithm. We find that at least 50% of all fly genes are organized into chromatin domains, which often consist of dozens of genes. The domains are characterized by various known and novel combinations of chromatin proteins. The genes in many of the domains are coregulated during development and tend to have similar biological functions. Furthermore, during evolution fewer chromosomal rearrangements occur inside chromatin domains than outside domains. Our results indicate that a substantial portion of the Drosophila genome is packaged into functionally coherent, multi-gene chromatin domains. This has broad mechanistic implications for gene regulation and genome evolution.
Feedback Valence Affects Auditory Perceptual Learning Independently of Feedback Probability

Previous studies have suggested that negative feedback is more effective in driving learning than positive feedback. We investigated the effect on learning of providing varying amounts of negative and positive feedback while listeners attempted to discriminate between three identical tones; an impossible task that nevertheless produces robust learning. Four feedback conditions were compared during training: 90% positive feedback or 10% negative feedback informed the participants that they were doing equally well, while 10% positive or 90% negative feedback informed them they were doing equally badly. In all conditions the feedback was random in relation to the listeners’ responses (because the task was to discriminate three identical tones), yet both the valence (negative vs. positive) and the probability of feedback (10% vs. 90%) affected learning. Feedback that informed listeners they were doing badly resulted in better post-training performance than feedback that informed them they were doing well, independent of valence. In addition, positive feedback during training resulted in better post-training performance than negative feedback, but only positive feedback indicating listeners were doing badly on the task resulted in learning. As we have previously speculated, feedback that better reflected the difficulty of the task was more effective in driving learning than feedback that suggested performance was better than it should have been given perceived task difficulty. But contrary to expectations, positive feedback was more effective than negative feedback in driving learning. Feedback thus had two separable effects on learning: feedback valence affected motivation on a subjectively difficult task, and learning occurred only when feedback probability reflected the subjective difficulty. To optimize learning, training programs need to take into consideration both feedback valence and probability.
Does a picture speak louder than words? The role of infographics as a concussion education strategy

Abstract Knowledge gaps exist regarding how to best educate audiences about concussion. Knowledge translation (KT) plays a critical role in how information is shared. In the field of concussion, infographics are becoming a popular KT strategy for synthesising and sharing information. Study objectives were to explore how infographics enhance concussion knowledge, infographic use and preferences across various stakeholders, and to determine their utility as a KT strategy. Six infographics were created to provide concussion information in a user-friendly and accessible format. A prospective design using a self-developed survey was conducted. Data were collected from youth (n = 78) and adults (n = 88) including students, teachers and healthcare professionals. Descriptive statistics exored perceived knowledge acquisition and infographic use. Thematic analysis of written feedback provided insight on participant responses. Participants identified that the infographics met their knowledge needs (91%) and provided them with new knowledge (87%). Participants also identified that they intend to use the infographics to build their knowledge (89%) and educate others (55%). Enhancement opportunities included incorporating graphics that appeal to different audiences and sharing the lived experiences of individuals who have a concussion. This study demonstrates the potential impact of infographics as a KT strategy that meets the knowledge needs of many audiences.
Robustness of Time Reversal vs. All-Rake Transceivers in Multiple Access Channels

Time reversal (TR) is an effective solution in both single user and multiuser communications for moving complexity from the receiver to the transmitter, in comparison to traditional postfiltering based on Rake receivers. Imperfect channel estimation may, however, affect pre- versus postfiltering schemes in a different way; this paper analyzes the robustness of time reversal versus All-Rake (AR) transceivers, in multiple access communications, with respect to channel estimation errors. Two performance indicators are adopted in the analysis: symbol error probability and spectral efficiency. Analytic expressions for both indicators are derived and used as the basis for simulation-based performance evaluation. Results show that while TR leads to slight performance advantage over AR when channel estimation is accurate, its performance is severely degraded by large channel estimation errors, indicating a clear advantage for AR receivers in this case, in particular when extremely short impulsive waveforms are adopted. Results however also show a stronger non-Gaussianity of interference in the TR case suggesting that the adoption of a receiver structure adapted to non-Gaussian interference might tilt the balance towards TR.
Altered brain activity in patients with strabismus and amblyopia detected by analysis of regional homogeneity: A resting-state functional magnetic resonance imaging study

Previous studies have demonstrated that strabismus or amblyopia can result in marked brain function and anatomical alterations. However, differences in spontaneous brain activity in strabismus and amblyopia (SA) patients as compared with control individuals remain unclear. The present study aimed to analyze the potential brain activity changes in SA patients and their association with behavioral performance. In total, 16 patients with SA (10 women and 6 men) and 16 healthy controls (HCs; 6 men and 10 women) with matched age and sex were recruited. All subjects were examined with resting-state functional magnetic resonance imaging (rs-fMRI), and changes in the spontaneous brain activity of SA patients were evaluated by the regional homogeneity (ReHo) method. The diagnostic ability of the ReHo method was assessed using receiver operating characteristic (ROC) curve analysis. In addition, the association between the mean ReHo value in different brain regions and the behavioral performance was explored by correlation analysis. It was observed that the ReHo value was significantly increased in SA patients compared with HCs in the following brain regions: left lingual gyrus, right middle occipital gyrus/precuneus, bilateral anterior cingulate, left middle occipital gyrus and bilateral precentral gyrus. By contrast, the ReHo value of the left inferior frontal gyrus was significantly lower than that in HCs. ROC curve analysis indicated that the ReHo method has certain credibility for the diagnosis of SA patients. In addition, no similar changes were detected in other brain regions. These results revealed abnormal spontaneous brain activity in certain parts of the brain in adult patients with SA, which suggests the involvement of the neuropathological or compensatory mechanism in these patients, and may be beneficial for clinical treatment.
Decreasing the number of MOPP courses reduces gonadal damage in survivors of childhood hodgkin disease

Children treated for Hodgkin disease are at risk for gonadal damage. Since most children were treated with radiotherapy (RT) in combination with chemotherapy, the presumed detrimental effect of MOPP (mustine, vincristine, procarbazine, and prednisone) (in contrast to schemes with less or without alkylating agents) could not be discerned completely from the effects of RT.
If I knew then what I know now: Advice to my younger self

ABSTRACT If we could go back and give ourselves advice to keep from making a mistake, most of us would probably take that opportunity. Using self-discrepancy theory as a theoretical framework, US workers on Amazon’s Mechanical Turk, who were at least 30 years of age, indicated in two studies what their advice to their younger selves would be, what pivotal event was influential for them, if they had regrets, and if following this advice would bring them closer to their ideal or ought self. Across both studies, most of the advice fell into the domains of relationships, education, and selfhood. Participants said following the advice would bring them more in line with their ideal than their ought self. Following the advice also led to more positive perceptions of the current self by the high school self. Ages at which pivotal events occurred provided strong support for the reminiscence bump.
Demographic and clinical characteristics reflect different phenotypes of osteoarthritis in the lumbar spine: the Johnston County Osteoarthritis Project.

OBJECTIVE Determine if associations between demographic, appendicular joint osteoarthritis (OA), clinical characteristics reflect different phenotypes of OA in the lumbar spine. METHODS Participants were from the Johnston County OA Project. Demographics consisted of age, sex, and race (White and African American [AA]) and clinical characteristics consisted of body mass index (BMI), low back pain and injury, and knee, hip and hand osteoarthritis (OA). Participants were categorized as spine OA (SOA), facet joint OA (FOA), both SOA and FOA, or neither SOA nor FOA (referent group). Multinomial regression models were used to determine odds ratios (OR) and 95% confidence intervals (CI). RESULTS The average age (n=1,793) was 66.2 years (SD=10.1) and BMI was 30.7 (SD=6.2). A majority (63.8%) were women (n=1,144) and 31.8% (n=570) AA. Neither SOA nor FOA was present in 18.0%; 22.8% had FOA, 13.2% had SOA and 46.0% had both SOA and FOA. In adjusted analyses, AA were less likely to have FOA (OR=0.68 95% CI 0.49, 0.95) and both SOA and FOA (OR=0.51 95% CI 0.37, 0.70). Women were more likely to have FOA (OR=1.71 95% CI 1.24, 2.36). BMI ≥30 kg/m2 was associated with FOA (OR=1.76 95% CI 1.28, 2.42) and both SOA and FOA (OR=1.85 95% CI 1.37, 2.51). Knee OA was associated with all three groups while lower back injury was associated with only SOA. Participants with hip OA were less likely to have FOA. CONCLUSION Race, sex, BMI, hip OA, and lower back injury may inform different OA phenotypes in the lumbar spine. This article is protected by copyright. All rights reserved.
How Does Acculturation Influence Smoking Behavior Among Latinos? The Role of Education and National Background.

Introduction As Latinos acculturate, they are assumed to smoke at higher rates. This study investigated the relationship between acculturation level, educational attainment, and cigarette smoking by gender and national background among Latinos. Methods Data from the 2009-2012 National Health Interview Survey were analyzed and participants included 1,111 Cubans, 813 Dominicans, 13,281 Mexicans, and 2,197 Puerto Ricans. Multivariable logistic regression was used to model acculturation and educational predictors of current smoking, stratified by gender and national background. Acculturation level was categorized into less acculturated, bicultural, and more acculturated by combining birthplace and language preference. Current cigarette smoking was defined by self-reported use every day or some days among those who ever smoked at least 100 cigarettes. Results Most respondents were interviewed in English (62%) and had a high school education or less (60%), but only 39% were US-born. Overall, 17.8% of men and 9.6% of women reported current smoking. By national background, smoking prevalence was highest among Puerto Ricans (16% of women and 23% of men) and lowest among Dominicans (6% of women and 10% of men). More acculturated Mexican women and men had significantly higher odds of current smoking (OR=2.94; 95% CI=2.01, 4.31 and OR=1.88; 95% CI=1.39, 2.55; respectively). Mexican men who were more acculturated and had greater levels of educational attainment had lower odds of smoking (OR=.84; 95% CI=.74, .96). Conclusions The relationship between acculturation and health behaviors among Latinos is influenced by education and should be considered by public health and clinician stakeholders when developing or adapting tobacco control strategies.
Effect of Processed Chickpea Flour Incorporation on Sensory Properties of Mankoushe Zaatar

Chickpea flour is known to have good nutritional values. Nevertheless, it is commonly made from ground grains, and characterized by an “off-flavor”. Processing of chickpea grains before flour formation reduces the intensity of the off-flavor. Therefore, two experiments were conducted: first to examine the effect of conventional processing (soaking, boiling, and drying) on the nutritional composition of the chickpea flour; and second, to investigate the impact of processed chickpea flour incorporation with different ratios on the sensory properties of mankoushe zaatar, a popular Lebanese pastry, usually made up of refined wheat flour. Chickpea flour was found to be nutritionally superior compared to refined wheat flour, and conventional processing of the flour was found not to affect its content of protein, fats, carbohydrates, and phosphorus, while total dietary and crude fibers were significantly increased. The fatty acid profile was minimally affected, while magnesium and potassium were reduced. The sensory test conducted among panelists (n = 60) showed that the incorporation of processed chickpea flour into the dough of mankoushe zaatar with ratios of 30% and 50% provided an end-product with better taste and overall acceptability compared to the regular mankoushe. Hence, conventionally processed chickpea flour can be used as a fortifier to improve the nutritional quality of bakery products without negatively affecting their sensory properties.
Mutation spectrum and clinical investigation of achromatopsia patients with mutations in the GNAT2 gene

Achromatopsia (ACHM) is a hereditary cone photoreceptor disorder characterized by the inability to discriminate colors, nystagmus, photophobia, and low‐visual acuity. Six genes have been associated with this rare autosomal recessively inherited disease, including the GNAT2 gene encoding the catalytic α‐subunit of the G‐protein transducin which is expressed in the cone photoreceptor outer segment. Out of a cohort of 1,116 independent families diagnosed with a primary clinical diagnosis of ACHM, we identified 23 patients with ACHM from 19 independent families with likely causative mutations in GNAT2, representing 1.7% of our large ACHM cohort. In total 22 different potentially disease‐causing variants, of which 12 are novel, were identified. The mutation spectrum also includes a novel copy number variation, a heterozygous duplication of exon 4, of which the breakpoint matches exactly that of the previously reported exon 4 deletion. Two patients carry just a single heterozygous variant. In addition to our previous study on GNAT2‐ACHM, we also present detailed clinical data of these patients.