Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Parent, Teacher, and Consultant Speech Exchanges and Educational Outcomes of Students With Autism During COMPASS Consultation

The significant increase in the numbers of students with autism combined with the need for better trained teachers (National Research Council, 2001) call for research on the effectiveness of alternative methods, such as consultation, that have the potential to improve service delivery. Data from 2 randomized controlled single-blind trials indicate that an autism-specific consultation planning framework known as the collaborative model for promoting competence and success (COMPASS) is effective in increasing child Individual Education Programs (IEP) outcomes (Ruble, Dalrymple, & McGrew, 2010; Ruble, McGrew, & Toland, 2011). In this study, we describe the verbal interactions, defined as speech acts and speech act exchanges that take place during COMPASS consultation, and examine the associations between speech exchanges and child outcomes. We applied the Psychosocial Processes Coding Scheme (Leaper, 1991) to code speech acts. Speech act exchanges were overwhelmingly affiliative, failed to show statistically significant relationships with child IEP outcomes and teacher adherence, but did correlate positively with IEP quality.
Dietary Patterns and Risk of Micronutrient Deficiencies: their Implication for Nutritional Intervention in Ethiopia

Background: Dietary patterns are the quantities, proportions, variety or combinations of different foods and beverages in diets, and the frequency with which they are habitually consumed. In Ethiopia, information on the dietary patterns and association of the proxies of dietary adequacy and quality with nutritional outcomes is scarce. The aims of this paper were to assess the interactions between dietary patterns, nutritional adequacy, nutritional quality and the risk of micronutrient deficiencies, and to highlight their implications in nutritional interventions. Methods: A community based cross-sectional study was carried out in North Shewa zone of Amhara Regional State, central Ethiopia from December 2014 to February 2015. Multistage sampling techniques were employed to recruit participants and 640 subjects involved in the study. Data were collected using structured and seven-day recall questionnaires. Chi-Square test, Kruskal-Walis test, Spearman correlation, multiple linear and multinomial regression models were used for inferential analyses. Results: The main dietary patterns included cereals, vegetables and legumes. Animal Source Foods (ASF) was consumed by 35.4% of participants. The median (range) of Food Variety Score (FVS) and Diet Diversity Score (DDS) were 16 (8-25) and 3.43 (1.14-5.57), respectively. About 28 % of subjects were malnourished. FVS had a positive correlation with DDS (r=0.502, p<0.001) and Body Mass Index (BMI) (r=0.145, p<0.001). DDS had also a positive correlation with BMI (r= 0.19, p<0.001). Family size and educational status were identified as determinant factors for FVS, but the later had a significant influence on DDS. The risks of vitamin A and iron deficiencies were 60.3% and 86.3%, respectively. The consumption of food groups rich in vitamin A and haem iron were significantly different across FVS and DDS (p<0.05). Conclusions: Dietary inadequacy, poor nutritional quality and high risk of micronutrient deficiencies were identified. These underlined the implications of nutritional interventions in central Ethiopia.
Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect

Comparative population genetics in asexual vs. sexual species offers the opportunity to investigate the impact of asexuality on genome evolution. Here, we analyse coding sequence polymorphism and divergence patterns in the fascinating Lineus ribbon worms, a group of marine, carnivorous nemerteans with unusual regeneration abilities, and in which asexual reproduction by fissiparity is documented. The population genomics of the fissiparous L. pseudolacteus is characterized by an extremely high level of heterozygosity and unexpectedly elevated πN/πS ratio, in apparent agreement with theoretical expectations under clonal evolution. Analysis of among‐species allele sharing and read‐count distribution, however, reveals that L. pseudolacteus is a triploid hybrid between Atlantic populations of L. sanguineus and L. lacteus. We model and quantify the relative impact of hybridity, polyploidy and asexuality on molecular variation patterns in L. pseudolacteus and conclude that (i) the peculiarities of L. pseudolacteus population genomics result in the first place from hybridization and (ii) the accumulation of new mutations through the Meselson effect is more than compensated by processes of heterozygosity erosion, such as gene conversion or gene copy loss. This study illustrates the complexity of the evolutionary processes associated with asexuality and identifies L. pseudolacteus as a promising model to study the first steps of polyploid genome evolution in an asexual context.
Single-visit or multiple-visit root canal treatment: systematic review, meta-analysis and trial sequential analysis

Objectives Single-visit root canal treatment has some advantages over conventional multivisit treatment, but might increase the risk of complications. We systematically evaluated the risk of complications after single-visit or multiple-visit root canal treatment using meta-analysis and trial-sequential analysis. Data Controlled trials comparing single-visit versus multiple-visit root canal treatment of permanent teeth were included. Trials needed to assess the risk of long-term complications (pain, infection, new/persisting/increasing periapical lesions ≥1 year after treatment), short-term pain or flare-up (acute exacerbation of initiation or continuation of root canal treatment). Sources Electronic databases (PubMed, EMBASE, Cochrane Central) were screened, random-effects meta-analyses performed and trial-sequential analysis used to control for risk of random errors. Evidence was graded according to GRADE. Study selection 29 trials (4341 patients) were included, all but 6 showing high risk of bias. Based on 10 trials (1257 teeth), risk of complications was not significantly different in single-visit versus multiple-visit treatment (risk ratio (RR) 1.00 (95% CI 0.75 to 1.35); weak evidence). Based on 20 studies (3008 teeth), risk of pain did not significantly differ between treatments (RR 0.99 (95% CI 0.76 to 1.30); moderate evidence). Risk of flare-up was recorded by 8 studies (1110 teeth) and was significantly higher after single-visit versus multiple-visit treatment (RR 2.13 (95% CI 1.16 to 3.89); very weak evidence). Trial-sequential analysis revealed that firm evidence for benefit, harm or futility was not reached for any of the outcomes. Conclusions There is insufficient evidence to rule out whether important differences between both strategies exist. Clinical significance Dentists can provide root canal treatment in 1 or multiple visits. Given the possibly increased risk of flare-ups, multiple-visit treatment might be preferred for certain teeth (eg, those with periapical lesions).
Resting-state functional connectivity predicts neuroticism and extraversion in novel individuals

Abstract The personality dimensions of neuroticism and extraversion are strongly associated with emotional experience and affective disorders. Previous studies reported functional magnetic resonance imaging (fMRI) activity correlates of these traits, but no study has used brain-based measures to predict them. Here, using a fully cross-validated approach, we predict novel individuals’ neuroticism and extraversion from functional connectivity (FC) data observed as they simply rested during fMRI scanning. We applied a data-driven technique, connectome-based predictive modeling (CPM), to resting-state FC data and neuroticism and extraversion scores (self-reported NEO Five Factor Inventory) from 114 participants of the Nathan Kline Institute Rockland sample. After dividing the whole brain into 268 nodes using a predefined functional atlas, we defined each individual’s FC matrix as the set of correlations between the activity timecourses of every pair of nodes. CPM identified networks consisting of functional connections correlated with neuroticism and extraversion scores, and used strength in these networks to predict a left-out individual’s scores. CPM predicted neuroticism and extraversion in novel individuals, demonstrating that patterns in resting-state FC reveal trait-level measures of personality. CPM also revealed predictive networks that exhibit some anatomical patterns consistent with past studies and potential new brain areas of interest in personality.
Macrophages are necessary for epimorphic regeneration in African spiny mice

How the immune system affects tissue regeneration is not well understood. In this study, we used an emerging mammalian model of epimorphic regeneration, the African spiny mouse, to examine cell-based inflammation and tested the hypothesis that macrophages are necessary for regeneration. By directly comparing inflammatory cell activation in a 4 mm ear injury during regeneration (Acomys cahirinus) and scarring (Mus musculus), we found that both species exhibited an acute inflammatory response, with scarring characterized by stronger myeloperoxidase activity. In contrast, ROS production was stronger and more persistent during regeneration. By depleting macrophages during injury, we demonstrate a functional requirement for these cells to stimulate regeneration. Importantly, the spatial distribution of activated macrophage subtypes was unique during regeneration with pro-inflammatory macrophages failing to infiltrate the regeneration blastema. Together, our results demonstrate an essential role for inflammatory cells to regulate a regenerative response. DOI: http://dx.doi. org/10.7554/eLife.24623. 001
Understanding Short-Horizon Bias in Stochastic Meta-Optimization

Careful tuning of the learning rate, or even schedules thereof, can be crucial to effective neural net training. There has been much recent interest in gradient-based meta-optimization, where one tunes hyperparameters, or even learns an optimizer, in order to minimize the expected loss when the training procedure is unrolled. But because the training procedure must be unrolled thousands of times, the meta-objective must be defined with an orders-of-magnitude shorter time horizon than is typical for neural net training. We show that such short-horizon meta-objectives cause a serious bias towards small step sizes, an effect we term short-horizon bias. We introduce a toy problem, a noisy quadratic cost function, on which we analyze short-horizon bias by deriving and comparing the optimal schedules for short and long time horizons. We then run meta-optimization experiments (both offline and online) on standard benchmark datasets, showing that meta-optimization chooses too small a learning rate by multiple orders of magnitude, even when run with a moderately long time horizon (100 steps) typical of work in the area. We believe short-horizon bias is a fundamental problem that needs to be addressed if meta-optimization is to scale to practical neural net training regimes.
Intestinal microbiome analysis revealed dysbiosis in sickle cell disease

REFERENCES [1] Duarte FB, Barbosa MC, Jesus Dos Santos TE, et al. Bone marrow fibrosis at diagnosis is associated with TP53 overexpression and adverse prognosis in low-risk myelodysplastic syndrome. Br J Haematol. In press. https://doi.org/10.1111/bjh.14656. [2] Dolgikh TY, Domnikova NP, Tornuev YV, Vinogradova EV, Krinitsyna YM. Incidence of myelofibrosis in chronic myeloid leukemia, multiple myeloma, and chronic lymphoid leukemia during various phases of diseases. Bull Exp Biol Med. 2017;162(4):483–487. [3] Barcellini W, Fattizzo B, Zaninoni A, et al. Clinical heterogeneity and predictors of outcome in primary autoimmune hemolytic anemia: a GIMEMA study of 308 patients. Blood. 2014;124(19):2930– 2936. [4] Arber DA, Orazi A, Hasserjian R, et al. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016;127(20):2391–2405. [5] Barcellini W, Fattizzo B, Zaninoni A, et al. Clinical evolution of autoimmune cytopenias to idiopathic cytopenias/dysplasias of uncertain significance (ICUS/IDUS) and bone marrow failure syndromes. Am J Hematol. 2017;92(3):E26–E29. [6] Mies A, Hermine O, Platzbecker U. Activin receptor II ligand traps and their therapeutic potential in myelodysplastic syndromes with ring sideroblasts. Curr Hematol Malign Rep. 2016;11(6):416–424.
Synchronization patterns: from network motifs to hierarchical networks

We investigate complex synchronization patterns such as cluster synchronization and partial amplitude death in networks of coupled Stuart–Landau oscillators with fractal connectivities. The study of fractal or self-similar topology is motivated by the network of neurons in the brain. This fractal property is well represented in hierarchical networks, for which we present three different models. In addition, we introduce an analytical eigensolution method and provide a comprehensive picture of the interplay of network topology and the corresponding network dynamics, thus allowing us to predict the dynamics of arbitrarily large hierarchical networks simply by analysing small network motifs. We also show that oscillation death can be induced in these networks, even if the coupling is symmetric, contrary to previous understanding of oscillation death. Our results show that there is a direct correlation between topology and dynamics: hierarchical networks exhibit the corresponding hierarchical dynamics. This helps bridge the gap between mesoscale motifs and macroscopic networks. This article is part of the themed issue ‘Horizons of cybernetical physics’.
Determinants of subjective well-being in representative samples of nations

Background Maximising the happiness and life satisfaction [i.e. subjective well-being (SWB)] of citizens is a fundamental goal of international governmental organizations' policies. In order to decide what policies should be pursued in order to improve SWB there is a need to identify what the key drivers of SWB are. However, to date most studies have been conducted in unrepresentative samples of largely 'developed' nations. Methods Data from the latest World Value Survey (2010-14) and gathered 85 070 respondents from 59 countries (Age 1-99 years, Mean = 42, SD = 16.54; 52.29% females) were pooled for the analysis. A cross-sectional multilevel random effects model was performed where respondents were nested by country. Results The average levels of SWB varied across countries and geographical regions. Among the lowest 10 SWB countries are nations from: Eastern Europe and Former Soviet Union and Middle East and North Africa. Factors driving SWB include state of health, financial satisfaction, freedom of choice, GDP per capita, income scale, importance of friends, leisure, being females, weekly religious attendance, unemployment and income inequality. Nevertheless, according to Cohen's rules of thumb, most of these factors have 'small' effect sizes. Thus, the main factors that possibly will improve the SWB of people across the globe are: state of health, household's financial satisfaction and freedom of choice. Conclusions To maximize the well-being of the population, policy makers may focus on health status, household's financial satisfaction and emancipative values. The levels of prosperity and political stability appear to positively improve the SWB of people.
Tracking Bioluminescent ETEC during In vivo BALB/c Mouse Colonization

Enterotoxigenic Escherichia coli (ETEC) is a leading cause of diarrhea worldwide. Adhesion to the human intestinal tract is crucial for colonization. ETEC adhesive structures have been extensively studied; however, colonization dynamics remain uncharacterized. The aim of this study was to track bioluminescent ETEC during in vivo infection. The promoter region of dnaK was fused with the luc gene, resulting in the pRMkluc vector. E. coli K-12 and ETEC FMU073332 strains were electroporated with pRMkluc. E. coli K-12 pRMkluc was bioluminescent; in contrast, the E. coli K-12 control strain did not emit bioluminescence. The highest light emission was measured at 1.9 OD600 (9 h) and quantified over time. The signal was detected starting at time 0 and up to 12 h. Streptomycin-treated BALB/c mice were orogastrically inoculated with either ETEC FMU073332 pRMkluc or E. coli K-12 pRMkluc (control), and bacterial colonization was determined by measuring bacterial shedding in the feces. ETEC FMU073332 pRMkluc shedding started and stopped after inoculation of the control strain, indicating that mouse intestinal colonization by ETEC FMU073332 pRMkluc lasted longer than colonization by the control. The bioluminescence signal of ETEC FMU073332 pRMkluc was captured starting at the time of inoculation until 12 h after inoculation. The bioluminescent signal emitted by ETEC FMU073332 pRMkluc in the proximal mouse ileum was located, and the control signal was identified in the cecum. The detection of maximal light emission and bioluminescence duration allowed us to follow ETEC during in vivo infection. ETEC showed an enhanced colonization and tropism in the mouse intestine compared with those in the control strain. Here, we report the first study of ETEC colonization in the mouse intestine accompanied by in vivo imaging.
Artocarpin, an isoprenyl flavonoid, induces p53-dependent or independent apoptosis via ROS-mediated MAPKs and Akt activation in non-small cell lung cancer cells

Artocarpin has been shown to exhibit cytotoxic effects on different cancer cells, including non-small cell lung carcinoma (NSCLC, A549). However, the underlying mechanisms remain unclear. Here, we explore both p53-dependent and independent apoptosis pathways in artocarpin-treated NSCLC cells. Our results showed that artocarpin rapidly induced activation of cellular protein kinases including Erk1/2, p38 and AktS473. Inhibition of these protein kinases prevented artocarpin-induced cell death. Moreover, artocarpin-induced phosphorylation of these protein kinases and apoptosis were mediated by induction of reactive oxygen species (ROS), as pretreatment with NAC (a ROS scavenger) and Apocynin (a Nox-2 inhibitor) blocked these events. Similarly, transient transfection of p47Phox or p91Phox siRNA attenuated artocarpin-induced NADPH oxidase activity and cell death. In addition, p53 dependent apoptotic proteins including PUMA, cytochrome c, Apaf-1 and caspase 3 were activated by artocarpin, and these effects can be abolished by antioxidants, MAPK inhibitors (U0126 and SB202190), but not by PI3K inhibitor (LY294002). Furthermore, we found that artocarpin-induced Akt phosphorylation led to increased NF-κB activity, which may act as an upstream regulator in the c-Myc and Noxa pathway. Therefore, we propose that enhancement of both ERK/ p38/ p53-dependent or independent AktS473/NF-κB/c-Myc/Noxa cascade by Nox-derived ROS generation plays an important role in artocarpin-induced apoptosis in NSCLC cells.
Neuroprotection of Transplanting Human Umbilical Cord Mesenchymal Stem Cells in a Microbead Induced Ocular Hypertension Rat Model

ABSTRACT Purpose: The purpose of this study is to investigate the potential therapeutic benefits of intravitreally transplanted human umbilical cord mesenchymal stem cells (UC-MSCs) in an animal model of microbead-injection-induced ocular hypertension (OHT). Methods: UC-MSCs were isolated from human umbilical cords and then cultured. The OHT model was induced via intracameral injection of polystyrene microbeads in Sprague–Dawley adult rat eyes. Fifty-four healthy adult rats were randomly divided into three groups: normal control, OHT model treated with intravitreal transplantation of UC-MSCs, or phosphate-buffered saline (PBS). Two days after OHT was induced, either 5 µl 105 UC-MSCs suspension or PBS was injected into the vitreous cavity of rats. UC-MSCs localization and integration were examined via immunohistochemistry. Neuroprotection was quantified by counting retinal ganglion cells (RGCs) and axons 2 weeks following transplantation. The expression levels of glial-derived neurotrophic factor (GDNF), brain-derived neurotrophic factor (BDNF), and glial fibrillary acidic protein (GFAP) were assessed via immunohistochemistry and Western blot. Functional recovery was assessed 2 weeks after transplantation via scotopic threshold response (STR) electroretinography. Results: Elevated IOP levels were sustained at least 3 weeks after intracameral microbead injection and the number of β-III-tubulin+ RGCs significantly declined compared to PBS-injected eyes. UC-MSCs survived for at least 2 weeks after intravitreal transplantation and predominantly located in the vitreous cavity. A fraction of cells migrated into the ganglion cell layer of host retina, but without differentiation. Intravitreal UC-MSC transplantation resulted in increased number of RGCs, axons, and increased expression of GDNF and BDNF but decreased expression of GFAP. Intravitreal delivery of UC-MSCs significantly improved the recovery of the positive STR. Conclusions: Intravitreal transplantation of UC-MSCs revealed the neuroprotection in the microbead-injection induced OHT. The effects could be related to the secretion of tropic factors (BDNF and GDNF) and the modulation of glial cell activation.
Evolution of nectar spur length in a clade of Linaria reflects changes in cell division rather than in cell expansion

Abstract Background and Aims Nectar spurs (tubular outgrowths of a floral organ which contain, or give the appearance of containing, nectar) are hypothesized to be a ‘key innovation’ which can lead to rapid speciation within a lineage, because they are involved in pollinator specificity. Despite the ecological importance of nectar spurs, relatively little is known about their development. We used a comparative approach to investigate variation in nectar spur length in a clade of eight Iberian toadflaxes. Methods Spur growth was measured at the macroscopic level over time in all eight species, and growth rate and growth duration compared. Evolution of growth rate was reconstructed across the phylogeny. Within the clade we then focused on Linaria becerrae and Linaria clementei, a pair of sister species which have extremely long and short spurs, respectively. Characterization at a micromorphological level was performed across a range of key developmental stages to determine whether the difference in spur length is due to differential cell expansion or cell division. Key Results We detected a significant difference in the evolved growth rates, while developmental timing of both the initiation and the end of spur growth remained similar. Cell number is three times higher in the long spurred L. becerrae compared with L. clementei, whereas cell length is only 1.3 times greater. In addition, overall anisotropy of mature cells is not significantly different between the two species. Conclusions We found that changes in cell number and therefore in cell division largely explain evolution of spur length. This contrasts with previous studies in Aquilegia which have found that variation in nectar spur length is due to directed cell expansion (anisotropy) over variable time frames. Our study adds to knowledge about nectar spur development in a comparative context and indicates that different systems may have evolved nectar spurs using disparate mechanisms.