Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancing a Somatic Maturity Prediction Model.

PURPOSE Assessing biological maturity in studies of children is challenging. Sex-specific regression equations developed using anthropometric measures are widely used to predict somatic maturity. However, prediction accuracy was not established in external samples. Thus, we aimed to evaluate the fit of these equations, assess for overfitting (adjusting as necessary), and calibrate using external samples. METHODS We evaluated potential overfitting using the original Pediatric Bone Mineral Accrual Study (PBMAS; 79 boys and 72 girls; 7.5-17.5 yr). We assessed change in R and standard error of the estimate (SEE) with the addition of predictor variables. We determined the effect of within-subject correlation using cluster-robust variance and fivefold random splitting followed by forward-stepwise regression. We used dominant predictors from these splits to assess predictive abilities of various models. We calibrated using participants from the Healthy Bones Study III (HBS-III; 42 boys and 39 girls; 8.9-18.9 yr) and Harpenden Growth Study (HGS; 38 boys and 32 girls; 6.5-19.1 yr). RESULTS Change in R and SEE was negligible when later predictors were added during step-by-step refitting of the original equations, suggesting overfitting. After redevelopment, new models included age × sitting height for boys (R, 0.91; SEE, 0.51) and age × height for girls (R, 0.90; SEE, 0.52). These models calibrated well in external samples; HBS boys: b0, 0.04 (0.05); b1, 0.98 (0.03); RMSE, 0.89; HBS girls: b0, 0.35 (0.04); b1, 1.01 (0.02); RMSE, 0.65; HGS boys: b0, -0.20 (0.02); b1, 1.02 (0.01); RMSE, 0.85; HGS girls: b0, -0.02 (0.03); b1, 0.97 (0.02); RMSE, 0.70; where b0 equals calibration intercept (standard error (SE)) and b1 equals calibration slope (SE), and RMSE equals root mean squared error (of prediction). We subsequently developed an age × height alternate for boys, allowing for predictions without sitting height. CONCLUSION Our equations provided good fits in external samples and provide an alternative to commonly used models. Original prediction equations were simplified with no meaningful increase in estimation error.
Analysis of Sequence Data Under Multivariate Trait-Dependent Sampling

High-throughput DNA sequencing allows for the genotyping of common and rare variants for genetic association studies. At the present time and for the foreseeable future, it is not economically feasible to sequence all individuals in a large cohort. A cost-effective strategy is to sequence those individuals with extreme values of a quantitative trait. We consider the design under which the sampling depends on multiple quantitative traits. Under such trait-dependent sampling, standard linear regression analysis can result in bias of parameter estimation, inflation of Type I error, and loss of power. We construct a likelihood function that properly reflects the sampling mechanism and uses all available data. We implement a computationally efficient EM algorithm and establish the theoretical properties of the resulting maximum likelihood estimators. Our methods can be used to perform separate inference on each trait or simultaneous inference on multiple traits. We pay special attention to gene-level association tests for rare variants. We demonstrate the superiority of the proposed methods over standard linear regression through extensive simulation studies. We provide applications to the Cohorts for Heart and Aging Research in Genomic Epidemiology Targeted Sequencing Study and the National Heart, Lung, and Blood Institute Exome Sequencing Project. Supplementary materials for this article are available online.
Plasma kisspeptin levels in lactational amenorrhea

Abstract The kisspeptin is a neuropeptide to play physiological roles in regulating gonadotropin-releasing hormone secretion in the hypothalamus. In human plasma, the kisspeptin concentration is measured, but gonadotropin-releasing hormone is not. This study aims to understand the physiological roles of the circulating kisspeptin in lactational amenorrhea in humans because prolactin reduces the kisspeptin expression and luteinizing hormone secretion resulting in anovulations in rodent brains. Plasma kisspeptin levels were measured in 11 subjects in lactational amenorrhea and in four cases with pathological amenorrhea by different etiologies for comparison using the enzyme immunoassay specific for human kisspeptin. The plasma kisspeptin levels in the 11 women with lactational amenorrhea were 15.2 ± 2.5 fmol/mL (mean ± SD) which were not significantly different as compared with 16.5 ± 4.8 fmol/mL (mean ± SD) in four age-matched women with menstrual cycles as we reported previously. In the four cases with pathological amenorrhea, their plasma kisspeptin levels were from 5.8 to 13.7 fmol/mL. This study demonstrated that the plasma kisspeptin levels were not totally reduced in lactational or pathological amenorrhea. These results suggest the physiological roles of the circulating kisspeptin are different from the role in the brain.
Methods Literature search The systematic review was conducted in accordance with the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-analyses

A systematic review and meta-analysis of randomised controlled trials was undertaken to determine the effects of almond consumption on blood lipid levels, namely total cholesterol (TC), LDL-cholesterol (LDL-C), HDL-cholesterol (HDL-C), TAG and the ratios of TC:HDL-C and LDL-C:HDL-C. Following a comprehensive search of the scientific literature, a total of eighteen relevant publications and twenty-seven almond-control datasets were identified. Across the studies, the mean differences in the effect for each blood lipid parameter (i.e. the control-adjusted values) were pooled in a meta-analysis using a random-effects model. It was determined that TC, LDL-C and TAG were significantly reduced by −0·153 mmol/l (P< 0·001), −0·124 mmol/l (P= 0·001) and −0·067 mmol/l (P= 0·042), respectively, and that HDL-C was not affected (−0·017 mmol/l; P= 0·207). These results are aligned with data from prospective observational studies and a recent large-scale intervention study in which it was demonstrated that the consumption of nuts reduces the risk of heart disease. The consumption of nuts as part of a healthy diet should be encouraged to help in the maintenance of healthy blood lipid levels and to reduce the risk of heart disease.
- 1-Inequality of Opportunities in the Labor Market : Evidence from Life in Transition Surveys in Europe and Central Asia

This paper attempts to quantify the degree of inequality of opportunity in labor market outcomes for a selection of countries in the Europe and Central Asia (ECA) region. We adapt the Human Opportunity Index (HOI) methodology that has been widely used to study opportunities of children to measures of inequality in the labor market for working age adults, using data from the Life in Transition Surveys (LiTS) conducted in 2006. We decompose the observed inequalities into components that are attributable to circumstances an individual was born into (e.g., gender, parents’ education, minority status, etc) and other characteristics (education and age). We conduct additional exercises with this measure, which examine: (i) comparisons with an expenditure-based measure of inequality of opportunity; (ii) the extent to which the measures of inequality resonate with individual perceptions of life satisfaction and fairness; and (iii) how the results for ECA countries compare with similar measures in the Latin America and the Caribbean (LAC) region. Our findings show substantial inequality of opportunity (attributable to circumstances that an individual was born into) in employment status in the ECA region and a high degree of heterogeneity across countries in the circumstances that matter the most for inequality. The correlations between measures and perceptions of inequality among citizens across ECA countries suggest that inequality between groups, including measures of inequality of opportunity, matter more than overall measures of inequality for citizen perceptions of ―fairness‖. The results are robust to different definitions of jobs as opportunities. 1 Poverty Reduction and Equity Department (PRMPR), World Bank. This was written as a background paper for the WDR (2013) and for regional studies in ECA region. We thank Francisco Ferreira and Luis-Felipe Lopez-Calva for their helpful comments as peer reviewers. The paper also benefited from comments and suggestions provided by Dena Ringold, Carolina Sanchez-Paramo, Jaime Saavedra, and participants of a Brown Bag Lunch organized by ECA PREM and the Second World Bank Conference on Equity. The paper is based on ideas that emerged from initial discussions with Francisco Ferreira, Jesko Hentschel, Dena Ringold and other members of the WDR 2013 team, for which we are much grateful. All remaining errors are our own.
Effects of substratum morphology on cell physiology

Among the host of substratum properties that affect animal cell behavior, surface morphology has received relatively little attention. The earliest effect of surface morphology on animal cells was discovered almost a century ago when it was found that cells became oriented in response to the underlying topography. This phenomenon is now commonly known as contact guidance. From then until very recentrly, little progress has been made in understanding the role of surface morphology on cell behavior, primarily due to a lack of defined surfaces with uniform morphologies. This problem has been solved recently with the development of photolithographic techniques to prepare substrata with well defined and uniform surface morphologies. Availability of such surfaces has facilitated systematic in vitro experiments to study influence of surface morphology on diverse cell physiological aspects such as adhesion, growth, and function. For example, these studies have shown that surfaces with uniform multipls parallel grooves can enhance cell adhesion by confining cells in grooves and by mechanically interlocking them. Several independent studies have demosterated that cell shape is a major determinant of cell growth and function. Because surface morphology has been shown to modulate the extent of cell spreading and cell shape, its effects on cell growth and function appear to be mediated via this biological coupling between cell shape and function. New evidence in the cell biology literature is emerging to suggest that surface morphology could affect other cell behavioral properties such as post‐translational modifications. Further elucidation of such effects will enable better designs for implant and cell culture substrata.
Development of bespoke machine learning and biocuration workflows in a BioC-supporting text mining workbench.

As part of our participation in the Collaborative Biocurator Assistant Task of BioCreative V, we developed methods and tools for recognising and normalising mentions denoting genes/proteins and organisms. A combination of different approaches were used in addressing these tasks. The recognition of gene/protein and organism names was cast as a sequence labelling problem to which the conditional random fields algorithm was applied. In training our models, various lexical and orthographic features were extracted over the CHEMDNER GPRO and S800 corpora which were leveraged as gold standard data. Our feature set was further enriched with semantic attributes drawn from matches between mentions in text and entries in relevant dictionaries. In normalising recognised names, i.e., assigning resource identifiers to recognised names in text, the Jaro-Winkler and Levenshtein distance measures were used to estimate string similarity and -rank candidate matches. Integration of the various techniques and resources was facilitated by the Web-based Argo text mining workbench which allows for the straightforward construction of automatic text processing workflows. Upon using our training workflow to produce gene/protein and organism name recognition models and subsequently evaluating them, micro-averaged F-scores of 70% and 72.87% were obtained, respectively. Curation workflows applying our models on the provided BioC corpus of 120 full-text PubMed Central documents generated normalised named entity annotations which were serialised in the required BioC format.
Acoustics of epenthetic vowels in Lebanese Arabic

We show that epenthetic and lexical vowels in Lebanese Arabic, which are often transcribed as identical, are acoustically distinct: epenthetic vowels are either shorter or backer or both. We argue that this incomplete neutralization is the result of phonetics optionally accessing an intermediate level of phonological derivation. This is formalized in Optimality Theory with Candidate Chains (OT-CC): epenthesis requires a multi-step candidate chain, and phonetics can access any step of the chain. Furthermore, we suggest that the acoustic distinction helps learners construct the correct candidate chains for words with epenthetic vs. lexical vowels.
Previous Research on Sentence Comprehension and Related Skills in Children With ASD

Purpose: Previous research has suggested that language comprehension might be particularly impaired in children with autism spectrum disorder (ASD), but this profile has been only broadly characterized. In the current study, the authors examined sentence comprehension in school-age boys with ASD, including a subgroup with intellectual disability (ID), with particular attention paid to errors that might differentiate between lexically and syntactically based difficulties. Method: Participants were boys with ASD (n = 45, ages 4–11 years) and younger typically developing boys (n = 45, ages 2–6 years). Comprehension was assessed with the Test for Reception of Grammar—Version 2 (TROG–2; Bishop, 2003). Error types were analyzed for a subset of items. Results: Boys with ASD did not differ from younger typically developing boys matched on receptive vocabulary in overall sentence comprehension on the TROG–2 or the number of lexical errors committed. In contrast, the subgroup of boys with ASD and ID (n = 16) had poorer overall performance and committed more lexical errors than younger typically developing boys matched on nonverbal cognition. Conclusions: On average, comprehension was delayed in school-ageboyswith ASDbut not beyond receptive vocabulary expectations. Boys with ASD and ID, however, had a weakness in sentence comprehension beyond nonverbal cognitive expectations.
Neurological Manifestations of Hemoglobinopathies

Hemoglobinopathies are among the most common inherited diseases around the world. Neurological manifestations in hemoglobinopathies may range from mild symptoms to serious complications. Early diagnosis and proper management of the basic disease require specialised hematological experties. In this review we discuss the current neurological manifestations, the management and prevention.
Coping With Stigma by Association and Family Burden Among Family Members of People With Mental Illness

Abstract In this study, we explored stigma by association, family burden, and their impact on the family members of people with mental illness. We also studied the ways in which family members coped with these phenomena. We conducted semistructured interviews with 23 immediate family members of people with mental illness. Participants reported various experiences of stigma by association and family burden. Social exclusion, being blamed, not being taken seriously, time-consuming caregiving activities, and exhaustion appeared to be the predominant forms of stigma by association and family burden experienced by the participants. The participants used problem-focused and emotion-focused coping strategies, separately or simultaneously, to cope with the negative impact of stigma by association and family burden. The results suggest that family members should have access to services to address these problems. Social, instrumental, and emotional support should be given to family members by community members and mental health professionals.
Impact of color temperature on the effectiveness of advertising spokesperson

Advertising spokesperson is one of the undeniably important factors affecting advertising effectiveness. However, advertising spokesperson has to have some particular features to be effective. Various previous researches resulted in determination of different features of advertising spokesperson and their effectiveness; i.e. type of a spokesperson (celebrity vs. a regular person); gender and race of a spokesperson; etc. were found to have an impact on the spokesperson’s effectiveness. However, the research on the impact of shooting color temperature on its effectiveness is still scarce. The aim of this paper is to fill this gap. Neuromarketing research methods were applied to substantiate the impact of color temperature on spokesperson effectiveness and to determine the guidelines for its usage in advertising.
Environmental margin and island evolution in Middle Eastern populations of the Egyptian fruit bat

Here, we present a study of the population genetic architecture and microevolution of the Egyptian fruit bat (Rousettus aegyptiacus) at the environmental margins in the Middle East using mitochondrial sequences and nuclear microsatellites. In contrast to the rather homogenous population structure typical of cave‐dwelling bats in climax tropical ecosystems, a relatively pronounced isolation by distance and population diversification was observed. The evolution of this pattern could be ascribed to the complicated demographic history at higher latitudes related to the range margin fragmentation and complex geomorphology of the studied area. Lineages from East Africa and Arabia show divergent positions. Within the northwestern unit, the most marked pattern of the microsatellite data set is connected with insularity, as demonstrated by the separate status of populations from Saharan oases and Cyprus. These demes also exhibit a reduction in genetic variability, which is presumably connected with founder effects, drift and other potential factors related to island evolution as site‐specific selection. Genetic clustering indicates a semipermeability of the desert barriers in the Sahara and Arabian Peninsula and a corridor role of the Nile Valley. The results emphasize the role of the island environment in restricting the gene flow in megabats, which is also corroborated by biogeographic patterns within the family, and suggests the possibility of nascent island speciation on Cyprus. Demographic analyses suggest that the colonization of the region was connected to the spread of agricultural plants; therefore, the peripatric processes described above might be because of or strengthened by anthropogenic changes in the environment.
Measurement of calcium transients in frog muscle by the use of arsenazo III

Intracellular injection of the calcium indicator dye arsenazo III was used to measure the calcium transients occurring during depolarization of frog skeletal muscle fibres. A quantitative estimate of the rise in intracellular free calcium during a twitch was made, and the relation between membrane potential and calcium release was examined. The results also indicate that calcium in the bathing solution plays no important part in the generation of calcium transients during single twitches.
Mutational Analysis of the Adeno-Associated Virus Type 2 (AAV2) Capsid Gene and Construction of AAV2 Vectors with Altered Tropism

ABSTRACT Adeno-associated virus type 2 (AAV2) has proven to be a valuable vector for gene therapy. Characterization of the functional domains of the AAV capsid proteins can facilitate our understanding of viral tissue tropism, immunoreactivity, viral entry, and DNA packaging, all of which are important issues for generating improved vectors. To obtain a comprehensive genetic map of the AAV capsid gene, we have constructed 93 mutants at 59 different positions in the AAV capsid gene by site-directed mutagenesis. Several types of mutants were studied, including epitope tag or ligand insertion mutants, alanine scanning mutants, and epitope substitution mutants. Analysis of these mutants revealed eight separate phenotypes. Infectious titers of the mutants revealed four classes. Class 1 mutants were viable, class 2 mutants were partially defective, class 3 mutants were temperature sensitive, and class 4 mutants were noninfectious. Further analysis revealed some of the defects in the class 2, 3, and 4 mutants. Among the class 4 mutants, a subset completely abolished capsid formation. These mutants were located predominantly, but not exclusively, in what are likely to be β-barrel structures in the capsid protein VP3. Two of these mutants were insertions at the N and C termini of VP3, suggesting that both ends of VP3 play a role that is important for capsid assembly or stability. Several class 2 and 3 mutants produced capsids that were unstable during purification of viral particles. One mutant, R432A, made only empty capsids, presumably due to a defect in packaging viral DNA. Additionally, five mutants were defective in heparan binding, a step that is believed to be essential for viral entry. These were distributed into two amino acid clusters in what is likely to be a cell surface loop in the capsid protein VP3. The first cluster spanned amino acids 509 to 522; the second was between amino acids 561 and 591. In addition to the heparan binding clusters, hemagglutinin epitope tag insertions identified several other regions that were on the surface of the capsid. These included insertions at amino acids 1, 34, 138, 266, 447, 591, and 664. Positions 1 and 138 were the N termini of VP1 and VP2, respectively; position 34 was exclusively in VP1; the remaining surface positions were located in putative loop regions of VP3. The remaining mutants, most of them partially defective, were presumably defective in steps of viral entry that were not tested in the preliminary screening, including intracellular trafficking, viral uncoating, or coreceptor binding. Finally, in vitro experiments showed that insertion of the serpin receptor ligand in the N-terminal regions of VP1 or VP2 can change the tropism of AAV. Our results provide information on AAV capsid functional domains and are useful for future design of AAV vectors for targeting of specific tissues.
An incremental clustering algorithm based on swarm intelligence theory

Although many clustering algorithms have been proposed so far, they seldom focused on high-dimensional and incremental databases. We present a new type of incremental clustering algorithm, which is based on the swarm intelligence theory. The new type of incremental clustering algorithm implements the clustering process by the actions of clustering agents. The clustering agents, which move in a three-dimensional space, have the abilities of memory, communication, analysis, judgement, coordination and so on. This new type of incremental clustering algorithm is applicable in periodically incremental environment. Experimental results have shown that this algorithm has many merits such as insensitivity to the order of the data, capability of dealing with the exceptional, high-dimensional and complicated data.
Does vertical integration enhance non-price efficiency? Evidence from the movie theater industry

This paper examines how vertical integration affects non-price efficiency in the movie theater industry. Adopting a discrete choice framework, we derive consumer welfare under capacity constraints and fixed prices, and show that allocating capacity proportionally to demand is efficient. Applying our approach to estimating the efficiency of movie theaters’ seat allocations, we show that integrated theaters may be more efficient than non-integrated ones at picking movies to screen and allocating seats across them. We propose a theoretical mechanism behind these results. Specifically, we show that integrated theaters have higher incentives to acquire demand information and hence can be more efficient in allocating the seats.