Miracle-dz/UniFAR-FTUs huggingface dataset:
Population structure and phylogeography reveal pathways of colonization by a migratory marine reptile (Chelonia mydas) in the central and eastern Pacific

Climate, behavior, ecology, and oceanography shape patterns of biodiversity in marine faunas in the absence of obvious geographic barriers. Marine turtles are an example of highly migratory creatures with deep evolutionary lineages and complex life histories that span both terrestrial and marine environments. Previous studies have focused on the deep isolation of evolutionary lineages (>3 mya) through vicariance; however, little attention has been given to the pathways of colonization of the eastern Pacific and the processes that have shaped diversity within the most recent evolutionary time. We sequenced 770 bp of the mtDNA control region to examine the stock structure and phylogeography of 545 green turtles from eight different rookeries in the central and eastern Pacific. We found significant differentiation between the geographically separated nesting populations and identified five distinct stocks (FST = 0.08–0.44, P < 0.005). Central and eastern Pacific Chelonia mydas form a monophyletic group containing 3 subclades, with Hawaii more closely related to the eastern Pacific than western Pacific populations. The split between sampled central/eastern and western Pacific haplotypes was estimated at around 0.34 mya, suggesting that the Pacific region west of Hawaii has been a more formidable barrier to gene flow in C. mydas than the East Pacific Barrier. Our results suggest that the eastern Pacific was colonized from the western Pacific via the Central North Pacific and that the Revillagigedos Islands provided a stepping-stone for radiation of green turtles from the Hawaiian Archipelago to the eastern Pacific. Our results fit with a broader paradigm that has been described for marine biodiversity, where oceanic islands, such as Hawaii and Revillagigedo, rather than being peripheral evolutionary “graveyards”, serve as sources and recipients of diversity and provide a mechanism for further radiation.
The Contribution of Phonological Awareness to Reading Fluency and Its Individual Sub-skills in Readers Aged 9- to 12-years

Research examining phonological awareness (PA) contributions to reading in established readers of different skill levels is limited. The current study examined the contribution of PA to phonological decoding, visual word recognition, reading rate, and reading comprehension in 124 fourth to sixth grade children (aged 9–12 years). On the basis of scores on the FastaReada measure of reading fluency participants were allocated to one of three reading ability categories: dysfluent (n = 47), moderate (n = 38) and fluent (n = 39). For the dysfluent group, PA contributed significantly to all reading measures except rate, but in the moderate group only to phonological decoding. PA did not influence performances on any of the reading measures examined for the fluent reader group. The results support the notion that fluency is characterized by a shift from conscious decoding to rapid and accurate visual recognition of words. Although PA may be influential in reading development, the results of the current study show that it is not sufficient for fluent reading.
Gene expression pattern Cloning and expression of the TALE superclass homeobox Meis2 gene during zebrafish embryonic development

Meis and Prep/Pknox (MEINOX family) proteins, together with Pbx (PBC family) proteins, belong to the TALE superfamily characterized by an atypical homeodomain containing three additional amino acids between helix 1 and helix 2. Members of the MEINOX and PBC families have been isolated in Caenorhabditis elegans, Drosophila, Xenopus, chick, mouse and human, and play crucial roles in many aspects of embryogenesis. Here, we report the isolation of meis2 in zebrafish. Expression of meis2 is first detected at the beginning of gastrulation. Later during embryogenesis, meis2 transcripts are found in distinct domains of the central nervous system with the strongest expression in the hindbrain. Expression was also detected in the isthmus, along the spinal cord and in the lateral mesoderm. As development proceeds, meis2 is also expressed in the developing retina, pharyngeal arches, and in the vicinity of the gut tube. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
Modelling complex software systems via weighted networks

It is well known that many large-scale software systems show the typical characteristics of complex networks. However, some recent research results indicate us that some essential features of general software networks topology are different from the corresponding functions of real-world software systems. To bridge the above gap, this paper aims at developing a weighted network model to model the practical large-scale software systems from the partial dependency of software systems. Based on the proposed model, we further investigate the statistical characteristics of several representative software systems. Furthermore, we compare the traditional general software network model and the proposed weighted software network model based on two software systems.
MicroRNAs in skeletal muscle: their role and regulation in development, disease and function

Maintaining skeletal muscle function throughout the lifespan is a prerequisite for good health and independent living. For skeletal muscle to consistently function at optimal levels, the efficient activation of processes that regulate muscle development, growth, regeneration and metabolism is required. Numerous conditions including neuromuscular disorders, physical inactivity, chronic disease and ageing are associated with perturbations in skeletal muscle function. A loss or reduction in skeletal muscle function often leads to increased morbidity and mortality either directly, or indirectly, via the development of secondary diseases such as diabetes, obesity, cardiovascular and respiratory disease. Identifying mechanisms which influence the processes regulating skeletal muscle function is a key priority. The discovery of microRNAs (miRNAs) provides a new avenue that will extend our knowledge of factors controlling skeletal muscle function. miRNAs may also improve our understanding and application of current therapeutic approaches as well as enable the identification of new therapeutic strategies and targets aimed at maintaining and/or improving skeletal muscle health. This review brings together the latest developments in skeletal muscle miRNA biology and focuses on their role and regulation under physiological and patho‐physiological conditions with an emphasis on: myogenesis, hypertrophy, atrophy and regeneration; exercise and nutrition; muscle disease, ageing, diabetes and obesity.
Did Post-Floyd et al. Reforms Reduce Racial Disparities in NYPD Stop, Question, and Frisk Practices? An Exploratory Analysis Using External and Internal Benchmarks

Various methodological approaches to constructing external and internal benchmarks have been applied to estimate racial bias in police stop, question, and frisk (SQF) patterns. We apply an external benchmark of the race of the residential population and an internal benchmark of similarly-situated stops to estimate if racial disparities in New York City SQF data were impacted by the Floyd, et al. v. City of New York court settlement. We find that after the settlement, the racial composition of census tracts were no longer significant predictors of the stop rate after controlling for reported crime, socioeconomic factors, and police precincts. We further find that differences in SQF outcomes and hit rates between Blacks and Hispanics and similarly-situated others diminished substantially after the settlement. These findings suggest that court reforms may be an effective method for reducing racial disparities in SQF patterns.
Random Forest and Filter Bank Common Spatial Patterns for EEG-Based Motor Imagery Classification

We propose using filter bank common spatial pattern (FBCSP) feature extraction algorithm, and random forest (RF) technique for classification of EEG motor imagery signals. FBCSP algorithm allows extracting features and dealing with subject variability by automatic selection of frequency bands. Performing random forest in the classification avoid the use of feature selection step, since RF combine a bagging (bootstrap aggregation) and a random selection of features. We evaluate our system on the dataset 2b of the Brain-Computer Interface BCI Competition IV. The proposed method is promising since it has outperformed the results obtained in BCI Competition for some subjects in term of accuracy and kappa.
Accounting for Imperfect Detection in Ecology: A Quantitative Review

Detection in studies of species abundance and distribution is often imperfect. Assuming perfect detection introduces bias into estimation that can weaken inference upon which understanding and policy are based. Despite availability of numerous methods designed to address this assumption, many refereed papers in ecology fail to account for non-detection error. We conducted a quantitative literature review of 537 ecological articles to measure the degree to which studies of different taxa, at various scales, and over time have accounted for imperfect detection. Overall, just 23% of articles accounted for imperfect detection. The probability that an article incorporated imperfect detection increased with time and varied among taxa studied; studies of vertebrates were more likely to incorporate imperfect detection. Among articles that reported detection probability, 70% contained per-survey estimates of detection that were less than 0.5. For articles in which constancy of detection was tested, 86% reported significant variation. We hope that our findings prompt more ecologists to consider carefully the detection process when designing studies and analyzing results, especially for sub-disciplines where incorporation of imperfect detection in study design and analysis so far has been lacking.
How do Students Experience Taking Key Stage 4/5 Public Examinations and What Works to Support them and Why?

This research focused on school life (assessments and transitions) as an area of change and insecurity in young people’s lives, which has been shown to generate stress and induce anxiety symptoms (Seiffge-Krenke, 1993). The experiences of nine students aged 15-17 years, who were taking Key stage 4 (Secondary level) and 5 (Further Education) public examinations were explored. Two school staff in pastoral roles were interviewed to gather their perceptions of student experiences. The research took place in one secondary school in the UK where I was on placement as a Trainee Educational Psychologist (TEP). Interpretative Phenomenological Analysis (IPA) was used to analyse the data. There are two UK based studies (Denscombe, 2000; Putwain, 2009) that have collected qualitative data on student experiences of taking exams. Whilst these studies have helped to highlight what factors might exacerbate feelings of exam stress within the school context, they do not consider the idiosyncratic nature of the exam experience and what factors help students to cope better. In choosing a case study approach with IPA as a methodology, it was possible to develop a rich picture of students’ unique experiences of the exam period. Three overarching concepts were identified in the data: the stress cycle, grades, expectations and identity, and resiliency and coping. Students who were better able to regulate feelings of stress, were those who had built a range of coping skills alongside key attachment figures. It is hoped that findings from the research can be used to inform EP practice in terms of the guidance that EPs might give to schools, particularly in developing effective supportive processes and practices in school.
A SOCIOLINGUISTIC ANALYSIS OF EMOTICON USAGE IN JAPANESE BLOGS: VARIATION BY AGE, GENDER, AND TOPIC

This study explores how Japanese older men and women express themselves in blogging (Curtain 2004), when aging population (65 years and up) is sharply on the rise. The internet proliferation among senior users is also rapidly increasing. In this demographic trend, though younger people’s online activities have heavily been studied, how senior users engage in online activities needs research (Smith 2014) both in the US and Japan. This study specifically examines understudied senior users’ linguistic behavior online from a sociolinguistic perspective (Coupland 2004). This paper is comprised of two parts. Part I makes a quantitative discussion on differences in linguistic and discourse specific features of emoticons between older and younger users for both genders, with respect to their diary-type blogs on everyday topics. Part II makes a qualitative analysis on blogs that discusses a specific topic, moral harassment, and examines how blogging on this particular topic differs from blogging on everyday topics, the latter of which comes from a subset used for the quantitative analyses. The study finds emoticon as the most salient feature that distinguishes younger and older men’s and women’s blogging, and blog topics as a determining factor on emoticon uses.
Schisandra chinensis Peptidoglycan-Assisted Transmembrane Transport of Lignans Uniquely Altered the Pharmacokinetic and Pharmacodynamic Mechanisms in Human HepG2 Cell Model

Schisandra chinensis (Turz Baill) (S. chinensis) (SC) fruit is a hepatoprotective herb containing many lignans and a large amount of polysaccharides. A novel polysaccharide (called SC-2) was isolated from SC of MW 841 kDa, which exhibited a protein-to-polysaccharide ratio of 0.4089, and showed a characteristic FTIR spectrum of a peptidoglycan. Powder X-ray diffraction revealed microcrystalline structures within SC-2. SC-2 contained 10 monosaccharides and 15 amino acids (essential amino acids of 78.12%w/w). In a HepG2 cell model, SC-2 was shown by MTT and TUNEL assay to be completely non-cytotoxic. A kinetic analysis and fluorescence-labeling technique revealed no intracellular disposition of SC-2. Combined treatment of lignans with SC-2 enhanced the intracellular transport of schisandrin B and deoxyschisandrin but decreased that of gomisin C, resulting in alteration of cell-killing bioactivity. The Second Law of Thermodynamics allows this type of unidirectional transport. Conclusively, SC-2 alters the transport and cell killing capability by a “Catcher-Pitcher Unidirectional Transport Mechanism”.
Preschool book-sharing and oral storytelling experiences in ethnically diverse, low-income families

ABSTRACT Children’s book-sharing and oral storytelling experiences were examined in 264 4-year-olds from low-income African-American, Dominican, Mexican, and Chinese families in the United States. Mothers reported on children’s book-sharing and oral storytelling experiences with mothers, fathers, and other people (siblings, grandparents, relatives, and family friends). Results showed that children’s book-sharing experiences were strongly associated with their oral storytelling experiences, suggesting that individual children had uniformly high or low participation in these activities. Mothers, fathers, and other people (especially siblings) participated in these activities with children. Family socio-economic status (i.e. parent education and employment), parental ethnicity, and household composition related to children’s experiences showing that learning experiences are embedded in ecological contexts. Future interventions should recognize the specific needs and advantages of families from diverse backgrounds, and involve multiple family members, including siblings.
Happy-productive groups: How positive affect links to performance through social resources

Abstract The current study extends the Broaden & Build theory to the collective (i.e. groups) level of analysis, focusing on the mediating role of group social resources (i.e. cohesion, coordination, teamwork, supportive team climate) between group positive affect (i.e. enthusiasm, optimism, satisfaction, comfort) and group performance (i.e. in-and extra-role performance, creative performance). To test our hypotheses, we conducted two studies using independent samples. Study 1 is a laboratory study with 449 participants nested in 112 small groups who performed an organizational simulation creative task. Study 2 is a field study that aggregated scores of 2159 employees nested in 417 groups. In both the lab and field studies, structural equation modeling results revealed that group social resources fully mediate the relationship between group positive emotions and performance.
Experiential and Learning Desires of Whale Watching Guides Versus Tourists in Bahía de Banderas, Puerto Vallarta, Mexico

ABSTRACT Whales are popular tourism attractions in many coastal areas of the world. Although not without disagreement, vessel-based whale viewing is widely considered to be a form of ecotourism, in which experiential and learning opportunities exist to engender pro-environmental awareness and behavior. Guides are considered to play an important interpretive role in this respect, although there is little research that explores what guides themselves desire to impart to their passengers. Using quantitative and qualitative methods, we compared what whale watching guides in Puerto Vallarta, Mexico (n = 9) desire their passengers experience and learn to that reported by the whale watchers themselves (n = 283). Guides placed a higher importance on education, while whale watchers indicated experiential elements such as viewing whales close up and spectacular behaviors. Furthermore, the guides held a strong view that emotional feelings of respect and love for whales were important for whale watchers to experience and learn about marine conservation.
Analysis of the metabolic properties of maintenance hemodialysis patients with glucose-added dialysis based on high performance liquid chromatography quadrupole time-of-flight mass spectrometry

The purpose of this study was to compare the metabolic properties of maintenance hemodialysis patients treated with glucose-containing and glucose-free dialysate using metabonomics. Pre- and post-dialysis serum samples from group G (−) using glucose-free dialysate, and group G (+) using glucose-added dialysate (glucose levels were 5.5 mmol/L) were analyzed and tested with high performance liquid chromatography quadrupole time-of-flight mass spectrometry. Orthogonal signal correction–partial least squares discriminate analysis revealed a significant difference in the post-dialysis metabolic properties between samples from the G (−) and G (+) groups, and concentrations of leucine and dihydroxyprostaglandin F2α were higher in the G (+) group than in the G (−) group. However, markers of reactive lipid mobilization and amino acid release, such as bile acids, aspartate, and valine, were lower in the G (+) group than in the G (−) group. There were no significant differences in excitatory neurotransmitters aspartate and phosphorylated anandamide. Use of liquid chromatography-tandem mass spectrometry metabonomics indicated that using glucose-added dialysate was superior to glucose-free dialysate in the protection of the central nervous system of maintenance hemodialysis patients, but had potential risks in stimulating oxidative stress.
Association of rs1800471 polymorphism of TGFB1 gene with chronic kidney disease occurrence and progression and hypertension appearance

Introduction Transforming growth factor β1 (TGF-β1) is a cytokine involved in the process of pathological tissue sclerosis, which is part of the pathophysiological mechanism of end stage renal disease development. The aim of the study was to evaluate the association of the single nucleotide polymorphism rs1800471 of the TGFB1 gene with chronic kidney disease (CKD) occurrence and progression as well as hypertension appearance. Material and methods It was a case-control study where 109 patients with CKD and 111 very old people were enrolled. The association of the studied polymorphism with mentioned diseases was assessed in the whole study group as well as in the subgroups stratified according to the underlying etiology of CKD: nephropathy in type 1 diabetes (n = 13), chronic glomerulonephritis (n = 50) and chronic interstitial nephritis (n = 46). Results No association of CKD progression with rs1800471 polymorphism was observed. The C allele was identified as the one associated with higher risk of the disease occurrence in the dominant model of inheritance (p = 0.035). The C allele in women, opposite to male gender, was associated with higher risk of CKD development (p = 0.038). GG genotype was associated with elevated risk of hypertension appearance (p = 0,0021). Conclusions Due to the lack of accordance with previously performed studies it is still impossible to state an unequivocal conclusion regarding the association between rs1800471 polymorphism of the TGFB1 gene and risk of CKD occurrence and progression as well as hypertension appearance. That is why it is necessary to perform further studies in this field.
Hue, saturation, and depth in planar images

Poorly saturated colors are closer to a pure grey than strongly saturated hues and, therefore, appear less "colorful". Color saturation is effectively manipulated in the visual arts for balancing conflicting sensations and moods and for inducing the perception of relative distance in the pictorial plane. While perceptual science has proven quite clearly that the luminance contrast of any hue acts as a self-sufficient cue to relative depth in visual images, the role of color saturation in such figure-ground organization has remained unclear. We presented configurations of colored inducers on grey 'test' backgrounds to human observers. Luminance and saturation of the inducers was uniform on each trial, but varied across trials. We ran two separate experimental tasks. In a relative background perception task, the perceptual judgments indicated whether the apparent brightness of the grey test background contrasted with, assimilated to, or appeared equal (no effect) to that of a comparison background with the same luminance contrast. Contrast polarity and its interaction with color saturation affected response proportions for contrast, assimilation and no effect. In a figure-ground (relative depth) perception task, perceptual judgments indicated whether the inducers appeared to lie in front of, behind, or in the same depth with the background. Strongly saturated inducers produced larger proportions of foreground effects indicating that these inducers stand out as figure against the background. Weakly saturated inducers produced significantly larger proportions of background effects, indicating that these inducers are perceived as lying behind the backgrounds. Saturation and contrast polarity interacted on foreground and background response proportions. We infer that color saturation modulates figure-ground organization, both directly by determining relative inducer depth, and indirectly, and in interaction with contrast polarity, by affecting apparent background brightness. The results point towards a hitherto undocumented functional role of color saturation in the genesis of form, and in particular figure-ground percepts in the absence of chromatic stereopsis.
Source and channel coding with action-dependent partially known two-sided state information

We consider a source coding problem where the encoder can take actions that influence the availability and/or quality of the side information which is available partially and noncausally at the encoder and the decoder. We then characterize the associated achievable tradeoffs between rate, distortion, and cost. In addition, we state and discuss a capacity result for the channel coding dual problem where the formula duality of special cases is recognized.