Miracle-dz/UniFAR-FTUs huggingface dataset:
A Phylogenetic Analysis of Chloroplast Genomes Elucidates the Relationships of the Six Economically Important Brassica Species Comprising the Triangle of U

The Brassica genus comprises many economically important worldwide cultivated crops. The well-established model of the Brassica genus, U’s triangle, consists of three basic diploid plant species (Brassica rapa, Brassica oleracea, and Brassica nigra) and three amphidiploid species (Brassica napus, Brassica juncea, and Brassica carinata) that arose through interspecific hybridizations. Despite being extensively studied because of its commercial relevance, several aspects of the origin of the Brassica species and the relationships within and among these six species still remain open questions. Here, we successfully de novo assembled 60 complete chloroplast genomes of Brassica genotypes of all six species. A complete map of the single nucleotide variants and insertions and deletions in the chloroplast genomes of different Brassica species was produced. The chloroplast genome consists of a Large and a Small Single Copy (LSC and SSC) region between two inverted repeats, and while these regions of chloroplast genomes have very different molecular evolutionary rates, phylogenetic analyses of different regions yielded no contradicting topologies and separated the Brassica genus into four clades. B. carinata and B. juncea share their chloroplast genome with one of their hybridization donors B. nigra and B. rapa, respectively, which fits the U model. B. rapa, surprisingly, shows evidence of two types of chloroplast genomes, with one type specific to some Italian broccoletto accessions. B. napus clearly has evidence for two independent hybridization events, as it contains either B. rapa chloroplast genomes. The divergence estimation suggests that B. nigra and B. carinata diverged from the main Brassica clade 13.7 million years ago (Mya), while B. rapa and B. oleracea diverged at 2.18 Mya. The use of the complete chloroplast DNA sequence not only provides insights into comparative genome analysis but also paves the way for a better understanding of the phylogenetic relationships within the Brassica genus.
Infants’ Responses to Affect in Music and Speech

Existing literature demonstrates that infants can discriminate between categories of infantdirected (ID) speech based on the speaker’s intended message – that is, infants recognize the difference between comforting and approving ID speech, and treat different utterances from within these two categories similarly. Furthermore, the literature also demonstrates that infants understand many aspects of music and can discriminate between happy and sad music. Building on these findings, the present study investigated whether exposure to happy or sad piano music would systematically affect infants’ preferences for comforting or approving ID speech. Fiveto nine-month-old infants’ preferences for comforting or approving ID speech were examined as a function of whether infants were exposed to sad or happy piano music. Seventeen (10 male, 7 female) full-term, healthy infants were included in the study. It was hypothesized that relative to infants exposed to happy music, infants exposed to sad music would demonstrate a stronger desire to hear comforting ID speech. The study employed an infant controlled, preferential looking procedure to test this hypothesis. The results of the study did not statistically support the researchers’ hypotheses. Limitations of the present work and suggestions for future research are discussed.
Data Science and its Relationship to Big Data and Data-Driven Decision Making

Companies have realized they need to hire data scientists, academic institutions are scrambling to put together data-science programs, and publications are touting data science as a hot-even "sexy"-career choice. However, there is confusion about what exactly data science is, and this confusion could lead to disillusionment as the concept diffuses into meaningless buzz. In this article, we argue that there are good reasons why it has been hard to pin down exactly what is data science. One reason is that data science is intricately intertwined with other important concepts also of growing importance, such as big data and data-driven decision making. Another reason is the natural tendency to associate what a practitioner does with the definition of the practitioner's field; this can result in overlooking the fundamentals of the field. We believe that trying to define the boundaries of data science precisely is not of the utmost importance. We can debate the boundaries of the field in an academic setting, but in order for data science to serve business effectively, it is important (i) to understand its relationships to other important related concepts, and (ii) to begin to identify the fundamental principles underlying data science. Once we embrace (ii), we can much better understand and explain exactly what data science has to offer. Furthermore, only once we embrace (ii) should we be comfortable calling it data science. In this article, we present a perspective that addresses all these concepts. We close by offering, as examples, a partial list of fundamental principles underlying data science.
Field study on thermal comfort in a UK primary school

This paper presents findings from a field survey in a naturally ventilated primary school building in Southampton, UK. The study included thermal comfort surveys and simultaneous measurements of indoor environmental variables. Approximately 230 pupils aged 7-11 in all 8 classrooms of the school were surveyed in repeated survey runs outside the heating season, from April to July 2011. In total 1314 responses were gathered. The survey involved questions on the thermal sensation and preference of the pupils. This paper investigates the children’s thermal sensation trends, their perception of overall comfort and tiredness. Furthermore, it compares the survey results to predictions achieved with current adult-based comfort standards, namely ISO 7730 and EN 15251. The results suggest that children have a different thermal perception than adults. Possible explanations are discussed in relation to the particularities and specific character of school environments.
Antiproliferative Effects of Two Amides, Piperine and Piplartine, from Piper Species

The present work evaluated the cytotoxicity of piplartine {5,6-dihydro-1-[1-oxo-3-(3,4,5- trimethoxyphenyl)-trans-2-propenyl]-2(1H)pyridinone} and piperine {1-[5-(1,3)-benzodioxol- 5-yl)-1-oxo-2,4-pentadienyl]piperidine}, components obtained from Piper species. The substances were tested for their cytotoxicity on the brine shrimp lethality assay, sea urchin eggs development, 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay using tumor cell lines and lytic activity on mouse erythrocytes. Piperine showed higher toxicity in brine shrimp (DL50 = 2.8 d 0.3 μg/ml) than piplartine (DL50 = 32.3 d 3.4 μg/ml). Both piplartine and piperine inhibited the sea urchin eggs development during all phases examined, first and third cleavage and blastulae, but in this assay piplartine was more potent than piperine. In the MTT assay, piplartine was the most active with IC50 values in the range of 0.7 to 1.7 μg/ml. None of the tested substances induced hemolysis of mouse erythrocytes, suggesting that the cytotoxicity of piplartine and piperine was not related to membrane damage.
Investing In People : The Social Benefits of Sustainable Design

This paper provides an overview of theory and research on the human benefits of building design. Identified benefits include improved health outcomes, psychological well being, reduced stress, improved cognitive performance, and improved work and life satisfaction. While many building variables affect these outcomes, there is growing evidence that the high impact design features are connection to nature, incorporation of daylight and sunlight in buildings, sensory change and variability, and improved personal control over ambient conditions.
Relative densities of synaptic and extrasynaptic GABAA receptors on cerebellar granule cells as determined by a quantitative immunogold method

Ion channels gated by the inhibitory neurotransmitter gamma- aminobutyric acid (GABA) are thought to be located in synaptic junctions, but they have also been found throughout the somatodendritic membrane of neurons independent of synapses. To test whether synaptic junctions are enriched in GABAA receptors, and to determine the relative densities of synaptic and extrasynaptic receptors, the alpha 1 and beta 2/3 subunits of the GABAA receptor were localized on cerebellar granule cells using a postembedding immunogold method in cats. Immunoparticle density for the alpha 1 and beta 2/3 subunits was approximately 230 and 180 times more concentrated, respectively, in the synaptic junction made by GABAergic Golgi cell terminals with granule cell dendrites than on the extrasynaptic somatic membrane. Quantification of immunoreactivity revealed one synapse population for the beta 2/3, but appeared to show two populations for the alpha 1 subunit immunoreactivity. The concentration of these subunits on somatic membrane was significantly lower than on the extrasynaptic dendritic membrane. Synaptic junctions with glutamatergic mossy fiber terminals were immunonegative. The results demonstrate that granule cells receiving GABAergic synapses at a restricted location on their distal dendrites exhibit a highly compartmentalized distribution of GABAA receptor in their plasma membrane.
The Mediating Effect of Social Support on the Relationship Between the Impact of Experienced Stigma and Mental Health

The impact of stigma and discrimination against persons with mental illness is well documented. Less well researched are the interpersonal and intrapersonal mechanisms that mediate how acts of discrimination impact persons with mental illness, specifically social support. Past research has focused on the buffering, or moderating impact of perceived social support. We hypothesize that perceived social support is a psychological process, changed by interactions with the outside world, including stressful interactions. In this study, we explore perceived social support as a mediator between the impact of experienced discrimination and mental health. We also test the moderating hypotheses as a way to determine if past research on the role of perceived social support is a better model than the mediating model. We used data from a subset of the Canadian Community Health Survey–Mental Health. We tested the mediating role of perceived social support using the bootstrapped estimate of the 95% confidence interval of the indirect effect. We also tested the buffering hypothesis of perceived social support, using the product of the impact of decimation measure and perceived social support measure. The results suggest that perceived social support does mediate the relationship between the impact of experienced discrimination and mental health. The buffering hypothesis did not hold. Results suggest a new way to model the relationship of perceived social support, stigma, and mental health. Further, the results provide insights into the importance of intervening at the point of discrimination.
Gender Differences in the Appetite Response to a Satiating Diet

We examined gender differences in appetite sensations when exposed to Mediterranean diet (MedDiet) meals and determined whether there are gender differences in the change in the satiating properties of the MedDiet over time. Thirty-eight men and 32 premenopausal women consumed a 4-week isoenergetic MedDiet under controlled conditions. Visual analogue scales were used to measure perceived appetite sensations before and immediately after each meal consumed over the course of one day (Wednesday) of the first and the fourth week of intervention. Women reported greater decreases for desire to eat, hunger, and appetite score than men in response to the consumption of the MedDiet meals (gender-by-meal interactions, resp., P = 0.04, P = 0.048, and P = 0.03). Fullness and prospective food consumption responses did not significantly differ between men and women. Between the first and the fourth week of intervention, premeal prospective food consumption increased with time in men (P = 0.0007) but not in women (P = 0.84; P for gender-by-time interaction = 0.04). These results indicate gender differences in appetite sensations when exposed to the MedDiet. These results may be useful in order to have a better understanding of gender issues for body weight management.
Blocking adenosine A2A receptor reduces peritoneal fibrosis in two independent experimental models.

BACKGROUND Long-term peritoneal dialysis (PD) is associated with peritoneal fibrosis and loss of function. It has been shown that activation of the adenosine A(2A) receptor (A(2A)R) promotes tissue repair, wound healing and extracellular matrix (ECM) production. We have previously shown that adenosine is a potent regulator of inflammation in the peritoneum. In the current study, we explored the role of adenosine and the A(2A)R in two experimental models. METHODS Collagen deposition was evaluated in primary peritoneal fibroblasts following treatment with an A(2A)R agonist and antagonist. In addition, peritoneal fibrosis was induced by i.p. injection of either chlorhexidine gluconate for 2 weeks or 4.25% glucose peritoneal dialysis fluid (PDF) for 1 month. The development of fibrosis was compared between wild-type (WT) and WT mice treated with caffeine (an A(2A)R antagonist) in drinking water or between (A(2A)R(+/+)) mice and A(2A)R-deficient mice (A(2A)R(-/-)). RESULTS Adenosine or the A(2A)R agonist CGS21680 stimulated collagen production by peritoneal fibroblasts in vitro and A(2A)R antagonists (ZM241385 and caffeine) blocked this effect. Consistent with these results, caffeine-treated WT or A(2A)R(-/-) mice had reduced submesothelial thickness, collagen deposition and mRNA levels of fibroblast-specific protein (FSP-1) and connective tissue growth factor (CTGF). In addition, treatment with caffeine in vitro and in vivo diminished A(2A)R and A(2B)R mRNA levels induced by CG or PDF while it upregulated A(1)R levels. CONCLUSION Our data suggest that adenosine through its A(2A)R promotes peritoneal fibrosis and therefore should be considered as a target for pharmacological intervention.
Language identification in Complex, Unoriented, and Degraded Document Images

We describe algorithms for identifying the language of text in document images which are complex, unoriented, and degraded. We distinguish among seven lan-page layouts may be complex, containing text blocks in unknown roughly Manhat-tan arrangements. The pages may be unoriented, that is, upright or rotated by 90, 180, or 270 degrees. The images may be degraded by digitization at coarse and unequal spatial sampling rates as in FAXes. We begin by segmenting the page into text lines in a manner oblivious to page skew and both page and text-line orientation. Then we distinguish between Asian and Latin scripts at any orientation. Chinese versus Japanese is decided at any orientation, and then their orientation is detected. On Latin scripts, we detect rst orientation and then language. A variety of decision procedures are used, some hand-crafted (e.g. using spatial features and optical density distributions) and others trainable (e.g. using word unigram relative entropy models). Tests on 1088 standard (low) resolution FAX images show that our method accurately identiies scripts (98.16%), and language and page orientations (94.76%).
Use of a novel double-antibody technique to describe the pharmacokinetics of rapid-acting insulin analogs.

OBJECTIVE To measure the contribution of bedtime intermediate-acting human insulin on the morning plasma insulin profiles after injection of the rapid-acting insulin analogs lispro and aspart in patients with type 1 diabetes. RESEARCH DESIGN AND METHODS A total of 14 patients with type 1 diabetes, aged 35 +/- 13 years (mean +/- SD), participated in this single-blind, randomized crossover study. After taking their usual injection of human intermediate-acting insulin the night before, they were given insulin aspart or insulin lispro (10 units) before a standardized breakfast. The contribution of continuing absorption of the human insulin was measured using a monoclonal antibody not cross-reacting with insulin aspart or lispro, whereas the contribution of the analogs was estimated by subtraction after measurement of all plasma free insulin using an antibody cross-reacting equally with human insulin and both analogs. RESULTS The correlation coefficient of the fasting free insulin concentrations measured with both insulin methods was 0.95. Fasting free insulin was 95 +/- 25 pmol/l before administration of insulin aspart, when determined with enzyme-linked immunosorbent assay detecting only human insulin, and 71 +/- 20 pmol/l before administration of insulin lispro (NS). Both insulin analogs gave marked peaks of free insulin concentrations, lispro at 40 +/- 3 min and aspart at 55 +/- 6 min after injection (P = 0.01). The later part of the profiles, from 4.5 to 5.5 h after injection, were similar and showed almost no contribution of the insulin analogs. CONCLUSIONS The combination of insulin assays that detect human insulin only or both human insulin and analogs provides a new tool for studying insulin pharmacokinetics. Using this technique, we showed that 4.5 h after administration of the rapid-acting insulin analogs lispro and aspart, the free insulin levels are almost only attributable to the intermediate-acting insulin given at bedtime.
Sentence Level Subjectivity and Sentiment Analysis Experiments in NTCIR-7 MOAT Challenge

This paper describes our supervised approach to the opinionated and the polarity subtasks in the NTCIR-7 MOAT Challenge. We apply a sequential tagging approach at the token level and use the learned token labels in the sentence level classification tasks. In our formal run submissions, we utilized SV M hmm in both tasks with syntactic and lexicon-based features. Additionally, we present our experiments with structural correspondence learning (SCL) for addressing the domain adaptation problem in sentiment analysis. We report experiments on three corpora: MPQA, NTCIR-6 and NTCIR-7, however our formal run submission is trained on MPQA. We reached an F-measure of 0.48 (lenient) in the opinionated and 0.27 (lenient) in the polarity subtasks.
Prevalence of Phantom Limb Pain, Stump Pain, and Phantom Limb Sensation among the Amputated Cancer Patients in India: A Prospective, Observational Study

Introduction: The phantom limb pain (PLP) and phantom limb sensation (PLS) are very common among amputated cancer patients, and they lead to considerable morbidity. In spite of this, there is a lack of epidemiological data of this phenomenon among the Asian population. This study was done to provide the data from Indian population. Methods: The prevalence of PLP, stump pain (SP), and PLS was prospectively analyzed from the amputated cancer patients over a period of 2 years in Dr. B.R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi. The risk factors and the impact of phantom phenomenon on patients were also noted. Results: The prevalence of PLP was 41% at 3 and 12 months and 45.3% at 6 months, whereas that of SP and PLS was 14.4% and 71.2% at 3 months, 18.75% and 37.1% at 6 months, 15.8% and 32.4% at 12 months, respectively. There was higher prevalence of PLP and PLS among the patients with history of preamputation pain, smoking with proximal level of amputation, receiving general anesthesia, receiving intravenous (IV) opioid postoperative analgesia, and developing neuroma or infection. Conclusion: The prevalence of PLP and PLS was higher among the cancer amputees as compared to SP, and a few risk factors responsible for their higher prevalence were found in our study. The PLP and PLS lead to considerable morbidity in terms of sleep disturbance and depression.
Teaching Who You Are: Connecting Teachers’ Civic Education Ideology to Instructional Strategies

Abstract This quantitative study uses survey data to test connections between 735 teachers’ civic education ideology (CivID) and their self-reported instructional practices. Analysis demonstrates teachers’ beliefs in relation to conservative, liberal, and critical civic education ideology as well as preference for instructional strategies, such as teacher–text and collaborative–research. Results indicate that high support for particular civic education ideologies are associated with preferences for particular instructional strategies. Endorsement of conservative civic education ideology was positively linked to teacher–text instruction, whereas liberal ideology held a negative association. Critical civic education ideology had a positive relationship with collaborative–research based instruction. Additional findings indicated differences in instructional preferences and CivID based on teachers’ gender, grade level, community type of school, racial makeup of school, and percent of students receiving free and reduced lunch.
Pengaruh Kompetensi dan Independensi Terhadap Kualitas Audit dengan Motivasi dan Etika Auditor sebagai Variabel Moderasi (Studi Empiris Pada Kantor Akuntan Publik di Jakarta)

This study aimed to determine the effect of competence and independence on audit quality with motivation and ethics of auditors as moderating variables The population in this study is auditors who work in Public Accounting Firm (KAP) listed in the IAI (Institute of Accountants Indonesia) in Jakarta as much as 237 KAP. Samples were selected by purposive sampling technique with certain criteria : KAP at least has 3 partmers which resulted 43 respondents. The results of study showed that only competence affected audit quality. Meanwhile independence did not significantly influence audit quality. In addition, motivation and ethics audit did not moderate the relationship of competence and audit quality as well as the relationship of independence and audit quality.
Safety in Beauty: Social Exclusion, Antisocial Responses, and the Desire to Reconnect

Individuals regularly exhibit antisocial responses after social exclusion. In four unregistered studies (1a, 1b, 2, and 3) and one preregistered experiment (Study 4), we tested the hypothesis that the excluder’s physical attractiveness reduces the relationship between social exclusion and negative responding. Results showed that exclusion by a highly attractive source caused less aggressive and more prosocial responses than exclusion by a less attractive source (Studies 1–3). The interaction effect was mediated by perceived likeability of the excluding person (Study 3). The preregistered experiment did not confirm the interactive effect between exclusion and attractiveness (Study 4); however, exploratory analyses indicated the effect on pro- (but not antisocial) responding. Inconsistent findings as well as the theoretical and practical implications are discussed.
Robust Lyapunov functions for Complex Reaction Networks: An uncertain system framework

We present a framework to transform the problem of finding a Lyapunov function for a Complex Reaction Network (CRN) in concentration coordinates with arbitrary monotone kinetics into finding a common Lyapunov function for a linear parameter varying system in reaction coordinates. This is applied to reinterpret previous results on Piecewise Linear in Rates Lyapunov function, and to introduce Piecewise Quadratic in Rates Lyapunov functions for CRNs. The results are illustrated by an example.