Miracle-dz/UniFAR-FTUs huggingface dataset:
Determining the conservation of DNA methylation in Arabidopsis

A high-resolution map of DNA methylation in Arabidopsis has recently been generated using high-throughput sequencing of bisulfite-converted DNA. This detailed profile measures the methylation state of most of the cytosines in the Arabidopsis genome, and allows us for the first time to address questions regarding the conservation of methylation across duplicated regions of the genome. To address these questions we measured the degree to which methylation is conserved in both duplicated genes and duplicated non-coding regions of the genome. Methylation is controlled by different mechanisms and methyltransferases depending on the genomic location. Methylation in genes occurs primarily at CG sites and is controlled by the maintenance methyltransferase MET1. In contrast, an RNAi mediated methylation pathway that leads to de novo methylation of asymmetric CHH sites along with CG and CHG sites by the methyltransferase DRM2, drives methylation at tandem and inverted repeats. We find that the cytosine methylation profile is strongly preserved between duplicated genes and repeat regions. The highest level of conservation can be found at CG sites in genes and CHH sites in repeat regions. By constructing substitution matrices between aligned genes we see that methylated cytosines often pair with thymines, which may be explained by the spontaneous deamination of methyl-cytosine to thymine. Despite this observation, we find that methylated cytosines are less often paired with other nucleotides than non-methylated cytosines within gene bodies indicating that they may play an important functional role.
Bullying, social power and heteronormativity: Girls' constructions of popularity

Literature on girls’ popularity posits a strong association between popularity, social power and bullying behaviours, some of which conflate the concepts ‘bully’ and ‘popular’. This study explores that association through links to concepts of popularity among girls in two demographically different high schools. Data are presented that were derived from the application of Q methodology to the problem of comparing girls’ attributions of popularity. Twenty-eight girls sorted items relating to attributes of popular girls. Despite the profound differences between the schools, all loaded heavily on one single factor: attractiveness to boys. The findings and the process have relevance for developing anti-bullying work in classrooms.
Dichloroacetate‐ and trichloroacetate‐induced oxidative stress in the hepatic tissues of mice after long‐term exposure

Dichoroacetate (DCA) and trichloroacetate (TCA) were found to be hepatotoxic and hepatocarcinogenic in rodents. To investigate the role of oxidative stress in the long‐term hepatotoxicity of the compounds, groups of mice were administered 7.7, 77, 154 and 410 mg kg−1 per day, of either DCA or TCA, by gavage, for 4 weeks (4‐W) and 13 weeks (13‐W), and superoxide anion (SA), lipid peroxidation (LP) and DNA‐single strand breaks (SSBs) were determined in the hepatic tissues. Significant increases in all of the biomarkers were observed in response to the tested doses of both compounds in the two test periods, with significantly greater increases observed in the 13‐W, as compared with the 4‐W, period. Hepatomegaly was only observed with a DCA dose of 410 mg kg−1 per day in the 13‐W treatment period, and that was associated with significant declines in the biomarkers, when compared with the immediately lower dose. With the exception of LP production in the 13‐W treatment period that was similarly induced by the two compounds, the DCA‐induced increases in all of the biomarkers were significantly greater than those of TCA. Since those biomarkers were significantly induced by the compounds' doses that were shown to be carcinogenic but at earlier periods than those demonstrating hepatotoxicity/haptocarcinogencity, they can be considered as initial events that may lead to later production of those long‐term effects. The results also suggest LP to be a more significant contributing mechanism than SA and DNA damage to the long‐term hepatotoxicity of TCA. Copyright © 2010 John Wiley & Sons, Ltd.
Adverse pregnancy outcomes: differences between US- and foreign-born women in major US racial and ethnic groups.

OBJECTIVES This study examined whether there were significant differentials between US-born and foreign-born women in risks of infant mortality, low birthweight, and preterm birth and whether these differentials, if they existed, varied across major US racial/ethnic groups. METHODS Multivariate logistic regression was applied to national linked birth/infant death records for 1985 through 1987 to estimate overall and ethnic-specific maternal nativity effects on pregnancy outcomes. RESULTS Substantial maternal nativity differences in risks of infant mortality and low birthweight were found, with the magnitude of the nativity effect varying significantly across racial/ethnic groups. Overall, foreign-born status was associated with 7% and 20% lower risks of low birthweight and infant mortality, respectively. However, the reduced risk of adverse pregnancy outcome associated with immigrant status tended to be substantially larger for Blacks, Cubans, Mexicans, and Chinese than for other ethnic groups. CONCLUSIONS Maternal nativity status, along with ethnicity, may serve as an important axis of differentiation in birth outcome studies. Further research needs to be conducted to assess the effects of behavioral, cultural, and psychosocial factors in explaining the nativity differentials observed here.
The recognition of mental states from dynamic and static facial expressions

The ability to recognize mental states from facial expressions is essential for effective social interaction. However, previous investigations of mental state recognition have used only static faces so the benefit of dynamic information for recognizing mental states remains to be determined. Experiment 1 found that dynamic faces produced higher levels of recognition accuracy than static faces, suggesting that the additional information contained within dynamic faces can facilitate mental state recognition. Experiment 2 explored the facial regions that are important for providing dynamic information in mental state displays. This involved using a new technique to freeze motion in a particular facial region (eyes, nose, mouth) so that this region was static while the remainder of the face was naturally moving. Findings showed that dynamic information in the eyes and the mouth was important and the region of influence depended on the mental state. Processes involved in mental state recognition are discussed.
A handcuff model for the cohesin complex

The cohesin complex is responsible for the accurate separation of sister chromatids into two daughter cells. Several models for the cohesin complex have been proposed, but the one-ring embrace model currently predominates the field. However, the static configuration of the embrace model is not flexible enough for cohesins to perform their functions during DNA replication, transcription, and DNA repair. We used coimmunoprecipitation, a protein fragment complement assay, and a yeast two-hybrid assay to analyze the protein–protein interactions among cohesin subunits. The results show that three of the four human cohesin core subunits (Smc1, Smc3, and Rad21) interact with themselves in an Scc3 (SA1/SA2)-dependent manner. These data support a two-ring handcuff model for the cohesin complex, which is flexible enough to establish and maintain sister chromatid cohesion as well as ensure the fidelity of chromosome segregation in higher eukaryotes.
Algorithm for an oriented multicast routing protocol

An increasing number of Internet applications and services will require the use of multicast in the near future. However, only a few techniques are currently used in network-layer multicast routing protocols, such as flooding, pruning or reverse path construction methods. We propose an algorithm to define a new way of multicasting. The base principle is to perform a limited multicast channeled around the unicast path joining the sender to a specific destination, hence the name "oriented". This algorithm is close to reverse path multicast algorithms but the flooding is much more controlled. A protocol based on our algorithm could have many applications such as performing network node searches in a specific area. The algorithm is tailored as to be scalable to enable its use in an inter-domain environment.
Column density distribution and cosmological mass density of neutral gas: Sloan Digital Sky Survey-III Data Release 9

We present the first results from an ongoing survey for damped Lyman-α systems (DLAs) in the spectra of z > 2 quasars observed in the course of the Baryon Oscillation Spectroscopic Survey (BOSS), which is part of the Sloan Digital Sky Survey (SDSS) III. Our full (non-statistical) sample, based on Data Release 9, comprises 12 081 systems with log N(Hi) ≥ 20, out of which 6839 have logN(Hi) ≥ 20.3. This is the largest DLA sample ever compiled, superseding that from SDSS-II by a factor of seven.
Growth and development in term infants fed long-chain polyunsaturated fatty acids: a double-masked, randomized, parallel, prospective, multivariate study.

OBJECTIVE To evaluate the effects of dietary intake of the long-chain polyunsaturated fatty acids, arachidonic acid (AA), and docosahexaenoic acid (DHA) on multiple indices of infant growth and development. DESIGN A double-masked, randomized, parallel trial was conducted with term infants fed formulas with or without AA+DHA for 1 year (N = 239). Reference groups of breastfed infants (N = 165) weaned to formulas with and without AA+DHA were also studied. Infants in the formula groups were randomized at </=9 days of age to a control formula with no AA or DHA (n = 77) or 1 of 2 otherwise identical formulas containing AA+DHA (AA, 0.46% and DHA, 0.14% of total fatty acids) from either egg-derived triglyceride (egg-DTG [n=80]) or fish oil and fungal oil (fish/fungal [n = 82]) at levels similar to the average in breast milk samples as measured in the reference group. All formulas contained 50% of energy from fat with the essential dietary fatty acids, linoleic acid (20% fatty acids) and alpha-linolenic acid (2% fatty acids). The main study outcomes were AA and DHA levels in plasma and red blood cells, and multiple measures of infant development at multiple ages from birth to 14 months: growth, visual acuity, information processing, general development, language, and temperament. RESULTS AA and DHA levels in plasma and red cells were higher in AA+DHA-supplemented groups than in the control formula group and comparable to those in reference groups. No developmental test results distinguished these groups. Expected differences in family demographics associated with breastfeeding were found, but no advantages to breastfeeding on any of the developmental outcome demonstrated. CONCLUSIONS These findings do not support adding AA+DHA to formulas containing 10% energy as linoleic acid and 1% energy as alpha-linolenic acid to enhance growth, visual acuity, information processing, general development, language, or temperament in healthy, term infants during the first 14 months after birth.infant development, breast feeding, infant formula, long-chain polyunsaturated fatty acids, docosahexaenoic acid.
An 802.11 a/b/g/n digital fractional-N PLL with automatic TDC linearity calibration for spur cancellation

This work presents a 1.9~5.6 GHz fractional-N DPLL with digi-phase spur canceller. It utilizes a ramp signal generated from the fractional-N accumulator to automatically calibrate the TDC linearity. The chip also includes an MMD that overcomes the division ration skipping problem associated with the prior art MMDs. The ADPLL achieves a worst fractional spur level of -55 dBc and an in-band phase noise of -109 dBc/Hz (0.63 ps integrated jitter) while consuming 9.9 mW.
Understanding Talk in Legal Settings: What Law and Society Studies Can Learn from a Conversation Analyst

One hope expressed by the founders of law and society studies in the 1960s was that it would be a truly interdisciplinary field, in which scholars from varied intellectual backgrounds would come together to pursue a shared interest in law and legal institutions. The field of language and law, which exists at the borders of sociology, anthropology, linguistics, and legal scholarship, is a good example of both the achievements and also limitations of this original vision. The achievements lie in a large body of scholarship on law and language, and the growing applied field of forensic linguistics (Gibbons 2003). There has even been a textbook, John Conley and William O’Barr’s (1998) Just Words , which has helped to establish courses in law schools. The limitations lie in the relatively small numbers working in this field (evident at law and society conferences), and a feeling that this kind of research is not properly understood or appreciated by legal scholars, and has only had a limited impact on sociology of law, or related fields like criminology. In their textbook, Conley and O’Barr present the different traditions constituting law and language research as part of an unified enterprise. Against this, one can argue that, although they have a shared interest in language and interactional analysis, these traditions have different assumptions not only about the nature of society, but also about the purpose of research.
Guideline adherence rates and interprofessional variation in a vignette study of depression

Objective: To assess the appropriateness of and variation in intention-to-treat decisions in the management of depression in the Netherlands. Design: Mailed survey with 22 paper cases (vignettes) based on a population study. Setting: A random sample from four professional groups in the Dutch mental healthcare system. Subjects: 264 general practitioners, psychiatrists, psychotherapists, and clinical psychologists. Main outcome measures: Each vignette contained information on a number of patient characteristics taken from three national depression guidelines. The distribution of patient characteristics was based on data from a population study. Respondents were asked to choose the best treatment option and the best treatment setting. For each vignette we examined which of the selected treatments was appropriate according to the recommendations of the three published Dutch clinical guidelines and a panel of experts. Results: 31% of all intention-to-treat decisions were not consistent with the guidelines. Overall, less severe depression, alcohol abuse, psychotic features, and lack of social resources were related to more inappropriate judgements. There was considerable variation between the professional groups: psychiatrists made more appropriate choices than the other professions although they had the highest rate of overtreatment. Conclusions: There is sufficient variation in the intentions to treat depression to give it priority in quality assessment and guideline development. Efforts to achieve appropriate care should focus on treatment indications, referral patterns, and overtreatment.
Symbolic signatures for deformable shapes

Recognizing classes of objects from their shape is an unsolved problem in machine vision that entails the ability of a computer system to represent and generalize complex geometrical information on the basis of a finite amount of prior data. A practical approach to this problem is particularly difficult to implement, not only because the shape variability of relevant object classes is generally large, but also because standard sensing devices used to capture the real world only provide a partial view of a scene, so there is partial information pertaining to the objects of interest. In this work, we develop an algorithmic framework for recognizing classes of deformable shapes from range data. The basic idea of our component-based approach is to generalize existing surface representations that have proven effective in recognizing specific 3D objects to the problem of object classes using our newly introduced symbolic-signature representation that is robust to deformations, as opposed to a numeric representation that is often tied to a specific shape. Based on this approach, we present a system that is capable of recognizing and classifying a variety of object shape classes from range data. We demonstrate our system in a series of large-scale experiments that were motivated by specific applications in scene analysis and medical diagnosis.
Crossings and Nestings in Set Partitions of Classical Types

In this article, we investigate bijections on various classes of set partitions of classical types that preserve openers and closers. On the one hand we present bijections for types $B$ and $C$ that interchange crossings and nestings, which generalize a construction by Kasraoui and Zeng for type $A$. On the other hand we generalize a bijection to type $B$ and $C$ that interchanges the cardinality of a maximal crossing with the cardinality of a maximal nesting, as given by Chen, Deng, Du, Stanley and Yan for type $A$. For type $D$, we were only able to construct a bijection between non-crossing and non-nesting set partitions. For all classical types we show that the set of openers and the set of closers determine a non-crossing or non-nesting set partition essentially uniquely.
Does Desegregation Help Close the Gap? (Testimony of Gary Orfield, March 22, 1996).

TAYLOR: . Dr. Orfield, have you followed the progress of the desegregation plans that were adopted pursuant to court order in 1980 and by consent decree in 1983 since the plans have been in effect? ORFIELD: Yes, I have. TAYLOR: Have you familiarized yourself with what has happened in St. Louis over the past decade or 12 years or so? ORFIELD: Well, I've reviewed the statistical reports that both parties have prepared, which have a great deal of data that's relevant; and I do think I could understand what's happened to the segregation levels. And we have computed those segregation levels independently in our project.
Using Structural Equation Modeling to Validate Online Game Players' Motivations Relative to Self-Concept and Life Adaptation

This study aimed to validate a systematic instrument to measure online players' motivations for playing online games (MPOG) and examine how the interplay of differential motivations impacts young gamers' self-concept and life adaptation. Confirmatory factor analysis determined that a hierarchical model with a two-factor structure of Social-engaging and Social-disengaging MPOG has better factorial validity than one-factor and two-factor models. The study found that individuals who play online games with Social-engaging MPOG are more likely to have a healthy self-concept and life adaptation, whereas players who have Social-disengaging MPOG have poorer self-concepts and experience a significant, negative, and indirect effect on life adaptation through their self-concept.
Psychological Dispositions That Facilitated and Sustained the Development of Knowledge of a Constructivist Approach to Physical Education

This case study tells the story of an in-service elementary physical education teacher, who made a large-scale change from an activities approach to a movement approach based, initially, on “Every Child a Winner” (Rockett & Owens, 1977). Five psychological dispositions facilitated the development of the teacher’s knowledge: (a) the disposition to understand the approach accurately and deeply and to do the job right, (b) the disposition to accept that the approach was difficult to learn and to persist in seeking clarification, (c) the disposition to justify and develop a practice in keeping with a sound educational philosophy and theoretical foundations, (d) the disposition toward change and to learn and implement new ideas, and (e) the disposition to suspend judgment of new ideas. Dispositions can be important aspects of teacher thinking and can help to explain successful knowledge development and teacher change.
A resource‐based perspective on human capital losses, HRM investments, and organizational performance

Reversing the focus on human capital accumulations in the resource-based literature, the authors examine the issue of human capital losses and organizational performance. They theorize that human capital losses markedly diminish the inimitability of human capital stores initially, but that the negative effects are attenuated as human capital losses increase. They argue further that these effects are more dramatic when human resource management (HRM) investments are substantial. As predicted, Study 1 shows that the human capital losses (voluntary turnover rates)-workforce performance relationship takes the form of an attenuated negative relationship when HRM investments are high. Study 2 shows stronger curvilinear effects of voluntary turnover rates on financial performance via workforce productivity under these conditions. Implications for resource-based theory and strategic HRM are addressed.
Statistical identification of differentially labeled peptides from liquid chromatography tandem mass spectrometry

LC‐MS/MS with certain labeling techniques such as isotope‐coded affinity tag (ICAT) enables quantitative analysis of paired protein samples. However, current identification and quantification of differentially expressed peptides (and proteins) are not reliable for large proteomics screening of complex biological samples. The number of replicates is often limited because of the high cost of experiments and the limited supply of samples. Traditionally, a simple fold change cutoff is used, which results in a high rate of false positives. Standard statistical methods such as the two‐sample t‐test are unreliable and severely underpowered due to high variability in LC‐MS/MS data, especially when only a small number of replicates are available. Using an advanced error pooling technique, we propose a novel statistical method that can reliably identify differentially expressed proteins while maintaining a high sensitivity, particularly with a small number of replicates. The proposed method was applied both to an extensive simulation study and a proteomics comparison between microparticles (MPs) generated from platelet (platelet MPs) and MPs isolated from plasma (plasma MPs). In these studies, we show a significant improvement of our statistical analysis in the identification of proteins that are differentially expressed but not detected by other statistical methods. In particular, several important proteins – two peptides for β‐globin and three peptides for von Willebrand Factor (vWF) – were identified with very small false discovery rates (FDRs) by our method, while none was significant when other conventional methods were used. These proteins have been reported with their important roles in microparticles in human blood cells: vWF is a platelet and endothelial cell product that binds to P‐selectin, GP1b, and GP IIb/IIIa, and β‐globin is one of the peptides of hemoglobin involved in the transportation of oxygen by red blood cells.
Creativity and Perceived Stress of Female Music Therapists and Hobbyists

Anecdotal and theoretical accounts suggest that creativity may reduce stress and enhance coping ability. We therefore hypothesized that higher levels of creativity would be associated with lower levels of stress. Ninety-five female nonprofessional musicians (49 music therapists and 46 music hobbyists) participated in the study. Analysis included a hierarchical multiple regression that used type of musician (therapist or hobbyist), creative thinking, creative personality, and creative behavior as predictors. A significant Type of Musician × Creative Thinking interaction indicated that lower stress levels were associated with higher levels of creative thinking for music hobbyists. For music therapists, there was no relation between creative thinking and stress. These findings implicate creative thinking as a coping resource in the stress-coping process for adult female music hobbyists.