Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenomic Changes during Leukemia Cell Differentiation: Analysis of Histone Acetylation and Cytosine Methylation Using CpG Island Microarrays

Dysregulation of epigenetic control is an important participant in carcinogenesis. The PML/RAR α translocation in acute promyelocytic leukemia (APL) is an example where the resultant fusion protein recruits histone deacetylase complexes to target genes resulting in their inappropriate transcriptional repression. All-trans-retinoic acid (ATRA) acts as a ligand that relieves this repression and produces an epigenetic transcriptional reprogramming of the cancer cell. CpG island microarrays were used to analyze the DNA methylation and histone acetylation state of the human APL cell line NB4 before and after differentiation with ATRA as well as normal peripheral blood mononuclear cells (PBMC). Over 70 CpG islands within 1 kb of transcription start of a known gene are aberrantly methylated in NB4 cells compared with PBMC; however, no changes in cytosine methylation were detected following ATRA-induced differentiation. With respect to histone H4 acetylation, over 100 single-copy CpG islands within 1 kb of transcription start of a known human gene became hyperacetylated following ATRA-induced differentiation. One CpG island was aberrantly methylated in NB4 cells, but became hyperacetylated and was induced following ATRA treatment and was associated with the HoxA1 gene, suggesting it may be a target gene of ATRA in APL. In addition to single-copy sequences, a selective increase in acetylation was detected in satellite DNA when compared with other high-copy sequences, such as Alu or rDNA. In summary, ATRA stimulates complex epigenomic changes during leukemic cell differentiation, and monitoring these changes may help to identify new targets of epigenetic dysfunction.
A Two-Step Hierarchical Algorithm for Model-Based Diagnosis

For many large systems the computational complexity of complete model-based diagnosis is prohibitive. In this paper we investigate the speedup of the diagnosis process by exploiting the hierarchy/locality as is typically present in well-engineered systems. The approach comprises a compile-time and a run-time step. In the first step, a hierarchical CNF representation of the system is compiled to hierarchical DNF of adjustable hierarchical depth. In the second step, the diagnoses are computed from the hierarchical DNF and the actual observations. Our hierarchical algorithm, while sound and complete, allows large models to be diagnosed, where compiletime investment directly translates to run-time speedup. The benefits of our approach are illustrated by using weak-fault models of real-world systems, including the ISCAS-85 combinatorial circuits. Even for these non-optimally partitioned problems the speedup compared to traditional approaches ranges in the hundreds.
Emotion Regulation, Parenting and Display of Social Reticence in Preschoolers

The study of social reticence in early childhood has focused primarily on those dispositional, intra-individual factors that might account for its demonstration among peers. Little is known, however, about the relations between social reticence and its association with the quality of parenting behaviors. Indeed, the independent and interactive "contributions" of dispositional and parenting factors to children's demonstration of socially reticent behavior have not received adequate attention. In this study, 188 preschool children and their mothers were observed during unstructured Free-play and a structured Lego-building teaching task. Additionally, the children were observed in quartets of same-sex, same-age unfamiliar peers. Results indicated that children's shy, socially reticent behavior was predicted by the extent to which mothers were over-solicitous during Free-play. In addition, preschooler's expressions of reticent behavior were predicted by the interactions between emotion dysregulation and the lack of maternal guidance and control during a teaching task. Emotionally dysregulated children whose mothers provided little control in this putatively stressful teaching task were more likely to be shy and reticent. This relation was non-significant for dysregulated children with mothers who provided high levels of guidance. The results suggest that early childhood educators offer reticent/shy children opportunities to explore their impersonal and social milieus and to warmly encourage such exploratory activities. Without such encouragement and opportunity building, reticent preschoolers may suffer from not having experienced sufficient exploration-to-play sequences thereby stifling the problem-solving competencies derived from such experiences.
Tomosyn Negatively Regulates CAPS-Dependent Peptide Release at Caenorhabditis elegans Synapses

The syntaxin-interacting protein tomosyn is thought to be a key regulator of exocytosis, although its precise mechanism of action has yet to be elucidated. Here we examined the role of tomosyn in peptide secretion in Caenorhabditis elegans tomosyn (tom-1) mutants. Ultrastructural analysis of tom-1 mutants revealed a 50% reduction in presynaptic dense-core vesicles (DCVs) corresponding to enhanced neuropeptide release. Conversely, overexpression of TOM-1 led to an accumulation of DCVs. Together, these data provide the first in vivo evidence that TOM-1 negatively regulates DCV exocytosis. In C. elegans, neuropeptide release is promoted by the calcium-dependent activator protein for secretion (CAPS) homolog UNC-31. To test for a genetic interaction between tomosyn and CAPS, we generated tom-1;unc-31 double mutants. Loss of TOM-1 suppressed the behavioral, electrophysiological, and DCV ultrastructural phenotypes of unc-31 mutants, indicating that TOM-1 antagonizes UNC-31-dependent DCV release. Because unc-31 mutants exhibit synaptic transmission defects, we postulated that loss of DCV release in these mutants and the subsequent suppression by tom-1 mutants could simply reflect alterations in synaptic activity, rather than direct regulation of DCV release. To distinguish between these two possibilities, we analyzed C. elegans Rim mutants (unc-10), which have a comparable reduction in synaptic transmission to unc-31 mutants, specifically attributed to defects in synaptic vesicle (SV) exocytosis. Based on this analysis, we conclude that the changes in DCV release in tom-1 and unc-31 mutants reflect direct effects of TOM-1 and UNC-31 on DCV exocytosis, rather than altered SV release.
Talking about Homelessness: A teaching and research initiative in East London

This article discusses a teaching and research initiative in which 12 third-year undergraduate students and a lecturer worked as volunteers at a local drop-in centre for homeless men and women, and subsequently conducted 49 life history interviews there. Students were asked to keep a diary, recording field observations and reflections on stories told, and to write a paper based on analysis and interpretation of interview transcripts. They were encouraged to think about relationships between the researcher and researched, and the ways in which accounts of the past are constructed. Overall, the initiative produced several positive outcomes. The lecturer was able to design and conduct an oral history research project, and write academic papers based on original data. Students learned about methodological issues through the process of actually participating in and documenting primary research and experienced working in the voluntary sector. Consequently, they also began to think more broadly about the range of employment possibilities open to them. Ongoing communication and a working relationship was established between university personnel and a local voluntary sector organisation. Drop-in centre staff began to perceive future benefits in working with university staff--in terms of making further use of research skills and access to a pool of potential volunteers.
Time to get emotional: Phronetic reflections on the concept of trust in International Relations

This article will engage with the growing literature on the subject of trust in international politics by pointing out remaining problems and contradictions in recent critiques against the rationalist mainstream. Although it finds itself in agreement with these critiques it will argue that despite its more nuanced appreciation of trust, this critical scholarship does not quite succeed in either leaving the rationalist conceptions behind or in achieving a more substantial account of the concept of trust. In order to do so the article will first challenge the remaining methodological framework in which trust scholarship is couched. Second, the article will proceed to show how the emotive element in acts of trust can be highlighted when approached through a phronetic lens and how the introduction of emotion into trust scholarship in IR will allow a richer and thicker study of the phenomenon of trust in international politics. Centrally, the article will claim that any study of trust which ignores the elementary emotional component will remain incomplete.
Emotional Intelligence and Social Interaction

Two studies found positive relationships between the ability to manage emotions and the quality of social interactions, supporting the predictive and incremental validity of an ability measure of emotional intelligence, the Mayer-Salovey-Caruso Emotional Intelligence Test (MSCEIT). In a sample of 118 American college students (Study 1), higher scores on the managing emotions subscale of the MSCEIT were positively related to the quality of interactions with friends, evaluated separately by participants and two friends. In a diary study of social interaction with 103 German college students (Study 2), managing emotions scores were positively related to the perceived quality of interactions with opposite sex individuals. Scores on this subscale were also positively related to perceived success in impression management in social interactions with individuals of the opposite sex. In both studies, the main findings remained statistically significant after controlling for Big Five personality traits.
An Exploratory Application of Rhetorical Structure Theory to Detect Coherence Errors in L2 English Writing: Possible Implications for Automated Writing Evaluation Software

This paper presents an initial attempt to examine whether Rhetorical Structure Theory (RST) (Mann & Thompson, 1988) can be fruitfully applied to the detection of the coherence errors made by Taiwanese low-intermediate learners of English. This investigation is considered warranted for three reasons. First, other methods for bottom-up coherence analysis have proved ineffective (e.g., Watson Todd et al., 2007). Second, this research provides a preliminary categorization of the coherence errors made by first language (L1) Chinese learners of English. Third, second language discourse errors in general have received little attention in applied linguistic research. The data are 45 written samples from the LTTC English Learner Corpus, a Taiwanese learner corpus of English currently under construction. The rationale of this study is that diagrams which violate some of the rules of RST diagram formation will point to coherence errors. No reliability test has been conducted since this work is at an initial stage. Therefore, this study is exploratory and results are preliminary. Results are discussed in terms of the practicality of using this method to detect coherence errors, their possible consequences about claims for a typical inductive content order in the writing of L1 Chinese learners of English, and their potential implications for Automated Writing Evaluation (AWE) software, since discourse organization is one of the essay characteristics assessed by this software. In particular, the extent to which the kinds of errors detected through the RST analysis match those located by Criterion (Burstein, Chodorow, & Leachock, 2004), a well-known AWE software by Educational Testing Service (ETS), is discussed.
Breaking the Crime/Drugs Cycle: The Birth of a New Approach?

This article outlines the findings of an evaluation of the Fast-Track programme currently operating in Plymouth and Torbay. Fast-Track is a coerced treatment scheme for offenders who are committing property crimes to fund a drug habit. Treatment for offenders revolves around a multi-agency initiative between criminal justice agencies and the medical profession, which is aimed at breaking the link between crime and drug abuse. The research findings themselves present a picture of a successful programme that enjoys support from all those involved, including the client group. As well as looking at the research findings, the article offers some thoughts on the implications.
Using Learning Analytics to Investigate Patterns of Performance and Engagement in Large Classes

Educators continue to face significant challenges in providing high quality, post-secondary instruction in large classes including: motivating and engaging diverse populations (e.g., academic ability and backgrounds, generational expectations); and providing helpful feedback and guidance. Researchers investigate solutions to these kinds of challenges from alternative perspectives, including learning analytics (LA). Here, LA techniques are applied to explore the data collected for a large, flipped introductory programming class to (1) identify groups of students with similar patterns of performance and engagement; and (2) provide them with more meaningful appraisals that are tailored to help them effectively master the learning objectives. Two studies are reported, which apply clustering to analyze the class population, followed by an analysis of a subpopulation with extreme behaviours.
Subculture, style, chavs and consumer capitalism: Towards a critical cultural criminology of youth

This article examines current controversies in youth culture studies and relates them to recent developments in ‘cultural criminology’. On the one hand, post-subcultural theorists argue the concept of ‘subculture’ is redundant and obsolete and should be replaced by less bounded or rigid concepts, such as ‘neo-tribe’, which supposedly better capture the essence of identity formation and lifestyle choices in postmodern consumer culture. On the other hand, critics argue postmodern subcultural theory is an apology for consumerism and posit the continuing relevance of social class as an analytical category. In the last decade or so, and unbeknownst to those working in youth culture studies, cultural criminologists have attempted to adapt ‘traditional’ subcultural theory to new experiences of ‘transgression’ which now emerge in the transition to late modernity. Cultural criminology nevertheless has poststructural tendencies. By examining the ‘chav’ phenomenon in Britain as well as research in youth transitions under ‘consumer capitalism’, this article argues that ‘old’ theories and concepts, such as subculture, ought not be so readily disregarded and discarded, and that the notion of ‘style’ remains applicable to some young people who are marginalized and disadvantaged. The article thus proposes a ‘critical cultural criminology’ of youth.
Fault Location on Branched Networks Using a Multiended Approach

Existing travelling-wave fault-location methods are known to perform poorly on branched networks. In this paper, a new fault-location method for use on highly branched networks is demonstrated. The method is based on the retrieval of global positioning system time-stamped arrival times of the fault-induced high-frequency transient. It is shown that for an unambiguous estimation of the fault location, a time-stamp is required from a fault recorder located in each of the two directions from the fault position; therefore, complete coverage of a network can be achieved with a fault recorder on each branch termination. The system is also capable of locating the origin of incipient faults and, therefore, provides a means of detecting potential future faults so remedial action can be taken.
Minocycline and Risperidone Prevent Microglia Activation and Rescue Behavioral Deficits Induced by Neonatal Intrahippocampal Injection of Lipopolysaccharide in Rats

Background Various signs of activation of microglia have been reported in schizophrenia, and it is hypothesized that microglia activation is closely associated with the neuropathology of schizophrenia. Methods Neonatal intrahippocampal injection of lipopolysaccharide (LPS), an activator of microglia, was performed in rats at postnatal day 7 (P7), and they were separately given saline, risperidone (0.5 mg/kg), minocycline (40 mg/kg) or a combination of both of them at P42 for consecutive 14 days. Behavioral changes (locomotion activity, social interaction, novel object recognition and prepulse inhibition) were examined and the number of microglia was assessed by using immunohistochemistry in adulthood. Results The adult rats in LPS-injected group showed obvious behavioral alteration (e. g. deficits in social interaction, novel object recognition and prepulse inhibition) and a dramatic increase of number of activated microglial cells in the hippocampus and other brain regions such as cerebral cortex and thalamus compared to those in saline-injected group. Interestingly, application of either minocycline, risperidone or both of them significantly rescued behavioral deficits and attenuated microglia activation. Conclusion Our results suggest that inhibition of microglia activation may be one of mechanisms underlying the antipsychotic effect of minocycline and risperidone.
AMP-Activated Protein Kinase Deficiency Enhances Myocardial Ischemia/Reperfusion Injury but Has Minimal Effect on the Antioxidant/Antinitrative Protection of Adiponectin

Background— Diabetes increases the morbidity/mortality of ischemic heart disease, but the underlying mechanisms are incompletely understood. Deficiency of both AMP-activated protein kinase (AMPK) and adiponectin occurs in diabetes, but whether AMPK is cardioprotective or a central mediator of adiponectin cardioprotection in vivo remains unknown. Methods and Results— Male adult mice with cardiomyocyte-specific overexpression of a mutant AMPK&agr;2 subunit (AMPK-DN) or wild-type (WT) littermates were subjected to in vivo myocardial ischemia/reperfusion (MI/R) and treated with vehicle or adiponectin. In comparison to WT, AMPK-DN mice subjected to MI/R endured greater cardiac injury (larger infarct size, more apoptosis, and poorer cardiac function) likely as a result of increased oxidative stress in these animals. Treatment of AMPK-DN mice with adiponectin failed to phosphorylate cardiac acetyl-CoA carboxylase as it did in WT mouse heart. However, a significant portion of the cardioprotection of adiponectin against MI/R injury was retained in AMPK-DN mice. Furthermore, treatment of AMPK-DN mice with adiponectin reduced MI/R-induced cardiac oxidative and nitrative stress to the same degree as that seen in WT mice. Finally, treating AMPK-DN cardiomyocytes with adiponectin reduced simulated MI/R-induced oxidative/nitrative stress and decreased cell death (P<0.01). Conclusions— Collectively, our results demonstrated that AMPK deficiency significantly increases MI/R injury in vivo but has minimal effect on the antioxidative/antinitrative protection of adiponectin.
Quench protection of very large superconducting magnets

The feasibility of utilization of cold switches for quench protection of very large superconducting magnets (e.g., for SMES) is considered. The scheme of quench protection of large SMES is suggested. The necessary number of sections can be easily evaluated. Destructive superconducting switches seem to be the best solution. The switch has to be properly designed to avoid arcing and to offer a possibility to change the destructive elements in a reasonable time without warming up large portions of the winding. A suggestion is also made to make use of the temperature dependence of the electrical resistance of the dump resistor. A proper choice of its mass can result in 25 percent decrease of a quench load. <<ETX>>
Benchmarking two techniques for Tor classification: Flow level and circuit level classification

Recently, many Internet users, who seek anonymity, use Tor, which is one of the most popular anonymity software solutions. Tor provides this anonymity by hiding the identity of the user from the destination that the user aims to reach. It also hides the user activities into encrypted cells. In this work, we investigate up to what level we can define what the user in Tor is doing. To this end, we extended on the previous work to classify the user activities using information extracted from Tor circuits and cells. Moreover, we developed a classification system to identify user activities based on traffic flow features. Our results show that flow based classification can reach up to the accuracy of the cell level classification as well as being more flexible.
Analysis on the Collaboration Between Global Search and Local Search in Memetic Computation

The synergy between exploration and exploitation has been a prominent issue in optimization. The rise of memetic algorithms, a category of optimization techniques which feature the explicit exploration-exploitation coordination, much accentuates this issue. While memetic algorithms have achieved remarkable success in a wide range of real-world applications, the key to successful exploration-exploitation synergies still remains obscure as conclusions drawn from empirical results or theoretical derivations are usually quite algorithm specific and/or problem dependent. This paper aims to provide a theoretical model that can depict the collaboration between global search and local search in memetic computation on a broad class of objective functions. In the proposed model, the interaction between global search and local search creates a set of local search zones, in which the global optimal points reside, within the search space. Based on such a concept, the quasi-basin class (QBC) which categorizes problems according to the distribution of their local search zones is adopted. The subthreshold seeker, taken as a representative archetype of memetic algorithms, is analyzed on various QBCs to develop a general model for memetic algorithms. As the proposed model not only well describes the expected time for a simple memetic algorithm to find the optimal point on different QBCs but also consists with the observations made in previous studies in the literature, the proposed model may reveal important insights to the design of memetic algorithms in general.
The Gesture as an Autonomous Nonlinear Dynamical System

ABSTRACT We propose a theory of how the speech gesture determines change in a functionally relevant variable of vocal tract state (e.g., constriction degree). A core postulate of the theory is that the gesture determines how the variable evolves in time independent of any executive timekeeper. That is, the theory involves intrinsic timing of speech gestures. We compare the theory against others in which an executive timekeeper determines change in vocal tract state. Theories that employ an executive timekeeper have been proposed to correct for disparities between theoretically predicted and experimentally observed velocity profiles. Such theories of extrinsic timing make the gesture a nonautonomous dynamical system. For a nonautonomous dynamical system, the change in state depends not just on the state but also on time. We show that this nonautonomous extension makes surprisingly weak kinematic predictions both qualitatively and quantitatively. We propose instead that the gesture is a theoretically simpler nonlinear autonomous dynamical system. For the proposed nonlinear autonomous dynamical system, the change in state depends nonlinearly on the state and does not depend on time. This new theory provides formal expression to the notion of intrinsic timing. Furthermore, it predicts experimentally observed relations among kinematic variables.