Miracle-dz/UniFAR-FTUs huggingface dataset:
Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type–specific gene expression profiles. Here, we performed Hi-C chromosome conformation capture sequencing to investigate how three-dimensional chromatin organization is disrupted in the context of copy-number variation, long-range epigenetic remodeling, and atypical gene expression programs in prostate cancer. We find that cancer cells retain the ability to segment their genomes into megabase-sized topologically associated domains (TADs); however, these domains are generally smaller due to establishment of additional domain boundaries. Interestingly, a large proportion of the new cancer-specific domain boundaries occur at regions that display copy-number variation. Notably, a common deletion on 17p13.1 in prostate cancer spanning the TP53 tumor suppressor locus results in bifurcation of a single TAD into two distinct smaller TADs. Change in domain structure is also accompanied by novel cancer-specific chromatin interactions within the TADs that are enriched at regulatory elements such as enhancers, promoters, and insulators, and associated with alterations in gene expression. We also show that differential chromatin interactions across regulatory regions occur within long-range epigenetically activated or silenced regions of concordant gene activation or repression in prostate cancer. Finally, we present a novel visualization tool that enables integrated exploration of Hi-C interaction data, the transcriptome, and epigenome. This study provides new insights into the relationship between long-range epigenetic and genomic dysregulation and changes in higher-order chromatin interactions in cancer.
Liminality competence: An interpretative study of mobile project workers’ conception of liminality at work

This study focuses on individuals working under transient and mobile conditions and the specific competences that they develop to deal with such work conditions. The article examines a specific type of knowledge worker, namely, the mobile project worker who is employed by a technical consultancy but who performs work on various client projects together with members from client organizations. The overall aim of this article is to improve our understanding of the differences among people’s abilities to handle fluid and flexible work conditions. We elaborate on the notion of “liminality” to denote a particular element of flexible work conditions, which consists of continuous movement among assignments and of simultaneous engagement with several organizations. Based on qualitative and interpretative research involving a combination of interviews, diaries, and workshops, this article identifies three levels of specific “liminality competence” that mobile project workers develop to deal with liminality at work.
Work, leisure and well-being

Both work and leisure are essential for well-being. Yet the ways in which we conceptualise work, leisure and well-being are in flux, reflecting, in part, the changing societal, economic and community contexts in which work and leisure take place. This paper first discusses the contested nature of work and leisure in relation to well-being, and then considers current evidence concerning the ways in which work and leisure are experienced in contemporary society. The emerging issues are then discussed drawing on two international studies which indicate the increasingly global nature of these concerns. The pervasiveness of the trend towards intensification of work, reducing time and energy for other activities, and the gendered impact of this trend are evident in both studies. Many commentators have noted the negative effects of current working patterns on well-being. Finally, some implications for guidance and counselling as well as future research, are explored.
U.S. reserve soldiers' combat exposure and intimate partner violence: Not more common but it is more violent

Combat exposure's influence on intimate partner violence (IPV) in reserve soldiers is not well understood. This work examines combat exposure's influence on IPV in U.S. Army Reserve/National Guard soldiers and partners. Data are from Operation: SAFETY, a longitudinal study of U.S. Army Reserve/National Guard soldiers and partners. Logistic regression models examined odds of sexual aggression, physical aggression, and physical injury with combat exposure, controlling for posttraumatic stress disorder symptoms, marital satisfaction, and age. Combat exposure was associated with greater physical injury, despite no association between combat exposure and physical aggression. This was significant for male soldier to female partner, as well as female partner to male soldier injury. In addition, female partners were more likely to be sexually aggressive against their male soldiers. Female soldiers' combat exposure was not associated with IPV or injury. Although men's combat exposure did not increase the likelihood of physical aggression, it increased the likelihood of IPV resulting in injury for both husband to wife and wife to husband aggression. Results indicate postdeployment programming should focus on conflict resolution and communication for both partners.
1 GENOMIC PREDICTION OF QUANTITATIVE TRAITS IN PLANT BREEDING USING MOLECULAR MARKERS AND PEDIGREE

ABSTRACT The availability of thousands of genome wide molecular markers has made possible the use of genomic selection in plants and animals. However, the evaluation of models for genomic selection in plant breeding populations is very limited. In this study, we provide an overview of several models for genomic selection, whose predictive ability we investigated using two plant data sets. One data set contains the historical phenotypic records of a series of wheat (Triticum aestivum L.) trials and recently generated genomic data. The other data set pertains to international maize (Zea mays L.) trials in which two disease traits (Exserohilum turcicum and Cercospora zeae-maydis) were measured in maize lines evaluated in five international environments. Results showed that models including marker information yield important gains in predictive ability, relative to that of a pedigree-based model––this, with a modest number of markers. Estimates of marker effects were different across environmental conditions, indicating that genotype × environment interaction is an important component of genetic variability. Overall, the study provides evidence from real populations indicating that genomic selection can be an effective tool for improving traits of economic importance in commercial crops.
Youth, marginalisation, and the city

Introduction A considerable amount of ‘mainstream’ research in education focuses on the central tendencies of a given practice or behaviour. Whether the focus is on average student achievement, median educational attainment, or modal teaching practices, the preponderance of educational inquiry is focused on what takes place on average. Yet often the most compelling story is in the dispersions or variances found at the margins. To a certain extent this latter emphasis summarises a key area of interest in critical scholarship. That is, critical scholars are often driven to understand not what is average or typical, but rather that which is seen as uncommon and atypical. Indeed, it is in what a society often defines as the margins and the marginal that defines what that society is really like. It is perhaps by definition, then, that as critical scholars we often find ourselves at the margins of our own practice. It is in the spirit of the margins that much of the ethnographic work on sub-cultural and, in particular, youth sub-cultural life has been approached. Widely read works such as Paul Willis’s (1977) Learning to Labor, Angela McRobbie’s (1978) ‘Working Class Girls and the Culture of Femininity’, and Phil Cohen’s (1972) Sub-cultural Conflict and Working Class Community are classic examples of the very best ethnographic glimpses into how life is experienced by those who live at the fringe of economic, cultural, and political fields of relations. Yet what separates these notable works from others is their attempt to go beyond describing the experiences of youth subcultural life and connecting these experiences to the relations of power that shape them in meaningful ways. Connecting the dots between the phenomenological and structural accounts of social life is far from an easy task. This is due, in part, to the fact that the phenomenological description operates at the level of direct experience – at the level of practice – whereas the structural explanation tends to operate beyond direct experience at the level of theory. In trying to understand the experience of a given individual or group, then, the critical analyst thus introduces a theoretical component to experience that is not constitutive of the Pedagogy, Culture & Society Vol. 20, No. 1, March 2012, 163–172
Testing-Context Analysis: Assessment is Just Another Part of Language Curriculum Development

In keeping with the theme of the International Language Testing Association/Language Testing Research Colloquium Conference in 2008, “Focusing on the Core: Justifying the Use of Language Assessments to Stakeholders,” I define stakeholder-friendly tests, defensible testing, and testing-context analysis. I then go on to discuss the rational for stakeholder-friendly testing and testing-context analysis and delineate the stages (and steps) involved in any testing-context analysis as follows: (a) get ready to do the testing-context analysis (define the purpose of the test, delimit the stakeholders, decide on options, recognize constraints, and select data collection procedures), (b) do the testing-context analysis (collect data, analyze data, and interpret results), and (c) use the testing-context analysis (determine the impact of the results on testing, implement testing procedures and decision making, report on the testing-context analysis, and decide on directions for further research). I also briefly describe and discuss an example testing-context analysis (the ongoing Eiken testing-context analysis) that illustrates how this framework can be applied. I end by considering the benefits that can be derived from testing-context analysis and how it can help justify the use of language assessments to stakeholders.
Nonlinear control of a quadrotor micro-UAV using feedback-linearization

Four-rotor micro aerial robots, so called quadrotor UAVs, are one of the most preferred type of unmanned aerial vehicles for near-area surveillance and exploration both in military and commercial in- and outdoor applications. The reason is the very easy construction and steering principle using four rotors in a cross configuration. However, stabilizing control and guidance of these vehicles is a difficult task because of the nonlinear dynamic behavior. In addition, the small payload and the reduced processing power of the onboard electronics are further limitations for any control system implementation. This paper describes the development of a nonlinear vehicle control system based on a decomposition into a nested structure and feedback linearization which can be implemented on an embedded microcontroller. Some first simulation results underline the performance of this new control approach for the current realization.
DNA methylation state of the galectin-3 gene represents a potential new marker of thyroid malignancy

In order to supplement the cytopathological assessment of thyroid tumors, there is a need for new markers to correctly diagnose malignant thyroid lesions and avoid unnecessary and potentially harmful therapies for patients. The immunohistochemical expression of galectin-3 is currently considered to be the most accurate stand-alone marker for thyroid cancer diagnosis. The aim of this study was to establish whether the methylation state of the galectin-3 gene is a candidate molecular marker for thyroid malignancy. Thyroid specimens from 50 patients were analyzed, including 5 normal thyroid, 3 goiters, 39 papillary and 3 anaplastic thyroid carcinoma cases. High-resolution methylation analyses was performed to investigate the methylation state of a large genomic region (from −89 to +408) encompassing the galectin-3 transcriptional start site. Within this region, 5 CpG sites (nucleotide positions +134, +137, +142, +147 and +156) were observed to be differentially methylated among the samples and were further analyzed by the quantitative pyrosequencing technique. The hypomethylation of the +134, +137, +142, +147 and +156 CpG sites was observed to be markedly associated with cancer. Although the methylation degree of each single site was highly variable in non-neoplastic tissues, the average methylation state of the 5 CpG sites clearly distinguished cancer from the nonneoplastic thyroid tissues.
Frequency-Dependent Selection and the Maintenance of Genetic Variation: Exploring the Parameter Space of the Multiallelic Pairwise Interaction Model

When individuals' fitnesses depend on the genetic composition of the population in which they are found, selection is then frequency dependent. Frequency-dependent selection (FDS) is often invoked as a heuristic explanation for the maintenance of large numbers of alleles at a locus. The pairwise interaction model is a general model of FDS via intraspecific competition at the genotypic level. Here we use a parameter-space approach to investigate the full potential for the maintenance of multiallelic equilibria under the pairwise interaction model. We find that FDS maintains full polymorphism more often than classic constant-selection models and produces more skewed equilibrium allele frequencies. Fitness sets with some degree of rare advantage maintained full polymorphism most often, but a wide variety of nonobvious fitness patterns were also found to have positive potential for polymorphism. An example is put forth suggesting possible explanations for multiallelic polymorphisms maintained despite positive FDS on individual alleles.
Correlates of Informal Caregiver Distress in Parkinson's Disease: A Meta-Analysis

Informal caregivers, mainly family members, of persons with Parkinson's disease (PD) are usually burdened with quite different loads of stress. Over the past decade, there is no consistent outcome on the association between characteristics of caregivers and patients (as stress sources), and caregiver distress. This meta-analysis integrated findings from 10 studies on the correlates of caregiver distress in terms of depressive symptoms, burden, as well as stress induced by the caregiving role. The results showed that motor symptoms of patients with PD had the strongest relationship with caregiver distress. Increased motor symptoms and higher dependency in activities of daily living showed the highest effect sizes on caregiver distress (|r| = .42 –.43) than did patients' higher level of depression (r = .37), more advanced disease stage (r = .33), longer duration of disease (r = .31), as well as poorer cognitive functioning level (|r|= .28). Among the characteristics of caregivers, only intensity of caregiving was significantly related to higher caregiver distress (r = .46).
Toward Tweets Normalization Using Maximum Entropy

The use of social network services and microblogs, such as Twitter, has created valuable text resources, which contain extremely noisy text. Twitter messages contain so much noise that it is difficult to use them in natural language processing tasks. This paper presents a new approach using the maximum entropy model for normalizing Tweets. The proposed approach addresses words that are unseen in the training phase. Although the maximum entropy needs a training dataset to adjust its parameters, the proposed approach can normalize unseen data in the training set. The principle of maximum entropy emphasizes incorporating the available features into a uniform model. First, we generate a set of normalized candidates for each out-ofvocabulary word based on lexical, phonemic, and morphophonemic similarities. Then, three different probability scores are calculated for each candidate using positional indexing, a dependency-based frequency feature and a language model. After the optimal values of the model parameters are obtained in a training phase, the model can calculate the final probability value for candidates. The approach achieved an 83.12 BLEU score in testing using 2,000 Tweets. Our experimental results show that the maximum entropy approach significantly outperforms previous well-known normalization approaches.
Fast hardware-software co-simulation using VHDL models

We describe a technique for hardware-software co-simulation that is almost cycle-accurate, and does nor require the use of interprocess communication for a C language interface for the software components. Software is modeled by using behavioral VHDL constructs, annotated with timing information derived from basic block-level timing estimates. Hardware is also modeled in VHDL, and can be either pre-existing intellectual property or synthesized to RTL from a functional specification. Execution of the VHDL processes modeling software tasks is coordinated by a process emulating the target RTOS behavior. The effects of changing the hardware/software partition can be quickly estimated by changing a process parameter defining its target implementation and the processor on which it is running.
Imaging tools for the clinical assessment of idiopathic inflammatory myositis

Purpose of reviewTo summarize advances in the imaging of idiopathic inflammatory myopathies. Recent findingsT2-weighted MRI with fat suppression or short tau inversion recovery sequences are the most sensitive and specific routine method of polymyositis and dermatomyositis imaging. MRI also represents an important aid in the identification of biopsy sites, with whole-body MRI sensitively visualizing the distribution of muscle involvement throughout the body. Ultrasound may be a cost-effective alternative to MRI, with contrast-enhanced ultrasound also permitting the assessment of muscle vascularization. PET sensitively detects increased muscle metabolism and simultaneously screens for underlying malignancies in dermatomyositis. Most scintigraphic techniques have a low sensitivity and specificity in the detection of muscle involvement, and it is unclear whether they provide an added benefit. New MRI techniques, such as T2 mapping, diffusion-weighted imaging and blood oxygenation level-dependent imaging, can provide information on muscle recruitment, myofibrillar structure and blood supply. SummaryIn suspected myositis, muscle imaging should be strongly considered prior to obtaining a muscle biopsy. Future research should prospectively study the use of muscle imaging in the evaluation of treatment response and muscle function.
Measurement of elasticity modulus using image processing

In this paper, we propose a scheme to measure the Elasticity Modulus of textile using image processing techniques, here the elasticity modulus is measured indirectly by measuring stiffness of the material. The material whose stiffness is to be measured is subjected to a known force, and the deformation caused in the material due to applied load is measured using image processing. The deformation caused depends on stiffness of the textile used, by making use of relation between stiffness and deformation we can calculate the stiffness. Using this stiffness, elasticity modulus is derived. Web camera is used for the purpose of capturing the image, which is then acquired on the LabVIEW platform for processing. The data is processed by image processing techniques to compute stiffness and elasticity. The system was subjected to test and results showed it had achieved desired objectives.
Memory for emotional words in the first and the second language: Effects of the encoding task*

Emotional words are better remembered than neutral words in the first language. Ferré, García, Fraga, Sánchez-Casas and Molero (2010) found this emotional effect also for second language words by using an encoding task focused on emotionality. The aim of the present study was to test whether the same effect can also be observed with encoding tasks not related to emotionality, as has been reported in monolinguals. We tested highly proficient bilinguals of Catalan and Spanish that were dominant in one of these two languages. At the encoding phase, we directed their attention to words’ features other than emotionality (participants had to either rate words’ concreteness or count the number of vowels they had). In both cases, we obtained an advantage for emotional words independently of the language in which they appeared. These results suggest that the emotional effect on memory has the same characteristics in the two languages of a bilingual.
Relay Selection with Physical-Layer Network Coding

We study relay selection with the physical-layer network coding (PNC), which is a major decode-and-forward (DF)-based bidirectional protocol. We consider a network consists of two different end-sources and multiple relays, where each relay adopts XOR-encoding to combine two received symbols from the two end-sources. For this network, we propose a relay selection scheme by modifying the well-known selection cooperation (SC) to use in the PNC protocol, and it is referred to as SC-PNC. The SC-PNC consists of two phases: a multiple access channel (MAC) phase and a broadcast channel (BC) phase. In the MAC phase, a set of relays that correctly decode two received symbols from the two end-sources is determined; in the BC phase, among the relays in the determined set, a single best relay is selected such that the minimum mutual information of the two links from each relay to the two end-sources is maximized. Finally, we derive the exact outage probability of the SC-PNC in closed-form.
Long-term effects of amyloid, hypometabolism, and atrophy on neuropsychological functions

Objective: To assess how amyloid deposition, glucose hypometabolism, and cerebral atrophy affect neuropsychological performance in patients with Alzheimer disease (AD) dementia, patients with mild cognitive impairment (MCI), and controls over time. Methods: A total of 41 patients with AD dementia, 28 patients with MCI, and 19 controls underwent [11C]–Pittsburgh compound B (11C-PiB) and [18F]-2-fluoro-2-deoxy-d-glucose (18F-FDG)–PET and MRI scans at baseline. We extracted global binding potential for 11C-PiB, the number of abnormal voxels for 18F-FDG, and gray matter volumes using SIENAX for MRI as measures of amyloid, hypometabolism, and atrophy. In addition, repeat neuropsychological testing was performed, including memory, attention, language, and executive tasks (mean follow-up 2.2 ± 0.7 years). Cross-sectional and longitudinal relationships between imaging markers and cognition were assessed using linear mixed models, including terms for the imaging markers, time, sex, age, diagnosis, and interactions for imaging marker × time and imaging marker × time × diagnosis. Results: Linear mixed models showed that baseline hypometabolism and atrophy were associated with poorer baseline performance on attention and executive functions (p < 0.05), whereas amyloid was not related to baseline cognition. Hypometabolism and amyloid were strongly associated with longitudinal decline in essentially all cognitive domains (pinteraction < 0.05), whereas atrophy was related specifically to future decline in Mini-Mental State Examination and memory (pinteraction < 0.05). Conclusion: Glucose hypometabolism and brain atrophy were associated with concurrent cognitive function, whereas brain amyloid was not. Amyloid deposition and glucose hypometabolism were predictors for decline of a wide variety of cognitive functions, while brain atrophy specifically predicted memory deterioration.