Miracle-dz/UniFAR-FTUs huggingface dataset:
Complex Chromosomal Rearrangements Mediated by Break-Induced Replication Involve Structure-Selective Endonucleases

DNA double-strand break (DSB) repair occurring in repeated DNA sequences often leads to the generation of chromosomal rearrangements. Homologous recombination normally ensures a faithful repair of DSBs through a mechanism that transfers the genetic information of an intact donor template to the broken molecule. When only one DSB end shares homology to the donor template, conventional gene conversion fails to occur and repair can be channeled to a recombination-dependent replication pathway termed break-induced replication (BIR), which is prone to produce chromosome non-reciprocal translocations (NRTs), a classical feature of numerous human cancers. Using a newly designed substrate for the analysis of DSB–induced chromosomal translocations, we show that Mus81 and Yen1 structure-selective endonucleases (SSEs) promote BIR, thus causing NRTs. We propose that Mus81 and Yen1 are recruited at the strand invasion intermediate to allow the establishment of a replication fork, which is required to complete BIR. Replication template switching during BIR, a feature of this pathway, engenders complex chromosomal rearrangements when using repeated DNA sequences dispersed over the genome. We demonstrate here that Mus81 and Yen1, together with Slx4, also promote template switching during BIR. Altogether, our study provides evidence for a role of SSEs at multiple steps during BIR, thus participating in the destabilization of the genome by generating complex chromosomal rearrangements.
Evaluation of Unsupervised Emotion Models to Textual Affect Recognition

In this paper we present an evaluation of new techniques for automatically detecting emotions in text. The study estimates categorical model and dimensional model for the recognition of four affective states: Anger, Fear, Joy, and Sadness that are common emotions in three datasets: SemEval-2007 "Affective Text", ISEAR (International Survey on Emotion Antecedents and Reactions), and children's fairy tales. In the first model, WordNet-Affect is used as a linguistic lexical resource and three dimensionality reduction techniques are evaluated: Latent Semantic Analysis (LSA), Probabilistic Latent Semantic Analysis (PLSA), and Non-negative Matrix Factorization (NMF). In the second model, ANEW (Affective Norm for English Words), a normative database with affective terms, is employed. Experiments show that a categorical model using NMF results in better performances for SemEval and fairy tales, whereas a dimensional model performs better with ISEAR.
Bringing Vygotsky and Bakhtin into the Second Language Classroom: A Focus on the Unfinalized Nature of Communication

Human development theories have influenced diverse areas of instruction, including second language teaching and learning. Acknowledging the importance of the bidirectional influences between theory and practice, the present paper grounds second language learning within the theories of Vygotsky and Bakhtin as they pertain to linguistic development. Both Vygotsky and Bakhtin endorsed a communication-based language learning based on their social primacy view of development. In addition, both theorists emphasized the dialogical nature of language and consciousness. This worldview allowed them to expand the scope of context to include multiple participants and perspectives in creating and understanding the meaning of any linguistic construction. The role of the teacher as a human mediator is emphasized in guiding the language learning process in the second language classroom with special attention to the instruction of pragmatic competence.
Increased risk of revision for infection in rheumatoid arthritis patients with total hip replacements

Background and purpose — Data from the national joint registries in Australia and England and Wales have revealed inferior medium-term survivorship for metal-on-metal (MoM) total hip arthroplasty (THA) than for metal-on-polyethylene (MoP) THA. Based on data from the Nordic Arthroplasty Register Association (NARA), we compared the revision risk of cementless stemmed THA with MoM and MoP bearings and we also compared MoM THA to each other. Patients and methods — We identified 32,678 patients who were operated from 2002 through 2010 with cementless stemmed THA with either MoM bearings (11,567 patients, 35%) or MoP bearings (21,111 patients, 65%). The patients were followed until revision, death, emigration, or the end of the study period (December 31, 2011), and median follow-up was 3.6 (interquartile range (IQR): 2.4–4.8) years for MoM bearings and 3.4 (IQR: 2.0–5.8) years for MoP bearings. Multivariable regression in the presence of competing risk of death was used to assess the relative risk (RR) of revision for any reason (with 95% confidence interval (CI)). Results — The cumulative incidence of revision at 8 years of follow-up was 7.0% (CI: 6.0–8.1) for MoM bearings and 5.1% (CI: 4.7–5.6) for MoP bearings. At 6 years of follow-up, the RR of revision for any reason was 1.5 (CI: 1.3–1.7) for MoM bearings compared to MoP bearings. The RR of revision for any reason was higher for the ASR (adjusted RR = 6.4, CI: 5.0–8.1), the Conserve Plus (adjusted RR = 1.7, CI: 1.1–2.5) and “other” acetabular components (adjusted RR = 2.4, CI: 1.5–3.9) than for MoP THA at 6 years of follow-up. Interpretation — At medium-term follow-up, the survivorship for cementless stemmed MoM THA was inferior to that for MoP THA, and metal-related problems may cause higher revision rates for MoM bearings with longer follow-up.
Query generation for semantic datasets

Due to the increasing volume of and interconnections between semantic datasets, it becomes a challenging task for novice users to know what are included in a dataset, how they can make use of them, and particularly, what queries should be asked. In this paper we analyse several types of candidate insightful queries and propose a framework to generate such queries and identify their relations. To verify our approach, we implemented our framework and evaluated its performance with benchmark and real world datasets.
Web Mining For Financial Market Prediction Based On Online Sentiments

Financial market prediction is a critically important research topic in financial data mining because of its potential commerce application and attractive profits. Previous studies in financial market prediction mainly focus on financial and economic indicators. Web information, as an information repository, has been used in customer relationship management and recommendation, but it is rarely considered to be useful in financial market prediction. In this paper, a combined web mining and sentiment analysis method is proposed to forecast financial markets using web information. In the proposed method, a spider is firstly employed to crawl tweets from Twitter. Secondly, Opinion Finder is offered to mining the online sentiments hidden in tweets. Thirdly, some new sentiment indicators are suggested and a stochastic time effective function (STEF) is introduced to integrate everyday sentiments. Fourthly, support vector regressions (SVRs) are used to model the relationship between online sentiments and financial market prices. Finally, the selective model can be serviced for financial market prediction. To validate the proposed method, Standard and Poor’s 500 Index (S&P 500) is used for evaluation. The empirical results show that our proposed forecasting method outperforms the traditional forecasting methods, and meanwhile, the proposed method can also capture individual behavior in financial market quickly and easily. These findings imply that the proposed method is a promising approach for financial market prediction.
Early T Cell Signalling Is Reversibly Altered in PD-1+ T Lymphocytes Infiltrating Human Tumors

To improve cancer immunotherapy, a better understanding of the weak efficiency of tumor-infiltrating T lymphocytes (TIL) is necessary. We have analyzed the functional state of human TIL immediately after resection of three types of tumors (NSCLC, melanoma and RCC). Several signalling pathways (calcium, phosphorylation of ERK and Akt) and cytokine secretion are affected to different extents in TIL, and show a partial spontaneous recovery within a few hours in culture. The global result is an anergy that is quite distinct from clonal anergy induced in vitro, and closer to adaptive tolerance in mice. PD-1 (programmed death -1) is systematically expressed by TIL and may contribute to their anergy by its mere expression, and not only when it interacts with its ligands PD-L1 or PD-L2, which are not expressed by every tumor. Indeed, the TCR-induced calcium and ERK responses were reduced in peripheral blood T cells transfected with PD-1. Inhibition by sodium stibogluconate of the SHP-1 and SHP-2 phosphatases that associate with several inhibitory receptors including PD-1, relieves part of the anergy apparent in TIL or in PD-1-transfected T cells. This work highlights some of the molecular modifications contributing to functional defects of human TIL.
Practice redesign to improve care for falls and urinary incontinence: primary care intervention for older patients.

BACKGROUND In primary care, medical care for age-associated conditions, such as falls and urinary incontinence (UI), is inadequate. In collaboration with the American College of Physicians, we augmented the Assessing Care of Vulnerable Elders practice redesign intervention to improve falls and UI care. METHODS We performed a controlled trial in 5 nonrandomly selected primary care intervention (26 physicians across sites) and control (18 physicians) practices from diverse communities. Patients 75 years and older who screened positive for falls or fear of falling and UI were included in the study. We conducted a multicomponent intervention between October 30, 2006, and December 31, 2007, that included efficient collection of data, medical record prompts, patient education materials, and physician decision support. Main outcome measures were quality of care for falls and UI comparing intervention and control sites. RESULTS Of 6051 patients screened, 2847 (47.1%) screened positive for falls or UI (46.1% in the intervention group and 48.8% in the control group). Across the 5 practices, 1211 patient medical records were evaluated after stratified random selection. Intervention patients received 60.0% of recommended care for falls vs 37.6% provided by control health care professionals (P < .001). Similarly, intervention health care professionals provided more recommended care for UI (47.2% vs 27.8%, P < .001). Intervention health care professionals more often performed a falls history, orthostatic blood pressure measurement, gait and balance examination, and UI history and tried UI behavioral treatments first. Knowledge about falls and UI increased more among intervention than control group health care professionals. CONCLUSIONS Practice redesign can improve the care that community-based primary care physicians provide for older patients with falls and UI. Outcomes of such care improvements require further evaluation.
A user-oriented test suite for transport protocols comparison in datagrid context

Standard TCP faces performance limitations in very high speed wide area networks. This is mainly due to the long end-to-end feedback loop and the conservative behaviour with respect to congestion. Many alternatives to TCP have been proposed to overcome these limitations. However, from a user perspective it is difficult to compare them quantitatively. The goal of this paper is to present a user-oriented test suite, called HSTTS, for helping users to select transport services adapted to their specific environment and traffic conditions. We detail the principles and the architecture of the tool and illustrate our proposal by experiments and results obtained on the Grid'5000 experimental facility.
Why Wind is Not Coal: On the Economics of Electricity

The economics of electricity is shaped by its physics. A well know example is the non-storability of electricity that causes its price to fluctuate widely. More generally, physical constraints cause electricity to be a heterogeneous good along three dimensions - time, space, and lead-time. Consequently, different generation technologies, such as coal and wind power, produce different economic goods that have a different marginal economic value. Welfare maximization or competitiveness analyses that ignore heterogeneity deliver biased estimates. This paper provides an analytical welfare-economic framework that accounts for heterogeneity for unbiased assessments of power generators. The framework offers a rigorous interpretation of commonly used cost indicators such as ‘levelized electricity costs’ and ‘grid parity’. Heterogeneity is relevant for all generators, but especially for variable renewables such as wind and solar power. We propose a definition of ‘variability’, derive the opportunity costs of variability, and link that concept to the ‘integration cost’ literature. A literature review shows that variability can reduce the value of wind power by 20-50%. Thus it is crucial that economic analysis accounts for the physics of electricity.
SNPselector: a web tool for selecting SNPs for genetic association studies

SUMMARY Single nucleotide polymorphisms (SNPs) are commonly used for association studies to find genes responsible for complex genetic diseases. With the recent advance of SNP technology, researchers are able to assay thousands of SNPs in a single experiment. But the process of manually choosing thousands of genotyping SNPs for tens or hundreds of genes is time consuming. We have developed a web-based program, SNPselector, to automate the process. SNPselector takes a list of gene names or a list of genomic regions as input and searches the Ensembl genes or genomic regions for available SNPs. It prioritizes these SNPs on their tagging for linkage disequilibrium, SNP allele frequencies and source, function, regulatory potential and repeat status. SNPselector outputs result in compressed Excel spreadsheet files for review by the user. AVAILABILITY SNPselector is freely available at http://primer.duhs. duke.edu/
The Effects of Using Diorama on 7th Grade Students' Academic Achievement and Science Learning Skills.

This study aims to investigate the effects of using diorama on 7th grade students’ academic achievement and science learning skills in “human being and Asia-Pacific Forum on Science Learning and Teaching, Volume 18, Issue 1, Article 2, p.2 (Jun., 2017) Hülya ASLAN EFE The effects of using diorama on 7th grade students’ academic achievement and science learning skills Copyright (C) 2017 EdUHK APFSLT. Volume 18, Issue 1, Article 2 (Jun., 2017). All Rights Reserved. environment relation” unit. The participants were 49 (E:25, C: 24) 7th grade students studying during 2015-16 academic year in Diyarbakir, Turkey. An achievement test and “science learning skills” scale was used to collect data. The study revealed that students in the experimental group were significantly more successful than the students in the control group in term of the academic achievement. Similarly, students taught with dioramas were better in science learning skills than those taught with traditional learning method. The study has implications for science teachers to include dioramas in their teaching activities and providing opportunities for teachers to develop diorama making skills.
POST-VALUED RECALL WEB PAGES: USER DISORIENTATION HITS THE BIG TIME

The growth in complexity of the World Wide Web, matched by the increase in user sophistication, has transformed the notion of user disorientation. While the retrieval of visited Web pages has been studied, the particular class of Web pages not initially recognized as being important enough to return to merits closer examination. Such pages, referred to as Post-Valued Recall (PVR) Web pages, tend to sit at the interface between the solitary act of surfing the Web and the social act of interacting with colleagues, who will often trigger the realization that a particular page is, in fact, of value. Results from a user study illustrate the effect of PVR in a social environment, as well as offer design guidelines for browser utilities that could diminish the negative impact of PVR.
Comparative Osteogenesis of Radiopaque Dicalcium Silicate Cement and White-Colored Mineral Trioxide Aggregate in a Rabbit Femur Model

The radiopaque dicalcium silicate cement (RDSC) displayed a shortened setting time and good biocompatibility. This study aimed to compare the regenerative potential of RDSC and white-colored mineral trioxide aggregate (WMTA) using a rabbit femur model. The animals were sacrificed at one, three and six months to accomplish histological and biochemical analyses. The results indicated that after one month of implantation, WMTA was associated with a greyish color alteration within its mass, while RDSC presented color stability even at six months. Histological assay with Masson’s Trichrome and Von Kossa stains showed the presence of newly formed bone surrounding the implanted sites in the rabbit femur. The histochemical data revealed that the RDSC group had significantly more bone regeneration than did the WMTA groups at three and six months. The conclusion drawn is that the encouraging results support the potential applications of RDSC as an improved alternative to WMTA for endodontic uses.
Biometrics: a tool for information security

Establishing identity is becoming critical in our vastly interconnected society. Questions such as "Is she really who she claims to be? ," "Is this person authorized to use this facility? ," or "Is he in the watchlist posted by the government? " are routinely being posed in a variety of scenarios ranging from issuing a driver's license to gaining entry into a country. The need for reliable user authentication techniques has increased in the wake of heightened concerns about security and rapid advancements in networking, communication, and mobility. Biometrics, described as the science of recognizing an individual based on his or her physical or behavioral traits, is beginning to gain acceptance as a legitimate method for determining an individual's identity. Biometric systems have now been deployed in various commercial, civilian, and forensic applications as a means of establishing identity. In this paper, we provide an overview of biometrics and discuss some of the salient research issues that need to be addressed for making biometric technology an effective tool for providing information security. The primary contribution of this overview includes: 1) examining applications where biometric scan solve issues pertaining to information security; 2) enumerating the fundamental challenges encountered by biometric systems in real-world applications; and 3) discussing solutions to address the problems of scalability and security in large-scale authentication systems.
Assessing online strategies aimed at enhancing campus safety

Purpose The purpose of this paper is to evaluate technological strategies (i.e. online training and university safety system) used at one southeastern four-year university to enhance campus safety. This paper investigates if an online training influenced rape myth acceptance (RMA) and if participation in the university safety system was associated with perceptions of campus safety. Design/methodology/approach Data from college students were collected via a survey that was distributed through the school’s e-mail system. The survey asked respondents about their perceptions of safety, experiences on campus, attitudes, and utilization of campus resources. In total, 1,583 students participated in the survey. Analyses were limited to 889 respondents not missing data. Findings RMA did not differ between those who completed the online training and those who did not complete the training. Regarding perceptions of campus safety, respondents who opted to receive emergency notifications were not significantly different from those who did not receive the notifications. Respondents who had the safety application felt safer on campus compared to those who did not have the application. Respondents who participated in the training, received notifications, and had the application felt safer on campus. Originality/value This study highlights the potential utility of the safety application as well as the limited effect of the online education program on RMA.
Variance-Gamma approximation via Stein's method

Variance-Gamma distributions are widely used in financial modelling and contain as special cases the normal, Gamma and Laplace distributions. In this paper we extend Stein's method to this class of distributions. In particular, we obtain a Stein equation and smoothness estimates for its solution. This Stein equation has the attractive property of reducing to the known normal and Gamma Stein equations for certain parameter values. We apply these results and local couplings to bound the distance between sums of the form $\sum_{i,j,k=1}^{m,n,r}X_{ik}Y_{jk}$, where the $X_{ik}$ and $Y_{jk}$ are independent and identically distributed random variables with zero mean, by their limiting Variance-Gamma distribution. Through the use of novel symmetry arguments, we obtain a bound on the distance that is of order $m^{-1}+n^{-1}$ for smooth test functions. We end with a simple application to binary sequence comparison.
Learning and work in the lives of young adults

It is clear that for many young people the balance between learning, work and leisure has shifted considerably over recent decades. Many students now work throughout the whole of their post‐compulsory education, entering the labour market well before any higher education applications have been made, and continue to work throughout their time at university. In part, this may be driven by: young people’s desires to maintain a particular ‘consumer lifestyles’; shifts towards flexible labour in many sectors of the economy that have provided more opportunities for student employment; as well as the increasing costs of studying for a degree. Within this context, many young people have become very practised at ‘juggling’ a job, an education and a social life. Drawing on a study of 30 graduates in their mid‐twenties, this paper explores whether the experience of combining education and employment may facilitate lifelong learning, through the ‘normalisation’ of these patterns or whether, conversely, the financial pressures that many young people experience during their post‐compulsory education act as a disincentive to pursue further learning.