Miracle-dz/UniFAR-FTUs huggingface dataset:
ExomeAI: detection of recurrent allelic imbalance in tumors using whole-exome sequencing data

SUMMARY Whole-exome sequencing (WES) has extensively been used in cancer genome studies; however, the use of WES data in the study of loss of heterozygosity or more generally allelic imbalance (AI) has so far been very limited, which highlights the need for user-friendly and flexible software that can handle low-quality datasets. We have developed a statistical approach, ExomeAI, for the detection of recurrent AI events using WES datasets, specifically where matched normal samples are not available. AVAILABILITY ExomeAI is a web-based application, publicly available at: http://genomequebec.mcgill.ca/exomeai. CONTACT JavadNadaf@gmail.com or somayyeh.fahiminiya@mcgill.ca SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Graphically Speaking Editor : André Stork Democratizing Digital Content Creation Using Mobile Devices with Inbuilt Sensors

“Digital content creation” covers the creation of literally every genre of consumable digital material. The growth of this multibillion dollar content creation market depends directly on developments in computer graphics, user interactions and other related elds. Traditionally, stationary desktop computing devices have ful lled the demands of casual and professional content creators, but the amount of graphical content produced on mobile devices is growing rapidly. In fact, over the past few years, the demand for mobile computing systems has grown at a much faster rate than the demand for desktop computing devices. Accordingly, new research directions that differ completely from traditional content creation practices are quickly emerging. Compared with traditional desktop-based platforms for content creation, a typical mobile computing system’s unique input and output modalities permit a more direct and natural interaction experience and thus motivate deeper levels of engagement during content creation tasks. We argue that investing in the development of techniques for creating content on handheld devices with inbuilt sensors, such as camera ashes and accelerometers, has the potential to extend computer graphics technologies to millions of mobile device users. In particular, some of the early barriers associated with creating graphics could be handled with novel sensing and input modalities.1 These barriers largely stem from a lack of support from the input devices, and interaction tasks and techniques associated with three basic human processes: perception, cognition, and motor activity. Although handheld computing platforms have their advantages, present-day mobile computing technology comes with its own limitations related to power supply, computational power, display, and interaction. In this article, we present the state of the art in digital content creation via mobile devices with inbuilt sensors and describe important research challenges and future directions. We aim to encourage both professional developers and novice users to leverage mobile devices’ novel sensing and input capabilities to create their own digital content.
DotCCG and VisCCG: Wiki and Programming Paradigms for Improved Grammar Engineering with OpenCCG

We present a suite of tools for simplifying the creation and maintenance of grammars for the OpenCCG parsing and realization system. The core of our approach relies on a terse but expressive textual format, DotCCG, for declaring CCG grammars. It supports powerful string expansions that allow grammar developers to eliminate redundancy in the declaration of both morphology and category definitions. Grammars written in this format are converted into the XML utilized by OpenCCG using the ccg2xml utility, which –like a programming language compiler– provides information regarding errors in the grammar, including the type of error and the line number on which it occurs. DotCCG grammars can be edited with VisCCG, a graphical interface which provides visualization of various components of the grammar and allows local editing of information in a manner inspired by wikis. We also report on resources developed to facilitate wide use of the OpenCCG tool suite presented in this paper and on recent uses of the tools in both academic research and classroom environments.
Nearest neighbour regression outperforms model-based prediction of specific star formation rate

Data in astronomy is rapidly growing with upcoming surveys producing 30 TB of images per night. Highly informative spectra are too expensive to measure for each detected object, hence ways of reliably estimating physical properties from images alone are paramount. The objective of this work is to test whether a “big data ready” k-nearest neighbour regression can successfully estimate the specific star formation rate (sSFR) from colours of low-redshift galaxies. The nearest neighbour algorithm achieves a root mean square error (RMSE) of 0.30, outperforming the state-of-the-art astronomical model achieving a RMSE of 0.36.
Identifying Social Influence in Viral Products Using Randomization over a Large Mobile Network

This paper analyzes the role of social influence in the diffusion of telecom related products across social networks. We study a subset of the products deployed by a large European mobile carrier and look at how their viral characteristics affect diffusion. We develop a theoretical model of the consumers’ incentives to adopt these products and find that apparently similar viral designs can result in very different adoption dynamics. We use randomization to identify social influence from observational data. In short, we shuffle adoption dates to create pseudo worlds where peer influence is inexistent, which allows us to capture, and thus separate, homophily. We find that for some products more adopters lead to more adoption. However, for other products more adopters lead to less adoption. These empirical results come in line with our theoretical model. To the best of our knowledge, our paper is the first to provide empirical evidence of social network effects that reduce adoption. These effects might limit considerably the diffusion of some products countering the potential benefits from viral designs.
Classroom Management and Loss of Time at the Lesson Start: A Preliminary Study.

Lesson starts are transitional events which may cause management problems for teachers. In this study 131 lesson starts of equally many teachers were observed in primary and secondary schools in Finland. The results indicated that, in general, the problems were minimal. However, for various reasons lesson starts were delayed by an average of about six minutes. Calculated on this basis, the total loss of instructional time in the whole school year was about five weeks of schooling. No statistically significant relationships were observed between disturbances in the classroom and any background variable studied including grade level, classroom type,(special or mainstream), group size, presence of classroom assistant, sex of the teacher, weekday, time of day of the lesson, or subject of the lesson. In order to maximise instructional time more attention should be paid in future to starting lessons promptly.
A Scoping Review of Strategies for the Prevention of Hip Fracture in Elderly Nursing Home Residents

Background Elderly nursing home residents are at increased risk of hip fracture; however, the efficacy of fracture prevention strategies in this population is unclear. Objective We performed a scoping review of randomized controlled trials of interventions tested in the long-term care (LTC) setting, examining hip fracture outcomes. Methods We searched for citations in 6 respective electronic searches, supplemented by hand searches. Two reviewers independently reviewed all citations and full-text papers; consensus was achieved on final inclusion. Data was abstracted in duplicate. Findings We reviewed 22,349 abstracts or citations and 949 full-text papers. Data from 20 trials were included: 7 - vitamin D (n = 12,875 participants), 2 - sunlight exposure (n = 522), 1 - alendronate (n = 327), 1 - fluoride (n = 460), 4 – exercise or multimodal interventions (n = 8,165), and 5 - hip protectors (n = 2,594). Vitamin D, particularly vitamin D3 ≥800 IU orally daily, reduced hip fracture risk. Hip protectors reduced hip fractures in included studies, although a recent large study not meeting inclusion criteria was negative. Fluoride and sunlight exposure did not significantly reduce hip fractures. Falls were reduced in three studies of exercise or multimodal interventions, with one study suggesting reduced hip fractures in a secondary analysis. A staff education and risk assessment strategy did not significantly reduce falls or hip fractures. In a study underpowered for fracture outcomes, alendronate did not significantly reduce hip fractures in LTC. Conclusions The intervention with the strongest evidence for reduction of hip fractures in LTC is Vitamin D supplementation; more research on other interventions is needed.
Policy and identity change in youth social work: From social-interventionist to neoliberal policy paradigms

Summary This article analyses – by drawing on ideology critical and psychoanalytical concepts from Slavoj Žižek and Glynos et al. – how political, social and fantasmatic logics interplay and form social workers’ professional identities within two youth social work institutions that operate within different social policy paradigms: a social-interventionist paradigm in 2002 and a neoliberal paradigm in 2010. Findings The article shows how the current neoliberalisation of public policy permeates social work practices through fantasmatic narratives that create professional identities to heal discrepancies in and conceal the political dimension of everyday life. In one institution, within a welfare state-based ideology a compensating-including social professional identity is created in response to the young people’s alleged deficiencies; in the other institution, within a neoliberal ideology a mobilising-motivating identity is created to meet the young people’s alleged excess. In both narratives, however, the young people risk bearing the blame for the failure of the social professional project. Applications Fantasies in both institutions conceal how social workers’ professional identities sustain dominant ideology through dislocating uncertainties, ambiguities and ambivalences implicated in professional social work. Whether rooted in the state-based welfare or market-oriented neoliberal policy paradigms, realisation of these dynamics may expose the basic interdependencies of state, civil society and market actors implicated in the project of professional social work.
Holistic energy consumption monitoring in buildings with IP-based wireless sensor networks

We present UBI-AMI v2 for holistic real-time monitoring of building energy consumption with two types of wireless sensors. A Mains sensor monitors the aggregate load at the root of the load tree and the individual loads of up to 30 circuit breakers using analog Hall sensors. A Socket sensor monitors the load of the connected individual appliances. The energy consumption is visualized in user interface in Web browser, through a proxy abstracting the wireless sensor network as a RESTful Web service. Data requests to the proxy are injected dynamically into the sensor network as computational tasks. These tasks can then be used as services for other tasks in the system and for the Web.
Vessel Segmentation with Automatic Centerline Extraction Using Tubular Tree Segmentation

The study of the coronary vessel structure is crucial to the diagnosis of atherosclerosis and other cardiovascular diseases, which together account for about 35% of all deaths in the United States per year. Vessel Segmentation from CTA data is challenging because of non-uniform image intensity along the vessel, and the branching and thinning geometry of the vessel tree. We present a novel method for vessel extraction that models the vasculature as a tubular tree and individual vessels as 3D tubes. We create an initial tube from a few seed points within the vessel tree, and then evolve this initial tube using a variational energy optimization approach to capture the vessel while automatically detecting branches in the vessel tree. A significant advantage of our proposed framework is that the center-line of the blood vessel tree, which is useful in defining cross sectional area of the vessel and evaluating stenoses, is detected automatically as the tubular tree evolves. Existing approaches on the other hand need an explicit step for skeletonization of the vessel volume after segmentation. Another benefit is that the parent-child relationships between branches are also automatically obtained, which is useful in fly-through visualization as well as clinical reporting.
The CHD remodeling factor Hrp1 stimulates CENP-A loading to centromeres

Centromeres of fission yeast are arranged with a central core DNA sequence flanked by repeated sequences. The centromere-associated histone H3 variant Cnp1 (SpCENP-A) binds exclusively to central core DNA, while the heterochromatin proteins and cohesins bind the surrounding outer repeats. CHD (chromo-helicase/ATPase DNA binding) chromatin remodeling factors were recently shown to affect chromatin assembly in vitro. Here, we report that the CHD protein Hrp1 plays a key role at fission yeast centromeres. The hrp1Δ mutant disrupts silencing of the outer repeats and central core regions of the centromere and displays chromosome segregation defects characteristic for dysfunction of both regions. Importantly, Hrp1 is required to maintain high levels of Cnp1 and low levels of histone H3 and H4 acetylation at the central core region. Hrp1 interacts directly with the centromere in early S-phase when centromeres are replicated, suggesting that Hrp1 plays a direct role in chromatin assembly during DNA replication.
A comparison and integration of capture-recapture models and the detection profile method

In order to control inspections, the number of remaining defects in software artifacts after their inspection should be estimated. This would allow, for example, deciding whether a reinspection of supposedly faulty artifacts is necessary. Several studies in software engineering have considered capture-recapture models for performing such estimations. These models were initially developed for estimating animal abundance in wildlife research. In addition to these models, researchers in software engineering have recently proposed an alternative approach, namely the detection profile method (DPM), that makes less restrictive assumptions than some capture-recapture models and that show promise in terms of estimation accuracy. The authors investigate how to select between these two approaches for defect content estimation. As a result of this investigation they present a selection procedure taking into account the strength and weaknesses of the two methods. A weakness known for capture-recapture models is that they tend to provide extreme under/over estimation. The existence of such extreme outliers can discourage their use because their consequences in terms of wasted effort or defect slippage can be substantial, and therefore it is not clear,whether a particular estimate can be trusted. The evaluation of the selection procedure with actual inspection data indicates that this selection procedure provides the same accuracy as capture-recapture models alone and DPM alone, and most importantly does not exhibit extreme over/under estimation.
A Selectable and Excisable Marker System for the Rapid Creation of Recombinant Poxviruses

Background Genetic manipulation of poxvirus genomes through attenuation, or insertion of therapeutic genes has led to a number of vector candidates for the treatment of a variety of human diseases. The development of recombinant poxviruses often involves the genomic insertion of a selectable marker for purification and selection purposes. The use of marker genes however inevitably results in a vector that contains unwanted genetic information of no therapeutic value. Methodology/Principal Findings Here we describe an improved strategy that allows for the creation of marker-free recombinant poxviruses of any species. The Selectable and Excisable Marker (SEM) system incorporates a unique fusion marker gene for the efficient selection of poxvirus recombinants and the Cre/loxP system to facilitate the subsequent removal of the marker. We have defined and characterized this new methodological tool by insertion of a foreign gene into vaccinia virus, with the subsequent removal of the selectable marker. We then analyzed the importance of loxP orientation during Cre recombination, and show that the SEM system can be used to introduce site-specific deletions or inversions into the viral genome. Finally, we demonstrate that the SEM strategy is amenable to other poxviruses, as demonstrated here with the creation of an ectromelia virus recombinant lacking the EVM002 gene. Conclusion/Significance The system described here thus provides a faster, simpler and more efficient means to create clinic-ready recombinant poxviruses for therapeutic gene therapy applications.
Three TFT pixel circuit with highly stable OLED current for AMOLED displays

This work proposes a novel voltage-programming pixel circuit for AMOLED using a-Si:H technology. The proposed 3T1C circuit can stabilize the output current regardless of VTH shift and OLED degradation. Experimental results indicate that the OLED current degradation is less than 3% over more than 16 h of operation.
Alphabet independent two dimensional matching

Alphabet Independent Two Dimensional Matching Amihood Amir* Gary Bensont Martin Farach$ Georgia Tech Univ. of Maryland DIMACS There are many solutions to the string matching pmZllem whkh are strictly linear in the input size and independent ofalphabet.size. Furthermore, the model of computation for these algorithms is very weak: they allow only simple arithmetic and comparisons of equality between characters of the input. In contrast, algorithm for two dimensional matching have needed stronger models of computation, most notably assuming a totally ordered alphabet. The fastest algorithms for two dimensional matching have therefore had a logarithmic dependence on the alphabet size. In the worst case, this givea an algorithm that runs in 0(n2 log m) with 0(rn2 log m) preprocessing. We show an algorithm for two dimensional matching with an 0(n2) text scanning phase. Furthermore, the text scan requires no special assumptions about the alphabet, i.e. it runs on the same model as standard linear time string matching algorithm. the *College of Computing, Georgia Institute of Technology, Atlanta, GA 30332-0280; (404) 853-0083; amir@cc.gatecb. edu; Partially supported by NSF ~ant IR.I-90-13055. tDept. of Computer Scienee, University of Maryland, College Park, MD 20742; (301) 405-2715; benaon@cs.umd. edq Partially supported by NSF grant IRI-90-13055. :DIMACS, Box 1179, Rutgers University, Piscataway, NJ 08855; (808) 932-592% farach@Xhu.acs. mtgers.edw, Supported by DIMACS under NSF contract STC-88-09648. Permission to copy without fee all or pert of thie material ie grantad provided that tha copies are not made or distributed for direct commercial advantage, the ACM copyright notice and the title of the publication and ite date appear, and notice is given that copying is by permission of the Association for Computing Machinery. To copy otherwise, or to republish, requires a fee and/or apacific permission. 24th ANNUAL ACM STOC 5/92/VICTORIA, B.C., CANADA a 1992 ACM 0-89791-51 2-7/9210004/0059 . $1 . 50
Gain-Scheduled Higher Harmonic Control for Full Flight Envelope Vibration Reduction

The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. ABSTRACT This paper investigates the dynamics of the SMART rotor, and presents a method to design a gain-scheduled controller to reduce the harmonic vibration throughout the flight envelope. The dynamics of the SMART rotor was examined at various flight conditions through nonlinear simulation. The simulation results showed that the dynamics is strongly dependent on the advance ratio, but only weakly dependent on the blade loading and the rotor shaft angle. To reduce the higher harmonic vibration throughout the flight envelope, a controller gain-scheduled on the advance ratio is presented. Output from linear time-invariant higher harmonic controllers designed for different flight conditions are blended to form the gain-scheduled controller. Closed-loop simulations of the helicopter rotor undergoing transitional flight with increasing advance ratio were conducted. The results from the closed-loop simulations show that the 5 per rev normal vibration was reduced by over 97% at the rotor hub.
Recent Advances in Cancer Therapy Targeting Proteins Involved in DNA Double-Strand Break Repair

Damage to genetic material represents a persistent and ubiquitous threat to genomic stability. Once DNA damage is detected, a multifaceted signaling network is activated that halts the cell cycle, initiates repair, and in some instances induces apoptotic cell death. In this article, we will review DNA damage surveillance networks, which maintain the stability of our genome, and discuss the efforts underway to identify chemotherapeutic compounds targeting the core components of DNA double-strand breaks (DSB) response pathway. The majority of tumor cells have defects in maintaining genomic stability owing to the loss of an appropriate response to DNA damage. New anticancer agents are exploiting this vulnerability of cancer cells to enhance therapeutic indexes, with limited normal tissue toxicity. Recently inhibitors of the checkpoint kinases Chk1 and Chk2 have been shown to sensitize tumor cells to DNA damaging agents. In addition, the treatment of BRCA1- or BRCA2-deficient tumor cells with poly(ADP-ribose) polymerase (PARP) inhibitors also leads to specific tumor killing. Due to the numerous roles of p53 in genomic stability and its defects in many human cancers, therapeutic agents that restore p53 activity in tumors are the subject of multiple clinical trials. In this article we highlight the proteins mentioned above and catalog several additional players in the DNA damage response pathway, including ATM, DNA-PK, and the MRN complex, which might be amenable to pharmacological interventions and lead to new approaches to sensitize cancer cells to radio- and chemotherapy. The challenge is how to identify those patients most receptive to these treatments. (Clin Cancer Res 2009;15(20):6314–20)
Omentin Plasma Levels and Gene Expression Are Decreased in Obesity

Central obesity and the accumulation of visceral fat are risk factors for the development of type 2 diabetes and cardiovascular disease. Omentin is a protein expressed and secreted from visceral but not subcutaneous adipose tissue that increases insulin sensitivity in human adipocytes. To determine the impact of obesity-dependent insulin resistance on the regulation of two omentin isoforms, gene expression and plasma levels were measured in lean, overweight, and obese subjects. Omentin 1 was shown to be the major circulating isoform in human plasma. Lean subjects had significantly higher plasma omentin 1 levels than obese and overweight subjects. In addition, higher plasma omentin 1 levels were detected in women compared with men. Plasma omentin 1 levels were inversely correlated with BMI, waist circumference, leptin levels, and insulin resistance as measured by homeostasis model assessment and positively correlated with adiponectin and HDL levels. Both omentin 1 and omentin 2 gene expression were decreased with obesity and were highly correlated with each other in visceral adipose tissue. In summary, decreased omentin levels are associated with increasing obesity and insulin resistance. Therefore, omentin levels may be predictive of the metabolic consequences or co-morbidities associated with obesity.