Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comprehensive Characterization of Genome-Wide Copy Number Aberrations in Colorectal Cancer Reveals Novel Oncogenes and Patterns of Alterations

To develop a comprehensive overview of copy number aberrations (CNAs) in stage-II/III colorectal cancer (CRC), we characterized 302 tumors from the PETACC-3 clinical trial. Microsatellite-stable (MSS) samples (n = 269) had 66 minimal common CNA regions, with frequent gains on 20 q (72.5%), 7 (41.8%), 8 q (33.1%) and 13 q (51.0%) and losses on 18 (58.6%), 4 q (26%) and 21 q (21.6%). MSS tumors have significantly more CNAs than microsatellite-instable (MSI) tumors: within the MSI tumors a novel deletion of the tumor suppressor WWOX at 16 q23.1 was identified (p<0.01). Focal aberrations identified by the GISTIC method confirmed amplifications of oncogenes including EGFR, ERBB2, CCND1, MET, and MYC, and deletions of tumor suppressors including TP53, APC, and SMAD4, and gene expression was highly concordant with copy number aberration for these genes. Novel amplicons included putative oncogenes such as WNK1 and HNF4A, which also showed high concordance between copy number and expression. Survival analysis associated a specific patient segment featured by chromosome 20 q gains to an improved overall survival, which might be due to higher expression of genes such as EEF1B2 and PTK6. The CNA clustering also grouped tumors characterized by a poor prognosis BRAF-mutant-like signature derived from mRNA data from this cohort. We further revealed non-random correlation between CNAs among unlinked loci, including positive correlation between 20 q gain and 8 q gain, and 20 q gain and chromosome 18 loss, consistent with co-selection of these CNAs. These results reinforce the non-random nature of somatic CNAs in stage-II/III CRC and highlight loci and genes that may play an important role in driving the development and outcome of this disease.
Transparent DFT: a design for testability and test generation approach for synchronous sequential circuits

This paper describes a design for testability (DFT) approach for synchronous sequential circuits that combines scan with nonscan DFT in a transparent way. DFT control inputs and scan chain inputs are used as primary inputs of the circuit, and scan chain outputs are used as primary outputs of the circuit during test generation to eliminate the distinction between functional clock cycles and the various types of nonfunctional clock cycles. The result is 1) short test application times due to the nonscan DFT modes and the ability to use limited scan operations and 2) the ability to detect all the combinationally irredundant faults due to the scan mode
Item Response Theory for Medical Educationists

Item analysis (IA) is commonly used to describe difficulty and discrimination indices of multiple true-false (MTF) questions. However, item analysis is basically a plain descriptive analysis with limited statistical value. Item response theory (IRT) can provide a better insight into the difficulty and discriminating ability of questions in a test. IRT consists of a collection of statistical models that allows evaluation of test items (questions) and test takers (examinees) at the same time. Specifically, this article focuses on two-parameter logistic IRT (2-PL IRT) model that is concerned with estimation of difficulty and discrimination parameters. This article shows how 2-PL IRT analysis is performed in R software environment, guides the interpretation of the IRT results and compares the results to IA on a sample of MTF questions.
Probe into performance of Ad hoc routing protocol at high velocity

With remarkable advantages over traditional networks on the aspect of flexible communication, Ad hoc networks have been applied widely in real implementations. Airborne network is a brand new Ad hoc application. In the case of airborne network, network node such as airplane keeps moving at fairly high speed. However, few researches attempted to probe into routing protocols performance with airborne velocity. In this paper we focus to research into performance of Ad hoc routing protocol at a specific high velocity (2 March) for the first time. Experiment results illustrate that the curve of performance variation in response to the increase of offered load can be distinctly different across different moving patterns with different maximum velocities. According to our simulation results, there is not an existing Ad hoc routing protocol which gives ideal performance at both normal velocity and airborne velocity. Proactive routing protocols using Bellman-Ford algorithm achieve relatively good performance compared to AODV and OLSR in lowly mobile network. Contrarily AODV outperforms OLSR and BF greatly in the case of airborne velocity. For airborne application, AODV is a relatively advisable choice for the moment.
R OBUST LDP B ASED F ACE D ESCRIPTOR

A BSTRACT This paper presents a novel LDP based image descriptor which is more robust to temporal face changes. LDP is a framework to encode directional pattern based on local derivative variations, hence LDP is highly directional. However texture based features extracted globally tend to average over the image area. Hence this paper proposes to divide the face image into multiple regions and perform LDP separately on each region. The procedure consists of using the texture descriptor to build several local descriptions of the face and combining them into a global description. Block based processing ensures robustness against pose, facial expressions and other temporal face changes. Also, a modification in Chi Square Distance is proposed to suit the spatial histogram matching of faces. Extensive experimental results on FERET, CAS-PEAL, CMU-PIE, and Extended Yale B databases show that the LDP based face descriptors consistently performs better than LDP extracted globally for both face identification and face verification under various conditions.
Abraham, Minkowski and "Hidden" Mechanical Momentum

This debate has been characterized by Ginzburg as a “perpetual problem” [1]. For a lengthy bibliography on this topic, see [2]. J.J. Thomson wrote the electromagnetic momentum as D × H/4πc in 1891 [5] and again in 1904 [6]. This form was also used Poincare in 1900 [7], following Lorentz’ convention [8] that the force on electric charge q be written q(D + v/c× H) and that the Poynting vector is (c/4π)D × H. For discussion of these forms, see, for example, [9]. Heaviside gave the form (3) in 1891, p. 108 of [11], and a derivation (1902) essentially that of Minkowski on pp. 146-147 of [12]. See also, for example, sec. 2.1 of [13].
ADDFuzzer: A New Fuzzing Framework of Android Device Drivers

Fuzzing has been widely used to discovery vulnerabilities in practice. Despite many linux system call fuzzers, few fuzzers of Android device drivers. In this paper, we research attack surface to Android device and present ADDFuzzer, a fuzz testing framework, especially for hunting Android device drivers' bugs and security issues. This fuzzing framework has two novel features: a flexible generator module for changing fuzzing strategy easily, and a unique mechanism for stably replaying a crash. Through a week's experiment, we also find some bugs which can cause denial-of-service attacks.
Can P2P Technology Benefit Eyeball ISPs? A Cooperative Profit Distribution Answer

Peer-to-Peer (P2P) technology has been promoting the development of Internet applications, like Video on Demand (VoD) and file sharing. However, under the traditional pricing mechanism, the fact that most P2P traffic flows among peers can dramatically decrease the profit of ISPs, who may take actions against P2P and impede the adoption of P2P-assisted applications. So far, there is no proper profit distribution mechanism to solve this problem. In this paper, we develop a mathematical framework to analyze such economic issues. Inspired by the idea from cooperative game theory, we propose a cooperative profit-distribution model based on Nash Bargaining Solution (NBS), in which both eyeball ISPs and Peer-assisted Content Providers (PCPs) form coalitions and compute a fair Pareto point to determine profit distribution. Moreover, we design a fair and feasible mechanism for profit distribution within each coalition and give a model to discuss the potential competition among ISPs. We show that such a cooperative method not only guarantees the fair profit distribution among network participants, but also improves the economic efficiency of the network system; and the potential competition among ISPs will make the network more efficient. This paper systematically studies solutions to unbalanced profit distribution caused by P2P and presents a feasible cooperative method to increase and fairly distribute the profit.
Analysis of Routing Protocols in AD HOC and Sensor Wireless Networks Based on Swarm Intelligence

There are various bio inspired and evolutionary approaches including genetic programming (GP), Neural Network, Evo lutionary programming (EP) exp loited for routing optimizat ion in MANETs and WSNs. The Swarm Intelligence based algorithmic approaches; Particle Swarm Optimization (PSO) and Ant Co lony Optimization (A CO) are more p ro mising in provid ing loop free, energy-aware, and mult i-path routing in mob ile ad hoc and wireless sensor networks. There are various constraints involved in ad hoc and sensor networks protocols due to the mobility and non infrastructure nature of the system. We study in this research work a probabilistic performance evaluation frameworks and Swarm Intelligence approaches (PSO, A CO) for routing protocols. The performance evaluation metrics employed for wireless and ad hoc routing algorith ms is , (a) routing overhead, (b) route optimality, and (c) energy consumption. Th is survey provides collection of Swarm Intelligence based algorithms for mobile ad hoc an d sensor networks and their critical analysis. The study concludes that PSO and ACO based protocols are advantageous than other approaches applied for the routing optimization in ad hoc and wireless sensor networks.
Keyboards without Keyboards: A Survey of Virtual Keyboards

Input to small devices is becoming an increasingly crucial factor in development for the ever-more powerful embedded market. Speech input promises to become a feasible alternative to tiny keypads, yet its limited reliability, robustness, and flexibility render it unsuitable for certain tasks and/or environments. Various attempts have been made to provide the common keyboard metaphor without the physical keyboard, to build “virtual keyboards”. This promises to leverage our familiarity with the device without incurring the constraints of the bulky physics. This paper surveys technologies for alphanumeric input devices and methods with a strong focus on touch-typing. We analyze the characteristics of the keyboard modality and show how they contribute to making it a necessary complement to speech recognition rather than a competitor.
A novel power control algorithm for CDMA systems

In this paper, a distributed power control scheme for the third generation wideband CDMA system is presented. In the algorithm, a kind of power update function of exponential type is presented. By adjusting parameter k in the power update function, the system can satisfy different performance requirement. Simulation results reveal that this algorithm has faster convergence speed and better system stability than the conventional distributed power control algorithm.
3 1 M ar 2 00 3 Onset of DNA Aggregation in Presence of Mono-and Multivalent Counterions ∗

We address theoretically aggregation of DNA segments by multivalent polyamines such as spermine and spermidine. In experiments, the aggregation occurs above a certain threshold concentration of multivalent ions. We demonstrate that the dependence of this threshold on the concentration of DNA has a simple form. When the DNA concentration c DNA is smaller than the monovalent salt concentration, the threshold multivalent ion concentration depends linearly on c DNA , having the form αc DNA + β. The coefficients α and β are related to the density profile of multivalent counterions around isolated DNA chains, at the onset of their aggregation. This analysis agrees extremely well with recent detailed measurements on DNA aggregation in the presence of spermine. From the fit to the experimental data, the number of condensed multivalent counterions per DNA chain can be deduced. A few other conclusions can then be reached: i) the number of condensed spermine ions at the onset of aggregation decreases with the addition of monovalent salt; ii) the Poisson-Boltzmann theory overestimates the number of condensed multivalent ions at high monovalent salt concentrations; iii) our analysis of the data indicates that the DNA charge is not over-compensated by spermine at the onset of aggregation.
Intense Tropical Thunderstorms Detected by the Special Sensor Microwave Imager/Sounder

The 150-GHz microwave window channel and the three water vapor channels, 183.3 plusmn 7, 183.3 plusmn 3, and 183.3 plusmn 1 GHz of the Defense Meteorological Satellite Programpsilas (DMSP) Special Sensor Microwave Imager/Sounder (SSMIS) are used to detect intense thunderstorms over the tropics (30deg S-30 deg N). This application utilizes the advantages of conical scanning and high surface horizontal resolution of the SSMIS compared to the same measurements made with cross-track scanning radiometers. The criteria to detect intense tropical thunderstorms are derived by the combination of the brightness temperature differences between the three water vapor channels and brightness temperatures at the four frequencies. One year of SSMIS data (December 2005-November 2006) is surveyed for intense tropical thunderstorms. The most intense tropical thunderstorms are predominant over land and are mainly concentrated over Central and South America, tropical west Africa, and northern Australia. Over most regions these very intense tropical thunderstorms have a strong regional dependence and a pronounced seasonal migration.
Breathing new life into the waterfall model

Imagine that you are in the market for some custom software. You’ve issued an RFP, prohibited any contact between bidders and your organization, and demanded a single price for the whole effort. In response, one of the prospective contractors pitches you the following scenario. “For US$35,000,” the contractor’s account executive says, “an cross-functional team of our best people will work with you for two weeks to define the opportunity, plan your future method of operations, write some thin requirements, and develop a simple prototype of the user interface. At the end of that period, we’ll probably offer you a proposal for doing the next stage of the work at a fixed price and within a fixed schedule. But we do reserve the right not to bid on the next stage. ” Should you be disgusted by the contractor’s insolence or delighted with their savvy approach? Many customers have come to believe the latter. The approach behind the pitch given above goes by many names, including staged contracts andmilestone-based development . Staged contracts are often used in an approach commonly called rapid applications development [1, 3]. (James Martin defined Rapid Application Development (RAD) in [2] as a particular set of tools and methodologies, but the term has since become a watered-down, overused buzzword. ) In this column I want to focus on the contracts and pricing policy used by companies such as Bellcore, Cambridge Technology Partners, Keane, and Sapient as part of their rapid applications development methodology. These companies have enjoyed significant, even explosive growth in their rapid apps divisions, and assign much of the credit to the processes that they use. I claim that staged contracts, while clearly inappropriate for some, offer an excellent choice of life-cycle model for many projects. A staged contract for custom software development means that the work is con-
Computer-aided Image Processing of Angiogenic Histological

This article reviews the questions regarding the image evaluation of angiogeneic histological samples, particularly the ovarian epithelial cancer. Review is focused on the principles of image analysis in the field of histology and pathology. The definition, classification, pathogenesis and angiogenesis regulation in the ovaries are also briefly discussed. It is hoped that the complex image analysis together with the patient’s clinical parameters will allow an acquiring of a clear pathogenic picture of the disease, extension of the differential diagnosis and become a useful tool for the evaluation of drug effects. The challenge of the assessment of angiogenesis activity is the heterogeneity of several objects: parameters derived from patient’s anamnesis as well as of pathology samples. The other unresolved problems are the subjectivity of the region of interest selection and performance of the whole slide scanning. Keywords Angiogenesis; Image processing; Microvessel density; Cancer; Pathology
Extracting Relations Within and Across Sentences

Previous work on relation extraction has focussed on identifying relationships between entities that occur in the same sentence (intra-sentential relations) rather than between entities in different sentences (inter-sentential relations) despite previous research having shown that intersentential relations commonly occur in information extraction corpora. This paper describes a SVM-based approach to relation extraction that is applied to both types. Adapted features and techniques for counter-acting bias in SVM models are used to deal with specific issues that arise in the inter-sentential case. It was found that the structured features used for intrasentential relation extraction can be easily adapted for the inter-sentential case and provides comparable performance.
The Protein Data Bank: A Case Study in Management of Community Data

As the sole repository for three-dimensional structure data of biological macro- molecules, the Protein Data Bank (PDB) is an important resource for research in the academic, pharmaceutical, and biotechnology sectors. Over the years, the methods and speed of structure determination have changed as technology has improved. At the same time the methods for data collection, archiving, and distribution of the structural data in the PDB have also evolved. Concurrently, the community of data depositors and users has expanded. As of October 2003, the PDB archive contains approximately 23,000 released structures and the website receives over 160,000 hits per day. The lessons learned from the development of the PDB may be applicable to the ongoing development of new data and knowledge resources in proteomics.
(Non-) Driving-Related Activities in the Car: Deﬁning Driver Activities for Manual and Automated Driving

The multitude of communication and infotainment features of modern cars enable drivers to perform many tasks on the go. If these tasks are not directly related to maneuvering the vehicle (i.e., the primary driving task), literature usually refers to such tasks as secondary or tertiary driving tasks. For automated driving the traditional separation into diﬀerent driving tasks needs to be adapted since the “old” primary driving task will become obsolete. In order to prevent the necessity of diﬀerent driving task deﬁnitions for automated and manual driving, we foster the use of alternative terms and provide a deﬁnition therefore: Driving-related activities comprise all tasks to safely control the vehicle while non-driving-related activities comprise all activities beyond maneuvering the vehicle. These terms can be used consistently for both automated and manual driving situations.
The relationship between resilience and job satisfaction in employees of supporting institution of Hormozgan province

The aim of this study is to determine the relation between resilience and job satisfaction in employees of supporting institution of Hormozgan province. This study is an applied and correlation. The research population of this study is employees institutions support Hormozgan province (Imam Khomeini Relief Committee (RA), Social Welfare,) have been selected. The sample size was based on Morgan table 276 people and selected by simple random sampling. For data analysis Pearson correlation coefficient was used. In this study, two questionnaires of Connor-Davidson for Resilience and Herzberg for job satisfaction were used. Result showed that there are relation between resilience and job satisfaction in employees of supporting institution of Hormozgan province.
Chaotic mutated bat algorithm optimized edge potential function for target matching

In this paper, we present a novel edge based matching approach to target recognition. To recognize the marker on a rotorcraft, a chaotic mutated bat algorithm optimized edge potential function approach is proposed to accomplish the matching between the sketch image and the scene in real applications. A novel type of attractive contour pattern is acquired using the edge potential function. These edge structures can be conveniently exploited for target matching. Bat algorithm is adopted for the optimization problem of searching the optimal match in the scene, and a chaotic mutated bat algorithm is proposed using the chaotic theory and a mutated operator. Thus, the target matching task is converted to optimizing the average of potential value by the processing of translating, reorienting and scaling the sketch image. Series of experiments are conducted to show that our method is superior to other methods. Our proposed method can achieve the higher fitness value over the standard optimization algorithms.
Supporting Reviewing of Warnings in Presence of Shared Variables: Need and Effectiveness

Clustering, breaking a large system into multiple clusters is commonly used technique to scale static analysis tools to large systems. Sound static analysis of resulted clusters requires conservative approach for the inter-cluster communication implemented through shared variables. We observe, this approach adds to the large number of warnings generated due to imprecision of static analysis. Further, manual reviewing of warnings resulted due to shared variables takes much more efforts as compared to efforts required in reviewing of the other class of warnings. This paper aims to assist reviewing of such warnings impacted by the shared variables so that reviewing effort is reduced. This is achieved by identification and reporting of suitable information about the impacting shared variables. The reported information includes - 1) marked warnings affected due to shared variables, 2) shared variables present in the code (such as warning point, and code slice) traversed while reviewing a warning, 3) intelligently selected write-points of the involved shared variables, depending on the type of warning, and 4) characteristics of the shared variables extracted from the code, that could potentially help to reduce the efforts further. Our experiments on two embedded systems indicated that the review assisting information presented to the user is quite effective to improve reviewing of warnings affected due to shared variables. The overall reduction in manual efforts varied from 45-70% depending on code size and complexity, type of warnings, reviewer skills, tool support used, etc.
Talk the Walk : Robotic NLP vs . Human Sublanguage Acquisition

The paper investigates the appropriateness of natural language processing (NLP) in the context of robotassisted navigation for the visually impaired. Several assumptions of corpus-based robotics are examined. It is argued that, in the short term, NLP may be inadequate and, in the long term, it may not be necessary to enable robotic guides to solicit route directions from bystanders. Human sublanguage acquisition is presented as one feasible alternative.