Miracle-dz/UniFAR-FTUs huggingface dataset:
Secreted Clusterin in Colon Tumor Cell Models and Its Potentialas Diagnostic Marker for Colorectal Cancer

We studied the specific changes of the secreted protein clusterin and its cytoplasmic precursor regarding colorectal tumorigenesis, using in vitro differentiation of Caco-2 cells. In tumor-like stage, we observed an overexpression of both precursor and secreted clusterin, corroborated in the cell line SW-480. Noticeably, SW-620 cells (from a tumoral node, thus with metastatic capacity) did not show overexpression of either precursor or secreted clusterin, suggesting a downregulation related to local metastasis. We further investigated clusterin in serum, finding a significant increase in colorectal cancer patients, with 81% sensitivity, 79% specificity, and an area under the ROC curve of 0.85.
Making subsequence time series clustering meaningful

The startling claim was made that sequential time series clustering is meaningless. This has important consequences for a significant amount of work in the literature, since such a claim invalidates this work's contribution. In this paper, we show that sequential time series clustering is not meaningless, and that the problem highlighted in these works stem from their use of the Euclidean distance metric as the distance measure in the subsequence vector space. As a solution, we consider quite a general class of time series, and propose a regime based on two types of similarity that can exist between subsequence vectors, which give rise naturally to an alternative distance measure to Euclidean distance in the subsequence vector space. We show that, using this alternative distance measure, sequential time series clustering can indeed be meaningful. We repeat a key experiment in the work on which the "meaningless" claim was based, and show that our method leads to a successful clustering outcome.
Comparison of joint strength produced by fsw, fssw and a novel technique friction stir linear spot welding

A comparison of joint strength of friction stir welded (FSW), friction stir spot welded (FSSW) and friction stir linear spot welded (FSLSW) 2 mm sheets of EN AW 5754 in a lap joint is presented. The optimal welding parameters were obtained based on maximal joint strengths at FSW. From the welds made using all three welding methods the tensile test specimens were prepared and the weld microstructure was analysed. The results show significant joint strength improvement when using FSLSW compared to FSSW. A FSLSW joint strength exceeded the strength of the base material at only small increase of welding time.
Postmortem: Never Leave a Project without It

Postmortem analysis (PMA) is a practical method for initiating knowledge management by capturing experience and improvement suggestions from completed projects. It requires little effort and quickly provides initial results, making it suitable even for small- and medium-size projects and companies. The authors describe their experiences with applying PMA techniques for collecting and analyzing experience in software organizations.
An efficient sequential SAT solver with improved search strategies

A sequential SAT solver, Satori, was recently proposed (Iyer, M.K. et al., Proc. IEEE/ACM Int. Conf. on Computer-Aided Design, 2003) as an alternative to combinational SAT in verification applications. This paper describes the design of Seq-SAT, an efficient sequential SAT solver with improved search strategies over Satori. The major improvements include: (1) a new and better heuristic for minimizing the set of assignments to state variables; (2) a new priority-based search strategy and a flexible sequential search framework which integrates different search strategies; (3) a decision variable selection heuristic more suitable for solving the sequential problems. We present experimental results to demonstrate that our sequential SAT solver can achieve orders-of-magnitude speedup over Satori. We plan to release the source code of Seq-SAT.
Casper: an efficient approach to call trace collection

Call traces, i.e., sequences of function calls and returns, are fundamental to a wide range of program analyses such as bug reproduction, fault diagnosis, performance analysis, and many others. The conventional approach to collect call traces that instruments each function call and return site incurs large space and time overhead. Our approach aims at reducing the recording overheads by instrumenting only a small amount of call sites while keeping the capability of recovering the full trace. We propose a call trace model and a logged call trace model based on an LL(1) grammar, which enables us to define the criteria of a feasible solution to call trace collection. Based on the two models, we prove that to collect call traces with minimal instrumentation is an NP-hard problem. We then propose an efficient approach to obtaining a suboptimal solution. We implemented our approach as a tool Casper and evaluated it using the DaCapo benchmark suite. The experiment results show that our approach causes significantly lower runtime (and space) overhead than two state-of-the-arts approaches.
Glimpse-Based Metrics for Predicting Speech Intelligibility in Additive Noise Conditions

The glimpsing model of speech perception in noise operates by recognising those speech-dominant spectro-temporal regions, or glimpses, that survive energetic masking; hence, a speech recognition component is an integral part of the model. The current study evaluates whether a simpler family of metrics based solely on quantifying the amount of supra-threshold target speech available after energetic masking can account for subjective intelligibility. The predictive power of glimpse-based metrics is compared for natural, processed and synthetic speech in the presence of stationary and fluctuating maskers. These metrics are raw glimpse proportion, extended glimpse proportion, and two further refinements: one, FMGP, incorporates a component simulating the effect of forward masking; the other, HEGP, selects speech-dominant spectro-temporal regions with above-average energy on the noisy speech. The metrics are compared alongside a state-of-the-art non-glimpsing metric, using three large datasets of listener scores. Both FMGP and HEGP equal or improve upon the predictive power of the raw and extended metrics, with across-masker correlations ranging from 0.81--0.92; both metrics equal or exceed the state-of-the-art metric in all conditions. These outcomes suggests that easily-computed measures of unmasked, supra-threshold speech can serve as robust proxies for intelligibility across a range of speech styles and additive masking conditions.
A system for visualizing and analyzing the evolution of the web with a time series of graphs

We propose WebRelievo, a system for visualizing and analyzing the evolution of the web structure based on a large Web archive with a series of snapshots. It visualizes the evolution with a time series of graphs, in which nodes are web pages, and edges are relationships between pages. Graphs can be clustered to show the overview of changes in graphs. WebRelievo aligns these graphs according to their time, and automatically determines their layout keeping positions of nodes synchronized over time, so that the user can keep track pages and clusters. This visualization enables us to understand when pages appeared, how their relationships have evolved, and how clusters are merged and split over time. Current implementation of WebRelievo is based on six Japanese web archives crawled from 1999 to 2003. The user can interactively browse those graphs by changing the focused page and by changing layouts of graphs. Using WebRelievo we can answer historical questions, and to investigate changes in trends on the Web. We show the feasibility of WebRelievo by applying it to tracking trends in P2P systems and search engines for mobile phones, and to investigating link spamming.
Evaluation of a Technique for Collision and Object Detection with the Z-buffer in Cyber Space

We propose a new technique to detect objects and collisions of geometric objects in cyber space. This technique uses depth values of the Z-buffer in rendering scene. We use the orthographic projection for collision detection. Our method uses two depth value sets. One is obtained through rendering the cyber space from the sensor object toward a target point. This set does not have the depth values of the sensor object. Another one is obtained through rendering only the sensor object in the reverse direction. From these two depth value sets, we obtain the distance between the sensor object and others for each pixel. This technique requires only one or two rendering processes and it is independent from the complexity of the object's shape, deformation or motion. In this paper we evaluate the efficiency of this method on the GPUs we currently use.
Fast GPU-based Monte Carlo simulations for LDR prostate brachytherapy

The aim of this study was to evaluate the potential of bGPUMCD, a Monte Carlo algorithm executed on Graphics Processing Units (GPUs), for fast dose calculations in permanent prostate implant dosimetry. It also aimed to validate a low dose rate brachytherapy source in terms of TG-43 metrics and to use this source to compute dose distributions for permanent prostate implant in very short times. The physics of bGPUMCD was reviewed and extended to include Rayleigh scattering and fluorescence from photoelectric interactions for all materials involved. The radial and anisotropy functions were obtained for the Nucletron SelectSeed in TG-43 conditions. These functions were compared to those found in the MD Anderson Imaging and Radiation Oncology Core brachytherapy source registry which are considered the TG-43 reference values. After appropriate calibration of the source, permanent prostate implant dose distributions were calculated for four patients and compared to an already validated Geant4 algorithm. The radial function calculated from bGPUMCD showed excellent agreement (differences within 1.3%) with TG-43 accepted values. The anisotropy functions at r = 1 cm and r = 4 cm were within 2% of TG-43 values for angles over 17.5°. For permanent prostate implants, Monte Carlo-based dose distributions with a statistical uncertainty of 1% or less for the target volume were obtained in 30 s or less for 1 × 1 × 1 mm3 calculation grids. Dosimetric indices were very similar (within 2.7%) to those obtained with a validated, independent Monte Carlo code (Geant4) performing the calculations for the same cases in a much longer time (tens of minutes to more than a hour). bGPUMCD is a promising code that lets envision the use of Monte Carlo techniques in a clinical environment, with sub-minute execution times on a standard workstation. Future work will explore the use of this code with an inverse planning method to provide a complete Monte Carlo-based planning solution.
Feature Assembly Framework: towards scalable and reusable feature models

Feature models have been commonly used to model the variability in software product lines. In this paper we present the Feature Assembly framework which is a new approach for creating feature models through feature composition and feature assembly. Furthermore, it promotes feature reusability by storing features in a so-called feature pool, which acts as a feature repository. The Feature Assembly Framework is based on the Feature Assembly feature modeling method, which will be briefly introduced. It is a multi-perspective approach for modeling variability, to deal with the complexity of large systems. The feature assembly modeling method also provides a simpler and easier to use modeling language, which separates the variability specifications from the feature specifications to allow reusing features in different contexts.
SFADiff: Automated Evasion Attacks and Fingerprinting Using Black-box Differential Automata Learning

Finding differences between programs with similar functionality is an important security problem as such differences can be used for fingerprinting or creating evasion attacks against security software like Web Application Firewalls (WAFs) which are designed to detect malicious inputs to web applications. In this paper, we present SFADIFF, a black-box differential testing framework based on Symbolic Finite Automata (SFA) learning. SFADIFF can automatically find differences between a set of programs with comparable functionality. Unlike existing differential testing techniques, instead of searching for each difference individually, SFADIFF infers SFA models of the target programs using black-box queries and systematically enumerates the differences between the inferred SFA models. All differences between the inferred models are checked against the corresponding programs. Any difference between the models, that does not result in a difference between the corresponding programs, is used as a counterexample for further refinement of the inferred models. SFADIFF's model-based approach, unlike existing differential testing tools, also support fully automated root cause analysis in a domain-independent manner. We evaluate SFADIFF in three different settings for finding discrepancies between: (i) three TCP implementations, (ii) four WAFs, and (iii) HTML/JavaScript parsing implementations in WAFs and web browsers. Our results demonstrate that SFADIFF is able to identify and enumerate the differences systematically and efficiently in all these settings. We show that SFADIFF is able to find differences not only between different WAFs but also between different versions of the same WAF. SFADIFF is also able to discover three previously-unknown differences between the HTML/JavaScript parsers of two popular WAFs (PHPIDS 0.7 and Expose 2.4.0) and the corresponding parsers of Google Chrome, Firefox, Safari, and Internet Explorer. We confirm that all these differences can be used to evade the WAFs and launch successful cross-site scripting attacks.
A hybrid system for concept-based web usage mining

A web site should be easy to browse by visitors. However, sometimes the reality is quite different. Situations like several unrelated topics in a single web page may lead to confusion and make harder to reach the information that the visitors are looking for. The design of the whole site (interface, content, structure, usability, etc.) is one of the most important aspects for any institution that wants to survive in the cyberspace. This work aims to extract new knowledge about how the visitors are using the web site and, in this way, to improve the site structure and content. We propose a hybrid system that combines the web usage mining (WUM) approach for analyzing the visitor browsing behavior and the conceptual classification of web pages for understanding the visitor text preferences in the site. The proposed system was tested in a real web site, which shows its effectiveness.
Thermomechanical modelling for fatigue damage of bituminous materials

To assess fatigue cracking performance, pavement materials are tested under cyclic loading during fatigue laboratory tests. Fatigue damage is generally assessed using the global specimen stiffness decrease. This classical fatigue life interpretation can be modified by the softening effect of thermal increase due to viscoelasticity which is not real micro-cracking induced damage. Here the material is modelled as a thermo-viscoelastic damageable material tested under sinusoidal loading. Both thermal and mechanical aspects and their coupling are taken into account leading to a complete constitutive model. Simulations are performed on cylindrical tension compression tests assuming a purely radial heat transfer. Comparison between the model and experimental data regarding temperature measurements and the global stiffness evolution lead to a good agreement. This approach points out the importance of thermal effects in fatigue tests and the limitation of classical approaches when thermal effects become important.
Estimated Patient Dose Indexes in Adult and Pediatric MDCT: Comparison of Automatic Tube Voltage Selection With Fixed Tube Current, Fixed Tube Voltage, and Weight-Based Protocols.

OBJECTIVE The purposes of this study were to determine the differences in estimated volumetric CT dose index (CTDIvol) obtained from the topogram before abdominal and pelvic MDCT in adult and pediatric patients using a scan type-based algorithm for selecting kilovoltage (CARE kV) and a fixed and a weight-based Quality Reference mAs for selecting tube (gmAs) current-exposure time product, in comparison with standard protocols, and to determine the bias and variability of estimated CTDIvol vis-à-vis actual CTDIvol using the standard protocols. MATERIALS AND METHODS During a 14-month period, 312 adult and pediatric patients referred for abdominal and pelvic MDCT were included in the study. For all patients, the estimated CTDIvol based on the topogram was recorded: protocol A, CARE kV on and 210 gmAs; protocol B, CARE kV on and 1 gmAs times patient weight (in pounds); and protocol C (standard protocol), CARE kV off, 120 kVp, and 1 gmAs times patient weight (in pounds). For the pediatric patients, estimated CTDIvol for the standard protocol D was calculated with 120 kVp and 150 gmAs. All patients were scanned with the standard protocols, and the actual CTDIvol was recorded. Linear regression models compared the CTDIvol of the three protocols in adults and the fourth for children. The estimated and actual CTDIvol were compared using a t test. RESULTS Protocol B yielded the lowest estimated CTDIvol (mean, 13.2 mGy for adults and 3.5 mGy for pediatric patients). The estimated CTDIvol overestimated the actual CTDIvol by, on average, 1.07 mGy for adults and 0.3 mGy for children. CONCLUSION CARE kV appears to reduce estimated CTDIvol vis-à-vis standard protocols only when a weight-based gmAs is used. Prescan estimated CTDIvol calculations appear to generally overestimate actual CTDIvol.
Proportional fair scheduling for dual-polarized multi-beam mobile satellite communications

The development of dual polarized digital beamforming techniques shows a bright prospect of high rate Mobile Satellite Communications (MSC). It is a Multi-User Multi-Input Multi-Output (MU-MIMO) network if all user terminals in this network are equipped with dual polarized antennas. The present work focuses on introducing the Proportional Fair (PF) scheduling into this network. The main problem is that the PF scheduling requires estimating the possible transmission rate of all users, but it is very difficult in the MSC because of the great satellite channel delay. In this paper we propose a solution for this problem and evaluate it through computer simulations.
Genetic variants associated with Lp(a) lipoprotein level and coronary disease.

BACKGROUND An increased level of Lp(a) lipoprotein has been identified as a risk factor for coronary artery disease that is highly heritable. The genetic determinants of the Lp(a) lipoprotein level and their relevance for the risk of coronary disease are incompletely understood. METHODS We used a novel gene chip containing 48,742 single-nucleotide polymorphisms (SNPs) in 2100 candidate genes to test for associations in 3145 case subjects with coronary disease and 3352 control subjects. Replication was tested in three independent populations involving 4846 additional case subjects with coronary disease and 4594 control subjects. RESULTS Three chromosomal regions (6q26-27, 9p21, and 1p13) were strongly associated with the risk of coronary disease. The LPA locus on 6q26-27 encoding Lp(a) lipoprotein had the strongest association. We identified a common variant (rs10455872) at the LPA locus with an odds ratio for coronary disease of 1.70 (95% confidence interval [CI], 1.49 to 1.95) and another independent variant (rs3798220) with an odds ratio of 1.92 (95% CI, 1.48 to 2.49). Both variants were strongly associated with an increased level of Lp(a) lipoprotein, a reduced copy number in LPA (which determines the number of kringle IV-type 2 repeats), and a small Lp(a) lipoprotein size. Replication studies confirmed the effects of both variants on the Lp(a) lipoprotein level and the risk of coronary disease. A meta-analysis showed that with a genotype score involving both LPA SNPs, the odds ratios for coronary disease were 1.51 (95% CI, 1.38 to 1.66) for one variant and 2.57 (95% CI, 1.80 to 3.67) for two or more variants. After adjustment for the Lp(a) lipoprotein level, the association between the LPA genotype score and the risk of coronary disease was abolished. CONCLUSIONS We identified two LPA variants that were strongly associated with both an increased level of Lp(a) lipoprotein and an increased risk of coronary disease. Our findings provide support for a causal role of Lp(a) lipoprotein in coronary disease.
Revisiting Doddington"s Zoo: A Systematic Method to Assess User-dependent Variabilities

A systematic analysis of user-dependent performance variability in the context of automatic speaker verification was first studied by Doddington \etal (1998). Different categories of users were distinguished and were called by animal names such as sheep, goats, lambs and wolves. Although such distinctions are important, it does not directly discriminate ``well-behaved'' users from ``badly behaved'' users. In our context, the badly behaved users are those who will bring the performance down when added to the system. We then extend such a study to formulate a user-specific score normalization (called F-norm's variant) and show that the user-dependent variability can be reduced to obtain an enhanced performance. By introducing some constraints, the proposed framework can also provide a stable user-dependent performance in terms of DET despite the fact that few (genuine) samples are available. In the context of multimodal biometrics, we show that it is possible to decide whether or not fusing the output of several systems is better than selecting any one of them, on a per user basis. This strategy is called an ``OR-switcher''. Based on 15 multimodal fusion experiments, the performance of OR-switcher is significantly better than the state-of-the-art score-level fusion algorithms.
The Coxiella burnetii Dot/Icm System Creates a Comfortable Home through Lysosomal Renovation

ABSTRACT Understanding the molecular pathogenesis of Coxiella burnetii, the causative agent of human Q fever, has historically been hindered by the technical difficulties of genetically manipulating obligate intracellular bacteria. The recent development of culture conditions suitable for axenic propagation of C. burnetii has paved the way for the application of a range of genetic techniques to address key questions within the field. Recent studies using mutational analysis have revealed that the C. burnetii Dot/Icm type 4 secretion system (T4SS) is an important virulence determinant that is essential for renovation of a lysosome into a mature Coxiella-containing vacuole (CCV) permissive of intracellular replication. Interestingly, a mutant of C. burnetii deficient in Dot/Icm function was found to be capable of replicating within the parasitophorous vacuole created by Leishmania amazonensis, which indicates that C. burnetii replication is not dependent on the cohort of Dot/Icm effector proteins per se but rather that the collective actions of effectors are required to create the specialized niche supportive of replication. Thus, a role for the Dot/Icm T4SS during the intracellular life cycle of C. burnetii has been more clearly defined by these studies, which demonstrate that advances in genetic analysis should allow future studies to focus on the intricacies of Dot/Icm effector functions that facilitate development of the unique CCV.