Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiscale Modeling and Simulation of Damage by Void Nucleation and Growth

Voids are observed to be generated under sufficient loading in many materials, ranging from polymers and metals to biological tissues. The presence of these voids can have drastic implications at the macroscopic level including strong material softening and more incipient fracture. Developing tools to appropriately account for these effects is therefore very desirable. This thesis is concerned with both, the appearance of voids (nucleation process) and the modeling and simulation of materials in the presence of voids. A particular nucleation mechanism based on vacancy aggregation in high purity metallic single crystals is analyzed. A multiscale model is developed in order to obtain an approximate value of the time required for vacancies to form sufficiently large clusters for further growth by plastic deformation. It is based on quantum mechanical results, kinetic Monte Carlo methods and continuum mechanics estimates calibrated with quasi-continuum results. The ultimate goal of these simulations is to determine the feasibility of this nucleation mechanism under shock loading conditions, where the temperature and tensions are high and vacancy diffusion is promoted. On the other hand, the effective behavior of materials with pre-existent voids is analyzed within the general framework of continuum mechanics and is therefore applicable to any material. The overall properties of the heterogeneous material are obtained through a two-level characterization: a representative volume element consisting of a hollow sphere is used to describe the "microscopic" fields, and an equivalent homogeneous material is used for the "macroscopic" behavior. A variational formulation of this two-scale model is presented. It provides a consistent definition of the macro-variables under general loading conditions, extending the well-known static averaging results so as to include microdynamic effects under finite deformations. This variational framework also provides a suitable starting point for time discretization and consistent definitions within discrete time. The spatial boundary value problem resulting from this multiscale model is solved with a particular spherical shell element specially developed for this problem. The approximation space is based on spherical harmonics, which respects the symmetries of the porous material and allows the representation of the fields on the sphere with very few degrees of freedom. Numerical tools, such as the exact representation of the boundary conditions and an exact quadrature rule, are also provided. The resulting numerical model is verified extensively, demonstrating good convergence results, and its applicability is shown through several material point calculations and a full two-scale finite element implementation.
Gain of ALK Gene Copy Number May Predict Lack of Benefit from Anti-EGFR Treatment in Patients with Advanced Colorectal Cancer and RAS-RAF-PI3KCA Wild-Type Status

Introduction Although cetuximab and panitumumab show an increased efficacy for patients with KRAS-NRAS-BRAF and PI3KCA wild-type metastatic colorectal cancer, primary resistance occurs in a relevant subset of molecularly enriched populations. Patients and Methods We evaluated the outcome of 68 patients with advanced colorectal cancer and RAS, BRAF and PI3KCA status according to ALK gene status (disomic vs. gain of ALK gene copy number – defined as mean of 3 to 5 fusion signals in ≥10% of cells). All consecutive patients received cetuximab and irinotecan or panitumumab alone for chemorefractory disease. Results No ALK translocations or amplifications were detected. ALK gene copy number gain was found in 25 (37%) tumors. Response rate was significantly higher in patients with disomic ALK as compared to those with gain of gene copy number (70% vs. 32%; p = 0.0048). Similarly, progression-free survival was significantly different when comparing the two groups (6.7 vs. 5.3 months; p = 0.045). A trend was observed also for overall survival (18.5 vs. 15.6 months; p = 0.885). Conclusion Gain of ALK gene copy number might represent a negative prognostic factor in mCRC and may have a role in resistance to anti-EGFR therapy.
Prüfer numbers: a poor representation of spanning trees for evolutionary search

The most important element in the design of a decoder-based evolutionary algorithm is its genotypic representation. The genotype-decoder pair must exhibit efficiency, locality, and heritability to enable effective evolutionary search. Prufer numbers have been proposed to represent spanning trees in evolutionary algorithms. Several researchers have made extravagant claims for the usefulness of this coding, but others have pointed out that Prufer numbers, though concise and easy to decode, lack the essential properties of locality and heritability. This conflict motivates our study. We examine the properties of Prufer numbers and compare Prufer numbers with other codings in evolutionary algorithms for four problems that involve spanning trees. Our conclusion is definite: Prufer numbers cause poor performance in evolutionary algorithms and should be avoided.
Parametric Study To Enhance The Genetic Algorithm's Performance When Using Transformation

Transformation is a biologically inspired genetic operator that, when incorporated in the standard Genetic Algorithm replacing crossover, can promote diversity in the population (Simoes and Costa 2001). The computational mechanism mimics the biological process and consists in the capacity of the individuals to absorb fragments of DNA from the environment. These gene segments are then reintegrated in the individuals' genome (see figure).
Source coding with side information at the decoder: Models with uncertainty, performance bounds, and practical coding schemes

We consider the problem of source coding with side information (SI) at the decoder only, when the joint distribution between the source and the SI is not perfectly known. Four parametric models for this joint distribution are considered, where uncertainty about the distribution is turned into uncertainty about the value of the parameters. More precisely, a prior distribution for the parameters may or may not be available. Moreover, the value of the parameters may either change at every symbol or remain constant for a while. This paper overviews the results on the performance of lossless source coding with SI at the decoder for the four models. The way LDPC-based encoding and decoding schemes should be designed to cope with model uncertainty is provided. Most of the proposed practical schemes perform close to the theoretical limits.
Characterizing large DNS traces using graphs

The increasing deployment of overlay networks that rely on DNS tricks has led to added interest in examining DNS traffic. In this paper we report on a characterization of DNS traffic gathered over a period of several weeks at Internet Gateway Routers (IGRs) in the AT&T Common Backbone. The characterization is carried out using several novel techniques to identify clients, local DNS servers, and authoritative DNS servers. Our techniques include passive and active measurements, graph-based analysis, examination of outliers, and explicit checks against data obtained from several external sources. Our contribution is the reduction of a very large data set (over 1 terabyte of raw data) into a significantly smaller representation that is ideally suited for answering protocol-specific semantic queries quickly. After categorizing the addresses, we use the network aware clustering technique to group local DNS servers. By juxtaposing the DNS server clusters with clusters formed by Web clients obtained from a large portal Web site, we determine the distribution of identified DNS servers in busy clusters. A variety of applications are examined, ranging from identifying suspected zombies to helping Content Distribution Networks in mapping location of DNS servers.
Pressure dressing in breast surgery: is this the solution for seroma formation?

PURPOSE Pressure dressing (PD) after modified radical mastectomy (MRM) for breast cancer is investigated here as an easy-to-apply method to reduce seroma formation and subsequent need for clinical care. PATIENTS AND METHODS Two hundred mastectomized patients who were treated with PD on the skin flaps and the axilla immediately postoperatively (group A) were compared with a similar non-PD group (B). Surgical technique and perioperative care were the same. Drains were removed when drain output was reduced to 30 ml per day, or on postoperative day 8 regardless of output. RESULTS Mean time with drains kept in situ was 4.9 and 5.5 days in group A and B, respectively. Five (2.5%) patients in group A and 16 (8%) in group B developed seromas after the removal of the drains. In total, 9 seroma needle aspirations were performed in group A and 26 in group B. Differences were statistically significant. CONCLUSION Our findings are supportive of PD as an effective, cheap and easy-to-apply method for the reduction (a) of the time with drains in situ after MRM, (b) of the number of patients developing seromas and (c) of the seroma aspirations. This can potentially reduce further complications, needed medical care and cut expenditure.
Homopolymer Length Filters

alignment is presented. The proposed “homopolymer-length-filter” replaces homopolymers with single characters in both the reads and the reference. In some sequencing technologies, this filter removes many of the machine-induced sequencing errors, but still allows the filtered read to be aligned to the filtered reference. In some sequencing and alignment technologies, this filter can increase the processing speed.
Correlates of Trabecular and Cortical Volumetric Bone Mineral Density of the Radius and Tibia in Older Men: The Osteoporotic Fractures in Men Study

Quantitative computed tomography (QCT) can estimate volumetric bone mineral density (vBMD) and distinguish trabecular from cortical bone. Few comprehensive studies have examined correlates of vBMD in older men. This study evaluated the impact of demographic, anthropometric, lifestyle, and medical factors on vBMD in 1172 men aged 69 to 97 years and enrolled in the Osteoporotic Fractures in Men Study (MrOS). Peripheral quantitative computed tomography (pQCT) was used to measure vBMD of the radius and tibia. The multivariable linear regression models explained up to 10% of the variance in trabecular vBMD and up to 9% of the variance in cortical vBMD. Age was not correlated with radial trabecular vBMD. Correlates associated with both cortical and trabecular vBMD were age (−), caffeine intake (−), total calcium intake (+), nontrauma fracture (−), and hypertension (+). Higher body weight was related to greater trabecular vBMD and lower cortical vBMD. Height (−), education (+), diabetes with thiazolidinedione (TZD) use (+), rheumatoid arthritis (+), using arms to stand from a chair (−), and antiandrogen use (−) were associated only with trabecular vBMD. Factors associated only with cortical vBMD included clinic site (−), androgen use (+), grip strength (+), past smoker (−), and time to complete five chair stands (−). Certain correlates of trabecular and cortical vBMD differed among older men. An ascertainment of potential risk factors associated with trabecular and cortical vBMD may lead to better understanding and preventive efforts for osteoporosis in men. © 2010 American Society for Bone and Mineral Research
Molecular methods (digital PCR and real-time PCR) for the quantification of low copy DNA of Phytophthora nicotianae in environmental samples.

BACKGROUND Currently, real-time polymerase chain reaction (qPCR) is the technique most often used to quantify pathogen presence. Digital PCR (dPCR) is a new technique with the potential to have a substantial impact on plant pathology research owing to its reproducibility, sensitivity and low susceptibility to inhibitors. In this study, we evaluated the feasibility of using dPCR and qPCR to quantify Phytophthora nicotianae in several background matrices, including host tissues (stems and roots) and soil samples. RESULTS In spite of the low dynamic range of dPCR (3 logs compared with 7 logs for qPCR), this technique proved to have very high precision applicable at very low copy numbers. The dPCR was able to detect accurately the pathogen in all type of samples in a broad concentration range. Moreover, dPCR seems to be less susceptible to inhibitors than qPCR in plant samples. Linear regression analysis showed a high correlation between the results obtained with the two techniques in soil, stem and root samples, with R(2) = 0.873, 0.999 and 0.995 respectively. CONCLUSIONS These results suggest that dPCR is a promising alternative for quantifying soil-borne pathogens in environmental samples, even in early stages of the disease.
A Factor Graph Approach to Exploiting Cyclic Prefix for Equalization in OFDM Systems

In OFDM systems, cyclic prefix (CP) insertion and removal enables the use of a set of computationally efficient single-tap equalizers at the receiver. Due to the extra transmission time and energy, the CP causes a loss in both spectrum efficiency and power efficiency. On the other hand, as a repetition of part of the data, the CP brings extra information and can be exploited for detection. Therefore, instead of discarding the CP observation as in the conventional OFDM system, we utilize all the received signals in a soft-input soft-output equalizer of a turbo equalization OFDM system. First, the models for both the CP part and the non-CP part of observation are presented in a Forney-style factor graph (FFG). Then based on the computation rules of the FFG and the Gaussian message passing (GMP) technique, we develop an equalization algorithm. With proper approximation, the complexity of the proposed algorithm is reduced to \changedmathcal O(2RNlog2N+4RGlog2G+2RG) per data block for R iterations, where N is the length of the data block and G is equal to P+L-1 with P the length of the CP and L the maximum delay spread of the channel. To justify the performance improvement, SNR analysis is provided. Simulation results show that the proposed approach achieves a significant gain over the conventional approach and the turbo equalization system converges within two iterations.
The CASIA statistical machine translation system for IWSLT 2009

This paper describes our statistical machine translation system (CASIA) used in the evaluation campaign of the International Workshop on Spoken Language Translation (IWSLT) 2008. In this year's evaluation, we participated in challenge task for Chinese-English and English-Chinese, BTEC task for Chinese-English. Here, we mainly introduce the overview of our system, the primary modules, the key techniques, and the evaluation results.
Approaches for estimating prevalence ratios

Recently there has been much interest in estimating the prevalence (risk, proportion or probability) ratio instead of the odds ratio, especially in occupational health studies involving common outcomes (for example, with prevalence rates above 10%). For example, if 80 out of 100 exposed subjects have a particular disease and 50 out of 100 non-exposed subjects have the disease, then the odds ratio (OR) is (80/20)/(50/50) = 4. However, the prevalence ratio (PR) is (80/100)/(50/100) = 1.6. The latter indicates that the exposed subjects are only 1.6 times as likely to have the disease as the non-exposed subjects, and this is the number in which most people would be interested. There is considerable literature on the advantages and disadvantages of OR versus PR (see Greenland,1 Stromberg,2 Axelson et al 3 and others). In this article we will review the existing methods and give examples and recommendations on how to estimate the PR. The most common method of modelling binomial (no/yes or 0/1) health outcomes today is logistic regression. In logistic regression one models the probability of the binomial outcome (Y = 1) of interest as: P(Y = 1| X1, X2, …, Xk) = eXβ/(1+eXβ) where Xβ = β+β1X1+β2X2+…+βkXk. Then exp(β1) = OR for a 1 unit increase in X1 adjusted for all other variables in the model. Logistic regression yields maximum likelihood estimates (MLEs) of the OR (adjusted for other covariates). If the adjusted OR is the parameter of interest, then these MLEs are generally considered the best estimators available. The adjusted OR can also be used to estimate the adjusted PR, but this should only be done for a rare disease (eg, one with a prevalence of 10% or less). This, together with the fact that …
Automatic Discovery of Action Taxonomies from Multiple Views

We present a new method for segmenting actions into primitives and classifying them into a hierarchy of action classes. Our scheme learns action classes in an unsupervised manner using examples recorded by multiple cameras. Segmentation and clustering of action classes is based on a recently proposed motion descriptor which can be extracted efficiently from reconstructed volume sequences. Because our representation is independent of viewpoint, it results in segmentation and classification methods which are surprisingly efficient and robust. Our new method can be used as the first step in a semi-supervised action recognition system that will automatically break down training examples of people performing sequences of actions into primitive actions that can be discriminatingly classified and assembled into high-level recognizers.
Application of reinforcement learning algorithms to software verification

This thesis presents a novel form of system verification through reinforcement learning algorithms. Large and complex software systems are often developed as a team effort. The aim of the development is to satisfy the customer by delivering the right product, with the right quality, and in time. Errors made by developers will always occur when a system is developed, but their effect can be reduced by removing them as early as possible. Software verification and validation are activities that are conducted to improve product quality. In this thesis we will adapt the techniques used in reinforcement learning to Software verification to verify if implemented system meets its specifications. This new approach can be used even if the complete model of the system is not available, which is new in probabilistic verification. This thesis main aim is not only to answer the question whether the system behaves according to its specifications but also to find the degree of divergence between the system and its specifications.
TUD-MMC at MediaEval 2016: Context of Experience task

This paper provides a three-step framework to predict user assessment of the suitability of movies for an inflight viewing context. For this, we employed classifier stacking strategies. First of all, using the different modalities of training data, twenty-one classifiers were trained together with a feature selection algorithm. Final predictions were then obtained by applying three classifier stacking strategies. Our results reveal that different stacking strategies lead to different evaluation results. A considerable improvement can be found for the F1-score when using the label stacking strategy.
Question Answering Evaluation Survey

Evaluating Question Answering (QA) Systems is a very complex task: state-of-the-art systems involve processing whose influences and contributions on the final result are not clear and need to be studied. We present some key points on different aspects of the QA Systems (QAS) evaluation: mainly, as performed during large-scale campaigns, but also with clues on the evaluation of QAS typical software components; the last part of this paper, is devoted to a brief presentation of the French QA campaign EQueR and presents two issues: inter-annotator agreement during campaign and the reuse of reference patterns.
Quadruped pronking on compliant terrains using a reaction wheel

While legged locomotion is a rapidly advancing area in robotics, several issues regarding the performance of such robots on deformable ground are still open. In this paper, we generate a pronking gait on a quadruped robot using a controller, which takes into account the effects of ground deformation. The controller, initially developed for monopods, is modified appropriately to operate for quadrupeds. The robot uses a reaction wheel to retain a desired body pitch. The dynamic models of leg motor drivetrains and of the reaction wheel are incorporated and their importance in the design of legged robots is highlighted. Simulation results show good performance in reaching commanded apex heights and forward velocities when traversing various deformable terrains, demonstrating that the developed controller is quite promising.
On challenges with mobile e-health: lessons from a game-theoretic perspective

Health portals play an important role in today's health care, and the increased mobility places demands on the portals to provide as accurate and few suggestions as possible. Often the information seekers may be in distress, lacking medical knowledge and expressing themselves in ways that make it difficult for the portal to interpret the seekers' needs. This raises the question on how portal providers may be able both to better model, or describe, the user behaviour and to predict the impact of changes in search algorithms to address these challenges. This paper highlights some possibilities and benefits of a theoretic framework, based on existing works on game-theoretic treatments of information retrieval and communication, to allow for both descriptive and predictive analysis of internet-based health communication. This is especially important in the context of increased mobility, demanding more accurate and fewer interactions. We also elaborate on how one of the fundamental results of game theory on equilibria may be used as a basis for improved information search. Possibly counter-intuitive, this is done not by tweaking the portal, but instead by trying to change the seekers' behaviour towards passing more diversifying queries.
Quantitative model for the interecho time dependence of the CPMG relaxation rate in iron‐rich gray matter

A quantitative model is proposed for computing the dependence on the interecho time of the NMR relaxation rate in iron‐rich gray matter obtained with a Carr‐Purcell‐Meiboom‐Gill sequence. The model consists of representing oligodendrocytes as identical magnetic spheres arranged in a spatially random pattern, and in approximating water diffusion as isotropic and unrestricted. Predictions of the model are calculated numerically using a Monte Carlo technique and, for the weak field limit, using an analytic formula. The model is shown to provide a good fit to experimental measurements of in vitro samples of monkey brain at field levels of 1.0 T and 1.5 T. These field levels are not sufficient to fully determine the model parameters, but it is argued that this may be possible at 3.0 T. The model is potentially of value for multiple‐spin‐echo MRI studies of iron‐related neurodegenerative disorders, such as Parkinson's disease. In particular, the model can be applied to correlate MRI data with the cellular distribution of iron in gray matter. Magn Reson Med 46:159–165, 2001. © 2001 Wiley‐Liss, Inc.