Miracle-dz/UniFAR-FTUs huggingface dataset:
Tracking and modelling small motions at grain scale in granular materials under compression by X-Ray microtomography and discrete simulations

The present work is motivated by the study of creep in granular materials at the microscopic scale.The first part of this thesis deals with displacement measurements by microtomography. Classical digital image correlation fails to catch time-dependent (possibly fast) phenomena such as short-term creep. A new method named emph{Discrete Digital Projection Correlation} is developed to overcome this limitation. This method requires very few projections (about 100 times less than classical methods) of the deformed state to perform the correlation and retrieve grain displacements. Therefore, the acquisition time is remarkably reduced, which allows to study time-dependent phenomena.The method is tested on experimental data. While its accuracy compares favorably to that of conventional methods, it only requires acquisition times of a few minutes. The origins of measurement errors are tracked by numerical means, on simulated grain displacements and rotations.The second part is a numerical simulation study, by the Discrete Element Method (DEM), of oedometric compression in model granular materials, carried out with a simple model material: assemblies of slightly polydisperse spherical beads interacting by Hertz-Mindlin contact elasticity and Coulomb friction. A wide variety of initial states are subject to compression, differing in density, coordination number and fabric anisotropy. Despite apparently almost reversible strains, oedometric compression proves an essentially anelastic and irreversible process,due to friction, with important internal state changes affecting coordination number and anisotropy. Elastic moduli only describe the response to very small stress increments about well equilibrated configurations. The ratio of horizontal stress to vertical stress (or coefficient of earth pressure at rest, commonly investigated in soil mechanics) only remains constant for initially anisotropic assemblies. A simple formula relates it to force and fabric anisotropy parameters, while elastic moduli are mainly sensitive to the latter. Further studies of contact network instabilities and rearrangements should pave the way to numerical investigations of creep behavior
Disruptive TP53 Mutation Is Associated with Aggressive Disease Characteristics in an Orthotopic Murine Model of Oral Tongue Cancer

Purpose: To characterize tumor growth and metastatic potential in head and neck squamous cell carcinoma (HNSCC) cell lines in an orthotopic murine model of oral tongue cancer and to correlate TP53 mutation status with these findings. Experimental Design: Cells from each of 48 HNSCC cell lines were orthotopically injected into the oral tongues of nude mice. Tumor volume, cervical lymph node metastasis, and mouse survival were recorded. Direct sequencing of the TP53 gene and Western blot analysis for the p53 protein after induction with 5-fluorouracil was conducted. Cell lines were categorized as either mutant TP53 or wild-type TP53, and lines with TP53 mutation were further categorized on the basis of type of mutation (disruptive or nondisruptive) and level of p53 protein expression. The behavior of tumors in these different groups was compared. Results: These 48 HNSCC cell lines showed a wide range of behavior from highly aggressive and metastatic to no tumor formation. Mice injected with cells harboring disruptive TP53 mutations had faster tumor growth, greater incidence of cervical lymph node metastasis, and shorter survival than mice injected with cells lacking these mutations. Conclusions: HNSCC cell lines display a wide spectrum of behavior in an orthotopic model of oral cancer. Cell lines with disruptive TP53 mutations are more aggressive in this system, corroborating clinical reports that have linked these mutations to poor patient outcome. Clin Cancer Res; 17(21); 6658–70. ©2011 AACR.
Prediction of clinical outcome with estrogen and progestin receptor concentrations and their relationships to clinical and histopathological variables in endometrial cancer.

Concentrations of cytosol estrogen (ERC) and cytosol progestin (PRC) receptors were assayed in malignant tissue specimens of 230 patients with endometrial cancer, and those of nuclear estrogen and nuclear progestin receptors, and 17 beta-hydroxysteroid dehydrogenase activities in about 100 specimens. Endometrial cancer was at an early stage in 205 and advanced in 25 patients. As a supplement to surgical and radiation therapy, all patients received p.o. medroxyprogesterone acetate (100 mg a day) for 2 years. The follow-up time varied from 12 to 96 months (median, 42 months). Concentrations of ERC, PRC, nuclear estrogen, and nuclear progestin receptors in endometrial cancer tissue were significantly lower in clinical stages III-IV than in clinical stage I. In clinical stage I, ERC and PRC appeared in significantly lower concentrations in anaplastic than in moderately and well differentiated malignancies. The concentrations of these receptors were increased in obese patients, and the activity of 17 beta-hydroxysteroid dehydrogenase was increased in patients younger than 50 years, suggesting that endogenous female steroid hormones modify the pattern of female steroid receptors in malignant endometrium. In clinical stage I, 13 of 153 patients with adequate therapy contracted a recurrent disease. Poor prognosis was predicted by anaplastic structure of the malignancy (P less than 0.001), low tissue concentrations (0-30 fmol/mg protein) of ERC alone (P = 0.006), PRC alone (P = 0.010), and ERC and PRC simultaneously (P = 0.004). All 101 patients who simultaneously had ERC and PRC in concentrations higher than 30 fmol/mg protein remained disease free for 2 years, whereas all recurrences in patients with receptor-poor tumors appeared during the 2 years of medroxyprogesterone acetate treatment. In clinical stage II, with 30 patients, no prognosis indicators predicted the clinical outcome, whereas in clinical stages III + IV, with 25 patients, low ERC concentrations were associated with a worsened prognosis (P = 0.045). Conclusively, cytosol and nuclear estrogen and nuclear progestin receptor concentrations and 17 beta-hydroxysteroid dehydrogenase activity give valuable information about the endocrine associations in endometrial cancer. Cytosol estrogen and cytosol progestin receptors appeared to be useful predictors of recurrent disease. They also have the potential to distinguish between patients expected to benefit from adjuvant progestin therapy and those expected to be unresponsive to the same treatment.
Quantifying Strength Size Effects in Polycrystalline Silicon and Aluminum with On-chip Test Platforms

IV List of Tables . IX List of Figures . X Chapter I: Introduction and Overview . 1 1.1 Motivation . 1 1.2 Deformation and Failure Mechanisms . 2 1.2-1 Polysilicon Fracture Mechanics . 2 1.2-2 Aluminum Deformation Mechanisms . 5 1.3 Test Platforms . 8 1.3-1 Test Platforms with Off-chip Actuators . 9 1.3-2 Test Platforms with On-chip Actuators . 13 1. 4 Test Set-up . 16 1.4-1 Probe Station . 16 1.4-2 Scanning Electron Microscopy . 17 1.5 Contributions . 17 1.6 Dissertation Organization. 19
A Framework for Cognitive Bias Detection and Feedback in a Visual Analytics Environment

This paper presents a framework that supports the detection and mitigation of cognitive biases in visual analytics environments for criminal analysis. Criminal analysts often use visual analytics environments for their analysis of large data sets, for gaining insights on criminal events and patterns of criminal events, and for drawing conclusions and making decisions. However, due to the nature of human cognition, these cognitive processes may lead to systematic errors, so-called cognitive biases. The most prominent and relevant cognitive bias in the intelligence field is the confirmation bias, in which an analyst disproportionally considers and selects information that supports the initial expectation and hypothesis. The framework presented in this paper describes a model, how the possible occurence of the confirmation bias can be detected automatically, while the analyst makes use of the visual environment. Moreover, based on this information, different feedback methods are employed that support and encourage the mitigation of the confirmation bias. This framework is in a work-in-progress state and contains research objectives and directions, the framework design, initial implementations, plans for further development and integration, as well as user-centric evaluation.
Health relevance of intestinal protein fermentation in young pigs

Abstract The physiological role of the gastrointestinal microbiota has become an important subject of nutrition research in pigs in the past years, and the importance of intestinal microbial activity in the etiology of disease is doubtless. This review summarizes the recent knowledge related to the microbial ecology of protein fermentation and the appearance of protein-derived metabolites along the pig intestine. The amount of fermentable protein depends on factors such as dietary protein concentration, protein digestibility due to secondary or tertiary structure, the interaction with dietary compounds or anti-nutritional factors, and the secretion of endogenous proteins into the gut lumen. High protein diets increase the luminal concentrations and epithelial exposure to putatively toxic metabolites and increase the risk for post-weaning diarrhea, but the mechanisms are not yet clarified. Although the use of fermentable carbohydrates to reduce harmful protein-derived metabolites in pigs is well-established, recent studies suggest that the inclusion of fermentable carbohydrates into diets with low protein digestibility or high dietary protein level may not ameliorate all negative effects with regard to epithelial response. Based on the current knowledge, the use of diets with low levels of high-quality protein may help to reduce the risk for intestinal disease in young pigs.
Efficient Localization Methods for Passivity Enforcement of Linear Dynamical Models

This paper describes a novel approach for passivity enforcement of compact dynamical models of electrical interconnects. The proposed approach is based on a parameterization of general state-space scattering models with fixed poles. We formulate the passivity constraints as a unitary boundedness condition on the H∞ norm of the system transfer function. When this condition is not verified, we use it as an explicit constraint within an iterative perturbation loop of the system state-space matrices. Since the resulting optimization framework is convex but nonsmooth, we solve it via localization based algorithms, such as the ellipsoid and the cutting plane methods. The proposed technique solves two critical bottleneck issues of the existing approaches for passivity enforcement of linear macromodels. Compared to quasi-optimal schemes based on singular value or Hamiltonian eigenvalue perturbation, we are able to guarantee convergence to the optimal solution. Compared to convex formulations based on direct Bounded Real Lemma constraints, we are able to reduce both memory and time requirements by orders of magnitude. We demonstrate the effectiveness of our approach on a number of cases for which existing algorithms either fail or exhibit very slow convergence.
[Alcohol, and tobacco consumption and sports practice in Mexican and Spanish university students and the association between quality of life and health and sensation seeking].

OBJECTIVE To analyze the alcohol, and tobacco consumption and sports practice for Mexican and Spanish and its relation to sensation seeking. Methods: 309 university students participated, 154 Spanish and 155 Mexican. We used the Sensation Seeking Scale (SSS-V), the health survey Short-Form 36 (SF-36) and a lifestyle questionnaire conducted ad hoc. RESULTS Mexican Students often have lower consumption of tobacco, alcohol and binge drinking and more frequent sport than Spanish students and receive higher scores on the SF-36. Disinhibition is a risk factor for alcohol consumption and physical inactivity and SSS-V for tobacco consumption. CONCLUSIONS The consumption of alcohol, tobacco and physical inactivity in universities in Spain and Mexico is low. The SSS-V full scale is a predictor of tobacco consumption and dimension DES of alcohol consumption and physical inactivity.
The construction of new scales: a framework and case study of the EUREGIO cross-border region

The article proposes a framework for analysing re-scaling processes and applies it to a case study of the Dutch-German EUREGIO cross-border region. While much of the scale debate focuses on the causes and consequences of re-scaling, the article addresses the conditions and circumstances in which new territorial scales emerge and suggests a framework of necessary components of re-scaling processes. Informed by neo-Gramscian thinking, the scales debate as well recent analyses of regionalisation, these are formulated as: political mobilisation, governance building and strategic unification. The case study locates the EUREGIO case with respect to these dimensions. The article concludes that this framework can be used for studying and comparing other re -scaling cases and presents an initial typology for classifying cross-border regions.
Emotion recognition in the noise applying large acoustic feature sets

Speech emotion recognition is considered mostly under ideal acoustic conditions: acted and elicited samples in studio quality are used besides sparse works on spontaneous fielddata. However, specific analysis of noise influence plays an important factor in speech processing and is practically not considered hereon, yet. We therefore discuss affect estimation under noise conditions herein. On 3 well-known public databases - DES, EMO-DB, and SUSAS - effects of postrecording noise addition in diverse dB levels, and performance under noise conditions during signal capturing, are shown. To cope with this new challenge we extend generation of functionals by extraction of a large 4k hi-level feature set out of more than 60 partially novel base contours. Such comprise among others intonation, intensity, formants, HNR, MFCC, and VOC19. Fast Information-Gain-Ratio filter-selection picks attributes according to noise conditions. Results are presented using Support Vector Machines as classifier.
Dangerous object recognition for visual surveillance

In this paper, we address a critical task, i.e. dangerous object recognition for web surveillance system. Instead of investigating how to define an object is dangerous by analyzing human's activities (e.g. leaving a bomb in public places), our research focus on how to capture the dangerous object immediately when he/she appears under surveillance camera again, to stop him/her do more bad things. Different with the existing template and feature matching based methods, we solve the dangerous object recognition problem by a classification based method. We train a SVM classifier by learning “bag of words” based dangerous and non-dangerous object representation. For obtaining more discriminative object descriptors, we fuse color and texture, two low level image features, to generate descriptors under “bag of words” frame. We evaluate the proposed method, along with template and feature matching methods. The experimental results validate our method.
Endothelial Differentiation of Mesenchymal Stromal Cells

Human mesenchymal stromal cells (hMSCs) are increasingly used in regenerative medicine for restoring worn-out or damaged tissue. Newly engineered tissues need to be properly vascularized and current candidates for in vitro tissue pre-vascularization are endothelial cells and endothelial progenitor cells. However, their use in therapy is hampered by their limited expansion capacity and lack of autologous sources. Our approach to engineering large grafts is to use hMSCs both as a source of cells for regeneration of targeted tissue and at the same time as the source of endothelial cells. Here we investigate how different stimuli influence endothelial differentiation of hMSCs. Although growth supplements together with shear force were not sufficient to differentiate hMSCs with respect to expression of endothelial markers such as CD31 and KDR, these conditions did prime the cells to differentiate into cells with an endothelial gene expression profile and morphology when seeded on Matrigel. In addition, we show that endothelial-like hMSCs are able to create a capillary network in 3D culture both in vitro and in vivo conditions. The expansion phase in the presence of growth supplements was crucial for the stability of the capillaries formed in vitro. To conclude, we established a robust protocol for endothelial differentiation of hMSCs, including an immortalized MSC line (iMSCs) which allows for reproducible in vitro analysis in further studies.
Frequency-Agile Radar Signal Processing

Modern radars may incorporate pulse-to-pulse carrier frequency modulation to increase probability of detection, to reduce Vulnerability to jamming, and to reduce probability of interception. However, if coherent processing is used for clutter rejection, the frequency of N consecutive pulses must be held constant for N-pulse clutter cancellation or Doppler filtering. If M pulses are transmitted during the time the antenna illuminates a target, there are M/N coherently integrated echoes available for noncoherent integration in the computer or the operator's display to further improve the signal-to-noise ratio (SNR). In this paper, analytical and simulation methods are employed to determine the balance between coherent and noncoherent integration that yields the greatest SNR improvement. Attention is focused upon a model using peak selection of fast Fourier transform (FFT) Doppler channels and is compared to a reference model involving only a single Doppler channel. Curves of detectable SNR as a function of M and N are presented for both models.
HELIOSPHERIC AND ASTROSPHERIC HYDROGEN ABSORPTION TOWARDS SIRIUS : NO NEEDFOR INTERSTELLAR HOT GAS

We use an updated self-consistent kinetic/gasdynamic model of the solar wind/interstellar flow interaction to compute the Lyman-alpha absorption by hydrogen atoms of both interstellar and solar origin generated in the heliospheric interface. We apply this model to the direction of the star Sirius. We show that the neutralized, compressed solar wind from the heliosheath explains the extra absorption at positive redshifts observed in the Lyman-alpha line with the HST/GHRS. This removes the need for the interstellar hot gas previously proposed to explain this extra absorption. We also show that extra absorption in the blue wing can possibly be explained by H atoms formed in an astrosphere around Sirius, providing the stellar wind is at least as massive and fast as the solar wind.
The Effects of Substance P on the Preconstricted Pulmonary Vasculature of the Anesthetized Dog

Abstract Substance P is a vasoactive peptide. Nerve fibers containing substance P are present in the media of pulmonary arteries but the physiologic function of substance P in the pulmonary vasculature is unknown. Several doses of substance P were infused intravenously in the anesthetized dog to ascertain its effects on the pulmonary vasculature, both during normoxia and following preconstriction with hypoxia (F1O2 0.1) or prostaglandin F2α (PGF2α 5 μg/kg/min). Substance P resulted in systemic vasodilatation during normoxia but had minimal effect on the pulmonary vasculature. During hypoxia and PGF2α-induced pulmonary vasoconstriction, substance P significantly lowered pulmonary artery pressure, pulmonary vascular resistance, mean aortic pressure, and total systemic resistance. It had no effect on cardiac output, wedge pressure, and arterial blood gases. To investigate possible mechanisms for substance P-induced vasodilatation, substance P was studied following pretreatment with N-acetylcysteine (a radical scavenging agent), methylene blue (an inhibitor of guanylate cyclase), meclofenamate (a cyclooxygenase inhibitor), and atropine (a muscarinic receptor antagonist). None of these agents impaired substance P-induced vasodilatation. Substance P given intravenously is a nonselective vasodilator in the dog but the mechanism of its action remains uncertain.
Recognizing articulated objects using a region-based invariant transform

In this paper, we present a new method for representing and recognizing objects, based on invariants of the object's regions. We apply the method to articulated objects in low-resolution, noisy range images. Articulated objects such as a back-hoe can have many degrees of freedom, in addition to the unknown variables of viewpoint. Recognizing such an object in an image can involve a search in a high-dimensional space that involves all these unknown variables. Here, we use invariance to reduce this search space to a manageable size. The low resolution of our range images makes it hard to use common features such as edges to find invariants. We have thus developed a new "featureless" method that does not depend on feature detection. Instead of local features, we deal with whole regions of the object. We define a "transform" that converts the image into an invariant representation on a grid, based on invariant descriptors of entire regions centered around the grid points. We use these region-based invariants for indexing and recognition. While the focus here is on articulation, the method can be easily applied to other problems such as the occlusion of fixed objects.
RNAi-based conditional gene knockdown in mice using a U6 promoter driven vector

RNA interference (RNAi) is a powerful tool widely used for studying gene function in a number of species. We have previously developed an approach that allows conditional expression of a polymerase III promoter based small hairpin RNA (shRNA) in mice using the Cre-LoxP system. This approach uses a U6 promoter, which is inactive due to the presence of a ploxPneo cassette in the promoter; this promoter can be activated after excision of the neo gene in transgenic mice that express a Cre recombinase transgene. As a proof of principle, we have previously knocked down over 95% of Fgfr2 transcripts in mouse germlines, leading to embryonic lethality, while restricting the knockdown to the progress zone of the limb results in live animals with malformation of digits of both the forelimbs and hindlimbs. We now provide a detailed protocol, including a simplified single-step cloning procedure for vector construction. This method provides a fast yet efficient way to decipher gene functions in vivo in a tissue specific manner.
Characterization of monoclonal antibodies to Acanthamoeba myosin-I that cross-react with both myosin-II and low molecular mass nuclear proteins

We characterized nine monoclonal antibodies that bind to the heavy chain of Acanthamoeba myosin-IA. Eight of these antibodies bind to myosin-IB and eight cross-react with Acanthamoeba myosin-II. All but one of the antibodies bind to a 30-kD chymotryptic peptide of myosin-IA that derives from the COOH terminus of the molecule, and to tryptic peptides as small as 17 kD, hence these epitopes are clustered closely together on the heavy chain. None of the antibodies prevent heavy chain phosphorylation by myosin-I heavy chain kinase. One antibody inhibits the K+-EDTA ATPase activity and three antibodies inhibit the actin- activated Mg++-ATPase activity of myosin-I under the set of conditions that we tested. When fluorescent antibody staining of both whole cells and isolated nuclei is done, several of these monoclonal antibodies react strongly with nuclei. These antibodies also stain the cytoplasmic matrix, especially the cortex near the plasma membrane. All nine of the monoclonal antibodies bind to polypeptides of 30-34 kD that are highly enriched in nuclei isolated from Acanthamoeba. There is no myosin-I in the isolated nuclei, so the 30-34-kD polypeptides, not myosin-I, are responsible for the nuclear staining.