Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemoprevention of prostate carcinogenesis by alpha-difluoromethylornithine in TRAMP mice.

Development of effective chemopreventive agents for human consumption requires conclusive evidence of their efficacy in animal models that have relevance to human diseases. Transgenic adenocarcinoma mouse prostate (TRAMP) is an excellent model of prostate cancer that mimics progressive forms of human disease inasmuch as 100% of males develop histological PIN by 8-12 weeks of age that progress to adenocarcinoma with distant site metastases by 24-28 weeks of age. In these animals, ornithine decarboxylase (ODC) activity (>3-fold) as well as protein expression (>4-fold) was found to be markedly higher in the dorsolateral prostate as compared with the nontransgenic littermates, suggesting their suitability to determine the chemopreventive effect of alpha-difluoromethylornithine (DFMO), an enzyme-activated irreversible inhibitor of ODC, against prostate cancer. Using male TRAMP mice, we studied the effect of oral consumption of DFMO on development of prostate carcinogenesis and surrogate end point biomarkers related to prostate cancer progression. In two independent experiments, each consisting of 8 animals on test, the cumulative incidence of prostatic cancer development at 28 weeks of age in 16 untreated TRAMP mice was 100% (16 of 16), whereas 94% (15 of 16) and 69% (11 of 16) of the animals exhibited distant site metastases to lymph nodes and lungs, respectively. Oral consumption of 1% DFMO (w/v) in the drinking water to TRAMP mice from 8 to 28 weeks of age resulted in a significant decrease in (a) weight (59%) and volume (66%) of prostate, (b) genitourinary weight (63%), and (c) ODC enzyme activity (52%) in the dorsolateral prostate. Importantly, in none of the DFMO-fed TRAMP mice were any distant metastases to lymph node and lungs observed. Furthermore, DFMO treatment resulted in the marked reduction in the protein expression of proliferation cell nuclear antigen, ODC, and probasin in the dorsolateral prostate. The protein expression of antimetastases markers, i.e., E-cadherin and alpha- and beta-catenin, was found to be restored in DFMO-fed animals as compared with the non-DFMO-fed mice. These chemopreventive effects of DFMO were further confirmed by immunohistochemical analysis of the dorsolateral prostate. Histological analysis of the dorsolateral prostate of DFMO-fed animals displayed marginal epithelial stratification, a small number of cribriform structures, elongated hyperchromatic epithelial nuclei, and a significant increase in apoptotic index. Non-DFMO-fed animals, on the other hand, displayed extensive epithelial stratification with profound cribriform structures accompanied with marked thickening, remodeling, and hypercellularity of the fibromuscular stroma. In nontransgenic littermates fed with DFMO, no significant alterations in the above parameters were evident. These data demonstrate that ODC represents a promising and rational target for chemoprevention of human prostate cancer and that TRAMP mice are excellent models for screening of novel drugs and chemopreventive regimens for potential human use.
A new maximum likelihood polarimetric interferometric synthetic aperture radar coherence change detection (ML-PolInSAR-CCD)

ABSTRACT Coherent change detection (CCD) use the sample degree of coherence as a measure of the temporal change collected between two complex-valued SAR images observed in the same area and using also the same geometry and polarization. The problem of classical CCD approaches shows a temporal change only when there are in areas of the image that have high clutter-to-noise power ratio. All experiments regarding the maximum-likelihood (ML) CCD, found to estimate useful information also in lower clutter-to-noise power ratio. Experiments used only electromagnetic transmissions in the same polarization. This work extends the formulation of the probability distribution function of the CCD in a multi-dimensional version useful for multi-polarization SAR data. Results of this ML-polarimetric interferometric SAR-CCD (ML-PolInSAR-CCD) show surprising recovery of both amplitude and phase CCD information. This information recovery is useful for improved interferometric SAR (InSAR), permanent scatterers interferometry (PS-InSAR) and SAR tomography applications.
Author Profile Pages in zbMATH - Improving Accuracy through User Interaction

A solid and distinctive online record of a scientist’s research achievements is nowadays a must, in particular for a researcher at an early career stage looking for a better university position, applying for a grant or a promotion, or trying to establish new contacts and build partnerships and projects. In the global world of science there are already numerous services offering research profile sites, such as Google Scholar, Scopus or ORCID. In the field of mathematics, however, the community still relies a lot on the traditional services MathSciNet and zbMATH, which stand for a high level of quality control regarding data inclusion and assignment. However, the enormously growing number of mathematical publications and new mathematicians begs the question of how to design author profile pages for mathematicians which fit the new trends of communication in the era of social networks, while keeping (or better increasing) the existing level of reliability. In our contribution we plan to present some ideas from the development team of zbMATH addressing this topic.
Changes in ultrasonographic echogenicity and visibility of needles with changes in angles of insonation.

PURPOSE To objectively compare the echogenicity of several types of needles at clinically important angles of insonation. MATERIALS AND METHODS Four commercial needles (Echotip, Mini-Stick, Echo-Coat, Surflo) and a prototype dimpled needle were tested in a liver phantom at angles of insonation ranging from 90 degrees to 15 degrees. Photodensity measurement determined echogenicity levels in arbitrary echogenicity units (EU). RESULTS At 90 degrees angles of insonation all needles were easily seen (60-76 EU) and echogenic levels were similar (P =.264). All values decreased with angulation. From the 35 degrees to 15 degrees angles, the prototype and Echotip needles were superior (P <.05). At 15 degrees the values were 43 EU for the prototype needle, 40 EU for the Echotip needle, 9.0 EU for the Echo-Coat needle, and 5.0 EU for the Surflo needle. CONCLUSION With angulation, all needles drop in echogenicity, with prototype dimpled and Echotip best maintaining visibility at clinically important angles.
Learning Number of Clusters in Unlabeled Dataset using Rotation Estimation

Most of the Clustering algorithms in Cluster Analysis, partition a dataset into a fixed number of clusters supplied by the user manually i.e. learning by Observation [1]. The estimation of number of clusters for partitioning the dataset is difficult in the case of large datasets, which leads to inefficient data distribution or majority outliers. Hence, in this paper we propose a novel method using rotation estimation also called Cross-Validation [2,3,4] which identifies a suitable number of clusters in a given unlabeled dataset without using prior knowledge about the number of clusters. In this paper, the k-means and Expectation Maximization(EM) Clustering Techniques are optimized and enhanced for typical applications in
Dendritic cells use macropinocytosis and the mannose receptor to concentrate macromolecules in the major histocompatibility complex class II compartment: downregulation by cytokines and bacterial products

We have previously demonstrated that human peripheral blood low density mononuclear cells cultured in granulocyte/macrophage colony-stimulating factor (GM-CSF) and interleukin (IL)-4 develop into dendritic cells (DCs) that are extremely efficient in presenting soluble antigens to T cells. To identify the mechanisms responsible for efficient antigen capture, we studied the endocytic capacity of DCs using fluorescein isothiocyanate-dextran, horseradish peroxidase, and lucifer yellow. We found that DCs use two distinct mechanisms for antigen capture. The first is a high level of fluid phase uptake via macropinocytosis. In contrast to what has been found with other cell types, macropinocytosis in DCs is constitutive and allows continuous internalization of large volumes of fluid. The second mechanism of capture is mediated via the mannose receptor (MR), which is expressed at high levels on DCs. At low ligand concentrations, the MR can deliver a large number of ligands to the cell in successive rounds. Thus, while macropinocytosis endows DCs with a high capacity, nonsaturable mechanism for capture of any soluble antigen, the MR gives an extra capacity for antigen capture with some degree of selectivity for non-self molecules. In addition to their high endocytic capacity, DCs from GM-CSF + IL-4-dependent cultures are characterized by the presence of a large intracellular compartment that contains high levels of class II molecules, cathepsin D, and lysosomal- associated membrane protein-1, and is rapidly accessible to endocytic markers. We investigated whether the capacity of DCs to capture and process antigen could be modulated by exogenous stimuli. We found that DCs respond to tumor necrosis factor alpha, CD40 ligand, IL-1, and lipopolysaccharide with a coordinate series of changes that include downregulation of macropinocytosis and Fc receptors, disappearance of the class II compartment, and upregulation of adhesion and costimulatory molecules. These changes occur within 1-2 d and are irreversible, since neither pinocytosis nor the class II compartment are recovered when the maturation-inducing stimulus is removed. The specificity of the MR and the capacity to respond to inflammatory stimuli maximize the capacity of DCs to present infectious non-self antigens to T cells.
Bivalirudin for Primary Percutaneous Coronary Interventions: Outcome Assessment in the Ottawa STEMI Registry

Background—Data from randomized trials has demonstrated the superiority of bivalirudin to glycoprotein IIb/IIIa inhibitors plus heparin in patients undergoing primary percutaneous coronary intervention. Real-world performance of bivalirudin in primary percutaneous coronary intervention and the benefit of bivalirudin over heparin remain unknown in an era of routine dual antiplatelet therapy. Methods and Results—From July 2004 to December 2010, 2317 consecutive patients were indexed in the University of Ottawa Heart Institute ST-segment–elevation myocardial infarction registry. During this period 748 patients received bivalirudin, 699 patients received glycoprotein IIb/IIIa inhibitors, and 676 patients received unfractionated heparin alone. The primary outcome was the rate of noncoronary artery bypass graft related thrombolysis in myocardial infarction major bleeding. Bivalirudin significantly reduced the primary outcome compared with heparin plus glycoprotein IIb/IIIa inhibitors (2.7% versus 7.3%, adjusted OR 2.96, 95% CI: 1.61–5.45, P<0.001) and the composite end point of death, stroke, reinfarction and major bleed (OR 1.66, 95% CI: 1.12–2.45, P=0.01). Compared with heparin alone, a reduction in major bleeds (OR 1.21, 95% CI: 0.60–2.44, P=0.59) or the composite end point (1.05, 95% CI: 0.68–1.63, P=0.83) with bivalirudin could not be demonstrated. Notably, major bleeding was associated with a 5-fold increase in the risk of mortality both in-hospital (3.5% versus 20.6%) and out to 180 days (5.6% versus 25.8%). Conclusions—Bivalirudin use compared with glycoprotein IIb/IIIa inhibitors plus heparin as an antithrombotic strategy in primary percutaneous coronary intervention results in less major bleeding in contemporary practice. A benefit of bivalirudin over heparin could not be established with this registry and requires additional investigations to either confirm or refute.
Persistently Low Extracellular Glucose Correlates with Poor Outcome 6 Months after Human Traumatic Brain Injury despite a Lack of Increased Lactate: A Microdialysis Study

Disturbed glucose brain metabolism after brain trauma is reflected by changes in extracellular glucose levels. The authors hypothesized that posttraumatic reductions in extracellular glucose levels are not due to ischemia and are associated with poor outcome. Intracerebral microdialysis, electroencephalography, and measurements of brain tissue oxygen levels and jugular venous oxygen saturation were performed in 30 patients with traumatic brain injury. Levels of glucose, lactate, pyruvate, glutamate, and urea were analyzed hourly. The 6-month Glasgow Outcome Scale extended (GOSe6) score was assessed for each patient. In regions of increased glucose utilization defined by positron emission tomography, the extracellular glucose concentration was less than 0.2 mmol/l. Extracellular glucose values were less than 0.2 mmol during postinjury days 0 to 7 in 19% to 30% of hourly samples on each day. Transient decreases in glucose levels occurred with electrographic seizures and nonischemic reductions in cerebral perfusion pressure and jugular venous oxygen saturation. Glutamate levels were elevated in the majority of low-glucose samples, but the lactate/pyruvate ratio did not indicate focal ischemia. Terminal herniation resulted in reductions in glucose with increases in the lactate/pyruvate ratio but not in lactate concentration alone. GOSe6 scores correlated with persistently low glucose levels, combined early low glucose levels and low lactate/glucose ratio, and with the overall lactate/glucose ratio. These results suggest that the level of extracellular glucose is typically reduced after traumatic brain injury and associated with poor outcome, but is not associated with ischemia.
Urban Revitalization, Urban Regimes, and Contemporary Gentrification Processes

tiers set limits and possibilities on subjacent levels. The research grounds itself in three Columbus, Ohio, neighborhoods, two of which have witnessed the emergence of neighborhood regimes: Weinland Park, King-Lincoln, and Olde Towne East. Methods include exploratory quantitative data and GIS analyses, archival research, and key informant interviews. Results indicate that the rise of the cognitive-cultural economy and consumer cities, along with demographic and cultural transitions, have fomented a new vitality for the CBD and surrounding areas. Coupled with ongoing shifts toward entrepreneurial governance, this has led to the current era of revitalization. Further, trends in community development (strategic geographic targeting) and foundation giving (smart philanthropy), combined with greater institutional involvement in surrounding neighborhoods, have encouraged a more placed-based approach from the public and civic spheres, which has, in turn, engendered the rise of neighborhood regimes.
HPV co-factors related to the development of cervical cancer: results from a population-based study in Costa Rica

We examined factors associated with high-grade squamous intraepithelial lesions (HSIL) and cervical cancer among human papillomavirus (HPV)-infected women in a prevalent case–control study conducted within a population-based cohort of 10 077 women in Costa Rica. We compared 146 women with HPV-positive HSIL or cancer (HSIL/CA) against 843 HPV-positive women without evidence of HSIL/CA. Subjects completed a risk factor questionnaire. We evaluated the associations between exposures and HSIL/CA among women positive for any HPV and restricted to those positive for high-risk HPV types. Risk of HSIL/CA increased with increasing number of live births (Ptrend= 0.04). Women who smoked 6+ cigarettes/day had a RR for HSIL/CA of 2.7 (95% CI = 1.1–6.7) compared to non-smokers. Current use of barrier contraceptives was associated with a reduction in risk of HSIL/CA (RR = 0.39; 95% CI = 0.16–0.96). Sexual behaviour and a self-reported history of sexually transmitted diseases (STDs) other than HPV were not associated with HSIL/CA. Oral contraceptive use was associated with HSIL/CA among women with <3 pregnancies. Effects were similar in analysis restricted to women positive for high-risk HPV types. Among women positive for high-risk HPV types, 44% of HSIL/CA could be attributed to multiparity (≥3 pregnancies) and/or smoking. Among HPV-positive women, multiparity and smoking are risk factors for HSIL/CA. Oral contraceptive use may be associated with HSIL/CA in subgroups of women. © 2001 Cancer Research Campaign http://www.bjcancer. com
Adaptive Mapping and Parameter Selection Scheme to Improve Automatic Code Generation for GPUs

Graphics Processing Units (GPUs) are today's most powerful coprocessors for accelerating massive data-parallel algorithms. However, programmers are forced to adopt new programming paradigms to take full advantage of their computing capabilities; this requires significant programming and maintenance effort. As a result, there is an increasing interest in the development of tools for automatic mapping of sequential code to GPUs. Current automatic tools require both a deep knowledge on the GPU architecture and the algorithm being mapped, which makes the mapping process a labor-intensive task. This paper proposes a technique that improves the code mapping of one of these tools, PPCG, removing the need for any user interaction. It relies on data reuse estimations to explore the mapping space and compute appropriate values for the number of threads per threadblock and tile sizes. Our results show speedups of 3x on average compared to the default code generated by PPCG.
Somatic recombination of duplicated genes: an hypothesis on the origin of antibody diversity.

The specificity of antibodies for different antigens appears to result from differences in the amino acid sequences of both the heavy and the light polypeptide chains of which antibody molecules are composed. -4 Although specific antibodies are too heterogeneous for complete amino acid sequence analysis, homogeneous iminunoglobulins may be obtained for this purpose from various plasma cell tumors. Bence-Jones proteins have been shown to be light polypeptide chains5' 6 and data have accumulated on the amino acid sequences of various samples of both humanl-9 and murine origin. '0'" These amino acid sequence analyses show that light polypeptide chains of type K (K chains) are composed of 212-214 amino acid residues. '2 From residue 1
Hydrological trade-offs due to different land covers and land uses in the Brazilian Cerrado

Abstract. Farmland expansion in the Brazilian Cerrado, considered one of the largest agricultural frontiers in the world, has the potential to alter water fluxes on different spatial scales. Despite some large-scale studies being developed, there are still few investigations in experimental sites in this region. Here, we investigate the water balance components in experimental plots and the groundwater table fluctuation in different land covers: wooded Cerrado, sugarcane, pasture and bare soil. Furthermore, we identify possible water balance trade-offs due to the different land covers. This study was developed between 2012 and 2016 in the central region of the state of São Paulo in southern Brazil. Hydrometeorological variables, groundwater table, surface runoff and other water balance components were monitored inside experimental plots containing different land covers; the datasets were analyzed using statistical parameters; and the water balance components uncertainties were computed. Replacing wooded Cerrado by pastureland and sugarcane shifts the overland flow (up to 42 mm yr−1) and the water balance residual (up to 504 mm yr−1) and may affect groundwater table behavior. This fact suggests significant changes in the water partitioning in a transient land cover and land use (LCLU) system, as the evapotranspiration is lower (up to 719 mm yr−1) in agricultural land covers than in the undisturbed Cerrado. We recommend long-term observations for continuing the evaluations initiated in this study, mainly because there are few basic studies on tropical environments at the hillslope scale and more assessments are needed for a better understanding of the real field conditions. Such efforts should be made to reduce uncertainties, validate the water balance hypothesis and catch the variability of hydrological processes.
Higher order spectra based deconvolution of ultrasound images

We address the problem of improving the spatial resolution of ulrasound images through blind deconvolution. The ultrasound image formation process in the RF domain can be expressed as a spatio-temporal convolution between the tissue response and the ultrasonic system response, plus additive noise. Convolutional components of the dispersive attenuation and aberrations introduced by propagating through the object being imaged are also incorporated in the ultrasonic system response. Our goal is to identify and remove the convolutional distortion in order to reconstruct the tissue response, thus enhancing the diagnostic quality of the ultrasonic image. Under the assumption of an independent, identically distributed, zero-mean, non-Gaussian tissue response, we were able to estimate distortion kernels using bicepstrum operations on RF data. Separate 1D distortion kernels were estimated corresponding to axial and lateral image lines and used in the deconvolution process. The estimated axial kernels showed similarities to the experimentally measured pulse-echo wavelet of the imaging system. Deconvolution results from B-scan images obtained with clinical imaging equipment showed a 2.5-5.2 times gain in lateral resolution, where the definition of the resolution has been based on the width of the autocovariance function of the image. The gain in axial resolution was found to be between 1.5 and 1.9.
Novel Repellent Activity of Motor Neurons in Commissural Axon Guidance BISC 494 Honors Thesis

During embryonic development, commissural axons, originating in the dorsal spinal cord, send axons ventrally towards the floor plate. The trajectory of these axons is mediated by both repulsive cues secreted from the roof plate, as well as attractive cues secreted from the floor plate. To investigate the guidance activity of the floor plate, we first attempted to examine the role of Sonic Hedgehog (Shh), a proposed chemoattractant in commissural axon guidance, by misexpressing Shh in chick embryos. While our misexpression experiments showed strong misexpression, we were unable to evaluate Shh’s role as a guidance cue due to drastic changes in spinal cord patterning. We then took a different approach and examined commissural axon trajectory in the absence of guidance cues from the floor plate. By analyzing the Gli2 mouse, which lacks a floor plate, we found that commissural axon trajectories become highly disorganized as they project through the medially and ventrally shifted population of motor neurons. Further investigation of the interaction between commissural axons and motor neurons revealed that commissural axons avoid areas rich in motor neurons and favor regions with few motor neurons as they navigate towards the ventral midline. Thus we propose motor neurons possess a repellent activity that facilitates the guidance of commissural axons in the ventral spinal cord.
A principled foundation for LCS

In this paper we explicitly identify the probabilistic model underlying LCS by linking it to a generalisation of the common Mixture-of-Experts model. Having an explicit representation of the model not only puts LCS on a strong statistical foundation and identifies the assumptions that the model makes about the data, but also allows us to use off-the-shelf training methods to train it. We show how to exploit this advantage by embedding the LCS model into a fully Bayesian framework that results in an objective function for a set of classifiers, effectively turning the LCS training into a principled optimisation task. A set of preliminary experiments demonstrate the feasibility of this approach.