gebhart/patrepeval huggingface dataset:
Positional Approaches to Cancer Genetics (2003)

Loss of genetic material accumulates during tumor development as cancer cells select for the physical removal or functional inactivation of genes whose encoded proteins regulate normal cellular behavior. The hallmark indication for this type of gene, now termed a tumor suppressor gene, is a genetic event resulting in loss or deletion of chromosomal material. Position-oriented approaches have taken advantage of the intimate involvement of tumor suppressor gene inactivation through deletion to localize, identify, and demonstrate the involvement of these genes in carcinogenesis. Since deletion of genetic material exceeds genomic amplifications in most cancer types, loss of gene function appears to play a prominent role in tumor formation. However, despite the intimate involvement of tumor suppressor genes in the neoplastic process, relatively few of these genes have been identified, leaving the identity of the majority unknown. Thus, the use of position-based strategies for mapping and isolating tumor suppressor genes remains a prime tool in their identification.
Carbonation-Induced Corrosion of Blended-Cement Concrete Mix Designs for Highway Structures (1998)

Abstract Corrosion of concrete reinforcing steel in highway structures has traditionally been related to chloride ions. However, another cause of reinforcing steel corrosion is concrete carbonation which decreases the pH of the pore solution. Carbonation-induced corrosion tends to develop later and proceeds at slower rates than chloride-induced corrosion. Since very long service life goals are currently proposed for new highway structures, concrete carbonation is a likely concern when projecting durability. The objective of this investigation was to establish the prognosis for development of carbonation-induced corrosion of concrete mix designs proposed for new construction projects. Accelerated laboratory carbonation exposures to 60% relative humidity with 0.5% and 4% CO2 were conducted with concrete mix designs containing from 20% to 50% pozzolanic cement replacement, 2 different water-to-cementitious ratios, and with small levels (~2 kg/m3) of Cl− contamination (non-contaminated specimens were also included) Both the carbonation and the electrochemical behavior were monitored as a function of time. Carbonation rates were found to be directly dependent on the pozzolanic content. Polarization Resistance measurements showed that steel corrosion rates at 60% RH were small where chloride contamination was not present but increased to ~0.2 μA/cm2 with moderate Cl− contamination. Corrosion rates increased by over one order of magnitude for all mixes (except a low water-to-cementitious ratio, 20% pozzolanic cement replacement mix) during a post-carbonation high humidity exposure.
Abstract 4956: A Risk Stratification Analysis of Predictors of Death or Transplant in Children with Hypertrophic Cardiomyopathy (2008)

We previously reported initial results from a univariate analysis of baseline predictors of death or heart transplant in children with hypertrophic cardiomyopathy (HCM). We present here the final multivariate analysis resulting in risk stratification rules for 6 HCM etiologic subgroups in children. The Pediatric Cardiomyopathy Registry collected longitudinal data on 882 children with HCM from 1990 –2003. The primary outcome was the earlier of death or heart transplantation. Cox regression was used to identify the 3 most important risk factors at time of diagnosis for each HCM subgroup; all echo measures were expressed as z-scores. Multivariate analysis revealed that children with idiopathic HCM diagnosed by 1 year were at higher risk of poor outcome if they had CHF, low BSA, or elevated LV mass, while risk factors for children diagnosed after 1 year were female gender, depressed fractional shortening, and elevated wall thickness. Risk factors for children with malformation syndrome were Black race, CHF and increased wall thickness; Black race, younger age, and elevated LV mass for children with inborn errors of metabolism; younger age, CHF, and increased wall thickness for children with mixed restrictive HCM; and decreased weight, family history of heart disease, and increased wall thickness for children with mixed dilated HCM. Children with multiple risk factors present at diagnosis had a significantly worse prognosis compared to those with 0 or 1 risk factors. (Figure ) Based on etiologic subtype and number of risk factors present at diagnosis, clinicians can reliably estimate the risk of death of transplant in children with HCM.
Gatifloxacin and the elderly: pharmacokinetic-pharmacodynamic rationale for a potential age-related dose reduction (2003)

The probability of a patient aged > or =65 years having an AUC0-24 > or =60-70 mg.h/L is markedly lower following a 200 mg regimen relative to a 400 mg regimen, suggesting a decreased risk of severe hyperglycaemia in a predisposed patient. Moreover, a dose reduction does not appear to significantly modify the likelihood of achieving the PK-PD target of gatifloxacin against S. pneumoniae.
Improving 64-bit java IPF performance by compressing heap references (2004)

64-bit processor architectures like the Intel/spl reg/ Itanium/spl reg/ processor family are designed for large applications that need large memory addresses. When running applications that fit within a 32-bit address space, 64-bit CPUs are at a disadvantage compared to 32-bit CPUs because of the larger memory footprints for their data. This results in worse cache and TLB utilization, and consequently lower performance because of increased miss ratios. This paper considers software techniques for virtual machines that allow 32-bit pointers to be used on 64-bit CPUs for managed runtime applications that do not need the full 64-bit address space. We describe our pointer compression techniques and discuss our experience implementing these for Java applications. In addition, we give performance results with our techniques for both the SPEC JVM98 and SPEC JBB2000 benchmarks. We demonstrate a 12% performance improvement on SPEC JBB2000 and a reduction in the number of garbage collections required for a given heap size.
Substrate Specificity of an Active Dinuclear Zn(II) Catalyst for Cleavage of RNA Analogues and a Dinucleoside (2006)

The cleavage of the diribonucleoside UpU (uridylyl-3'-5'-uridine) to form uridine and uridine (2',3')-cyclic phosphate catalyzed by the dinuclear Zn(II) complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (Zn(2)(1)(H(2)O)) has been studied at pH 7-10 and 25 degrees C. The kinetic data are consistent with the accumulation of a complex between catalyst and substrate and were analyzed to give values of k(c) (s(-)(1)), K(d) (M), and k(c)/K(d) (M(-)(1) s(-)(1)) for the Zn(2)(1)(H(2)O)-catalyzed reaction. The pH rate profile of values for log k(c)/K(d) for Zn(2)(1)(H(2)O)-catalyzed cleavage of UpU shows the same downward break centered at pH 7.8 as was observed in studies of catalysis of cleavage of 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) and uridine-3'-4-nitrophenyl phosphate (UpPNP). At low pH, where the rate acceleration for the catalyzed reaction is largest, the stabilizing interaction between Zn(2)(1)(H(2)O) and the bound transition states is 9.3, 7.2, and 9.6 kcal/mol for the catalyzed reactions of UpU, UpPNP, and HpPNP, respectively. The larger transition-state stabilization for Zn(2)(1)(H(2)O)-catalyzed cleavage of UpU (9.3 kcal/mol) compared with UpPNP (7.2 kcal/mol) provides evidence that the transition state for the former reaction is stabilized by interactions between the catalyst and the C-5'-oxyanion of the basic alkoxy leaving group.
Pattern of Surgical Treatment for Early Gastric Cancers in Upper Third of the Stomach (2011)

There is a huge variety of surgical treatment for U-ECG in general hospitals in our country. A multi-institutional large cohort randomized trial might be urgent to establish the standard surgical procedure of this infrequent disease.
Measuring web quality (2013)

Measuring the quality of web content, either at page level or website level, is at the heart of several key challenges in the Web. Without doubt, the main one is web search, to be able to rank results. However, there are other important problems such as web reputation or trust, and web spam detection and filtering. However, measuring intrinsic web quality is a hard problem, because of our limited (automatic) understanding of text semantics, which is even worse for other media. Hence, similarly to human trust assessing, where we use past actions, face expressions, body language, etc; in the Web we need to use indirect signals that serve as surrogates for web quality. In this keynote we attempt to present the most important signals as well as new signals that are or can be used to measure quality in the Web. We divide them using the traditional web content, structure, and usage trilogy. We also characterize them according to how easy is to measure these signals, who can measure them, and how well they scale to the whole Web.
Miller Cycle Application to the Scuderi Split Cycle Engine (by Downsizing the Compressor Cylinder) (2012)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;The Scuderi engine is a split cycle design that divides the four strokes of a conventional combustion cycle over two paired cylinders, one intake/compression cylinder and one power/exhaust cylinder, connected by a crossover port. This configuration provides potential benefits to the combustion process, as well as presenting some challenges. A Miller cycle configuration of the engine is made possible by turbocharging with a downsized compressor cylinder and has been modeled in 1-dimensional cycle simulation software. Several positive interactions were found between the split cycle engine and Miller cycle operating principles, namely: &lt;ol class="list nostyle"&gt;&lt;li class="list-item"&gt;&lt;span class="li-label"&gt;1&lt;/span&gt;&lt;div class="htmlview paragraph"&gt;The reduced compression stroke facilitates actual displacement (and physical size) reduction of the split cycle engine, providing a more advantageous brake mean effective pressure (BMEP) characteristic compared to traditional reciprocating internal combustion engines (RICE) with Miller cycle operation.&lt;/div&gt;&lt;/li&gt;&lt;li class="list-item"&gt;&lt;span class="li-label"&gt;2&lt;/span&gt;&lt;div class="htmlview paragraph"&gt;Reduction of the compression cylinder displacement allows Miller cycle operation while still closing the intake valve at an optimum trapped mass condition. This results in more favorable pumping work than the Miller cycle applied to traditional RICE, due to the avoidance of closing the intake valve during a period of high piston velocity.&lt;/div&gt;&lt;/li&gt;&lt;li class="list-item"&gt;&lt;span class="li-label"&gt;3&lt;/span&gt;&lt;div class="htmlview paragraph"&gt;The extremely high turbulence and resulting fast combustion and late fuel addition provides a natural knock avoidance characteristic that allow the utilization of higher boost levels than are typically achievable with stoichiometric, spark-ignited engines.&lt;/div&gt;&lt;/li&gt;&lt;/ol&gt;&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Parametric variations are made across the operating range of the engine, investigating a range of potential Miller factors and boost levels. Analysis is performed to determine engine performance sensitivity to turbomachinery performance. At low load, a secondary level Miller cycle is applied through the use of early intake valve closure to provide near throttle-less load control. Simulation results indicate that high BMEP and good thermal efficiency are achievable in the main operating region. The resulting improvements in thermal efficiency and maximum BMEP provide the potential for significant fuel energy savings in an automotive application. BMEP provides benefits both through the effect of downsizing reducing the mass and size of the engine payload that must be transported, as well as by allowing the engine to operate at a higher operational BMEP and therefore higher efficiency during typical driving conditions.&lt;/div&gt;&lt;/div&gt;
Wavelength-tunable 2-D bioimaging and tomography based on a coherent detection imaging method with widely tunable lasers (1991)

We report further progress in our experimental demonstration of computer-assisted tunable laser absorption tomography (Laser CT) of biological organisms and samples. This was achieved by coherent detection imaging based on the laser heterodyne detection technique and the projection slice theorem. Its operating principle and simple demonstration have already been published. 1 , 2 Although the idea of optical imaging inside the living body is appealing, strong light scattering by the tissues and other optical distortions create severe practical difficulties. To overcome such a diffuse optical image quality in highly turbid, scattering media, we have proposed and verified, we believe for the first time, the use of the optical heterodyne method utilizing tunable coherent laser beams. It should be stressed that this method possesses both the properties of a highly sensitive receiver and an extremely directional antenna, so that ballistic photons can be detected passing straight through multiple-forward scattering in the tissues and systems.
Cytokine Receptor Expression on Hematopoietic Stem and Progenitor Cells (1997)

Hematopoietic stem and progenitor cell populations were obtained by fluorescence activated cell sorting of murine bone marrow (BM) cells into Rhodamine-123io lineage-Ly6A/ E+ c-kit+ (primitive stem cells highly enriched for long-term BM repopulating activity), Rhodamine-123med/hl lineage- Ly6A/E+ c-kit+ (mature stem cells highly enriched for shortterm BM repopulating activity and day 13 spleen colony-forming activity) and lineage- Ly6A/E- c-kit+ (enriched for in vitro colony forming cells) populations. Neither stem cell population responds to single cytokines in vitro and each requires the synergistic action of two or more cytokines for proliferation, whereas the progenitor cell population proliferates in response to single cytokines. Since each of these cell populations was sorted as c-kit+, they express receptors for stem cell factor. Cell populations were also analyzed by autoradiography for their ability to specifically bind iodinated cytokines and this revealed that both stem cell populations expressed receptors for interleukin-1 alpha (IL-1 alpha), IL-3, IL-6, and granulocyte colony-stimulating factor (G-CSF), but lacked receptors for macrophage colony-stimulating factor (M-CSF), granulocyte-macrophage colony stimulating factor (GM-CSF), and leukemia inhibitory factor (LIF). Cells within the progenitor cell population specifically bound IL-3, GM-CSF, G-CSF, IL-6, and IL-1 alpha, whereas no receptors were detected for M-CSF and LIF. Within each cell population examined, heterogeneity was observed in the percentage of cells labeled and the number of receptors per cell. These results suggest that stem cell populations can be further subdivided according to their cytokine receptor profile and it will be of interest to determine if such subpopulations have distinctive functional properties.
Synchrotron Radiation Therapy from a Medical Physics point of view (2010)

Synchrotron radiation (SR) therapy is a promising alternative to treat brain tumors, whose management is limited due to the high morbidity of the surrounding healthy tissues. Several approaches are being explored by using SR at the European Synchrotron Radiation Facility (ESRF), where three techniques are under development: Synchrotron Stereotactic Radiation Therapy (SSRT), Microbeam Radiation Therapy (MRT) and Minibeam Radiation Therapy (MBRT).
Lightfield Completion (2004)

A light field is a 4D function representing radiance as a function of ray position and direction in 3D space. In this paper we describe a method for recovering gaps in light fields of scenes that contain significant occluders. In these situations, although a large fraction of the scene may be blocked in any one view, most scene points are visible in at least some views. As a consequence, although too much information is missing to employ 2D completion methods that operate within a single view, it may be possible to recover the lost information by completion in 4D the full dimensionality of the light field. The proposed light field completion method has three main steps: registration, initial estimation, and high dimensional texture synthesis and/or inpainting. At the registration stage, the set of images are shifted and re-projected so that the corresponding pixels from different images are aligned in the reconstructed light Held. Following this, the estimation step uses a naive technique to fill-in parts of gaps using the available information from the multiple images. This serves as the initial condition for the next and last step, where the missing information is recovered via high dimensional texture synthesis and/or inpainting. These two steps of initial condition and completion are iterated. The algorithm is illustrated with real examples.
Cellular Responses to Electrochemical Killing Process by Applying a Constant Potential in Synchronously Cultured Saccharomyces Cerevisiae (2008)

To elucidate the mechanism of the electrochemical killing, the global gene expression of synchronously cultured Saccharomyces cerevisiae exposed to electrochemical stimulus was analyzed using DNA microarray. By applying a potential of 1.0 V vs. saturated calomel electrode (SCE), oxidative stress related genes were expressed after only 5 minutes. The gene for cta1 exhibited the highest expression level, while ROS gradually accumulated inside the cells. Genes for signal transduction which may be related to cellular apoptosis were also seen expressed.
Transition metal and rare earth-doped ZnO: a comparison of optical, magnetic, and structural behavior of bulk and thin films (2007)

Recent theoretical predictions of ferromagnetic behavior in transition metal (TM)-doped ZnO have focused significant attention on these materials for use as spintronic materials. Moreover, rare earth (RE) elements in wide bandgap semiconductors would be useful not only in spintronics but also in optoelectronic applications. This work presents results obtained from an investigation into the optical, magnetic, and structural properties of transition-metal (TM)- doped ZnO and rare earth (RE) doped ZnO (TM = Mn, Co, Ni, and Fe; RE = Gd, Eu, and Tb) bulk crystals and thin films. Properties of TM- and RE-doped ZnO bulk crystals and thin films were studied and compared in order to better understand the nature of these dopant centers and their effects on the properties of the host crystal. Optical properties confirm the incorporation of substitutional transition metal ions on cation sites. While most thin film samples show ferromagnetic behavior, the magnetic response of the bulk crystals varies. This suggests that the magnetic behavior of TM-doped ZnO is highly dependent on growth conditions, and growth conditions which favor the formation of grain boundaries and interfaces may be more likely to result in ferromagnetic behavior. Origins of this ferromagnetic behavior are still under investigation. Defect luminescence observed in the RE-doped samples suggests that these materials may prove useful in optoelectonic applications as well.
Phase autocorrelation (PAC) features in entropy based multi-stream for robust speech recognition (2004)

Methods to improve noise robustness of speech recognition systems often result in degradation of recognition performance for clean speech. Recently proposed phase autocorrelation (PAC) based features (S. Ikbal et al., Proc. ICASSP-03, p.II-133-6, 2003; Proc. IEEE ASRU 2003 Workshop, 2003), while showing noticeable improvement in noise robustness, also suffer from this drawback. We try to alleviate this problem by using the PAC based features along with regular speech features in a multi-stream framework. The multi-stream system uses the entropy of the posterior probability distribution, computed during recognition, as a confidence measure to combine evidence from different feature streams adaptively (Misra, H. et al., Proc. ICASSP-03, p.II-741-4, 2003). Experimental results obtained on OGI Numbers95 database and Noisex92 noise database show that such a system yields the best possible recognition performance in all conditions. Actually, the combination always performs better than the best performing stream for all the conditions.
The Biologically Relevant Targets and Binding Affinity Requirements for the Function of the Yeast Actin-Binding Protein 1 Src-Homology 3 Domain Vary With Genetic Context (2007)

Many protein-protein interaction domains bind to multiple targets. However, little is known about how the interactions of a single domain with many proteins are controlled and modulated under varying cellular conditions. In this study, we investigated the in vivo effects of Abp1p SH3 domain mutants that incrementally reduce target-binding affinity in four different yeast mutant backgrounds in which Abp1p activity is essential for growth. Although the severity of the phenotypic defects observed generally increased as binding affinity was reduced, some genetic backgrounds (prk1 Delta and sla1 Delta) tolerated large affinity reductions while others (sac6 Delta and sla2 Delta) were much more sensitive to these reductions. To elucidate the mechanisms behind these observations, we determined that Ark1p is the most important Abp1p SH3 domain interactor in prk1 Delta cells, but that interactions with multiple targets, including Ark1p and Scp1p, are required in the sac6 Delta background. We establish that the Abp1p SH3 domain makes different, functionally important interactions under different genetic conditions, and these changes in function are reflected by changes in the binding affinity requirement of the domain. These data provide the first evidence of biological relevance for any Abp1p SH3 domain-mediated interaction. We also find that considerable reductions in binding affinity are tolerated by the cell with little effect on growth rate, even when the actin cytoskeletal morphology is significantly perturbed.