gebhart/patrepeval huggingface dataset:
Beyond loss of frataxin: the complex molecular pathology of Friedreich ataxia. (2014)

Friedreich ataxia (FRDA) is a devastating neurodegenerative disease caused by mutations in the frataxin gene (FXN). Frataxin is an essential protein which localizes to the mitochondria and is required for the synthesis of iron-sulfur clusters and heme. Most individuals with FRDA are homozygous for trinucleotide GAA.TTC repeat expansions in intron 1 of FXN. The instability of these GAA.TTC repeats, the formation of non-B DNA GAA.TTC structures, and accompanying epigenetic changes lead to reduced FXN transcript and frataxin protein. This 'loss of frataxin' is considered the main driver of disease pathology with mitochondria-rich tissues such as the heart and the brain most affected. While our understanding of FRDA etiology has advanced in recent years, exactly how reduced frataxin leads to disease remains largely unknown. Most therapeutic strategies aim to increase frataxin, yet there are other underlying aspects of the molecular pathology that could impact disease progression and severity. These include RNA toxicity due to antisense RNAs, dysregulated splicing and microRNAs, and repeat-associated protein toxicity via RAN translation. Here we review the diverse array of molecular events that have been shown to influence clinical outcome in FRDA. We also examine additional pathogenic factors from other trinucleotide repeat diseases which could be potentially important in FRDA.
Corneal imaging in localization and HMD interaction (2014)

The human eyes perceive our surroundings and are one of, if not our most important sensory organs. Contrary to our other senses the eyes not only perceive but also provide information to a keen observer. However, thus far this has been mainly used to detect reflection of infrared light sources to estimate the user's gaze. The reflection of the visible spectrum on the other hand has rarely been utilized. In this dissertation we want to explore how the analysis of the corneal image can improve currently available eye-related solutions, such as calibration of optical see-through head-mounted devices or eye-gaze tracking and point of regard estimation in arbitrary environments. We also aim to study how corneal imaging can become an alternative for established augmented reality tasks such as tracking and localization.
Joint signal precoding in the downlink of spread-spectrum systems (2003)

The downlink capacity tends to be the limiting factor in future communications systems. We propose two schemes for the downlink of code-division multiple-access systems that help reduce the multiuser interference by jointly precoding the transmitted signal based on knowledge of the downlink channel. Methods that operate on blocks of bits are first developed and a bitwise simplification of these for systems with large processing gains are derived. The use of multiple transmit antennas are also considered. These methods provide a substantial capacity increase without requiring complex multiuser detectors at the mobile terminals, and can be applied for instance to time-division duplex systems, which have reciprocal channels.
A Statistical Engine to Model Well Operations and Evaluate Asset Performance (2018)

Summary Holistic understanding of well operations can play a key role in optimization and maintenance of assets. The traditional process for understanding well operations mainly involves fitting a curve through all of the historical production data and extending the curve to forecast production without modeling the stochastic nature of production history, considering impact of any well interventions, or feeding any a priori information into curve-fitting workflows. This leads to unreliable production and reserves estimates which, in turn, impact the strategy and planning process for asset management. A novel workflow was developed learns the production characteristics of a well through a statistical framework using principles of signal processing and Bayesian inferences. Using this workflow, high-fidelity empirical production performance forecasts can be obtained for all the wells in the asset in an automated fashion. This novel workflow aims to significantly simplify interpretation of well operations, reduce the turnaround time for analyzing and modeling well performance, and improve the quality of reserves estimates.
Optical properties of gallium phosphide (GaP) nanowires (2012)

The linear and non-linear optical properties of different geometrical structures of gallium phosphide (GaP) nanowires have been studied by employing ab initio method. We have calculated the optical response of four different GaP nanowires, viz., two atom linear wire, two atom zigzag wire, four atom square wire and six atom hexagonal wire. We have investigated imaginary part of the zz component of the linear dielectric tensor and second order susceptibility for different structures along with bulk material. We revealed that strongest absorption occurs for four atom square nanowire configuration.
Protecting grapevines from winter injury (2008)

Published March 2008. Reviewed July 2017. Please check for up-to-date information in the OSU Extension Service Catalog: http://extension.oregonstate.edu/catalog
Suppression of Apoptosis by Dominant Negative Mutants of Cyclin-dependent Protein Kinases (1996)

In many cell types, position in the cell cycle appears to play a role in determining susceptibility to apoptosis (programmed cell death), and expression of various cyclins and activation of cyclin-dependent kinases (CDKs) have been shown to correlate with the onset of apoptosis in a number of experimental systems. To assess the role of CDK-mediated cell cycle events in apoptosis, we have expressed CDK dominant negative mutants in human HeLa cells. Dominant negative mutants of CDC2, CDK2, and CDK3 each suppressed apoptosis induced by both staurosporine and tumor necrosis factor alpha, whereas a dominant negative mutant of CDK5 was without effect. Like CDC2 and CDK2, CDK3 was shown to form a complex with cyclin A in vivo. CDK5 did not bind cyclin A to any detectable extent. Overexpression of wild type CDC2, CDK2, CDK3, or cyclin A (but not cyclin B) markedly elevated the incidence of apoptosis in BCL-2+ cells, which otherwise fail to respond to these agents. These results help identify cell cycle events that are also important for efficient apoptosis.
Quantitative assessment of hematopoietic chimerism by quantitative real-time polymerase chain reaction of sequence polymorphism systems after hematopoietic stem cell transplantation. (2011)

This SP-based real-time PCR assay provides a rapid, sensitive, and accurate quantitative assessment of mixed chimerism that can be useful in predicting graft rejection and early relapse.
Aminoglycoside−Arginine Conjugates That Bind TAR RNA:  Synthesis, Characterization, and Antiviral Activity (2000)

Regulation of HIV gene expression is crucially dependent on binding of the trans-activator protein, Tat, to the trans-activation response RNA element, TAR, found at the 5' end of all HIV-1 transcripts. Tat-TAR interaction is mediated by a short arginine-rich domain of the protein. Disruption of this interaction could, in theory, create a state of complete viral latency. A new class of small-molecule peptidomimetic TAR RNA binders, conjugates of aminoglycosides and arginine, was recently designed [Litovchick, A., Evdokimov, A. G., and Lapidot, A. (1999) FEBS Lett. 445, 73-79]. Two of these compounds, the tri-arginine derivative of gentamicin C (R3G) and the tetra-arginine derivative of kanamycin A (R4K), bind efficiently and specifically to TAR RNA. These compounds display negligible toxicity while being transported and accumulated in cell nuclei. Here we present a detailed synthesis and chemical characterization of the aminoglycoside-arginine conjugates R3G and R4K as well as GB4K, the tetra-gamma-guanidinobutyric derivative of kanamycin A. Their binding sites on TAR RNA were assigned by RNase A, uranyl nitrate, and lead acetate footprinting. The conjugates interact with TAR RNA in the widened major groove, formed by the UCU bulge and the neighboring base pairs of the upper stem portion of TAR, the binding site of Tat protein, and Tat-derived peptides (e.g., R52). Our results suggest an additional binding site of R4K and R3G compounds, in the lower stem-bulge region of TAR. The antiviral activity of the conjugates in cultured equine dermal fibroblasts infected with equine infectious anemia virus, used as a model system of HIV-infected cells, is also presented.
Ultra Low Power Bioelectronics: Fundamentals, Biomedical Applications, and Bio-Inspired Systems (2010)

Learn how to architect ultra low power robust electronics and how bio-inspired principles can revolutionize low power electronics design with this all-inclusive guide.
Rigorous Coupling of Geomechanics and Multiphase Flow with Strong Capillarity (2013)

Summary We study sequential formulations for coupled multiphase flow and reservoir geomechanics. First, we identify the proper definition of effective stress in multiphase-fluid systems. Although the average pore-pressure p¯ —defined as the sum of the product of saturation and pressure of all the fluid phases that occupy the pore space—is commonly used to describe multiphase-fluid flow in deformable porous media, it can be shown that the "equivalent" pore pressure pE —defined as p¯ minus the interfacial energy—is the appropriate quantity (Coussy 2004). We show, by means of a fully implicit analysis of the system, that only the equivalent pore pressure pE leads to a continuum problem that is thermodynamically stable (thus, numerical discretizations on the basis of the average pore pressure p¯ cannot render unconditionally stable and convergent schemes). We then study the convergence and stability properties of sequential-implicit coupling strategies. We show that the stability and convergence properties of sequential-implicit coupling strategies for single-phase flow carry over for multiphase systems if the equivalent pore pressure pE is used. Specifically, the undrained and fixed-stress schemes are unconditionally stable, and the fixed-stress split is superior to the undrained approach in terms of convergence rate. The findings from stability theory are verified by use of nonlinear simulations of two-phase flow in deformable reservoirs.
MHC Universal Cells Survive in an Allogeneic Environment after Incompatible Transplantation (2013)

Cell, tissue, and organ transplants are commonly performed for the treatment of different diseases. However, major histocompatibility complex (MHC) diversity often prevents complete donor-recipient matching, resulting in graft rejection. This study evaluates in a preclinical model the capacity of MHC class I-silenced cells to engraft and grow upon allogeneic transplantation. Short hairpin RNA targeting β2-microglobulin (RN_shβ2m) was delivered into fibroblasts derived from LEW/Ztm (RT1(l)) (RT1-A(l)) rats using a lentiviral-based vector. MHC class I (RT1-A-) expressing and -silenced cells were injected subcutaneously in LEW rats (RT1(l)) and MHC-congenic LEW.1W rats (RT1(u)), respectively. Cell engraftment and the status of the immune response were monitored for eight weeks after transplantation. In contrast to RT1-A-expressing cells, RT1-A-silenced fibroblasts became engrafted and were still detectable eight weeks after allogeneic transplantation. Plasma levels of proinflammatory cytokines IL-1 α , IL-1 β , IL-6, TNF- α , and IFN- γ were significantly higher in animals transplanted with RT1-A-expressing cells than in those receiving RT1-A-silenced cells. Furthermore, alloantigen-specific T-cell proliferation rates derived from rats receiving RT1-A-expressing cells were higher than those in rats transplanted with RT1-A-silenced cells. These data suggest that silencing MHC class I expression might overcome the histocompatibility barrier, potentially opening up new avenues in the field of cell transplantation and regenerative medicine.
{SDN} and Optical Flow Steering for Network Function Virtualization (2014)

Introduction Middlebox traffic steering, the capability of routing traffic through different sequences of middleboxes, has been a popular application in software-define networks (SDN) [5]. In this work, we focus on network function virtualization (NFV) [2][3], especially on core virtualized network functions that process high-volume traffic, such as session border controllers (SBCs) and serving/gateway GPRS support node (SGSN/GGSN). While these core network functions (NFs) run in a virtualized environment in a data center/cloud instead of dedicated hardware, their locations are more dynamic and thus there is a strong need to steer traffic through them dynamically. Similar to [5], traffic will need to be routed across various intermediate NFs before reaching its destination, e.g. at the customer PE. This process is called traffic steering for NFV. Different from traditional middleboxes, the core NFs handle much higher volumes of traffic, and usually don't have the same fine-grained traffic steering requirements that normal middleboxes do. Thus, we argue that existing Layer2/Layer3 packet based traffic steering will have scalability issue for large traffic volume, and may also be associated with high energy cost.
Structural Glazing Failure — Five Case Studies (2004)

Silicone sealant manufacturers produce extensive amounts of information instructing users of silicone structural glazing material on proper use of their material, including design guidelines, compatibility analysis, material storage, handling and application, including surface preparation and installation instructions. What are usually not shared are the results of not following the manufacturers' instructions. The following five case studies are examples of actual projects where structural silicone sealant failure occurred as a result of improper use of the material. The case studies are followed by commentary on what might be done to prevent failure in the future.
The specificity of collagen cross-links as markers of bone and connective tissue degradation (1995)

The availability of a specific and convenient biochemical assay for quantifying bone turnover would aid in the clinical management of osteoporosis and other metabolic bone diseases. Recently, several immunoassays for bone metabolites have been reported in the research literature, with data suggesting that certain of them may now have the required specificity and responsiveness to bone cell activity and convenience for routine clinical use.
Tenth SPE Comparative Solution Project: A Comparison of Upscaling Techniques (2001)

Abstract This paper presents the results of the Tenth SPE Comparative Solution Project on Upscaling. Two problems were chosen. The first problem was a small 2D gas injection problem, chosen so that the fine grid could be computed easily, and both upscaling and pseudoisation methods could be used. The second problem was a waterflood of a large geostatistical model chosen so that it was hard (though not impossible) to compute the true fine grid solution. Nine participants provided results for one or both problems.
Mechanoenzymatic peptide and amide bond formation (2017)

Mechanochemical chemoenzymatic peptide and amide bond formation catalysed by papain was studied by ball milling.
A critical discussion of intraclass correlation coefficients (1994)

Abstract In general, intraclass correlation coefficients (ICC's) are designed to assess consistency or conformity between two or more quantitative measurements. They are claimed to handle a wide range of problems, including questions of reliability, reproducibility and validity. It is shown that care must be taken in choosing a suitable ICC with respect to the underlying sampling theory. For this purpose a decision tree is developed. It may be used to choose a coefficient which is appropriate for a specific study setting. We demonstrate that different ICC's may result in quite different values for the same data set, even under the same sampling theory. Other general limitations of ICC's are also addressed. Potential alternatives are presented and discussed, and some recommendations are given for the use of an appropriate method.
Coronary-Artery Stenting Compared with Balloon Angioplasty for Restenosis after Initial Balloon Angioplasty (1998)

Elective coronary stenting was effective in the treatment of restenosis after balloon angioplasty. Stenting resulted in a lower rate of recurrent stenosis despite a higher incidence of subacute thrombosis.
It Takes Two: The Reciprocal Relationship Between Social Capital and Democracy (1999)

What is the relationship between social capital and democracy?Some scholars, following Tocqueville, argue that social capital is an important precondition to democracy (Inglehart 1997;Putnam 1993).Others argue that social capital is in fact "endogenous" to democratic institutions (Jackman and Miller 1998).This paper explores a third possibility, often acknowledged but not yet tested empirically: a reciprocal relationship between social capital and democracy.Drawing on the 1990-93 World Values Survey and a variety of other cross-national data, I first present evidence that democracy and social capital are related at the bivariate level, and that this relationship persists in more fully specified models.I then estimate a structural equations model, allowing for a reciprocal linkage between interpersonal trust and the quality of democracy in particular.The results indicate a degree of reciprocity, although democracy's impact on social trust is much greater than social trust's impact on democracy.Thus these results also provide some confirmation of the endogeneity thesis.
Simulation of congenital heart defects: a novel way of training in echocardiography (2009)

According to this validation the prototype simulator could make a significant contribution to training in the use of echocardiography in congenital heart disease.
Poppable display: A display that enables popping, breaking, and tearing interactions with people (2013)

We previously developed a display using a soap film as a screen. This screen can display various appearances of the projected images by changing its reflectance property by controlling ultrasound waves. Further, the soap film has other advantages of being very thin and disposable. This research aims to make use of these advantages to realize new interactions with a display. The soap screen pops out and breaks. Users can insert their fingers into the screen. When the screen breaks, it can be replaced easily. This display is expected to contribute to entertainment computing communities by acting as a deformable and physically interactive display. In this paper, the details of the proposed display, the related experimental results, discussion and future work are presented.
Determination of a Patient's Speed and Stride Length Minimizing Hardware Requirements (2011)

Within biomedical engineering, the use of wearable wireless accelerometers for gait analysis can provide useful information for multiple health-related applications. The minimization of hardware for an accurate and simple estimation of the patient's velocity and stride length represents a difficult task. In this paper we propose a new methodology to determine the velocity and stride length of the patient through the application of the wavelet transform to the waist acceleration signal minimizing the hardware requirements. We introduce 4 novel formulations to take into account the trade-off between accuracy and computational costs, showing that an adaptive optimum approach can deliver results with average errors below 5%.
Travel advice for clients with pre-existing medical conditions (2003)

Overseas travel, especially long-haul, can have risks that are not only associated with infection but also the mode of transport, climate, lifestyle and conditions at the destination. These risks may be magnified if the individual has a pre-existing medical condition.
Internet of Blockchains: Techniques and Challenges Ahead (2018)

Recently, we have witnessed a trend that many industries are forming consortiums and attempting to accelerate efficiency and reduce cost by using blockchain technology. Nevertheless, there is a clear missing capability of cross-industry and cross-blockchain interoperability. Currently, most blockchain business networks operate in isolation without external data transfer or multi-blockchain interactions. For blockchain technology to ultimately deliver on its promise, blockchain networks must be able to scale from networks addressing individual business processes to very large scale networks of interconnected decentralized autonomous organizations addressing much larger business problems at the level of entire industries and across industries. In this paper, we envision the inception of Internet of Blockchains (IoB), where homogeneous and heterogeneous decentralized networks communicate to facilitate cross-chain transactions of value, data and state transition. In addition, we also discuss interledger techniques that are essential for enabling industry-scale blockchain networks as well as achieving scalable interconnectivity between disparate, distributed ledgers.
Direct Potentiometric Measurement of Potassium in Blood Serum with Liquid Ion-Exchange Electrode (1970)

Abstract A new liquid ion-exchange electrode is described which has a selectivity for K+ over Na+ of 93:1 in 0.1 mol/kg solutions. Its response is Nernstian in the range 5 x 10-4 to 5 x 10-1 mol KCl per kg. The dip-type electrode responds to small changes in K+ in mixed salt solutions containing the same quantities of KCl and NaCl as human blood serum. A miniaturized form of the electrode was adapted to a capillary flow-through system for blood sera. It gives results for K+ in the normal range that agree with flame photometric values without correction for Na+ in the concentrations normally present. The effect of pH on the K+ response and the response of the electrode to Mg++, Ca++, NH4+, Rb+, and Cs+ are also illustrated.
USE OF AN ELECTROLYTIC RESPIROMETER TO STUDY DENITRIFICATION IN SOIL (1958)

An electrolytic respirometer and gas-sampling attachment suitable for soil denitrification studies is described. With this apparatus, control of moisture and oxygen content in incubating soils is obtained over long periods while at the same time small quantities of gases released by denitrilication are retained for estimation. Experiments using N 13 confirmed the value of this apparatus. Only slight denitrification was found under aerobic conditions in a Walla Walla silt loam soil, and the conditions under which denitrification took place indicated the specific role of substrate level and the related gas-exchange characteristics of the system.
Impact of 4 Lactobacillus plantarum capsular polysaccharide clusters on surface glycan composition and host cell signaling (2012)

Our study reveals that modulation of surface glycan characteristics in L. plantarum highlights the role of these molecules in shielding of cell envelope embedded host receptor ligands. Although the apparently complete cps clusters (cps2A-J and cps4A-J) contributed individually to this shielding, the removal of all cps clusters led to the strongest signaling enhancement. Our findings provide new insights into cell surface glycan biosynthesis in L. plantarum, which bears relevance in the context of host-cell signaling by probiotic bacteria.