gebhart/patrepeval huggingface dataset:
Demonstration of a hepatitis C virus-specific antigen predicted from the putative core gene in the circulation of infected hosts (1992)

An ELISA was used to detect a protein derived from the core gene of the hepatitis C virus (HCV) in human plasma. The solid phase antibody in the assay was a murine monoclonal antibody against a synthetic peptide deduced from the putative core gene of HCV (residues 39 to 74). An enzyme-labelled affinity-purified human antibody directed at another region within the HCV core (residues 5 to 23) was the second antibody tracer. The ELISA had a sensitivity capable of detecting a few ng/ml of the HCV core polypeptide expressed in Escherichia coli. Core antigen activity in plasma of infected hosts was detected after treatment of HCV RNA-rich fractions from buoyant density centrifugation with the detergent Tween 80. There was a direct correlation between core antigen ELISA values of a plasma fraction and intensities of polymerase chain reaction signals for HCV RNA. These observations are consistent with the proposal that the N-terminal sequence of the predicted polyprotein of HCV is a nucleocapsid protein, and that improved core antigen assays may correlate with viraemia.
Smartphone-based Indoor Localization for Blind Navigation across Building Complexes (2018)

Continuous and accurate smartphone-based localization is a promising technology for supporting independent mobility of people with visual impairments. However, despite extensive research on indoor localization techniques, they are still not ready for deployment in large and complex environments, like shopping malls and hospitals, where navigation assistance is needed. To achieve accurate, continuous, and real-time localization with smartphones in such environments, we present a series of key techniques enhancing a probabilistic localization algorithm. The algorithm is designed for smartphones and employs inertial sensors on a mobile device and Received Signal Strength (RSS) from Bluetooth Low Energy (BLE) beacons. We evaluate the proposed system in a 21,000 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> shopping mall which includes three multi-story buildings and a large open underground passageway. Experiments in this space validate the effect of the proposed technologies to improve localization accuracy. Field experiments with visually impaired participants confirm the practical performance of the proposed system in realistic use cases.
Time resolved properties of acoustic pulses generated in water and in soft tissue by pulsed proton beam irradiation—A possibility of doses distribution monitoring in proton radiation therapy (1991)

Time-resolved acoustic pulses generated in water and in soft tissue by pulsed proton beam irradiation were observed. The spatial resolution of depth dose distribution in the clinically applied beam intensity is estimated about 3 mm by means of TOF measurement. The dependence of the acoustic signal intensity on the temperature of medium was examined. Proportionality of acoustic pulse intensity to absorbed dose per pulse was confirmed as well. These results suggest the possibility of clinical application to monitor dose distribution in the patient's body during irradiation of pulsed proton beam.
Applications of glycosyltransferases in the site-specific conjugation of biomolecules and the development of a targeted drug delivery system and contrast agents for MRI (2008)

The modified glycan residues introduced at specific sites on the cargo molecule make it possible to conjugate fluorophores for ELISA-based assays, radionuclides for imaging and immunotherapy applications, lipids for the assembly of immunoliposomes, cytotoxic drugs, cytokines, or toxins for antibody-based cancer therapy and the development of a targeted drug delivery system.
Probing the Conformation of the Sugar Transport Inhibitor Phlorizin by 2D-NMR, Molecular Dynamics Studies, and Pharmacophore Analysis (2000)

Sodium/D-glucose cotransport, one of the prototypes for sodium gradient-driven symport systems in kidney and intestine, is known to be inhibited by aromatic and aliphatic glucosides (Diedrich, D. F. Biochim. Biophys. Acta 1963, 71, 688-700; Diedrich, D. F. Arch. Biochem. Biophys. 1966, 117, 248-256; Kipp, H.; et al. Biochim. Biophys. Acta 1996, 1282, 124-130; Ramaswamy, K.; et al. Biochim. Biophys. Acta 1976, 433, 32-38). The conformation in which the most potent inhibitor, phlorizin, interacts with the transport protein was investigated with different approaches. Phlorizin consists of the glucose moiety and two aromatic rings (A and B) joined by an alkyl spacer. First the interaction of these various parts of the molecule was determined by two-dimensional (2D) solution NMR. From the 2D-NOESY (nuclear Overhauser effect) measurements spatial distances (up to 5 A) between various interacting H atoms could be detected. Using these values as distance constraints, conformations of phlorizin were calculated and analyzed by the valence force-field method. As a result, a set of conformations could be obtained. The most probable phlorizin conformation shows a nearly perpendicular arrangement of the two aromatic rings (A and B) with the ring B situated above the sugar ring. A very similar conformation could be found by using molecular dynamics simulations when water was chosen as the solvent. This phlorizin conformation in aqueous solution then served as a template for conformational analysis of various phlorizin derivatives. The resulting conformations of derivatives were taken as input to establish a pharmacophore model using the DISCO calculation. As a result, the essential elements of phlorizin for interaction with its binding pocket could be deduced: namely hydrogen bonding via hydroxyl groups of the pyranoside at C(2), C(3), C(4), and C(6) and at C(4) and C(6) of aromatic ring A and hydrophobic interactions via the pyranoside ring and aromatic ring A. Finally, from these conformational features of the pharmacophore the dimension of the phlorizin binding site on the sodium/D-glucose cotransporter was estimated to be 17 x 10 x 7 A(3).
SynTF: Synthetic and Differentially Private Term Frequency Vectors for Privacy-Preserving Text Mining (2018)

Text mining and information retrieval techniques have been developed to assist us with analyzing, organizing and retrieving documents with the help of computers. In many cases, it is desirable that the authors of such documents remain anonymous: Search logs can reveal sensitive details about a user, critical articles or messages about a company or government might have severe or fatal consequences for a critic, and negative feedback in customer surveys might negatively impact business relations if they are identified. Simply removing personally identifying information from a document is, however, insufficient to protect the writer's identity: Given some reference texts of suspect authors, so-called authorship attribution methods can reidentfy the author from the text itself. One of the most prominent models to represent documents in many common text mining and information retrieval tasks is the vector space model where each document is represented as a vector, typically containing its term frequencies or related quantities. We therefore propose an automated text anonymization approach that produces synthetic term frequency vectors for the input documents that can be used in lieu of the original vectors. We evaluate our method on an exemplary text classification task and demonstrate that it only has a low impact on its accuracy. In contrast, we show that our method strongly affects authorship attribution techniques to the level that they become infeasible with a much stronger decline in accuracy. Other than previous authorship obfuscation methods, our approach is the first that fulfills differential privacy and hence comes with a provable plausible deniability guarantee.
<i>ato</i> Operon: a Highly Inducible System for Acetoacetate and Butyrate Degradation in <i>Escherichia coli</i> (1972)

1 Growth of Escherichia coli in the presence of acetoacetate as inducer stimulates the rate of synthesis of two enzymes, an acetoacetyl-CoA: acetate CoA-transferase and a thiolase by a factor of 3000. The combined action of these enzymes allows for the degradation of acetoacetate to acetate and acetyl-CoA. 2 The structural genes for these enzymes, called ato A (CoA-transferase) and atoB (thiolase), and a regulatory gene, atoC, are closely linked, forming an operon (ato operon) with the order his…atoCAB…nalA on the bacterial chromosome. 3 The regulatory gene atoC is defined by a spontaneous mutation to the atoCc state which allows E. coli to grow on butyrate and to synthesize the enzymes of the ato operon constitutively. This mutation can only be selected for when the enzymes of the C-3 oxidation pathway are themselves formed constitutively. The atoCc state is required for butyrate degradation because this acid does not serve as inducer of the ato operon but requires the CoA-transferase for activation. 4 The evidence so far available indicates that the atoCc mutation is trans- dominant over the inducible atoC+ state suggesting a positive mechanism of control. 5 The uptake of butyrate is reduced or completely suppressed when mutational lesions prevent the further metabolism of this substrate.
The axis-inducing activity, stability, and subcellular distribution of beta-catenin is regulated in Xenopus embryos by glycogen synthase kinase 3. (1996)

The serine/threonine kinase Xgsk-3 and the intracellular protein beta-catenin are necessary for the establishment of the dorsal-ventral axis in Xenopus. Although genetic evidence from Drosophila indicates that Xgsk-3 is upstream of beta-catenin, direct interactions between these proteins have not been demonstrated. We demonstrate that phosphorylation of beta-catenin in vivo requires an in vitro amino-terminal Xgsk-3 phosphorylation site, which is conserved in the Drosophila protein armadillo. beta-catenin mutants lacking this site are more active in inducing an ectopic axis in Xenopus embryos and are more stable than wild-type beta-catenin in the presence of Xgsk-3 activity, supporting the hypothesis that Xgsk-3 is a negative regulator of beta-catenin that acts through the amino-terminal site. Inhibition of endogenous Xgsk-3 function with a dominant-negative mutant leads to an increase in the steady-state levels of ectopic beta-catenin, indicating that Xgsk-3 functions to destabilize beta-catenin and thus decrease the amount of beta-catenin available for signaling. The levels of endogenous beta-catenin in the nucleus increases in the presence of the dominant-negative Xgsk-3 mutant, suggesting that a role of Xgsk-3 is to regulate the steady-state levels of beta-catenin within specific subcellular compartments. These studies provide a basis for understanding the interaction between Xgsk-3 and beta-catenin in the establishment of the dorsal-ventral axis in early Xenopus embryos.
Development of a GFP reporter gene for <i>Chlamydomonas reinhardtii</i> chloroplast (2002)

Reporter genes have been successfully used in chloroplasts of higher plants, and high levels of recombinant protein expression have been reported. Reporter genes have also been used in the chloroplast of Chlamydomonas reinhardtii, but in most cases the amounts of protein produced appeared to be very low. We hypothesized that the inability to achieve high levels of recombinant protein expression in the C. reinhardtii chloroplast was due to the codon bias seen in the C. reinhardtii chloroplast genome. To test this hypothesis, we synthesized a gene encoding green fluorescent protein (GFP) de novo, optimizing its codon usage to reflect that of major C. reinhardtii chloroplast-encoded proteins. We monitored the accumulation of GFP in C. reinhardtii chloroplasts transformed with the codon-optimized GFP cassette (GFPct), under the control of the C. reinhardtii rbcL 5'- and 3'-UTRs. We compared this expression with the accumulation of GFP in C. reinhardtii transformed with a non-optimized GFP cassette (GFPncb), also under the control of the rbcL 5'- and 3'-UTRs. We demonstrate that C. reinhardtii chloroplasts transformed with the GFPct cassette accumulate approximately 80-fold more GFP than GFPncb-transformed strains. We further demonstrate that expression from the GFPct cassette, under control of the rbcL 5'- and 3'-UTRs, is sufficiently robust to report differences in protein synthesis based on subtle changes in environmental conditions, showing the utility of the GFPct gene as a reporter of C. reinhardtii chloroplast gene expression.
Substrate recognition and fidelity of strand joining by an archaeal DNA ligase (2002)

We have previously identified a DNA ligase (LigTk) from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1. The enzyme is the only characterized ATP-dependent DNA ligase from a hyperthermophile, and allows the analysis of enzymatic DNA ligation reactions at temperatures above the melting point of the substrates. Here we have focused on the interactions of LigTk with various DNA substrates, and its specificities toward metal cations. LigTk could utilize Mg2+, Mn2+, Sr2+ and Ca2+ as a metal cation, but not Co2+, Zn2+, Ni2+, or Cu2+. The enzyme displayed typical Michaelis-Menten steady-state kinetics with an apparent Km of 1.4 microm for nicked DNA. The kcat value of the enzyme was 0.11*s-1. Using various 3' hydroxyl group donors (L-DNA) and 5' phosphate group donors (R-DNA), we could detect ligation products as short as 16 nucleotides, the products of 7 + 9 nucleotide or 8 + 8 nucleotide combinations at 40 degrees C. An elevation in temperature led to a decrease in reaction efficiency when short oligonucleotides were used, suggesting that the formation of a nicked, double-stranded DNA substrate preceded enzyme-substrate recognition. LigTk was not inhibited by the addition of excess duplex DNA, implying that the enzyme did not bind strongly to the double-stranded ligation product after nick-sealing. In terms of reaction fidelity, LigTk was found to ligate various substrates with mismatched base-pairing at the 5' end of the nick, but did not show activity towards the 3' mismatched substrates. LigTk could not seal substrates with a 1-nucleotide or 2-nucleotide gap. Small amounts of ligation products were detected with DNA substrates containing a single nucleotide insertion, relatively more with the 5' insertions. The results revealed the importance of proper base-pairing at the 3' hydroxyl side of the nick for the ligation reaction by LigTk.
Array element localization for towed marine seismic arrays (2001)

This paper presents an approach to array element localization (AEL) for towed marine seismic arrays based on regularized inversion of direct and bottom-reflected acoustic ray travel times picked from recorded seismic sections. Depth-sensor measurements at a number of points along the array are included as a priori estimates (with uncertainties) in the inversion. The smoothest array shape consistent with the acoustic data and prior estimates is determined by minimizing the array curvature or roughness. A smooth array shape is physically reasonable; in addition, minimizing curvature provides a priori information about the correlation between hydrophone positions that allows the estimation of both the offset and depth of hydrophones that record only one (or even no) acoustic arrival due to the shadowing effects of water-column refraction or reflection from arbitrary bathymetry. The AEL inversion is applied to a 102-sensor, 1.2-km towed array to correct receiver positions in the seismic velocity analysis of a seabed gas hydrate survey.
The Measurement and Development of Professional Performance: An Introduction to the Topic and a Background to the Design and Origin of This Book (2009)

Developments in technology and software engineering are making many types of traditional jobs, such as bookkeeping, accounting, routine design, and document indexing, virtually obsolete (Rasmussen, 2000). The rapid improvements in technology and automated work methods challenge even the traditional idea of stable job competence, as well as the ability to predict the length and the nature of current or future professional careers. Today's work conditions require ongoing adaptations by employees and entrepreneurs to new demands and competitive opportunities through continuing education and training. Technological innovations, such as the World Wide Web, broadband communication, and highly portable communication and work devices, have reduced the constraints of geography on work. Today, many services can be provided with an equivalent level of quality irrespective of whether the provider is in the office next door or on a different continent. It is, indeed, becoming an age of global consumerism in which one can “work with anyone, anytime, anywhere.” Additionally, many specialized skills previously performed by human beings are now the purview of automated systems, and can often be conducted anywhere in the world at a fraction of the cost if carried out in Western Europe and North America. This technological revolution suggests that the competitive advantage of any country aspiring to economic prosperity is increasingly dependent on the capability of both its research and development groups and its skilled workforce, not only to create and develop new and improved products that are at the cutting edge, but also to quickly react and adapt to market forces.
Nonlinear and anisotropic behavior of high performance fibers (1993)

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 1993.
Improvement of biomass through lignin modification (2008)

Lignin, a major component of the cell wall of vascular plants, has long been recognized for its negative impact on forage quality, paper manufacturing, and, more recently, cellulosic biofuel production. Over the last two decades, genetic and biochemical analyses of brown midrib mutants of maize, sorghum and related grasses have advanced our understanding of the relationship between lignification and forage digestibility. This work has also inspired genetic engineering efforts aimed at generating crops with altered lignin, with the expectation that these strategies would enhance forage digestibility and/or pulping efficiency. The knowledge gained from these bioengineering efforts has greatly improved our understanding of the optimal lignin characteristics required for various applications of lignocellulosic materials while also contributing to our understanding of the lignin biosynthetic pathway. The recent upswing of interest in cellulosic biofuel production has become the new focus of lignin engineering. Populus trichocarpa and Brachypodium distachyon are emerging as model systems for energy crops. Lignin research on these systems, as well as on a variety of proposed energy crop species, is expected to shed new light on lignin biosynthesis and its regulation in energy crops, and lead to rational genetic engineering approaches to modify lignin for improved biofuel production.
Induction of long-term H-Y-specific tolerance in female mice given male lymphoid cells while transiently depleted of CD4+ or CD8+ T cells. (1993)

Rejection of H-Y-bearing primary skin grafts and generation of H-Y-specific cytolytic T cells by female mice requires the participation of both CD4+ and CD8+ T lymphocytes. Studies were conducted to investigate long-term tolerance of H-Y antigen induced in female mice by transiently depleting them of CD4+ and/or CD8+ T cells and, at the same time, giving them an injection of male lymphoid cells. We confirmed that after recovery of CD4+ to normal levels, female mice that had been transiently depleted of CD4+ cells and concurrently given an injection of male spleen cells were unable to generate H-Y-specific cytolytic T cells. Tolerance was also manifest by greatly extended survival (probably permanent in most cases) of male skin grafts. Further investigations revealed that female mice transiently depleted of CD8+ cells, and concurrently given an injection of male spleen cells, were similarly tolerant of H-Y antigen later when numbers of CD8+ T cells returned to normal. Moreover, small numbers of male cells were detectable in spleen and lymph nodes of tolerant females long after they had been given an injection of male cells and depleted of either CD4+ or CD8+ T cells, whereas no male cells were detected in (nontolerant) females given male cells and control antibodies. These findings show that tolerance of the relatively weak transplantation antigen, H-Y, can be achieved simply by giving male antigen-bearing spleen cells to the host while it is transiently depleted of a type of cell it needs in order to reject those cells, thus allowing the male cells to persist in the host. Furthermore, depletion of helper cells is not obligatory to achieve tolerance. It has been hypothesized that tolerance of H-Y antigen in females given male lymphoid cells while temporarily depleted of CD4+ lymphocytes results from unresponsiveness (anergy) induced in H-Y-specific CD8+ cells that are exposed to H-Y antigen in the absence of help from CD4+ cells. Interpretations of our findings are discussed in relation to this hypothesis.
Performance Improvement for Multicore Processors Using Variable Page Technologies (2011)

In order to improve system performance, many modern processors support super page technology, which is also called variable page. It improves TLB coverage greatly without increasing TLB size. But supporting super page brings great challenge to operating systems. In this paper, we implement two variable page technologies, including the static variable page and dynamic variable page, in Linux kernel on Godson-3 four-core processors. The static variable page technology is implemented on the basis of hugetlbfs pseudo file system. The dynamic one chooses proper page sizes according to the address spaces of applications adaptively. Experiment results show that static variable page technology improves the performance of scientific applications such as large matrix multiplication significantly. The number of TLB misses is reduced by 99% and the speed of large-scale matrix multiplication is improved by over 50%. The dynamic self-adapting variable page technology can bring an average performance improvement of 15% to SPECCPU 2000 benchmarks. Compared with system of single large page (64KB), the file system performance of system supporting dynamic variable page is significantly improved by about 25%.
Reversal of dyskinesias in an animal model of Parkinson's disease by continuous L-DOPA delivery using rAAV vectors (2005)

Dyskinesias are a major complication of long-term l-3,4-dihydroxyphenylalanine (L-DOPA) treatment in Parkinson's disease, and are believed to result from the intermittent and pulsatile supply of L-DOPA. Daily injections of L-DOPA can prime similar abnormal involuntary movements of the limb, orolingual and axial muscles in rats rendered parkinsonian by destruction of the nigrostriatal dopamine (DA) neurons. In this study we used 33 rats with severe nigrostriatal dopamine depletion and showed that in vivo gene transfer of the DA-synthetic enzymes tyrosine hydroxylase (TH) and GTP cyclohydrolase 1 (GCH1) using recombinant adeno-associated virus vectors can provide a constant source of DOPA production locally in the striatum, at a level that is effective in reducing L-DOPA-induced dyskinesias by >85%, and reverse lesion-induced motor impairments. Furthermore, the abnormal expression of DeltaFosB, prodynorphin and preproenkephalin mRNA within the striatal projection neurons normally seen in dyskinetic animals was completely reversed by TH-GCH1 gene transfer. These findings form a strong basis for replacing, or supplementing, conventional systemic L-DOPA therapy by continuous intrastriatal DOPA using in vivo gene transfer in the treatment of patients with advanced Parkinson's disease.