gebhart/patrepeval huggingface dataset:
Fast photorefractive response in B_12SiO_20 in the near infrared (2000)

The polarization self-modulation effect was applied for effective measurement of the characteristic response time of nominally pure Bi(12)SiO(20) (BSO) at wavelengths of 810 and 980 nm. Owing to oxygen deficiency in the crystal lattice, the BSO crystals showed unusual photorefractive sensitivity and remarkable operation speed in the near-infrared spectral region. A response time of 130 ms was measured at 810 nm, and a response time of 540 ms was measured at 980 nm, with incident intensities of 110 and 200mW/cm(2), respectively. To our knowledge, this is the first experimental evidence of a subsecond response in the infrared for a nonsemiconductor photorefractive material.
Effect of defined point mutations in the pneumolysin gene on the virulence of Streptococcus pneumoniae (1995)

The thiol-activated toxin pneumolysin is a known pneumococcal virulence factor, with both cytotoxic (hemolytic) and complement activation properties. Copies of the pneumolysin gene carrying defined point mutations affecting either or both of these properties were introduced into the chromosome of Streptococcus pneumoniae D39 by insertion-duplication mutagenesis. The virulences of these otherwise isogenic strains were then compared. There was no significant difference in either the median survival time or overall survival rate between mice challenged with D39 derivatives producing the wild-type toxin and those expressing a pneumolysin gene with an Asp-385-->Asn mutation, which abolishes the complement activation property. However, mice challenged with strains carrying either His-367-->Arg or Trp-433-->Phe plus Cys-428-->Gly mutations, which reduce hemolytic activity to approximately 0.02 and 0.0001% of the wild-type level, respectively, had significantly greater median survival times and overall survival rates than mice challenged with D39 derivatives expressing a wild-type pneumolysin gene. No additional reduction in virulence was observed when mice were challenged with a D39 derivative carrying Trp-433-->Phe, Cys-428-->Gly, and Asp-385-->Asn, rather than Trp-433-->Phe and Cys-428-->Gly, mutations in the pneumolysin gene. Thus, it appears that in the intraperitoneal challenge model, the contribution of pneumolysin to virulence is largely attributable to its hemolytic (cytotoxic) properties rather than to its capacity to activate complement. Interestingly, however, the amount of pneumolysin required for full virulence may be very small, as D39 derivatives carrying the Trp-433-->Phe mutation (which reduces hemolytic activity to 0.1% of the wild-type level) had intermediate virulence.
Current Status: Site-Specific Antibody Drug Conjugates (2016)

Antibody drug conjugates (ADCs), a promising class of cancer biopharmaceuticals, combine the specificity of therapeutic antibodies with the pharmacological potency of chemical, cytotoxic drugs. Ever since the first ADCs on the market, a plethora of novel ADC technologies has emerged, covering as diverse aspects as antibody engineering, chemical linker optimization and novel conjugation strategies, together aiming at constantly widening the therapeutic window for ADCs. This review primarily focuses on novel chemical and biotechnological strategies for the site-directed attachment of drugs that are currently validated for 2nd generation ADCs to promote conjugate homogeneity and overall stability.
Gene copy number alteration profile and its clinical correlation in B-cell acute lymphoblastic leukemia (2016)

The genes related to B-cell development are frequently altered in B-cell acute lymphoblastic leukemia (B-ALL). One hundred sixty-two newly diagnosed B-ALL cases, median age 8.5 years (2 months-67 years), were prospectively analyzed for copy number alterations (CNAs) in CDKN2A/B, IKZF1, PAX5, RB1, ETV6, BTG1, EBF1, and pseudoautosomal region genes (CRLF2, CSF2RA, IL3RA) using multiplex ligation-dependent probe amplification. The CNAs were detected in 114 (70.4%) cases; most commonly affected genes being CDKN2A/B-55 (34%), PAX5-51 (31.5%), and IKZF1-43 (26.5%). IKZF1 and RB1 deletions correlated with higher induction failure. Patients classified as good-risk, according to the integrated CNA profile and cytogenetic criteria, had lower induction failure [5 (8.6%) vs. 20 (25.3%); p = 0.012]. Those classified as good-risk, based on CNA profile irrespective of cytogenetics, also showed lower induction failure [6 (9.4%) vs. 19 (26%); p = 0.012]. The CNA profile identified patients with better induction outcome and has a potential role in better risk stratification of B-ALL.
Improving Integrated Circuit Performance Through the Application of Hardness-by-Design Methodology (2008)

Increased space system performance is enabled by access to high-performance, low-power radiation-hardened microelectronic components. While high performance can be achieved using commercial CMOS foundries, it is necessary to mitigate radiation effects. This paper describes approaches to fabricating radiation-hardened components at commercial CMOS foundries by the application of novel design techniques at the transistor level, the cell level, and at the system level. This approach is referred to as hardness-by-design. In addition, trends in the intrinsic radiation hardness of commercial CMOS processes will be discussed.
Bayesian Experimental Design: A Review (1995)

This paper reviews the literature on Bayesian experimental design. A unified view of this topic is presented, based on a decision-theoretic approach. This framework casts criteria from the Bayesian literature of design as part of a single coherent approach. The decision-theoretic structure incorporates both linear and nonlinear design problems and it suggests possible new directions to the experimental design problem, motivated by the use of new utility functions. We show that, in some special cases of linear design problems, Bayesian solutions change in a sensible way when the prior distribution and the utility function are modified to allow for the specific structure of the experiment. The decision-theoretic approach also gives a mathematical justification for selecting the appropriate optimality criterion.
Ribonuclease activity and substrate preference of human eosinophil cationic protein (ECP) (1991)

The eosinophil cationic protein (ECP), a potent helminthotoxin with considerable neurotoxic activity, was recently shown to also have ribonucleolytic activity. In this work the substrate preference of ECP ribonuclease action was studied in detail. With single-stranded RNA or synthetic polyribonucleotide substrates ECP showed significant but low activity, 70- to 200-fold less than that of bovine RNase A. ECP hydrolyzed RNA more rapidly than it did any synthetic polynucleotide. Poly(U) was degraded more rapidly than poly(C), and poly(A) and double-stranded substrates were extremely resistant. Defined low molecular weight substrates in the form of the 16 dinucleoside phosphates (NpN') and uridine and cytidine 2',3'-cyclic phosphates were tested, and none showed hydrolysis by ECP at a significant rate. The results link ECP ribonucleolytic activity to the 'non-secretory' liver-type enzymes rather than to the 'secretory' pancreatic-type RNases.
The World Health Organization's global strategy for prevention and assessment of HIV drug resistance (2008)

Antiretroviral treatment (ART) for HIV is being scaled up rapidly in resource-limited countries. Treatment options are simplified and standardized, generally with one potent first-line regimen and one potent alternate first-line regimen recommended. Widespread HIV drug resistance (HIVDR) was initially feared, but reports from resource-limited countries suggest that initial ART programmes are as effective as in resource-rich countries, which should limit HIV drug resistance if programme effectiveness continues during scale-up. ART interruptions must be minimized to maintain viral suppression on the first-line regimen for as long as possible. Lack of availability of appropriate second-line drugs is a concern, as is the additional accumulation of resistance mutations in the absence of viral load testing to determine failure. The World Health Organization (WHO) recommends a minimum-resource strategy for prevention and assessment of HIVDR in resource-limited countries. The WHO's Global Network HIVResNet provides standardized tools, training, technical assistance, laboratory quality assurance, analysis of results and recommendations for guidelines and public health action. National strategies focus on assessments to guide immediate public health action to improve ART programme effectiveness in minimizing HIVDR and to guide regimen selection. Globally, WHO HIVResNet collects and analyses data to support evidence-based international policies and guidelines. Financial support is provided by major international organizations and technical support from HIVDR experts worldwide. As of December 2007, 25 countries were planning or implementing the strategy; seven countries report results in this supplement.
Effect of ultrasound on transdermal drug delivery to rats and guinea pigs. (1989)

The effect of therapeutic range ultrasound (1 MHz) on skin permeation of D-mannitol, a highly polar sugar alcohol, inulin, a high molecular weight polysaccharide and physostigmine, a lipophilic anticholinesterase drug was studied in rats and guinea pigs. D-Mannitol and inulin are totally and rapidly excreted, once they have penetrated through the skin into the blood stream, permitting direct in vivo monitoring. For evaluating skin penetration of physostigmine the decrease of whole blood cholinesterase was measured. Ultrasound nearly completely eliminated the lag time usually associated with transdermal delivery of drugs. 3-5 min of ultrasound irradiation (1.5 W/cm2 continuous wave or 3 W/cm2 pulsed wave) increased the transdermal permeation of inulin and mannitol in rats by 5-20-fold within 1-2 h following ultrasound application. Ultrasound treatment also significantly increased (P less than 0.05) the inhibition of cholinesterase during the first hour after application in both physostigmine treated rats and guinea pigs: while in control guinea pigs no significant inhibition of cholinesterase could be detected during the first 2 h after application of physostigmine, the ultrasound treated group showed a 15 +/- 5% (mean +/- SEM) decrease in blood cholinesterase 1 h after ultrasound application. For physostigmine-treated rats the level of cholinesterase inhibition 1 h after ultrasound application was 53 +/- 5% in the ultrasound-treated group and 35 +/- 5% in the controls.
Displacement mapping using flow fields (1994)

Existing displacement mapping techniques operate only in directions normal to the surface, a restriction which limits the richness of the set of representable objects. This work removes that restriction by allowing displacements to be defined along curved trajectories of flow fields. The main contribution of this generalized technique, which will be referred to as flow mapping, is an alternative model of offset surfaces that extends the class of shapes that can be modelled using displacement maps. The paper also discusses methods for synthesizing homogeneous displacement textures. Finally, it introduces the concept of a texture atlas for efficient sampling and reconstruction of distorted textures.
Microarray analysis of gene expression in lupus. (2003)

Recent advances in the study of global patterns of gene expression with the use of microarray technology, coupled with data analysis using sophisticated statistical algorithms, have provided new insights into pathogenic mechanisms of disease. Complementary and reproducible data from multiple laboratories have documented the feasibility of analysis of heterogeneous populations of peripheral blood mononuclear cells from patients with rheumatic diseases through use of this powerful technology. Although some patterns of gene expression, including increased expression of immune system cell surface activation molecules, confirm previous data obtained with other techniques, some novel genes that are differentially expressed have been identified. Most interesting is the dominant pattern of interferon-induced gene expression detected among blood mononuclear cells from patients with systemic lupus erythematosus and juvenile dermatomyositis. These data are consistent with longstanding observations indicating increased circulating interferon-alpha in the blood of patients with active lupus, but draw attention to the dominance of the interferon pathway in the hierarchy of gene expression pathways implicated in systemic autoimmunity.
Spatio-temporal analysis using tensors (2003)

Summary form only given. A fundamental issue in the problem of finding an efficient algorithm for estimation of 3D orientation is how 3D orientation should be represented. A representation is regarded as suitable if it meets the three basic requirements of uniqueness, uniformity, and polar separability. A tensor representation suitable in the above sense has been obtained. The uniqueness requirement implies a mapping that maps all pairs of 3D vectors x and -x onto the same tensor T. Uniformity implies that the mapping implicitly carries a definition of distance between 3D planes (and lines) that is rotation invariant and monotone with the angle between the planes. Polar separability means that the norm of the representing tensor T is rotation invariant. One way to describe the mapping is that it maps a 3D sphere into 6D in such a way that the surface is uniformly stretched and all pairs of antipodal points map onto the same tensor. It has been demonstrated that the above mapping can be implemented by sampling the 3D space using a specific class of symmetrically distributed quadrature filters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lymphoma models for B cell activation and tolerance IV. Growth inhibition by anti‐Ig of CH31 and CH33 B lymphoma cells (1986)

CH31 and CH33 are B cell lymphomas whose growth in vitro is inhibited by anti-Ig reagents, including both polyclonal and monoclonal anti-mu antibodies, and an anti-idiotype antiserum. Antibodies against class I or class II major histocompatibility complex antigens do not affect the growth of these cells. Inhibition is dependent on surface Ig cross-linking and does not require ligand binding to Fc receptors. Interestingly, the inhibition of growth by anti-mu is reversed in CH31 (but not CH33) by E. coli lipopolysaccharide. These lymphomas should provide excellent models to study the mechanisms of growth inhibition mediated by surface Ig cross-linking and the pathways of its reversal.
Longitudinal in Vivo Positron Emission Tomography Imaging of Infected and Activated Brain Macrophages in a Macaque Model of Human Immunodeficiency Virus Encephalitis Correlates with Central and Peripheral Markers of Encephalitis and Areas of Synaptic Degeneration (2008)

Human immunodeficiency virus encephalitis is characterized by infiltration of the brain with infected and activated macrophages; however, it is not known why disease occurs after variable lengths of infection in 25% of immunosuppressed acquired immune deficiency syndrome patients. We determined in vivo correlates (in peripheral blood and the central nervous system) for the development and progression of lentiviral encephalitis by longitudinally following infected and activated macrophages in the brain using positron emission tomography (PET). Using human postmortem brain tissues from both lentivirus-infected encephalitic patients and cell culture systems, we showed that the PET ligand [(3)H](R)-PK11195 bound specifically to virus-infected and activated macrophages. We longitudinally imaged infected and activated brain macrophages in a cohort of macaques infected with simian immunodeficiency virus using [(11)C](R)-PK11195. [(11)C](R)-PK11195 retention in vivo in the brain correlated with viral burden in the brain and cerebrospinal fluid, and with regions of both presynaptic and postsynaptic damage. Finally, longitudinal changes in [(11)C](R)-PK11195 retention in the brain in vivo correlated with changes in circulating monocytes as well as in both natural killer and memory CD4(+) T cells in the periphery. Our results suggest that development and progression of simian immunodeficiency virus encephalitis in vivo correlates with changes in specific cell subtypes in the periphery. A combination of PET imaging and the assessment of these peripheral immune parameters may facilitate longitudinal assessment of lentiviral encephalitis in living patients as well as evaluation of therapeutic efficacies.
Parallelization of a local similarity algorithm (1992)

The local similarity problem is to determine the similar regions within two given sequences. We recently developed a dynamic programming algorithm for the local similarity problem that requires only space proportional to the sum of the two sequence lengths, whereas earlier methods use space proportional to the product of the lengths. In this paper, we describe how to parallelize the new algorithm and present results of experimental studies on an Intel hypercube. The parallel method provides rapid, high-resolution alignments for users of our software toolkit for pairwise sequence comparison, as illustrated here by a comparison of the chloroplast genomes of tobacco and liverwort.
Further studies on the homogeneous hydrogenation of olefins using tris(triphenylphosphine)halogenorhodium(I) catalysts (1967)

Studies on the homogeneous hydrogenation of olefinic hydrocarbons and other unsaturated substrates using tris(triphenylphosphine)halogenorhodium(I), RhX(PPh3)3(X = Cl or Br), as catalyst in benzene solution have been extended. The activation enthalpies and entropies for a number of olefins have been determined and, for other substrates, the relative rates of hydrogenation under standard conditions have been compared. The data can be broadly explained in terms of steric factors but electronic effects are clearly also important. Quantitative studies have been made of the kinetic isotope effect and the influence of the halide and of solvents.
DNA vaccines for prophylactic or therapeutic immunization against hepatitis B virus. (1999)

DNA vaccines, with which the antigen is synthesized in vivo after direct introduction of its encoding sequences, offer a unique method of immunization that may overcome many of the deficits of traditional antigen-based vaccines. By virtue of the sustained in vivo antigen synthesis and the comprised stimulatory CpG motifs, plasmid DNA vaccines appear to induce strong and long-lasting humoral (anti-bodies) and cell-mediated (T-help, other cytokine functions and cytotoxic T-cells) immune responses. In animal models, DNA vaccines against hepatitis B virus (HBV) give humoral and cell-mediated immunity superior to that of the current traditional antigen-based vaccines, indicating the possibility of a more effective prophylactic vaccine against HBV. Furthermore, DNA vaccines can overcome tolerance to and expression of HBV proteins in a transgenic mouse model of the HBV chronic carrier, opening up the possibility of an effective therapeutic DNA vaccine to treat chronic carriers of HBV.
Standards, Options and Recommendations for the use of appetite stimulants in oncology (2000) (2003)

Anorexia and cachexia are serious complications frequently found in patients with cancer (Bozetti, 1995; Donnelly and Walsh, 1995). They are present in about 10% of patients at the time of diagnosis (Bozetti et al, 1989). Multiple factors are involved in their aetiology (Puccio and Nathanson, 1997). The resultant malnutrition is associated with a poorer response to anticancer treatment and an impaired quality of life (Holmes and Dickerson, 1987; Bozetti, 1995; De Conno et al, 1998). Many clinical trials have been undertaken to evaluate the efficacy of drugs thought to be appetite stimulants.
Improving Kd-tree quality at a reasonable construction cost (2008)

We consider construction of high-quality kd-tree and investigate the effect of techniques based on perfect splits. The main idea of perfect splits is clipping of objects straddling the splitting planes during the construction. This effectively results in reducing the number of references in leaves while also generating new potential split positions. We derive an efficient algorithm for triangle clipping/assignment and show how to avoid problems for parallel construction using clipping. Investigating the influence of using clipping results at different kd-tree construction stages, we finally come up with on-the-fly pruning algorithm that improves rendering performance by up to 25% decreasing construction time as well.
Novel Dry Polymer Foam Electrodes for Long-Term EEG Measurement (2011)

A novel dry foam-based electrode for long-term EEG measurement was proposed in this study. In general, the conventional wet electrodes are most frequently used for EEG measurement. However, they require skin preparation and conduction gels to reduce the skin-electrode contact impedance. The aforementioned procedures when wet electrodes were used usually make trouble to users easily. In order to overcome the aforesaid issues, a novel dry foam electrode, fabricated by electrically conductive polymer foam covered by a conductive fabric, was proposed. By using conductive fabric, which provides partly polarizable electric characteristic, our dry foam electrode exhibits both polarization and conductivity, and can be used to measure biopotentials without skin preparation and conduction gel. In addition, the foam substrate of our dry electrode allows a high geometric conformity between the electrode and irregular scalp surface to maintain low skin-electrode interface impedance, even under motion. The experimental results presented that the dry foam electrode performs better for long-term EEG measurement, and is practicable for daily life applications.
Effects of carbon nanotubes on electro-optical characteristics of liquid crystal cell driven by in-plane field (2007)

Homogeneously aligned nematic liquid crystal (LC) cells doped with carbon nanotubes (CNTs) driven by an in-plane field were fabricated and their electro-optic characteristics were investigated. The effective cell retardation values showed no difference between doped and undoped LC cells in the absence of electric field. However, in the presence of electric field, it was smaller in the CNT-doped cell than in the undoped cell, resulting in the decrease of transmittance. Furthermore, the CNT-doped cell exhibited a slight increase in the driving voltage due to the increase of the twist elastic constant (K22) and the decrease in the decay response time due to the decrease in the rotational viscosity (γ) and γ∕K22 compared to the undoped cell.