gebhart/patrepeval huggingface dataset:
Immunological evaluation of personalized peptide vaccination monotherapy in patients with castration‐resistant prostate cancer (2009)

We previously reported that personalized peptide vaccine (PPV) therapy in combination with leutenizing hormone-releasing hormone (LH-RH) analog and estramustine phosphate in certain cases is safe and capable of inducing both immune responses and clinical responses for metastatic castration-resistant prostate cancer (CRPC) patients. In the present study, PPV monotherapy was given to CRPC patients. Twenty-three patients with metastatic CRPC were treated with PPV without any additional treatment modalities, including LH-RH analogs. Samples were analyzed for peptide-specific cytotoxic T-lymphocyte (CTL) precursor analysis and peptide-reactive IgG. Toxicity and immunological and clinical responses were assessed on a three-monthly basis. Seventeen patients were available for immunological and clinical evaluation. The vaccines were well tolerated, with grade 3 erythema at injection sites in only one patient. Augmentation of CTL or IgG responses to at least one of the peptides was observed in six of 17 (35%) and 15 of 17 (88%) patients tested, respectively. Among 57 peptides used, 9 and 36 peptides induced CTL and IgG responses, respectively. Delayed-type hypersensitivity reaction was observed in eight of 17 patients. More than 30% prostate-specific antigen (PSA) decline was observed in four of 17 patients. Of these, one patient achieved a complete PSA response and another patient showed a partial PSA response with profound shrinking of lymph node metastases and prostate. The overall median survival time was 24 months (range, 5-37 months). These results suggest that PPV monotherapy appears to be safe and capable of inducing peptide-specific immune responses and clinical responses in CRPC patients. This trial was registered with University Hospital Medical Information Network (UMIN) number R000003339.
Digital imaging of cephalometric radiographs, Part 2: Image quality. (1996)

The aim of this study was to compare the diagnostic quality of conventional cephalometric radiographs with that of digital image counterparts. The random error associated with angular and linear measurements recorded on the digital images was greater than on the conventional radiographs. In addition, there was a systematic error producing statistically significant differences in the majority of angular and linear measurements between the digital images and the conventional radiographs. The errors that occurred with some measurements were of sufficient magnitude to be of clinical significance, particularly in a cephalometric situation where a high degree of accuracy is required. It is therefore suggested that, for digital imaging of cephalometric radiographs, a pixel matrix larger than 512 x 512 with more than 64 gray levels is required to maintain the diagnostic quality of the original radiograph.
Crystal Structure of the Antioxidant Enzyme Glutathione Reductase Inactivated by Peroxynitrite (2002)

As part of our studies on the nitric oxide-related pathology of cerebral malaria, we show that the antioxidative enzyme glutathione reductase (GR) is inactivated by peroxynitrite, with GR from the malarial parasite Plasmodium falciparum being more sensitive than human GR. The crystal structure of modified human GR at 1.9-A resolution provides the first picture of protein inactivation by peroxynitrite and reveals that this is due to the exclusive nitration of 2 Tyr residues (residues 106 and 114) at the glutathione disulfide-binding site. The selective nitration explains the impairment of binding the peptide substrate and thus the nearly 1000-fold decrease in catalytic efficiency (k(cat)/K(m)) of glutathione reductase observed at physiologic pH. By oxidizing the catalytic dithiol to a disulfide, peroxynitrite itself can act as a substrate of unmodified and bisnitrated P. falciparum glutathione reductase.
Lazy abstraction (2002)

One approach to model checking software is based on the abstract-check-refine paradigm: build an abstract model, then check the desired property, and if the check fails, refine the model and start over. We introduce the concept of lazy abstraction to integrate and optimize the three phases of the abstract-check-refine loop. Lazy abstraction continuously builds and refines a single abstract model on demand, driven by the model checker, so that different parts of the model may exhibit different degrees of precision, namely just enough to verify the desired property. We present an algorithm for model checking safety properties using lazy abstraction and describe an implementation of the algorithm applied to C programs. We also provide sufficient conditions for the termination of the method.
Human Pharmacokinetics and Safety Evaluation of SonoVue™, a New Contrast Agent for Ultrasound Imaging (2000)

SonoVue was shown to be rapidly removed from the blood. The route of SF6 elimination was by means of the lungs in the expired air. SonoVue appeared to be safe and well tolerated in healthy subjects.
Colour texture fusion of multiple range images (2004)

Texture mapping of manifolds that were reconstructed from different range views requires the fusion of the texture maps acquired from different views. Illumination conditions and camera technology prevents colour continuity in the fusion process leading to observable discontinuities in the colour (and also lightness). We present a simple method for the correction of this discontinuity. First a global correction is applied that largely removes the systematic differences between the individual texture maps. Local corrections refine the small observable variations in colour that may still exist near the fusion boundaries.
Dextran hydrogel scaffolds enhance angiogenic responses and promote complete skin regeneration during burn wound healing (2011)

Neovascularization is a critical determinant of wound-healing outcomes for deep burn injuries. We hypothesize that dextran-based hydrogels can serve as instructive scaffolds to promote neovascularization and skin regeneration in third-degree burn wounds. Dextran hydrogels are soft and pliable, offering opportunities to improve the management of burn wound treatment. We first developed a procedure to treat burn wounds on mice with dextran hydrogels. In this procedure, we followed clinical practice of wound excision to remove full-thickness burned skin, and then covered the wound with the dextran hydrogel and a dressing layer. Our procedure allows the hydrogel to remain intact and securely in place during the entire healing period, thus offering opportunities to simplify the management of burn wound treatment. A 3-week comparative study indicated that dextran hydrogel promoted dermal regeneration with complete skin appendages. The hydrogel scaffold facilitated early inflammatory cell infiltration that led to its rapid degradation, promoting the infiltration of angiogenic cells into the healing wounds. Endothelial cells homed into the hydrogel scaffolds to enable neovascularization by day 7, resulting in an increased blood flow significantly greater than treated and untreated controls. By day 21, burn wounds treated with hydrogel developed a mature epithelial structure with hair follicles and sebaceous glands. After 5 weeks of treatment, the hydrogel scaffolds promoted new hair growth and epidermal morphology and thickness similar to normal mouse skin. Collectively, our evidence shows that customized dextran-based hydrogel alone, with no additional growth factors, cytokines, or cells, promoted remarkable neovascularization and skin regeneration and may lead to novel treatments for dermal wounds.
Deep Extreme Cut: From Extreme Points to Object Segmentation (2018)

This paper explores the use of extreme points in an object (left-most, right-most, top, bottom pixels) as input to obtain precise object segmentation for images and videos. We do so by adding an extra channel to the image in the input of a convolutional neural network (CNN), which contains a Gaussian centered in each of the extreme points. The CNN learns to transform this information into a segmentation of an object that matches those extreme points. We demonstrate the usefulness of this approach for guided segmentation (grabcut-style), interactive segmentation, video object segmentation, and dense segmentation annotation. We show that we obtain the most precise results to date, also with less user input, in an extensive and varied selection of benchmarks and datasets. All our models and code are publicly available on http://www.vision.ee.ethz.ch/~cvlsegmentation/dextr/.
Promoting educational encouragement for success (2012)

Present article attempted to highlight the importance of Educational Encouragement in Adolescent’s Academic Achievement. It is believed that if parents and teachers prepare adolescents for success by boosting up and focusing on efforts and strengths rather than outcome and weaknesses. It is suggested that educational encouragement can be one of the most important motivator to enhance academic achievement of adolescents. Encouragers always focus on endeavor rather than perfect results. The present study has implications for teachers and counselors and the framework used for this study suggests the intervention focused on the adolescents’ achievement.
Bandwidth specification for adaptive optics systems* (1977)

A simplified expression for the bandwidth of an adaptive optics system is found to depend on a weighted path integral of the turbulence strength, where the weighting is transverse wind velocity to the 5/3 power. The wave-front corrector is conservatively assumed to match the phase perfectly, at least spatially, if not temporally. For the case of astronomical imaging from a mountaintop observatory, the necessary bandwidth is found to be less than 200 Hz.
Low-Voltage Organic Field-Effect Transistors and Inverters Enabled by Ultrathin Cross-Linked Polymers as Gate Dielectrics (2005)

The quest for high-performance organic thin-film transistor (OTFT) gate dielectrics is of intense current interest. Beyond having excellent insulating properties, such materials must meet other stringent requirements for optimum OTFT function: efficient low-temperature solution fabrication, mechanical flexibility, and compatibility with diverse gate materials and organic semiconductors. The OTFTs should function at low biases to minimize power consumption, hence the dielectric must exhibit large gate capacitance. We report the realization of new spin-coatable, ultrathin (<20 nm) cross-linked polymer blends exhibiting excellent insulating properties (leakage current densities approximately 10(-)(8) Acm(-)(2)), large capacitances (up to approximately 300 nF cm(-)(2)), and enabling low-voltage OTFT functions. These dielectrics exhibit good uniformity over areas approximately 150 cm(2), are insoluble in common solvents, can be patterned using standard microelectronic etching methodologies, and adhere to/are compatible with n(+)-Si, ITO, and Al gates, and with a wide range of p- and n-type semiconductors. Using these dielectrics, complementary invertors have been fabricated which function at 2 V.
Transfection and physical properties of various saccharide, poly(ethylene glycol), and antibody‐derivatized polyethylenimines (PEI) (1999)

Background The ideal non-viral vector should be cell-type directed and form complexes with DNA that are physically stable, small and electrically neutral. Methods We have synthesized several PEI derivatives that coat the PEI/DNA complexes with water-soluble residues able to stabilize the particles, to mask their surface charge and eventually to direct them to a particular tissue. The morphologies and sizes of the complexes were observed by TEM and DLS techniques, and their apparent surface charge was quantitated by zeta potential measurements; in vitro transfection efficacies were determined in serum-containing cell culture medium. Results When compared to DNA complexes formed with the unmodified PEI, extensive grafting with maltose (15–25% of the amine functions) led to beneficial electrostatic shielding of the particle surface, but was unable to prevent aggregation in physiological salt concentration. More extended hydrophilic residues were therefore explored as a mean of physical repulsion between the particles. Low grafting (2.7%) with a linear dextran nonasaccharide led to small and stable toroids having no apparent surface charge, yet still reaching effective transfection levels. Electron microscopy of complexes with a higher extent of grafting showed worm-like structures unsuited for cell entry. Conjugation of PEI with as little as 0.5% of a terminally galactose-derivatized polyethyleneglycol (PEG)-3400 also gave neutral complexes of another worm-like structure that failed to transfect receptor-expressing hepatocytes. Conclusion These results show that conjugation of large and flexible hydrophilic residues to PEI, while protecting the complexes from parasitic interactions also interfere with DNA condensation. PEG conjugation after PEI/DNA complex formation may avoid this problem, provided intracomplex reorganization is slow. Finally an anti-GD2 antibody (mAb) grafted with PEI was synthesized. The corresponding protein-coated DNA complexes were compact and small (50–60 nm), yet did not enhance transfection of GD2 ganglioside-expressing cells. Copyright © 1999 John Wiley & Sons, Ltd.
Hate Crime Laws and Sexual Orientation (1999)

This article provides definitions for hate crimes, a summary of national data on hate crime incidents, and descriptions of federal and state hate crime laws. The author presents various arguments in support of and against hate crime laws, and the inclusion of sexual orientation in such laws. The author contends that it is illogical and a violation of the Fourteenth Amendment to exclude sexual orientationf rom hate crime laws. The perpetratorso f hate crime incidents, regardess of the target group, have similar motives and perpetrate similar types of assaults; the victims experience similar physical and psychological harm. Excluding a class of persons who are targets of hate crimes denies them equal protection under the law because the Equal Protection Clause of the Fourteenth Amendment establishes a fundamental right to equal benefit of laws protecting personal security.
Conserved functional organization of the human immunodeficiency virus type 1 and visna virus Rev proteins (1991)

Visna virus encodes a posttranscriptional regulatory protein that is functionally analogous to the Rev trans activator of human immunodeficiency virus type 1. Here, we demonstrate that the known functional organization of the human immunodeficiency virus type 1 Rev trans activator is shared by the distantly related visna virus Rev protein. In particular, both Rev proteins contain an N-terminal domain marked by a highly basic core motif that determines RNA sequence specificity, as well as a second C-terminal domain containing an essential leucine-rich motif that functions as an activation domain. Chimeric proteins consisting of the binding domain of one Rev protein fused to the activation domain of the other were fully functional in the viral sequence context cognate for the binding domain. We also describe derivatives of visna virus Rev bearing a defective activation domain that displayed a trans-dominant negative phenotype in transfected cells. These visna virus Rev mutants may prove useful in the derivation of transgenic animals resistant to this agriculturally important retroviral pathogen.
Microbial ecology and adaptation in cystic fibrosis airways (2011)

Chronic infections in the respiratory tracts of cystic fibrosis (CF) patients are important to investigate, both from medical and from fundamental ecological points of view. Cystic fibrosis respiratory tracts can be described as natural environments harbouring persisting microbial communities with Pseudomonas aeruginosa as a dominant pathogen. Various factors contribute to the complexity of this ecosystem, including community composition, dynamics and interactions, as well as heterogeneous distribution and fluctuation of components of the immune system, antibiotics and nutrients. All these elements constitute the selective forces that drive the evolution of the microbes after they migrate from the outer environment to human airways. Pseudomonas aeruginosa adapts to the new environment through genetic changes and exhibits a special lifestyle in chronic CF airways. Understanding the persistent colonization of microbial pathogens in CF patients in the context of ecology and evolution will expand our knowledge of the pathogenesis of chronic infections and improve therapeutic strategies.
Disruption of the Active Site Solvent Network in Carbonic Anhydrase II Decreases the Efficiency of Proton Transfer (1996)

The importance of maintaining the active site water network for efficient proton transfer was investigated by substituting amino acids of varying size at position 65 in carbonic anhydrase II (including four amino acids found in other CA isozymes, F, L, S, and T, and two amino acids that do not occur naturally at position 65, G and H) and measuring the rate constants for the proton transfer reactions in the variant carbonic anhydrases. Intramolecular proton transfer between zinc-bound water and H64 is significantly inhibited by the introduction of bulky residues at position 65; kcat for CO2 hydration decreases up to 26-fold, comparable to the observed decrease in intramolecular proton transfer caused by removal of H64 [Tu, C., Silverman, D. N., Forsman, C., Jonsson, B.-H., & Lindskog, S. (1989) Biochemistry 28, 7913-7918]. Intermolecular proton transfer between protonated H64 and external buffer is also inhibited, although to a lesser degree. Furthermore, an alternative proton transfer pathway, consisting of an active site solvent-mediated proton transfer from zinc-water to imidazole buffer, is inhibited in the A65F, A65L, and A65H CAII variants. Therefore, the active solvent bridge between zinc-bound water and H64 is disrupted by substitutions at position 65. The inhibition of proton transfer reactions correlates with the disruption of the crystallographically observed solvent network in the CA active site and rotation of the proton acceptor, H64 [Scolnick, L. R., & Christianson, D. W. (1996) Biochemistry 35, 16429-16434], suggesting that this solvent network, including water molecules 292, 264, and 369, or a structurally related network, forms the proton transfer pathway in CAII for both intramolecular proton transfer and stimulation of proton transfer in imidazole buffers.
Simple Purification and Properties of Bovine Pancreatic Deoxyribonuclease I (1980)

A simple purification method for pancreatic deoxyribonuclease I (DNase I) [EC 3.1.4.3] was developed by utilizing the technique of isoelectric focusing. The active protein was resolved in to at least four forms with different isoelectric points; the major components a, b, and c had isoelectric points at pH 5.2, 4.9, and 4.8, respectively, and that of the minor component d was at 4.7. The four components (a, b, c, and d) exhibited peaks similar to those observed by Salnikow et al. after phosphocellulose chromatography (A, B, C, and D). The four components were all free from RNase and protease activities and were very stable at 0-2 degrees C for at least four weeks. Further, each of the four peaks exhibited a single protein band after polyacrylamide electrophoresis. DNase I-a antibody was prepared; it was very specific for DNase I and precipitated with the other components (b, c, and d). The mode of endonucleolytic action of pancreatic DNase I-a purified from Worthington DP grade DNase I was investigated. The sedimentation patterns in neutral sucrose gradients of digest of circular duplex DNA in an early stage of hydrolysis suggested that DNase I produces single strand scissions in the initial attack in the presence of divalent metal ions.
Toxicity of Insecticides to <I>Halyomorpha halys</I> (Hemiptera: Pentatomidae) Using Glass-Vial Bioassays (2008)

A scintillation glass-vial bioassay was used to test technical grade insecticides against the non-native stink bug Halyomorpha halys (Stål). Halyomorpha halys (Stål) (Hemiptera: Pentatomidae) is emerging as an important pest in the Mid-Atlantic States, especially in tree fruits and as a homeowner nuisance during the winter. Pyrethroid insecticides, especially bifenthrin, caused mortality against H. halys at low doses, with LC50 values of 0.03-0.49 (microg [AI]/cm2) (mg body mass(-1)). Three nicotinoids were tested against adults with LC50 values ranging between 0.05 and 2.64 (microg [AI]/cm2) (mg body mass(-1)). Phosmet had LC50 values that were up to 3.6-fold higher than other classes of insecticides tested. Fifth instars of H. halys were evaluated against selected chemicals, and they were generally susceptible at lower rates than the adults. Due to significant differences in weight, males and females were individually weighed, tested, and analyzed separately. Sex-related differences in susceptibility were found in the responses to thiomethoxam with males being less susceptible despite having a smaller body mass.
Thermogravimetric and differential thermal analysis of cellulose, hemicellulose, and lignin (1970)

Abstract The thermal degradation of samples of cellulose, hemicellulose, and lignin have been investigated using the techniques of thermogravimetric analysis (TGA) and differential thermal analysis (DTA) between room temperature and 600°C. The results calculated from static and dynamic TGA indicated that the activation energy E for thermal degradation for different cellulosic, hemicellulose, and lignin samples is in the range 36–60, 15–26, and 13–19 kcal/mole, respectively. DTA of all the wood components studied showed an endothermic tendency around 100°C in an atmosphere of flowing nitrogen and stationary air. However, in the presence of flowing oxygen this endothermic effect was absent. In the active pyrolysis temperature range in flowing nitrogen and stationary air atmospheres, thermal degradation of Avicel cellulose occurred via a sharp endothermic and a sharp exothermic process, the endothermic nadir and exothermic peak being at 320° and 360°C, respectively. In the presence of oxygen, combustion of Avicel cellulose occurred via two sharp exothermic processes. DTA studies of different cellulose samples in the presence of air showed that the shape of the curve depends on the sources from which the samples were prepared as well as on the presence of noncellulosic impurities. Potassium xylan recorded a sharp exothermic peak at 290°C in a nitrogen atmosphere, and in a stationary air atmosphere it yielded an additional peak at 410°C, while in the presence of oxygen the curve showed two sharp exothermic peaks. DTA traces of periodate lignin in flowing nitrogen and air were the same and showed two exothermic peaks at 320° and 410°C, while in the presence of oxygen there were two exothermic peaks in the temperature range 200°–500°C.
A microfluidic device for practical label-free CD4+ T cell counting of HIV-infected subjects (2006)

Practical HIV diagnostics are urgently needed in resource-limited settings. While HIV infection can be diagnosed using simple, rapid, lateral flow immunoassays, HIV disease staging and treatment monitoring require accurate counting of a particular white blood cell subset, the CD4(+) T lymphocyte. To address the limitations of current expensive, technically demanding and/or time-consuming approaches, we have developed a simple CD4 counting microfluidic device. This device uses cell affinity chromatography operated under differential shear flow to specifically isolate CD4(+) T lymphocytes with high efficiency directly from 10 microliters of unprocessed, unlabeled whole blood. CD4 counts are obtained under an optical microscope in a rapid, simple and label-free fashion. CD4 counts determined in our device matched measurements by conventional flow cytometry among HIV-positive subjects over a wide range of absolute CD4 counts (R(2) = 0.93). This CD4 counting microdevice can be used for simple, rapid and affordable CD4 counting in point-of-care and resource-limited settings.