gebhart/patrepeval huggingface dataset:
Antibody‐dependent cell cytotoxicity: immunotherapy strategies enhancing effector NK cells (2017)

Antibody-dependent cellular cytotoxicity (ADCC) is a set of mechanisms that target cells coated with IgG antibodies of the proper subclasses (IgG1 in the human) to be the prey of cell-to-cell cytolysis executed by immune cells expressing FcRIIIA (CD16A). These effectors include not only natural killer (NK) cells but also other CD16<sup>+</sup> subsets such as monocyte/macrophages, NKT cells or γδ T cells. In cancer therapy, ADCC is exploited by antibodies that selectively recognize proteins on the surface of malignant cells. An approach to enhance antitumor activity is to act on effector cells so they are increased in their numbers or enhanced in their individual (on a cell per cell basis) ADCC performance. This enhancement can be therapeutically attained by cytokines (that is, interleukin (IL)-15, IL-21, IL-18, IL-2); immunostimulatory monoclonal antibodies (that is, anti-CD137, anti-CD96, anti-TIGIT, anti-KIR, anti-PD-1); TLR agonists or by adoptive infusions of ex vivo expanded NK cells which can be genetically engineered to become more efficient effectors. In conjunction with approaches optimizing IgG1 Fc affinity to CD16, acting on effector cells offers hope to achieve synergistic immunotherapy strategies.
Carotenoids as Singlet Oxygen Quenchers in Marine Organisms (1996)

To understand the roles of carotenoids as singlet oxygen quenchers in marine organisms, quenching activities of eight major carotenoids, astaxanthin, canthaxanthin, β-carotene, zeaxanthin, lutein, tunaxanthin, fucoxanthin and halocynthiaxanthin were examined according to the method using a thermodissociable endoperoxide of 1, 4-dimethylnaphthalene as a singlet oxygen generator. The second-order rate constant for the singlet oxygen quenching activity by each carotenoid was determined, suggesting that an increasing number of conjugated double bonds in carotenoid was proportional to greater quenching activity. The quenching activity of each carotenoid was found to be approximately 40 to 600 times greater than that of α-tocopherol. The potency of these carotenoids suggests that they may play a role in protecting marine organisms from active oxygen species.
Production of the constant domain of murine T‐cell receptor β‐chain in Escherichia coli (1987)

T-cell antigen receptor is a heterodimer of disulfide-linked alpha- and beta-chains. Although the essential features of T-cell receptor seem to be rather similar to those of immunoglobulin, the amount of T-cell receptor expressed on the surface of a T-cell is not large enough to be analyzed physcio-chemically. In this study, the DNA fragment encoding 120 amino acids from the 116th to the 235th of the murine beta-chain which corresponds to the presumed constant domain was inserted into an expression vector in E. coli. A large amount of this 18 kDa protein was observed to be synthesized in E. coli, and might be a good source for the three dimensional analysis of the T-cell receptor molecule.
Intratumoral administration of recombinant circularly permuted interleukin-4-Pseudomonas exotoxin in patients with high-grade glioma. (2000)

Human glioblastoma but not normal brain cells express numerous receptors for the cytokine interleukin (IL)-4. To target these receptors, we have investigated the safety and activity of directly infusing IL-4(38-37)-PE38KDEL, a chimeric protein composed of circularly permuted IL-4 and a truncated form of Pseudomonas exotoxin (PE), into recurrent malignant high-grade gliomas. IL-4(38-37)-PE38KDEL (IL-4-toxin) was infused over a 4-8-day period into gliomas of nine patients by one to three stereotactically placed catheters. No apparent systemic toxicity occurred in any patient. The infusion of IL-4-toxin in six of nine patients showed glioma necrosis as evidenced by diminished gadolinium enhancement on magnetic resonance imaging. Seven of nine patients underwent craniotomy because of increased intracranial pressure at 16-101 days after the beginning of infusion. In six of these seven patients, partial-to-extensive tumor necrosis with edema was confirmed pathologically. No histological evidence of neurotoxicity to normal brain was identified in any patient. Two patients were not operated on; by magnetic resonance imaging, one showed mottled gadolinium enhancement, and the other showed extensive necrosis of tumor leading to complete remission; this patient remains disease-free > 18 months after the procedure. We conclude that direct glioma injection of IL-4(38-37)-PE38KDEL is safe without systemic toxicity. Local toxicity seemed attributable mainly to tumor necrosis or occasionally to the volume of infusion. Histological evidence of toxicity to normal brain was not observed and in many patients, could be pathologically excluded. Additional patients are being treated to determine the maximal tolerated concentration and volume of IL-4(38-37)-PE38KDEL.
Cloning and expression of cDNAs for polymorphic and monomorphic arylamine N-acetyltransferases from human liver. (1990)

To elucidate the molecular basis of human N-acetylation polymorphism, cDNA clones encoding human liver N-acetyltransferases (EC 2.3.1.5) were isolated from lambda gt10 cDNA libraries using the 32P-labeled cDNA of rabbit liver N-acetyltransferase recently cloned in this laboratory. Three types of cDNAs (D-14, O-7, and D-24) were isolated and their nucleotide sequences were determined, from which the amino acid sequences of human N-acetyltransferases were deduced. All the cDNAs coded for 290 amino acids. Between D-14 and O-7 cDNAs, there was only a single-base substitution in the coding region, which replaced glutamic acid in D-14 cDNA for glycine in O-7 cDNA. There were considerable differences between O-7/D-14 and D-24 cDNAs, with 80% homology in amino acid sequences. When the cDNAs were inserted into pEF321 expression vector and introduced into Chinese hamster ovary cells, N-acetyltransferase activity was expressed in three groups of the transfected cells. The activity in cells transfected with D-14 cDNA was only 9-17% of the activity in O-7 cells. Immunoblot analysis of the transfected cells indicated that the difference in the enzyme activity between O-7 and D-14 cells was possibly due to a difference in the amount of enzyme proteins. The substrate specificity of the expressed enzymes indicated that O-7 and D-14 cDNAs code for polymorphic N-acetyltransferase whereas D-24 cDNA codes for monomorphic enzyme. Southern blot analysis indicated that the polymorphic and monomorphic N-acetyltransferases were encoded in separate genes and that there was restriction fragment length polymorphism with KpnI digestion in the polymorphic N-acetyltransferase gene.
The Extracellular Domain of the Epidermal Growth Factor Receptor (1994)

The binding of epidermal growth factor (EGF) or an EGF-like growth factor to the EGF receptor is the initial event which leads to receptor activation, and consequently the induction of cell growth. In order to study this binding interaction in detail, we produced the extracellular domain of the EGF receptor (EGFR) using the baculovirus expression system. Affinity-labeling and Western-blot analyses revealed that the baculovirus-infected insect cells secrete active EGFR extracellular domain relatively efficiently, however a significant amount of inactive EGFR extracellular domain is retained within the cells. The apparent dissociation constant (Kd) of the secreted EGFR extracellular domain for EGF and transforming growth factor alpha (TGF-alpha), as determined using an immobilized receptor binding assay, was approximately 200 nM. Interestingly, this Kd value is 30-40-fold lower than that of the full-length EGFR derived from detergent-solubilized A431 cell membranes. The stoichiometry of binding of the EGFR extracellular domain to EGF and TGF-alpha was examined by band-shift analysis on non-denaturing PAGE and was estimated to be 1:1. We have also shown, using sedimentation equilibrium analysis, that ligand binding induces significant dimerization of the EGFR extracellular domain. Finally, we carried out site-specific mutagenesis on the EGFR extracellular domain in order to define the ligand-binding region. We identified amino acid residues which are close to the binding site since they are common to the epitopes of several ligand-competitive monoclonal antibodies. However, these residues do not contribute directly to ligand binding since the affinity of the mutated EGFR extracellular domain for EGF and TGF-alpha was unaffected.
Insulin‐like growth factors and binding proteins in multiple sclerosis plaques (1999)

Insulin-like growth factors (IGFs) play an important role in development and myelination in the central nervous system (CNS) as well as in the proliferation and differentiation of cells of the immune system. To assess the influence of this growth factor family on demyelination and repair in multiple sclerosis (MS), the expression of IGF-I, IGF-II, insulin, IGF binding proteins (IGFBP) 1-3 and IGF-I receptor (IGF-IR) in CNS tissue from MS and normal control cases was studied by immunocytochemistry. In active MS lesions, the expression of IGF-I, insulin and IGFBP1 was detected in hypertrophic astrocytes while that of IGF-II and IGFBP2 and 3 was confined to foamy macrophages within lesions and activated microglia in adjacent white matter. IGF-IR, the major IGF receptor, was immunolocalized in macrophages and an astrocyte subpopulation in plaques. Oligodendrocytes in normal-appearing white matter expressed only IGFBP1, not IGFs or IGF-IR. As the remyelinating capacity of oligodendrocytes could be impaired owing to the absence of IGF-IR, the prevailing role of IGFs in inflammatory demyelination may be to promote phagocytosis of myelin and astrogliosis.
Overcoming Laryngospasm by Electrical Stimulation of the Posterior Cricoarytenoid Muscle (1989)

The intent of this study was to demonstrate that the technique of transmucosal electrical stimulation of laryngeal muscles may be of clinical use in airway management. Specifically, its ability to overcome laryngospasm was evaluated. Laryngospasm was induced in eight tracheotomized dogs by hyperventilating each dog, and then applying 0.1 M ammonia to the laryngeal mucosa while administering continuous positive airway pressure (CPAP). Laryngospasm was defined by steady apposition of the vocal cords, massive electromyographic activity in the laryngeal adductor muscles, absence of such activity in the posterior cricoarytenoid muscle (PCA), and intraglottic pressure greater than 80 mm Hg. Upon transmucosal application of 10 mAmp current to the PCA bilaterally, the vocal cords abducted for the duration of the stimulus. We theorize that overcoming laryngospasm by electrostimulation involves a reflexive inhibition of the laryngeal adductors. This study provides an objective model for laryngospasm, and demonstrates that electrical manipulation of the vocal cords may have clinical relevance.
Tight Clustering: A Resampling‐Based Approach for Identifying Stable and Tight Patterns in Data (2005)

In this article, we propose a method for clustering that produces tight and stable clusters without forcing all points into clusters. The methodology is general but was initially motivated from cluster analysis of microarray experiments. Most current algorithms aim to assign all genes into clusters. For many biological studies, however, we are mainly interested in identifying the most informative, tight, and stable clusters of sizes, say, 20-60 genes for further investigation. We want to avoid the contamination of tightly regulated expression patterns of biologically relevant genes due to other genes whose expressions are only loosely compatible with these patterns. "Tight clustering" has been developed specifically to address this problem. It applies K-means clustering as an intermediate clustering engine. Early truncation of a hierarchical clustering tree is used to overcome the local minimum problem in K-means clustering. The tightest and most stable clusters are identified in a sequential manner through an analysis of the tendency of genes to be grouped together under repeated resampling. We validated this method in a simulated example and applied it to analyze a set of expression profiles in the study of embryonic stem cells.
Scanning Tunneling Microscopy and Atomic Force Microscopy: Application to Biology and Technology (1988)

The scanning tunneling microscope (STM) and the atomic force microscope (AFM) are scanning probe microscopes capable of resolving surface detail down to the atomic level. The potential of these microscopes for revealing subtle details of structure is illustrated by atomic resolution images including graphite, an organic conductor, an insulating layered compound, and individual adsorbed oxygen atoms on a semiconductor. Application of the STM for imaging biological materials directly has been hampered by the poor electron conductivity of most biological samples. The use of thin conductive metal coatings and replicas has made it possible to image some biological samples, as indicated by recently obtained images of a recA-DNA complex, a phospholipid bilayer, and an enzyme crystal. The potential of the AFM, which does not require a conductive sample, is shown with molecular resolution images of a nonconducting organic monolayer and an amino acid crystal that reveals individual methyl groups on the ends of the amino acids. Applications of these new microscopes to technology are demonstrated with images of an optical disk stamper, a diffraction grating, a thin-film magnetic recording head, and a diamond cutting tool. The STM has even been used to improve the quality of diffraction gratings and magnetic recording heads.
Localized and Delocalized Electronic States in Single-Wall Carbon Nanotubes (1998)

We present momentum-dependent measurements of the density response function of bulk samples of purified single-wall nanotubes probed by electron energy loss spectroscopy. Carbon nanotubes support excitations between both delocalized and localized electronic states. The $\ensuremath{\pi}$ plasmon exhibits a q dependence similar to that of the graphite plane, signaling the graphitelike nature of the nanotube electron system along the tube axis. In contrast, the interband excitations between the singularities in the nanotube electronic density of states observed at low energy have vanishingly small dispersion in q, and can be used to show that our samples contain significant quantities of semiconducting and metallic single-wall nanotubes.
Mitochondria-related male infertility (2006)

Approximately 15% of human couples are affected by infertility, and about half of these cases of infertility can be attributed to men, through low sperm motility (asthenozoospermia) or/and numbers (oligospermia). Because mitochondrial genome (mtDNA) mutations are identified in patients with fertility problems, there is a possibility that mitochondrial respiration defects contribute to male infertility. To address this possibility, we used a transmitochondrial mouse model (mito-mice) carrying wild-type mtDNA and mutant mtDNA with a pathogenic 4,696-bp deletion (ΔmtDNA). Here we show that mitochondrial respiration defects caused by the accumulation of ΔmtDNA induced oligospermia and asthenozoospermia in the mito-mice. Most sperm from the infertile mito-mice had abnormalities in the middle piece and nucleus. Testes of the infertile mito-mice showed meiotic arrest at the zygotene stage as well as enhanced apoptosis. Thus, our in vivo study using mito-mice directly demonstrates that normal mitochondrial respiration is required for mammalian spermatogenesis, and its defects resulting from accumulated mutant mtDNAs cause male infertility.
Density Functional Theory Studies of Negishi Alkyl–Alkyl Cross-Coupling Reactions Catalyzed by a Methylterpyridyl-Ni(I) Complex (2008)

Density functional theory calculations were done to examine the potential energy surfaces of Ni(I)-catalyzed Negishi alkyl-alkyl cross-coupling reactions by using propyl iodide and isopropyl iodide as model alkyl electrophiles and CH 3ZnI as a model alkyl nucleophile. A four-step catalytic cycle involving iodine transfer, radical addition, reductive elimination, and transmetalation steps were characterized structurally and energetically. The reaction mechanism for this catalytic cycle appears feasible based on the calculated free energy profiles for the reactions. The iodine transfer step is the rate-determining step for the Ni(tpy)-CH 3 (tpy = 2,2'6',2''-terpyridine) reactions with alkyl iodides. For secondary alkyl electrophiles, the oxidative addition intermediate, Ni(III), prefers to undergo decomposition over reductive elimination, whereas for the primary alkyl electrophiles, Ni(III) prefers to undergo reductive elimination over decomposition based on comparison of the relative reaction rates for these two types of steps. In addition, thermodynamic data were employed to help explain why the yield of the coupled product is very low from the Ni(II)-alkyl halide reactions with organozinc reagents.
Restriction endonuclease map of the nontoxigenic corynephage gamma c and its relationship to the toxigenic corynephage beta c (1982)

Clear-plaque-forming mutant gamma tox- corynephages were isolated independently from nontoxigenic lysogenic Corynebacterium diphtheriae strains C7s(gamma tox-) and C4(gamma tox-). A physical map was constructed by using restriction endonucleases BamHI, EcoRI, HindIII, and KpnI. A comparison of nontoxigenic gamma c with toxigenic corynephage beta c revealed large areas of homology, including common regions for cohesive ends (cos) and attachment sites (att). Localization of the att sites on the beta prophage and correlation of the physical and genetic maps defined the orientation of the diphtheria tox operon. Diphtheria tox sequence homologies were mapped on gamma c by hybridizing 32P-labeled diphtheria tox mRNA to restriction fragments of gamma c DNA. Two regions of heterogeneity between phages beta c and gamma c were localized and these regions accounted for the 3-kilobase larger molecular size of gamma c compared with beta c. One change occurs near the tox promoter and may explain the nontoxigenic phenotype of corynephage gamma tox-.
The appearances of wear on polyethylene—a comparison of in vivo and in vitro wear surfaces (1978)

Abstract An examination has been made of the wear surfaces of 21 ultra‐high‐molecular‐weight polyethylene components of hip and knee joint prostheses removed from patients. Both light optics and scanning electron microscope systems of examination have been used. The appearances are compared with specimens subjected to two different in vitro wear tests. Surface appearances related to the wear experience have been classified into seven modes. At least four of these are evidences of what may be four different wear mechanisms. Entrapment of bone‐cement particles between articulating surfaces is fundamentally extraneous but is seen to generate the most severe wear. In the absence of bone‐cement particles, in vivo , wear seems to be mild. Wear in vitro produces similar surface modes but with different relative emphasis.
60-70 dB isolation 2-19 GHz MMIC switches (2003)

High-isolation switches are made with p-i-n diodes in a channelized microwave-integrated-circuit structure. Although the performance of these switches is acceptable, they are difficult and costly to produce. GaAs high-isolation switches that offer a high-performance, low-cost, reproducible alternative are presented. A number of novel high-isolation features have been incorporated, all using standard monolithic-microwave-integrated-circuit (MMIC) processing. Isolation greater than 70 dB for a single-pole, single-throw switch and 62 dB for a single-pole, double-throw switch has been achieved. This represents a substantial improvement over the present 40-dB state-of-the-art isolation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Relaxation‐compensated fast multislice amide proton transfer (APT) imaging of acute ischemic stroke (2008)

Amide proton transfer (APT) imaging is a variant form of chemical exchange saturation transfer (CEST) imaging that is based on the magnetization exchange between bulk water and labile endogenous amide protons. Given that chemical exchange is pH-dependent, APT imaging has been shown capable of imaging ischemic tissue acidosis, and as such, may serve as a surrogate metabolic imaging marker complementary to perfusion and diffusion MRI. In order for APT imaging to properly diagnose heterogeneous pathologies such as stroke and cancer, fast volumetric APT imaging has to be developed. In this study the evolution of CEST contrast after RF irradiation was solved showing that although the CEST steady state is reached by the apparent longitudinal relaxation rate, the decreases of CEST contrast after irradiation is governed by the intrinsic relaxation constant. A volumetric APT imaging sequence is proposed that acquires multislice images immediately after a single long continuous wave (CW) RF irradiation, wherein the relaxation-induced loss of CEST contrast is compensated for during postprocessing. The proposed technique was verified by numerical simulation, a tissue-like dual-pH phantom, and demonstrated on an embolic stroke animal model. In summary, our study has established a fast volumetric pH-weighted APT imaging technique, allowing further investigation to fully evaluate its diagnostic power.
Optimal number of stimulation contacts for coordinated reset neuromodulation (2013)

In this computational study we investigate coordinated reset (CR) neuromodulation designed for an effective control of synchronization by multi-site stimulation of neuronal target populations. This method was suggested to effectively counteract pathological neuronal synchrony characteristic for several neurological disorders. We study how many stimulation sites are required for optimal CR-induced desynchronization. We found that a moderate increase of the number of stimulation sites may significantly prolong the post-stimulation desynchronized transient after the stimulation is completely switched off. This can, in turn, reduce the amount of the administered stimulation current for the intermittent ON-OFF CR stimulation protocol, where time intervals with stimulation ON are recurrently followed by time intervals with stimulation OFF. In addition, we found that the optimal number of stimulation sites essentially depends on how strongly the administered current decays within the neuronal tissue with increasing distance from the stimulation site. In particular, for a broad spatial stimulation profile, i.e., for a weak spatial decay rate of the stimulation current, CR stimulation can optimally be delivered via a small number of stimulation sites. Our findings may contribute to an optimization of therapeutic applications of CR neuromodulation.
Phase 1 Trial of Malaria Transmission Blocking Vaccine Candidates Pfs25 and Pvs25 Formulated with Montanide ISA 51 (2008)

ClinicalTrials.gov NCT00295581.
Vibration Problems in Engineering - fourth edition (1974)

Keywords: vibration ; amortissement ; elasticite Reference Record created on 2005-11-18, modified on 2016-08-08