gebhart/patrepeval huggingface dataset:
In vitro characterization of cardiac radiofrequency ablation lesions using optical coherence tomography (2010)

Currently, cardiac radiofrequency ablation (RFA) is guided by indirect signals. We demonstrate optical coherence tomography (OCT) characterization of RFA lesions within swine ventricular wedges. Untreated tissue exhibited a consistent birefringence artifact within OCT images due to the organized myocardium, which was not present in treated tissue. Birefringence artifacts were detected by filtering with a Laplacian of Gaussian (LoG) to quantify gradient strength. The gradient strength distinguished RFA lesions from untreated sites (p=5.93 x 10(-15)) with a sensitivity and specificity of 94.5% and 86.7% respectively. This study demonstrates the potential of OCT for monitoring cardiac RFA, confirming lesion formation and providing feedback to avoid complications.
Single Amino Acid Substitutions Globally Suppress the Folding Defects of Temperature-sensitive Folding Mutants of Phage P22 Coat Protein (1999)

The amino acid sequence of a polypeptide defines both the folding pathway and the final three-dimensional structure of a protein. Eighteen amino acid substitutions have been identified in bacteriophage P22 coat protein that are defective in folding and cause their folding intermediates to be substrates for GroEL and GroES. These temperature-sensitive folding (tsf) substitutions identify amino acids that are critical for directing the folding of coat protein. Additional amino acid residues that are critical to the folding process of P22 coat protein were identified by isolating second site suppressors of the tsf coat proteins. Suppressor substitutions isolated from the phage carrying the tsf coat protein substitutions included global suppressors, which are substitutions capable of alleviating the folding defects of numerous tsf coat protein mutants. In addition, potential global and site-specific suppressors were isolated, as well as a group of same site amino acid substitutions that had a less severe phenotype than the tsf parent. The global suppressors were located at positions 163, 166, and 170 in the coat protein sequence and were 8-190 amino acid residues away from the tsf parent. Although the folding of coat proteins with tsf amino acid substitutions was improved by the global suppressor substitutions, GroEL remained necessary for folding. Therefore, we believe that the global suppressor sites identify a region that is critical to the folding of coat protein.
Assay of plasma homocysteine: light sensitivity of the fluorescent 7-benzo-2-oxa-1, 3-diazole-4-sulfonic acid derivative, and use of appropriate calibrators (1996)

The recognition of homocysteine as a vascular risk factor has led to increased clinical interest in assaying plasma homocysteine concentrations. Our aim was to improve the reliability of a widely used assay based on HPLC of the fluorescent 7-benzo-2-oxa-1, 3-diazole-4-sulfonic acid (SBD) derivative. We found that SBD derivatives of homocysteine, cysteine, and N-acetylhomocysteine were highly unstable in light but essentially stable in the dark for several hours at either 0 degree C or 25 degrees C. As our primary calibrator, we chose homocystine added to human serum for more consistent results than homocysteine or homocystine in an aqueous buffer. N-acetylcysteine was effective as an internal recovery standard. We observed a previously unreported peak with a prolonged elution time in some plasma samples from subjects who had ingested methionine. Our findings suggest improvements in this and other assay procedures for plasma homocysteine.
The crystal structure of human α‐amino‐β‐carboxymuconate‐ε‐semialdehyde decarboxylase in complex with 1,3‐dihydroxyacetonephosphate suggests a regulatory link between NAD synthesis and glycolysis (2009)

The enzyme alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase (ACMSD) is a zinc-dependent amidohydrolase that participates in picolinic acid (PA), quinolinic acid (QA) and NAD homeostasis. Indeed, the enzyme stands at a branch point of the tryptophan to NAD pathway, and determines the final fate of the amino acid, i.e. transformation into PA, complete oxidation through the citric acid cycle, or conversion into NAD through QA synthesis. Both PA and QA are key players in a number of physiological and pathological conditions, mainly affecting the central nervous system. As their relative concentrations must be tightly controlled, modulation of ACMSD activity appears to be a promising prospect for the treatment of neurological disorders, including cerebral malaria. Here we report the 2.0 A resolution crystal structure of human ACMSD in complex with the glycolytic intermediate 1,3-dihydroxyacetonephosphate (DHAP), refined to an R-factor of 0.19. DHAP, which we discovered to be a potent enzyme inhibitor, resides in the ligand binding pocket with its phosphate moiety contacting the catalytically essential zinc ion through mediation of a solvent molecule. Arg47, Asp291 and Trp191 appear to be the key residues for DHAP recognition in human ACMSD. Ligand binding induces a significant conformational change affecting a strictly conserved Trp-Met couple, and we propose that these residues are involved in controlling ligand admission into ACMSD. Our data may be used for the design of inhibitors with potential medical interest, and suggest a regulatory link between de novo NAD biosynthesis and glycolysis.
Bone Morphogenetic Protein 7 (BMP-7) Influences Tendon-Bone Integration In Vitro (2015)

Our findings indicated a role for BMP-7 as an adjuvant therapeutic agent in the treatment of ligamentous injuries, and they emphasized the importance of the transdifferentiation process of tendinous fibroblasts at the tendon-bone interface.
ICD-9: The Annual Update (2001)

This article will update readers on the annual additions to and deletions from the coding manual that are most pertinent to family physicians and feature an updated version of our coding reference card, ICD-9 Codes for Family Practice: The FPM Short List.
Superfine Laser Position Control Using Statistically Enhanced Resolution In Real Time (1985)

An electronic control system is described which analyzes digitized TV images to simultaneously position 96 time-and-space multiplexed beams for a large KrF laser system. Degra-dation of position resolution due to the intervals between digitization is discussed, and improvement of this resolution by using inherent system noise is demonstrated. The methods shown resolve arbitrary intensity boundaries to a small fraction of the discrete sample spacing.
A simple method for detecting single base substitutions and its application to HLA-DPB1 typing (1994)

We have developed a simple and reliable method, PCR-PHFA (polymerase chain reaction dependent preferential homoduplex formation assay), for detection of single base substitutions within PCR amplicons. This technique is based upon strand competition during hybridization between a double labeled amplicon, prepared from biotin and DNP labeled primers, and an unlabeled amplicon. Under the precisely controlled temperature gradient, the preferential formation of a homoduplex over a heteroduplex occurs. After annealing, the identical sequence of the double labeled and unlabeled amplicon resulted in a low population of regenerated double labeled dsDNA due to strand exchange between them. Even when the two differed by only a single base substitution, double labeled molecule was regenerated efficiently because of preferential homoduplex formation. The regenerated double labeled molecule was captured onto a streptavidin coated microtiter plate and quantified enzymatically with a chromogenic substrate. The technique has been successfully applied in HLA-DPB1 typing. Furthermore, we detected a mutated gene even in the presence of a large excess of the corresponding normal gene.
Manipulating particles with light: radiation and gradient forces (2017)

The manipulation of matter with electromagnetic radiation is a capacity that has been known for over a century. However, the prominence of such optical effects only grew rapidly following the invention of optical tweezers in the 1980s. While both the original theory and the early trapping techniques are based on the radiation force, optical tweezing uses the gradient force. This paper aims to differentiate between these two clearly distinct types of optical forces, which are sometimes confused in the literature. We also discuss three completely separate forms of optical torque that can be applied to a particle, also due to an electromagnetic field. These involve the transfer of either spin or orbital angular momentum from the beam to the particle, depending on the character of the light, or the often overlooked alignment effect that can act on a cylindrical particle due to a gradient force.
Regulation of high-affinity IgE receptor-mediated mast cell activation by murine low-affinity IgG receptors. (1995)

Allergic symptoms result from the release of granular and lipidic mediators and of cytokines by inflammatory cells. The whole process is initiated by the aggregation of mast cell and basophil high-affinity IgE receptors (Fc epsilon RI) by IgE and antigen. We report here that IgE-induced release of mediator and cytokine can be inhibited by cross-linking Fc epsilon RI to low-affinity IgG receptors (Fc gamma RII) which are constitutively expressed on mast cells and basophils. Using a model of stable transfectants in RBL-2H3 cells expressing endogeneous rat Fc epsilon RI and recombinant murine Fc gamma RII, we showed that inhibition requires that Fc epsilon RI be crosslinked to Fc gamma RII by the same multivalent ligand. Inhibition of cross-linked receptors left non-cross-linked Fc epsilon RI capable of triggering mediator release and was reversible upon disengagement. Both isoforms of wild-type Fc gamma RII were equally capable of inhibiting Fc epsilon RI-mediated mast cell activation provided they had an intact intracytoplasmic domain. Our results demonstrate that mast cell secretory responses triggered by high-affinity receptors for IgE may be controlled by low-affinity receptors for IgG. This regulation of Fc epsilon RI-mediated mast cell activation is of potential interest in mast cell physiology and in allergic pathology.
Murine Tumor Cells Metastasizing Selectively in the Liver: Ability to Produce Hepatocyte‐activating Cytokines Interleukin‐1 and/or ‐6 (1991)

Increasing evidence suggests that an intimate correlation may exist between the production of a cytokine, granulocyte-macrophage colony-stimulating factor (GM-CSF) and the ability to metastasize spontaneously in the lungs in murine transplantable tumors. In the present study, we further examined the cytokine production by tumor cells with the ability to metastasize in the liver. Four out of 8 test tumors, which produced metastasis in the lungs but not in the liver, exhibited the ability to produce GM-CSF activity in culture. Three other tumors produced metastasis in the liver but not in the lungs. These tumor cells exhibited no ability to produce GM-CSF, but two of them expressed an interleukin-6 (IL-6) mRNA and also produced IL-6 activity in the culture fluids. One of the two IL-6-producing tumors and the remaining liver metastatic tumor produced interleukin-1 (IL-1) as revealed by bioassay and neutralization test. In the tumor cells producing pulmonary metastasis, neither IL-6 gene expression nor IL-1 production could be detected. The last test tumor, which produced no metastasis either in the lungs or liver, produced neither GM-CSF, IL-1 nor IL-6. Furthermore, injection of antisera reactive to recombinant murine IL-6 caused a marked decrease of the number of liver metastases of an IL-6-producing tumor, but not lung metastases of a GM-CSF-producing tumor, which could be markedly inhibited by injection of anti-recombinant murine GM-CSF sera. These results suggest the possibility that there may be a correlation between the cytokines produced by tumor cells and their organ specificity in spontaneous metastasis, and also indicate that these tumor models may provide a useful tool for studies on the role of cytokines in tumor metastasis.
Distinct immunological mechanisms of CTLA-4 and PD-1 blockade revealed by analyzing TCR usage in blood lymphocytes (2014)

Targeting immune inhibitory receptors has brought excitement, innovation and hope to cancer patients. Our recent work revealed the immunological effects of blocking the CTLA4 and PD-1 immune checkpoints on T cell receptor usage among peripheral blood cells, and further uncovers how the expansion of the T cell repertoire matches the immunotoxicity profile of the therapy.
Pulse propagation near highly reflective surfaces: Applications to photonic band-gap structures and the question of superluminal tunneling times (1995)

We address the physics of pulse propagation, energy flow, and field dynamics as described by Maxwell's equations. After deriving the form of the Poynting vector for pulses that vary slowly in time only, we show that interference terms nontrivially affect the momentum and the energy density of an electromagnetic pulse that scatters from highly reflective materials. Inside such materials, we conclude that the magnetic- and electric-field amplitudes are strongly out of phase. We then apply our findings to the study of layered periodic structures; specifically, we examine the propagation of apparently ``superluminal'' pulses. By monitoring the local momentum and energy densities in the structure at all times, we explicitly show that the canonical energy velocity can never exceed the vacuum speed of light c at any point in the crystal.
The effects of gas phase convection on mass transfer in spin coating (1993)

The thickness uniformity of photoresist films deposited by spin coating critically influences the resolution of photolithography. This thickness uniformity depends on uniform evaporation from the film during drying. Simple scaling arguments demonstrate that, if the mass transfer coefficient at the surface of the wafer does not vary with radial position, then the dry coated resist film thickness will be independent of radial position. A model is presented for the compressible, laminar, steady-state, axisymmetric air flow in a spin coating apparatus for 6-in.-diam wafers. Flow fields computed by a finite-element–Newton method are used to evaluate the radial profile of the mass transfer coefficient at the surface of the rotating wafer, and to calculate the trajectories of particles that are generated as photoresist is flung from the edge of the spinning wafer. At a spin speed of 2000 revolutions/min and exhaust flow rate of 100 ℓ/min through the coater, the calculations predict that the mass transfer coefficient should be independent of radius. Comparison with film contours measured from experiments at these conditions indicates radial nonuniformities in the film thickness and suggests the importance of hydrodynamic instabilities in the gas on the uniformity of the coating.
High-Resolution Analysis of Gene Copy Number Alterations in Human Prostate Cancer Using CGH on cDNA Microarrays: Impact of Copy Number on Gene Expression (2004)

Identification of target genes for genetic rearrangements in prostate cancer and the impact of copy number changes on gene expression are currently not well understood. Here, we applied high-resolution comparative genomic hybridization (CGH) on cDNA microarrays for analysis of prostate cancer cell lines. CGH microarrays identified most of the alterations detected by classic chromosomal CGH, as well as a number of previously unreported alterations. Specific recurrent regions of gain (28) and loss (18) were found, and their boundaries defined with sub-megabasepair accuracy. The most common changes included copy number decreases at 13q, and gains at 1q and 5p. Refined mapping identified several sites, such as at 13q (33-44, 49-51, and 74-76 Mbp from the p-telomere), which matched with minimal regions of loss seen in extensive loss of heterozygosity mapping studies of large numbers of tumors. Previously unreported recurrent changes were found at 2p, 2q, 3p, and 17q (losses), and at 3q, 5p, and 6p (gains). Integration of genomic and transcriptomic data revealed the role of individual candidate target genes for genomic alterations as well as a highly significant (P <.0001) overall association between copy number levels and the percentage of differentially expressed genes. Across the genome, the overall impact of copy number on gene expression levels was, to a large extent, attributable to low-level gains and losses of copy number, corresponding to common deletions and gains of often large chromosomal regions.
The Evolution of Suture Anchors in Arthroscopic Rotator Cuff Repair (2013)

The advancement of suture anchor design and technology has fostered the transition from open to arthroscopic rotator cuff repair. Current suture-bridging constructs have greatly surpassed the biomechanical strength parameters of transosseous repairs and have shown impressive healing rates after arthroscopic rotator cuff repair. This review describes this evolution and discusses the important characteristics of suture anchors.
1H-[13C] NMR measurements of [4-13C]glutamate turnover in human brain. (1992)

A limitation of previous methods for studying human brain glucose metabolism, such as positron emission tomography, is that metabolic steps beyond glucose uptake cannot be studied. Nuclear magnetic resonance (NMR) has the advantage of allowing the nondestructive measurement of 13C distribution in specific carbon positions of metabolites. In this study 1H-[13C] NMR spectroscopy in conjunction with volume localization was used to measure the rate of incorporation of 13C isotope from infused enriched [1-13C]glucose to human brain [4-13C]glutamate. In three studies C4 glutamate turnover time constants of 25, 20, and 17 min were measured in a 21-cm3 volume centered in the region of the visual cortex. Based on an analysis of spectrometer sensitivity the spatial resolution of the method can be improved to < 4 cm3. In conjunction with metabolic modeling and other NMR measurements this method can provide a measure of regional rates of the brain tricarboxylic acid cycle and other metabolic pathways.
Micropreparative Fraction Collection in Microfluidic Devices (2002)

Micropreparative fraction collection following microchip-based electrophoretic analysis of biomolecules is of major importance for a variety of biomedical applications. In this paper, we present a microfabricated device-based fraction collection system. Various size DNA fragments were separated and collected by simply redirecting the desired portions of the detected sample zones to corresponding collection wells using appropriate voltage manipulations. The efficiency of sampling and collection of the fractions was enhanced by placing a cross channel at or downstream of the detection point. Following the detection of the band of interest, the potentials were reconfigured to sampling/collection mode, so that the selected sample zone migrated to the appropriate collection well of the microdevice. The potential distribution assured that the rest of the analyte components in the separation column was retarded, stopped, or reversed, increasing in this way the spacing between the sample zone being collected and the immediately following one. By this means, a precise collection of spatially close consecutive bands could be facilitated. Once the target sample fraction reached the corresponding collection well, the potentials were switched back to separation mode. Alternation of the separation/detection and sampling/collection cycles was repeated until all required sample zones were physically isolated. The integrated device consists of a sample introduction, separation, fraction sampling, and fraction collection compartments. The feasibility of the fraction collection technique was tested on a mixture of dsDNA fragments. The amounts of DNA collected in this way were enough for further downstream sample processing, such as conventional PCR-based analysis.
Novel Therapies Based on Mechanisms of HIV-1 Cell Entry (2003)

Inhibitors of human immunodeficiency virus type 1 (HIV-1) enzymes are central to the treatment of HIV-1 infection, but the development of resistant viruses remains a problem. Another approach is to thwart the entry of the virus into cells by preventing the fusion of the viral envelope with the cell surface. This article reviews the way in which HIV-1 enters cells and potential means of denying the virus admission to cells.
Continuous Glucose Monitoring by Means of the Microdialysis Technique: Underlying Fundamental Aspects (2003)

The microdialysis technique allows extraction of substances (e.g., glucose) from fluids in the human body for quantitative measurements ex vivo. The microdialysis catheter can be inserted in many different tissues; for continuous glucose monitoring it is most often implanted in the subcutaneous fat tissue in the abdominal region. Perfusion of the thin catheter with an isotonic solution without glucose leads to a diffusion of glucose available in the interstitial fluid along the concentration gradient across the semipermeable membrane into the catheter. The glucose levels in the dialysate are measured quantitatively outside the body by means of specific sensors. A number of factors have a profound impact on the amount of glucose extracted (i.e., the glucose levels in the dialysate can be considerably lower than that in the interstitial fluid). However, as long as this proportion remains constant (independent of the prevailing glucose level), the sensor signal, which is related to the glucose level in the interstitial fluid, can be calibrated to the blood glucose level by means of a conventional blood glucose measurement. The microdialysis systems that are commercially available or in clinical development allow (after a run-in phase of some hours) continuous glucose monitoring with a good reliability over several days. Insertion of the microdialysis catheters cannot be performed by the patients themselves but requires professional help. From a technological point of view the microdialysis technique is demanding; consequently the costs of continuous glucose monitoring using this approach are considerable. However, further developments probably will allow development of cheaper patient self-care systems that can be used for longer periods of time.
Proton-Translocating Adenosine Triphosphatase Activity in Lactic Acid Bacterial (1991)

Streptococcus thermophilus 19258 and 573, Luctococcus luctis ssp. lucris C2, Lactococcus luctis ssp. cremoris HP, and Luctobucillus cusei 685 were grown in various media and assayed for protontranslocating ATPase (H+-ATPase) activity. The H+-ATPase was extracted from the membrane fractions of protoplasted cells using a French pressure cell, and activity was measured by the release of inorganic phosphate from ATP. The pH optima for the H+-ATPase, assayed in vitro, were 7.5 for S. thermophilus and Lactococcus luctis ssp. cremoris HP and 5.0 for Lactobacillus casei 685. In contrast, for cells grown in batch culture the H+-ATPase activity was always greatest when the cytoplasmic pH was less than the optimum for the enzyme. The H+-ATPase activity generally increased as the pH decreased until an extracellular pH of 5.0 was reached. Below an extracellular pH of 5.0, activities of this enzyme dropped markedly. The aciduric lactic acid bacterium, Lactobacillus cusei 685, had higher basal levels of this enzyme than the streptococci and lactococci. Results suggest that this enzyme may be involved in regulation of the intracellular pH in lactic acid bacteria.
Evaluation of induction of porcine dermatitis and nephropathy syndrome in gnotobiotic pigs with negative results for porcine circovirus type 2 (2008)

These data suggested that PDNS is a manifestation of disseminated intravascular coagulation in swine. For the experimental conditions reported here, combined infection with g1-TTV and PRRSV was implicated in the genesis of these lesions.