gebhart/patrepeval huggingface dataset:
Identification of a restriction fragment length polymorphism by a CR1 cDNA that correlates with the number of CR1 on erythrocytes. (1986)

A genetic basis for the regulation of the number of CR1 on E of different normal individuals was investigated by probing Southern blots of their genomic DNA with a 0.75-kb fragment of CR1 cDNA. Using Hind III, we observed a RFLP involving fragments of 7.4 kb and 6.9 kb that correlated with the number of CR1 on E. 32 individuals having only the 7.4-kb restriction fragment had a mean of 661 +/- 33 (SEM) CR1/E, 11 donors having both restriction fragments had a mean of 455 +/- 52 CR1/E, and 7 individuals having only the 6.9-kb fragment had a mean of 156 +/- 13 CR1/E, all means being significantly different (p less than 0.005). Cosegregation in a normal family of the Hind III restriction fragments with the S, F, and F' structural allotypes of CR1 confirmed that the regulatory element identified by these fragments is linked to the CR1 gene. Moreover, an analysis of the relative expression on E of these structural allotypes in association with either the 7.4-kb Hind III fragment or the 6.9-kb fragment showed that this regulatory element is cis-acting. In contrast, quantitation of CR1 of B lymphocytes and neutrophils revealed no differences in total CR1 expression between individuals homozygous for the 7.4-kb and 6.9-kb Hind III fragments. Thus, we have identified a genomic polymorphism that is linked to the CR1 gene and is associated with a cis-acting regulatory element for the expression of CR1 on E.
Integrated Kidney Exosome Analysis for the Detection of Kidney Transplant Rejection (2017)

Kidney transplant patients require life-long surveillance to detect allograft rejection. Repeated biopsy, albeit the clinical gold standard, is an invasive procedure with the risk of complications and comparatively high cost. Conversely, serum creatinine or urinary proteins are noninvasive alternatives but are late markers with low specificity. We report a urine-based platform to detect kidney transplant rejection. Termed iKEA (integrated kidney exosome analysis), the approach detects extracellular vesicles (EVs) released by immune cells into urine; we reasoned that T cells, attacking kidney allografts, would shed EVs, which in turn can be used as a surrogate marker for inflammation. We optimized iKEA to detect T-cell-derived EVs and implemented a portable sensing system. When applied to clinical urine samples, iKEA revealed high level of CD3-positive EVs in kidney rejection patients and achieved high detection accuracy (91.1%). Fast, noninvasive, and cost-effective, iKEA could offer new opportunities in managing transplant recipients, perhaps even in a home setting.
Bioluminescence resonance energy transfer (2005)

Abstract Bioluminescence Resonance Energy Transfer (BRET) has become a method of choice to monitor and quantify both constitutive and regulated interactions among proteins in intact cells. Despite the fact that BRET cannot be used to visualize the subcellular compartment where the interaction between two proteins occurs, it offers a number of practical advantages over FRET, including higher sensitivity in microplate‐based high‐throughput assays. The advantages of BRET‐based approaches are illustrated by some significant advances obtained in various fields, such as protein oligomerization, ligand‐induced conformational changes, and regulated movement of proteins between subcellular compartments.
Total Synthesis of (+)- Dihydronepetalactone (1991)

Journal Article Total Synthesis of (+)- Dihydronepetalactone Get access Shinji Tanimori, Shinji Tanimori Department of Agricultural Chemistry, College of Agriculture, University of Osaka Prefecture, Sakai, Osaka 591, Japan Search for other works by this author on: Oxford Academic Google Scholar Mitsuru Nakayama Mitsuru Nakayama Department of Agricultural Chemistry, College of Agriculture, University of Osaka Prefecture, Sakai, Osaka 591, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 55, Issue 4, 1 April 1991, Pages 1181–1183, https://doi.org/10.1080/00021369.1991.10870697 Published: 01 April 1991 Article history Received: 02 November 1990 Published: 01 April 1991
Prime subprogram parsing of a program (1980)

A parsing method based on the triconnected decomposition of a biconnected graph is presented. The parsing algorithm runs in linear time and handles a large class of flow graphs. The applications of this algorithm to flow analysis and to the automatic structuring of programs are discussed.
An open label phase 1b/2 trial of TRC105 and sorafenib in patient with advanced/metastatic hepatocellular carcinoma (HCC) (NCT01806064). (2018)

301 Background: Endoglin plays a critical role in angiogenesis and is implicated in resistance to VEGF inhibition. TRC105, an endoglin antibody potentiates anti-tumor activity of sorafenib (S) in preclinical HCC models. The combination of TRC105 and S demonstrated encouraging evidence of activity, including a 33% partial response rate (5/15 pts) by RECIST, at RP2D doses of TRC105 in HCC ( Clin Can Res 2017). Adverse events characteristic of each drug were not increased in frequency or severity when the two drugs were administered concurrently, and most commonly included epistaxis, fatigue, headache and anemia. Methods: Following dose escalation, 21 pts will be enrolled at the RP2D. Four objective responses are required to reject the null hypothesis that the true response rate probability is < 5% with an alpha level of 0.1 and 80% power. Secondary endpoints: DR, PFS, frequency and severity of AEs, PK, immunogenicity, angiogenic biomarkers. Key inclusion criteria: disease not amendable to surgical or local therapies, ECOG ≤ 1; Child-Pugh A or B (7 points) classification. Results: Four pts have been enrolled in phase 1b at TRC105 10 mg/kg (n=4) weekly for four doses and 15 mg/kg every other week thereafter + S 800 mg daily without DLT. One of 3 evaluable pts achieved PR (41% reduction), ongoing at month 4. Serum levels of TRC105 exceeded the target concentration following 4 weekly doses of TRC105 at 10 mg/kg (mean = 59 µg/ml, range 43-80). Mean trough concentration decreased following every other week dosing (mean = 21 µg/ml, range 17-31). Common TRC105 related AEs included ≤ G2 epistaxis and G1 headache. Common S related AEs included G3 hand foot syndrome, ≤G3 periodontal disease, G2 hypertension, ≤G2 increased lipase, ≤G2 fatigue and G1 epistaxis. Conclusions: TRC105 dosed by a hybrid schedule of 10 mg/kg weekly for four doses followed by every other week dosing at 15 mg/kg was tolerable and did not potentiate the toxicity of S. The combination of TRC105 + S demonstrated additional signs of activity, including a PR in 1/3 evaluable pts. 21 pts will be enrolled at the RP2D to assess the primary endpoint of ORR by RECIST. Clinical trial information: NCT01806064.
Concurrent control of multiple BIT structures (1988)

A generic control graph for activating common built-in test structures is derived and its microprogrammed and hardwired implementations described. Three designs for activating multiple BIT structures concurrently are also presented along with simulation results of area/test time tradeoffs. Two designs for this generic controller are presented. The first design augments the classical microprogrammed controller with some circuitry used for counting. This design is most useful when a microprogrammable controller already exists for normal control operations. The second design is a hardwire unit which efficiently implements the generic controller. A complete circuit-level implementation is described. The controller can be easily made self-testing by modifying an existing register to support signature analysis. In addition, the controller is quite simple and can be incorporated on-chip. >
Targeted delivery of polyamidoamine-paclitaxel conjugate functionalized with anti-human epidermal growth factor receptor 2 trastuzumab (2015)

TMAB can serve as an effective targeting agent, and the TMAB-conjugated PAMAM can be exploited as a potential targeted chemotherapeutic drug delivery system for tumors that overexpress HER2.
HTLV-III/LAV-LIKE RETROVIRUS PARTICLES IN THE BRAINS OF PATIENTS WITH AIDS ENCEPHALOPATHY (1983)

It has been postulated that the retrovirus HTLV-III/LAV thought to be the etiologic agent of AIDS also infects the central nervous system and directly causes AIDS encephalopathy. Electron microscopical studies performed on brain sections from three patients with AIDS complicated by progressive encephalopathy revealed structures morphologically consistent with HTLV-III/LAV retrovirus particles. The particles were located principally within multinucleated giant cells but were also present in astrocytes. Many particles were also noted in the extracellular space.
Molecular markers of extracellular matrix remodeling in glioblastoma vessels: Microarray study of laser‐captured glioblastoma vessels (2007)

Glioblastoma multiforme (GBM) are the most malignant and vascularized brain tumors. The aberrant vascular phenotype of GBM could be exploited for diagnosis or therapeutic targeting. This study identified new molecular markers of GBM vessels, using a combination of laser capture microdissection (LCM) microscopy, RNA amplification, and microarray analyses to compare vessels from nonmalignant human brain and GBM tumors. Forty-two genes were differentially expressed in GBM vessels compared to nonmalignant brain vessels. Validation of differentially expressed genes was performed by literature mining, Q-PCR, and immunohistochemistry. Among the differentially expressed genes, only 64% were previously associated with vessels, angiogenesis, gliomas, and/or cancer. The upregulation of genes encoding secreted extracellular proteins IGFBP7 and SPARC was confirmed by Q-PCR in LCM-captured vessels. Whereas SPARC and IGFBP7 protein were absent in nonmalignant brain vessels, a distinct immunoreactivity patterns were observed in GBM sections whereby SPARC was strongly expressed in perivascular cells adjacent to GBM vessels while GBM endothelial cells were immunostained for IGFBP7. IGFBP7 immunoreactivity was also detected on the abluminal side of GBM vessels deposited between strands of vascular basal lamina. The study discerns unique molecular characteristics of GBM vessels compared with nonmalignant brain vessels that could potentially be used for diagnostic or therapeutic purposes.
Homeostatic reinforcement learning for integrating reward collection and physiological stability (2014)

Efficient regulation of internal homeostasis and defending it against perturbations requires adaptive behavioral strategies. However, the computational principles mediating the interaction between homeostatic and associative learning processes remain undefined. Here we use a definition of primary rewards, as outcomes fulfilling physiological needs, to build a normative theory showing how learning motivated behaviors may be modulated by internal states. Within this framework, we mathematically prove that seeking rewards is equivalent to the fundamental objective of physiological stability, defining the notion of physiological rationality of behavior. We further suggest a formal basis for temporal discounting of rewards by showing that discounting motivates animals to follow the shortest path in the space of physiological variables toward the desired setpoint. We also explain how animals learn to act predictively to preclude prospective homeostatic challenges, and several other behavioral patterns. Finally, we suggest a computational role for interaction between hypothalamus and the brain reward system.
<i>In vitro</i> expansion of gamma delta T cells with anti‐myeloma cell activity by Phosphostim and IL‐2 in patients with multiple myeloma (2007)

T-cell-mediated immunotherapy is a promising therapeutic option for multiple myeloma (MM). Gamma-delta T cells (gammadelta T cells) recognize phosphoantigens and display strong anti-tumour cytotoxicity. The synthetic agonist Phosphostim (bromohydrin pyrophosphate, BrHPP) has been shown to selectively activate Vgamma9Vdelta2 T cells. This study aimed to evaluate the expansion capacity and anti-myeloma cell cytotoxicity of circulating gammadelta T cells from MM patients at different time points throughout the disease, using Phosphostim and interleukin 2 (IL-2). Circulating gammadelta T cell counts in patients with newly diagnosed MM or in relapse did not differ from those in healthy donors. A 14-d culture of peripheral blood mononuclear cells with Phosphostim and IL-2 triggered a 100-fold expansion of gammadelta T cells in 78% of newly diagnosed patients. Gammadelta T cells harvested at the time of haematopoietic progenitor collection or in relapsing patients expanded less efficiently. Expanded gammadelta T cells killed 13/14 myeloma cell lines as well as primary myeloma cells, but not normal CD34 cells. Their killing efficiency was not affected by 2-d IL-2 starvation. This study demonstrated the ability of Phosphostim and IL-2 to expand gammadelta T cells from MM patients, and the efficient and stable killing of human myeloma cells by gd T cells.
2D and 3D elastic wavefield vector decomposition in the wavenumber domain for VTI media (2010)

Abstract A pragmatic decomposition of a vector wavefield into P- and S-waves is based on the Helmholtz theory and the Christoffel equation. It is applicable to VTI media when the plane-wave polarization is continuous in the vicinity of a given wavenumber and is uniquely defined by that wavenumber, except for the kiss singularities on the VTI symmetry axis. Unlike divergence and curl, which separate the wavefield into a scalar and a vector field, the decomposed P- and S-wavefields are both vector fields, with correct amplitude, phase, and physical units. If the vector components of decomposed wavefields are added, they reconstruct those of the original input wavefield. Wavefield propagation in any portions of a VTI medium that have the same polarization distribution (i.e., the same eigenvector) in the wavenumber domain have the same decomposition operators and can be recon-structed with a single 3D Fourier transform for each operator (e.g., one for P-waves and one for S-waves). This applies to isotropic wavefields and to VTI anisotropic wavefields, if the polarization distribution is constant, regardless of changes in the velocity. Because the anisotropic phase polarization is local, not global, the wavefield decomposition for inhomogeneous anisotropic media needs to be done separately for each region that has a different polarization distribution. The complete decomposed vector wavefield is constructed by combining the P-, SV-, and SH-wavefields in each region into the corresponding composite P-, SV-, and SH-wavefields that span the model. Potential practical applications include extraction of separate images for different wave types in prestack reverse time migration, inversion, or migration velocity analysis, and calculation of wave-propagation directions for common-angle gathers.
Echinocandins in antifungal pharmacotherapy (2017)

The subtle differences in echinocandins with respect to their pharmacology, clinical therapy and the mechanisms of resistance are emerging at a rapid pace from the current pool of research which could potentially aid in extending their utility in the fungal infections of the eye, heart and nervous system.
Procedures for Wavelength Calibration and Spectral Response Correction of CCD Array Spectrometers (2009)

This work describes a procedure for acquiring a spectrum of an analyte over an extended range of wavelengths and validating the wavelength and intensity assignments. To acquire a spectrum over an extended range of wavelengths with a spectrometer with a charge coupled device (CCD) array detector, it is necessary to acquire many partial spectra, each at a different angular position of the grating, and splice the partial spectra into a single extended spectrum. The splicing procedure exposes instrument dependent artifacts. It is demonstrated that by taking a spectrum of a reference irradiance source and making spectral correction, the artifacts exposed by the splicing are removed from the analyte spectrum. This is because the irradiance reference spectrum contains the same artifacts as the analyte spectrum. The artifacts exposed by the splicing depend on the wavelength of the splice; therefore it is important to measure the irradiance reference spectrum for the same range of wavelengths used to measure the spectrum of the analyte solution. In other words, there is no general spectral correction factor which is applicable to spectra taken for different range of wavelengths. The wavelength calibration is also carried out by splicing many partial spectra from a source like a krypton lamp. However the wavelength assignments are not sensitive to the splicing procedure and the same wavelength calibration can be used for spectra acquired over different extended wavelength ranges. The wavelength calibration checks the validity of the setting of the grating angular position, and the assignment of wavelengths to individual pixels on the CCD array detector. The procedure is illustrated by measuring the spectrum of an orange glass and the spectrum of a suspension of microalgae.
High range resolution performance of frequency stepped radar signal (2002)

The high range resolution performance of frequency stepped radar signal under the influence of thermal noise, target fluctuation, frequency jitter and target motion is analysed; the minimum target velocity unit needed to be compensated is calculated.
Studies on Parkinson's Disease Including X-Ray Fluorescent Spectroscopy of Formalin Fixed Brain Tissue (1968)

Journal Article Studies on Parkinson's Disease Including X-Ray Fluorescent Spectroscopy of Formalin Fixed Brain Tissue Get access Kenneth M. Earle, M.D. Kenneth M. Earle, M.D. Washington, D.C. Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Neuropathology & Experimental Neurology, Volume 27, Issue 1, January 1968, Pages 1–14, https://doi.org/10.1097/00005072-196801000-00001 Published: 01 January 1968
Simple, efficient protocol for enzymatic synthesis of uniformly 13C, 15N-labeled DNA for heteronuclear NMR studies (1998)

The use of uniformly 13C,15N-labeled RNA has greatly facilitated structural studies of RNA oligonucleotides by NMR. Application of similar methodologies for the study of DNA has been limited, primarily due to the lack of adequate methods for sample preparation. Methods for both chemical and enzymatic synthesis of DNA oligonucleotides uniformly labeled with 13C and/or 15N have been published, but have not yet been widely used. We have developed a modified procedure for preparing uniformly 13C,15N-labeled DNA based on enzymatic synthesis using Taq DNA polymerase. The highly efficient protocol results in quantitative polymerization of the template and approximately 80% incorporation of the labeled dNTPs. Procedures for avoiding non-templated addition of nucleotides or for their removal are given. The method has been used to synthesize several DNA oligonucleotides, including two complementary 15 base strands, a 32 base DNA oligonucleotide that folds to form an intramolecular triplex and a 12 base oligonucleotide that dimerizes and folds to form a quadruplex. Heteronuclear NMR spectra of the samples illustrate the quality of the labeled DNA obtained by these procedures.
A parametric algorithm for drawing pictures of solid objects composed of quadric surfaces (1976)

An algorithm for drawing pictures of three-dimensional objects, with surfaces made up of patches of quadric surfaces, is described. The emphasis of this algorithm is on calculating the intersections of quadric surfaces. A parameterization scheme is used. Each quadric surface intersection curve (QSIC) is represented as a set of coefficients and parameter limits. Each value of the parameter represents at most two points, and these may easily be distinguished. This scheme can find the coordinates of points of even quartic (fourth-order) intersection curves, using equations of no more than second order. Methods of parameterization for each type of QSIC are discussed, as well as surface bounding and hidden surface removal.
Dietary Sodium Bicarbonate and Magnesium Oxide for Early Postpartum Lactating Dairy Cows: Effects of Production, Acid-Based Metabolism, and Digestion (1982)

In two experiments with cows in early lactation fed 40% corn silage and 60% concentrate diets (dry basis), we examined effects of 1.0% dietary sodium bicarbonate and .8% magnesium oxide in a 2 x 2 factorial arrangement on performance, acid-base metabolism, and digestion. In Experiment 1 with 20 Holstein and 4 Jersey cows, intake and milk production were not affected by treatment through 12 wk postpartum. In digestion trials at 3, 6, 9, and 12 wk postpartum, addition of magnesium oxide increased digestibility of dry matter 1.8% units by sodium bicarbonate whereas acid detergent fiber digestion increased 9 to 12% units with addition of either buffer. In Experiment 2, with four fistulated Holstein cows in a Latin square design, intake per unit body weight was increased .18% units by dietary sodium bicarbonate while milk production was unaffected. Dry matter and acid detergent fiber digestion were increased slightly by sodium bicarbonate plus magnesium oxide addition whereas nitrogen balance increased 23 g/day in cows fed magnesium oxide alone. Because of the low fiber content of the ration, milk fat percent increased .5 to .9% by addition of either buffer in both experiments and resulted in corresponding increased in fat-corrected milk. Sodium bicarbonate and magnesium oxide prevented rapid declines in rumen pH associated with feeding in Experiment 2, which related to changes in acid detergent fiber digestion. Blood acid-base metabolites were relatively unchanged by treatment in either experiment. Urinary bicarbonate and net acid excretion rates were changed on the average by +41 and +43 meq/h by sodium bicarbonate or magnesium oxide but could not be related to changes in intake and production.
Design of a new counter-balancing stackable mechanism (2014)

This paper describes design and application of a novel counter-balancing stackable parallel mechanism. The stackable mechanism is designed by combining a five-bar and a couple of parallelograms. This design allows a compact design and wide workspace as compared to prior parallel type counter-balancing mechanisms. A linear geometry of this mechanism guarantees static balancing in the whole workspace. This mechanism was successfully applied to otologic.
16S rRNA-based probes and polymerase chain reaction method to detect Listeria monocytogenes cells added to foods (1992)

A rapid polymerase chain reaction (PCR) method was developed for detection of Listeria monocytogenes in foods. This method used a pair of primers based on a unique region in the 16S rRNA sequence of L. monocytogenes, which were previously reported by us to yield a specific nucleic acid probe. Our method included use of a shorter denaturing time, a shorter annealing time, a rapid transition, and an increase in the number of cycles, resulting in good sensitivity. Just 3 h for PCR plus 1 h for electrophoresis was required. Additional time for DNA isolation and DNA hybridization was not needed. This method detected as few as 2 to 20 CFU of L. monocytogenes in pure cultures and as few as 4 to 40 CFU of L. monocytogenes in inoculated (10(8) CFU), diluted food samples. Seven of eight foods, including four poultry products, gave positive results. Only one food sample, soft cheese, gave interference. An internal probe hybridization test was used to confirm that the PCR products were from L. monocytogenes. A specificity test indicated that this PCR method was positive for all 13 strains of L. monocytogenes tested but negative for the other 6 species of Listeria, including 6 strains of L. innocua, and negative for 17 other gram-positive and gram-negative bacteria tested.