gebhart/patrepeval huggingface dataset:
A New NMR Method of Fluid Characterization in Reservoir Rocks: Experimental Confirmation and Simulation Results (2000)

Abstract A new magnetic resonance fluid (MRF) characterization method for fluids in porous rocks has been developed. The method uses suites of spin-echo measurements that can be acquired in the laboratory or by a nuclear magnetic resonance (NMR) logging tool. In general, the data suites consist of spinecho measurements with different echo spacings, polarization times, applied magnetic field gradients, and numbers of echoes. These measurements are sensitive to the viscosities and molecular diffusion coefficients of the fluids and therefore provide the information needed for fluid characterization. The MRF method is based on the inversion of a general multifluid relaxational model that describes the decay of the transverse magnetization in porous rocks containing reservoir fluids. In its most general form, the relaxational model consists of separate contributions to the measured spin-echo signals from all of the fluids that can be present in reservoir rocks; i.e., brine, oil, gas, and oil-base mud filtrate (OBMF), including mixtures of gas dissolved in oil or OBMF. A key ingredient in the multifluid relaxational model is a new phenomenological microscopic constituent viscosity model (CVM) for hydrocarbon mixtures that links diffusion-free relaxation and molecular diffusion in crude oils. The CVM significantly improves the robustness of the inversion so that accurate fluid characterization is possible even when the brine and crude oil T1 and T2 distributions overlap one another. We present experimental results on live and dead hydrocarbon mixtures and crude oils that confirm the validity of the CVM. The results of a Monte Carlo simulation for a model carbonate formation containing brine, crude oil, gas, and OBMF demonstrate the robustness and accuracy of the inversion. Monte Carlo simulations conducted for different types of rocks containing different amounts and types of fluids demonstrate that the inversion provides quantitative estimates of total porosity, fluid saturations, fluid volumes, bulk volume irreducible water, crude oil viscosity, hydrocarbon-corrected permeability, crude oil T1 and T2 relaxation time distributions, crude oil diffusion coefficient distributions, brine T2 distributions, and apparent brine T1/T2 ratios. The MRF method was also tested in the laboratory on partially saturated Berea 100 and Indiana limestone rocks containing brine and oil. The water saturations estimated from the NMR data by inversion of the multifluid relaxational model are shown to agree well with the water saturations that were independently estimated from differential weight measurements. The oil viscosity estimates are also shown to be in good agreement with the known viscosity of the oil.
[Comparison of the transcription of the fetal type acetylcholine receptor and myogenin in rhabdomyosarcoma]. (1998)

Myogenin and the fetal type acetylcholine receptor (AChR) subunits are specific immunohistochemical markers for the diagnosis of rhabdomyosarcomas. In spite of light microscopy and immunohistochemistry, the diagnosis of doubtful cases and small biopsies of rhabdomyosarcomas remains a challenge. Therefore, a PCR-based highly sensitive approach, would be a valuable diagnostic adjunct and should be free from the risk of contamination of the tumor sample with normal tissue. We studied the transcription of myogenin and fetal type AChR in rhabdomyosarcomas, other childhood and adult tumors and normal tissues. In all embryonal and alveolar rahbdomyosarcomas transcripts of both myogenin and fetal type AChR could be detected. The detection of myogenin mRNA however was not specific for rhabdomyosarcomas but occurred in normal muscle and the majority of other normal tissues and childhood tumors. In contrast the transcription of fetal type AChR, which is defined by an alpha subunit AChR/gamma subunit AChR ratio < 1 was encountered only in rhabdomyosarcomas and denervated muscle. Therefore we suggest, that mRNA of the fetal type AChR but not myogenin is a highly specific and sensitive target for the PCR-based diagnosis of rhabdomyosarcomas.
The Effects of Changes in Pa CO 2 Cerebral Blood Volume, Blood Flow, and Vascular Mean Transit Time (1974)

The relationships between cerebral blood volume (CBV), cerebral blood flow (CBF), and the cerebral vascular mean transit time (t v ) during acute changes in the Pa CO 2 over a range of 15 to 76 torr were investigated in vivo in rhesus monkeys by serially determining the mean transit time of a vascular tracer, 15 O-labeled carboxyhemoglobin, and the mean transit time of a diffusible tracer, 15 O-labeled water. Over this range of Pa CO 2 , a significant linear relationship of CBV = 0.041 Pa CO 2 + 2.0 was found. For each one torr change in Pa CO 2 , there is a change in CBV of 0.041 ml/100 gm of perfused tissue. At a normocarbic value of Pa CO 2 (37 torr), an average value of 3.5 ml/100 gm was found. A nonlinear relationship of CBV and CBF was found. This relationship is expressed in the equation, CBV = 0.80 CBF 0.38 . A significant linear relationship was found between CBF and Pa CO 2 . This was described by the equation, CBF = 1.8 Pa CO 2 - 16.75. For each one torr change in the PaCO 2 , there is a 1.8 ml/100 gm per minute change in the CBF. At a normocarbic value of Pa CO 2 (37 torr), an average value of CBF of 50 ml/100 gm per minute was found. The relationship of CBV and t v was nonlinear and was expressed in the equation, t C15O = 41 CBF -0.62 .
Special multicolor illumination and numerical tilt correction in volumetric digital holographic microscopy (2014)

We introduce a color imaging method in our digital holographic microscope system (DHM). This DHM can create color images of freely floating, or moving objects inside a large volume by simultaneously capturing three holograms using three different illumination wavelengths. In this DHM a new light source assembly is applied, where we use single mode fibers according to the corresponding wavelengths that are tightly and randomly arranged into a small array in a single FC/PC connector. This design has significant advantages over the earlier approaches, where all the used illuminations are coupled in the same fiber. It avoids the coupling losses and provides a cost effective, compact solution for multicolor coherent illumination. We explain how to determine and correct the different fiber end positions caused tilt aberration during the hologram reconstruction process. To demonstrate the performance of the device, color hologram reconstructions are presented that can achieve at least 1 µm lateral resolution.
Calpain‐Induced Proteolysis of Normal Human Tau and Tau Associated with Paired Helical Filaments (1995)

The major components of neurofibrillary tangles (NFT) in Alzheimer's disease are bundles of paired helical filaments (PHF) which are primarily composed of highly phosphorylated tau proteins (PHF-tau). To further understand the mechanism of PHF accumulation in NFT, we examined the calpain-induced proteolysis of highly purified and primarily non-aggregated PHF and normal tau proteins with various contents of phosphate isolated from either fetal (F-tau) or adult human brain (N-tau). The extent of proteolysis was determined by decreases in tau immunoreactivity using Western-blot analysis and a panel of site-specific tau antibodies (Alz 50, Tau-2, Tau 14, Tau-1, AT8, E-11, AH-1 and PHF-1). We found that full-size polypeptides of N-tau and F-tau were similarly and rapidly proteolyzed in vitro by calpain (calpain II, 3.3 units/mg protein) during a 10-min incubation at 30 degrees C, and that their half lives (t1/2) were 1.5 min and 1.8 min, respectively. Analysis of immunoblots suggests that full-length polypeptides of tau are first degraded into large fragments similar in size to that generated endogenously, then into smaller fragments. Since both endogenous and in-vitro-generated tau fragments retained N-terminal epitopes, the results suggest that most of the calpain-sensitive sites may be located in the C-terminal half of the tau molecule. In contrast, PHF were extremely resistant to degradation and only a fivefold higher concentration of calpain (16.7 units/mg protein) induced partial proteolysis of PHF. A major calpain-generated fragment was a 45-kDa polypeptide derived from the C-terminal region of PHF-tau, which forms a core of filaments. The results suggest that the inaccessibility of potential calpain-digestion sites in the filament core could contribute to the resistance of PHF to calpain and subsequently lead to the accumulation of PHF in Alzheimer's disease. The results also suggest that hyperphosphorylation of tau may be marginally involved in the resistance of PHF to degradation by calpain. Ultrastructural examination revealed that, in contrast to previous studies with trypsin, calpain did not alter the morphologic appearance of filaments; after incubation with calpain, the majority of PHF remained short and disperse and the number of PHF aggregated into NFT-like clusters was not significantly increased. The results suggest that the role of calpain in promoting the aggregation and clustering of filaments is limited.
Chromosomal Localization of the Human Homolog (c- sis ) of the Simian Sarcoma Virus onc Gene (1982)

Nonrandom chromosome rearrangements of chromosome 22 have been identified in different human malignancies. As a result of Southern blot hybridization of a c-sis probe to DNA's from mouse-human somatic cell hybrids, the human homolog (c-sis) of the transforming gene of simian sarcoma virus was assigned to chromosome 22. Hybrids between thymidine kinase-deficient mouse cells and human fibroblasts carrying a translocation of the region q11-qter of chromosome 22 to chromosome 17 were also analyzed. These studies demonstrate that the human c-sis gene is on region 22q11 greater than qter.
The genes for leukemia inhibitory factor and interleukin-6 are expressed in mouse blastocysts prior to the onset of hemopoiesis. (1990)

We have investigated the role that hemopoietic regulatory molecules may play in mouse embryogenesis prior to the appearance of hemopoietic stem cells or their microenvironments. Using polymerase chain reaction analysis, we detected mRNA transcripts for interleukin-6 (IL-6) and leukemia inhibitory factor (LIF) but not for granulocyte-macrophage colony-stimulating factor (GM-CSF) or IL-3 in mouse blastocysts at 3.5 days of gestation. Functional IL-6 protein was also detected in cultured blastocysts as a secreted product, as was an activity consistent with the presence of LIF protein. The expression of IL-6 and LIF in blastocysts prior to hemopoiesis suggests that these proteins may regulate the growth and development of trophoblasts or embryonic stem cells.
Glucose Metabolism Regulates T Cell Activation, Differentiation, and Functions (2015)

The adaptive immune system is equipped to eliminate both tumors and pathogenic microorganisms. It requires a series of complex and coordinated signals to drive the activation, proliferation, and differentiation of appropriate T cell subsets. It is now established that changes in cellular activation are coupled to profound changes in cellular metabolism. In addition, emerging evidence now suggest that specific metabolic alterations associated with distinct T cell subsets may be ancillary to their differentiation and influential in their immune functions. The "Warburg effect" originally used to describe a phenomenon in which most cancer cells relied on aerobic glycolysis for their growth is a key process that sustain T cell activation and differentiation. Here, we review how different aspects of metabolism in T cells influence their functions, focusing on the emerging role of key regulators of glucose metabolism such as HIF-1α. A thorough understanding of the role of metabolism in T cell function could provide insights into mechanisms involved in inflammatory-mediated conditions, with the potential for developing novel therapeutic approaches to treat these diseases.
Identification and characterization of nuclear retinoic acid-binding activity in human myeloblastic leukemia HL-60 cells. (1989)

Specific [3H]retinoic acid (RA)-binding sites in nuclear and cytosolic extracts prepared from human myeloblastic leukemia HL-60 cells have been detected by sucrose density gradient sedimentation and size-exclusion high-performance liquid chromatography (HPLC) analyses. This RA-binding activity migrated as a single peak with an apparent molecular weight of 50,000 and greater than 95% of the total binding activity was associated with the nuclear extract. Nuclear extracts prepared from COS-1 cells transfected with an expression vector for the nuclear RA receptors RAR alpha or RAR beta were enriched (20- to 100-fold) with a RA-binding activity that coeluted by size-exclusion HPLC with the putative RAR from HL-60 cells. The HL-60 nuclear receptor exhibited high-affinity binding of RA and its benzoic acid analogs Ch55, Ch30, Ro 13-7410, and SRI 6409-40 and low-affinity binding of retinol, Ro 8-8717, and SRI 5442-60, correlating well with the biological activity of these compounds in HL-60 cells. Saturation binding and Scatchard plot analyses of the binding of RA to the nuclear HL-60 receptor yielded an apparent dissociation constant of approximately 0.46 nM and 1400 +/- 100 receptor sites per cell. Northern blot analyses of poly(A)+ RNA with cDNA probes specific for RAR alpha and RAR beta indicated that HL-60 cells contain predominantly transcripts encoded by the RAR alpha gene. Our results suggest that the observed nuclear RA-binding activity in HL-60 cells might mediate the action of RA in these cells.
Speckle Interferometry, Image Reconstruction By Speckle Masking, Speckle Spectroscopy, Multiple-Mirror Interferometry (1985)

The atmosphere of the earth restricts the resolution of conventional astrophotography to about 1&quot;. We will discuss various high-resolution speckle methods which can overcome image degradation caused by the atmosphere and telescope aberrations. All methods yield diffraction-limited resolution, for example 0.03&quot; for a 3.6m telescope. We will show various astronomical applications of speckle interferometry, observations of asteroids, Pluto/Charon, double stars and the gravitational-lens triple quasar. Speckle interferometry can yield a true diffraction-limited image if there is a point source (reference star) in the isoplanatic neighbourhood of the object (holographic speckle interferometry). We show an application of holographic speckle interferometry to the central object R136a of the 30 Doradus nebula in the Large Magellanic Cloud. A true diffraction-limited image of R136a has been reconstructed. The image shows that R136a consists of 8 stars. Speckle masking is a triple correlation method which yields diffraction-limited images of general astronomical objects. A point source near the object is not required. We will describe an application of speckle masking to the central object in the giant H II region NGC 3603. The reconstructed image shows that this central object is a star cluster of 4 stars with magnitudes 11m, 12m, 13m and 13m. The signal-to-noise ratio of the speckle masking image is about the same as the signal-to-noise ratio of the speckle interferometry autocorrelation. Speckle spectroscopy is a speckle method which yields diffraction-limited objective prism spectra. It is also possible to apply speckle masking to multiple-mirror interferometers or long-baseline interferometers on the ground or in space. True images of very high angular resolution can be obtained by these techniques. We will show computer simulations which illustrate the dependence of the signal-to-noise ratio on photon noise.
Gamma-carboxylated isoforms of recombinant human protein S with different biologic properties (1990)

Human protein S (HPS), a regulator of hemostasis, is a vitamin K- dependent plasma protein with potential clinical utility. We have obtained high-level expression of the cDNA for HPS in two mammalian cell lines. Both cell lines secreted single chain recombinant HPS (rHPS) in serum-free medium as determined by Western blot analysis. The ability of the rHPS from both cell lines to act as a cofactor for human protein C (HPC) was determined; the rHPS secreted from the human 293 cell line had an activity six times that of the rHPS from the AV12–664 Syrian hamster cell line. Furthermore, the relative specific cofactor activity of rHPS from the 293 cell line was actually 2.5-fold higher than that of single-chain human plasma-derived HPS. Essentially all of the rHPS secreted from the 293 cell line exhibited a calcium-dependent elution profile on anion exchange chromatography, whereas only 25% to 35% of the hamster cell-derived rHPS exhibited this profile. However, the calcium-eluted rHPS from the AV12 cell line had a high specific cofactor activity, equivalent to that of the 293-derived rHPS. A NaCl- elutable rHPS fraction (calcium nondependent) was isolated from the recombinant AV12–664 cell line, further purified, and found to have reduced activity, only 40% that of the calcium-dependent rHPS. The only observable difference in the calcium-dependent and nondependent rHPS molecules was in the content of gamma-carboxyglutamic acid (Gla); the calcium-dependent material contained approximately 10 mol Gla/mol protein whereas the calcium-nondependent material contained only approximately 8 mol Gla/mol of protein. In addition, the calcium- nondependent rHPS had reduced ability to interact with phospholipid vesicles as evidenced by an eightfold increase in the apparent kd. Our data demonstrate the isolation of rHPS with high specific activity, and show that a reduction in as few as two Gla residues dramatically decreases its functional cofactor activity for HPC, due to a reduction in ability to interact with the phospholipid bilayer.
Chronic Dysfunction of Astrocytic Inwardly Rectifying K+ Channels Specific to the Neocortical Epileptic Focus After Fluid Percussion Injury in the Rat (2010)

Astrocytic inwardly rectifying K(+) currents (I(KIR)) have an important role in extracellular K(+) homeostasis, which influences neuronal excitability, and serum extravasation has been linked to impaired K(IR)-mediated K(+) buffering and chronic hyperexcitability. Head injury induces acute impairment in astroglial membrane I(KIR) and impaired K(+) buffering in the rat hippocampus, but chronic spontaneous seizures appear in the perilesional neocortex--not the hippocampus--in the early weeks to months after injury. Thus we examined astrocytic K(IR) channel pathophysiology in both neocortex and hippocampus after rostral parasaggital fluid percussion injury (rpFPI). rpFPI induced greater acute serum extravasation and metabolic impairment in the perilesional neocortex than in the underlying hippocampus, and in situ whole cell recordings showed a greater acute loss of astrocytic I(KIR) in neocortex than hippocampus. I(KIR) loss persisted through 1 mo after injury only in the neocortical epileptic focus, but fully recovered in the hippocampus that did not generate chronic seizures. Neocortical cell-attached recordings showed no loss or an increase of I(KIR) in astrocytic somata. Confocal imaging showed depletion of KIR4.1 immunoreactivity especially in processes--not somata--of neocortical astrocytes, whereas hippocampal astrocytes appeared normal. In naïve animals, intracortical infusion of serum, devoid of coagulation-mediating thrombin activity, reproduces the effects of rpFPI both in vivo and at the cellular level. In vivo serum infusion induces partial seizures similar to those induced by rpFPI, whereas bath-applied serum, but not dialyzed albumin, rapidly silenced astrocytic K(IR) membrane currents in whole cell and cell-attached patch-clamp recordings in situ. Thus both acute impairment in astrocytic I(KIR) and chronic spontaneous seizures typical of rpFPI are reproduced by serum extravasation, whereas the chronic impairment in astroglial I(KIR) is specific to the neocortex that develops the epileptic focus.
Rift Valley Fever Virus-induced Encephalomyelitis and Hepatitis in Calves (1992)

Three calves (Nos. 1, 2 = 7 days old; No. 3 = 21 days old) were inoculated subcutaneously with virulent Rift Valley fever (RVF) virus. All calves became viremic and clinically ill, but the two 7-day-old calves were moribund and were euthanatized subsequently on post-inoculation day (PID) 3. Highest viral titers were measured in the serum, with lesser concentrations in the brain, heart, spleen, and liver of these animals. Viral antigens were detected by immunohistochemical analysis only in the livers, where positive staining was localized in coalescing foci of hepatocellular necrosis. The 21-day-old calf appeared to recover after viremia and pyrexia but became lethargic and ataxic and was euthanatized on PID 9. The calf was no longer viremic, and RVF virus was isolated only from the brain. Microscopic examination of the central nervous system revealed diffuse perivascular infiltrates of lymphocytes and macrophages, multifocal meningitis, and focal areas of neuronal necrosis and aggregates of macrophages, lymphocytes, and neutrophils throughout all regions of the brain and cervical spinal cord. There was positive immunohistochemical staining for viral antigens within the cytoplasm of neurons and glial cells throughout the central nervous system. Thus, RVF virus can cause encephalomyelitis in calves, and the specific virologic diagnosis can be made by immunohistochemical localization of viral antigens in formalin-fixed tissues.
Primary chronic cold agglutinin disease: An update on pathogenesis, clinical features and therapy (2007)

Chronic cold agglutinin disease (CAD) is a subgroup of autoimmune hemolytic anemia. Primary CAD has traditionally been defined by the absence of any underlying or associated disease. The results of therapy with corticosteroids, alkylating agents and interferon-alpha have been poor. Cold reactive immunoglobulins against erythrocyte surface antigens are essential to pathogenesis of CAD. These cold agglutinins are monoclonal, usually IgMkappa autoantibodies with heavy chain variable regions encoded by the V(H)4-34 gene segment. By flowcytometric and immunohistochemical assessments, a monoclonal CD20+kappa+B-lymphocyte population has been demonstrated in the bone marrow of 90% of the patients, and lymphoplasmacytic lymphoma is a frequent finding. Novel attempts at treatment for primary CAD have mostly been directed against the clonal B-lymphocytes. Phase 2 studies have shown that therapy with the chimeric anti-CD20 antibody rituximab produced partial response rates of more than 50% and occasional complete responses. Median response duration, however, was only 11 months. In this review, we discuss the clinical and pathogenetic features of primary CAD, emphasizing the more recent data on its close association with clonal lymphoproliferative bone marrow disorders and implications for therapy. We also review the management and outline some perspectives on new therapy modalities.
Monte Carlo methods for signal processing: a review in the statistical signal processing context (2005)

In this article, MCMC (Markov chain Monte Carlo methods) and SMC (sequential Monte Carlo methods) are introduced to sample and/or maximize high-dimensional probability distributions. These methods enable to perform likelihood or Bayesian inference for complex non-Gaussian signal processing problems.