gebhart/patrepeval huggingface dataset:
Post-transplant nuclear renal scans correlate with renal injury biomarkers and early allograft outcomes (2011)

Renal scans reflect early transplant function and allow for a more objective assessment of scores predicting early outcome and for identification of biomarkers. The study shows that transcript levels of AKI genes correlate better with renal scans than clinical- or histopathology-based scores.
Factor X and its deficiency states (1997)

Factor X is one of the vitamin-K-dependent serine proteases. As a result of its position at the convergence of the intrinsic and extrinsic pathways of the clotting cascade, it plays a crucial role in blood coagulation. Factor X interacts with components of both pathways of coagulation, leading to its activation and the formation of the prothrombinase complex. The gene for factor X has been cloned and sequenced and maps to the long arm of chromosome 13, approximately 2.8 kb downstream of the factor VII gene. Each of the exons of factor X encodes a specific functional domain within the protein. In terms of its gene structure and amino acid sequence, factor X shows significant homology with other vitamin-K-dependent clotting factors, suggesting an origin in some common ancestral protein. Factor X deficiency is one of the rarest of the inherited coagulation disorders. Such deficiencies are inherited in an autosomal recessive manner and are characterized by a variable bleeding tendency. In its homozygous form, factor X deficiency has an estimated prevalence of 1:500 000 but in its heterozygous form it has an estimated frequency of ∼1:500 although affected individuals are often clinically asymptomatic. Acquired deficiencies of factor X are uncommon and in isolation are seen most frequently in patients with amyloidosis and in association with upper respiratory tract infections. Treatment of the deficiency state involves factor X replacement with either fresh frozen plasma or prothrombin complex concentrates. However, the latter may be associated with an increased risk of thrombosis.
Optimization of Perforation Distribution for Horizontal Wells (1991)

Abstract In a high permeability reservoir, significant pressure drop can occur in a horizontal well, causing nonuniform inflow due to the variation in pressure drawdown along the well. A mathematical model is described for investigating how perforation distribution affects the performance of a horizontal well producing under steady state inflow. The model couples the Darcy flow into each perforation with the one-dimensional momentum equations for pipe flow. The perforated well is treated like a pipe manifold with T-junctions representing the perforations along the wellbore. A number of examples are presented demonstrating how the model may be used to determine the optimal perforation distribution for different production requirements.
Arginine-Rich Peptide Conjugation to Morpholino Oligomers:  Effects on Antisense Activity and Specificity (2005)

Noncharged antisense compounds, such as phosphorodiamidate morpholino oligomers (PMOs), do not readily enter mammalian cells in culture. A simple and effective means for cellular delivery of PMOs is through their conjugation to arginine-rich peptides. Understanding the effect of peptide conjugation on the efficacy, toxicity, and specificity of PMOs is important to the successful application of this antisense delivery method. We investigated the effects of conjugation of arginine-rich peptides to PMO on the thermal stability, efficacy and specificity for targeted RNA of the resulting compound. In vitro translation assays showed that (1) R9F2-PMO generated antisense activity 3-25-fold higher than corresponding nonconjugated PMO, (2) the level of antisense activity enhancement by R9F2-PMO over a corresponding nonconjugated PMO is related to the GC content of the PMO sequence, (3) R9F2 conjugation reduced the minimum length of a PMO required to inactivate a target RNA from 20 bases to 14 bases, and (4) nonspecific effects of R9F2-PMO occur at lower concentrations than corresponding PMO alone. Thermal stability of heteroduplexes of PMO and complementary RNA were increased by conjugation of PMO to R9F2 peptide, likely accounting for the increased specific antisense activity of conjugated over nonconjugated PMO. A cell-culture based assay demonstrated that while conjugation to unnatural peptides increased PMO efficacy without causing nonspecificity at concentrations < or = 10 microM, only L-peptide conjugation retained high specificity at higher concentrations. This study demonstrates that conjugation of PMO to an arginine-rich peptide generally increases the binding affinity of the PMO to complementary RNA and increases its antisense potency. Additionally, it is shown that the enzymatic stability of an L- or unnatural peptide used for PMO conjugation affects the antisense properties of the resulting compound.
Specificity Determinants of Substrate Recognition by the Protein Kinase DYRK1A (2000)

DYRK1A is a dual-specificity protein kinase that is thought to be involved in brain development. We identified a single phosphorylated amino acid residue in the DYRK substrate histone H3 (threonine 45) by mass spectrometry, phosphoamino acid analysis, and protein sequencing. Exchange of threonine 45 for alanine abolished phosphorylation of histone H3 by DYRK1A and by the related kinases DYRK1B, DYRK2, and DYRK3 but not by CLK3. In order to define the consensus sequence for the substrate specificity of DYRK1A, a library of 300 peptides was designed in variation of the H3 phosphorylation site. Evaluation of the phosphate incorporation into these peptides identified DYRK1A as a proline-directed kinase with a phosphorylation consensus sequence (RPX(S/T)P) similar to that of ERK2 (PX(S/T)P). A peptide designed after the optimal substrate sequence (DYRKtide) was efficiently phosphorylated by DYRK1A (K(m) = 35 microM) but not by ERK2. Both ERK2 and DYRK1A phosphorylated myelin basic protein, whereas only ERK2, but not DYRK1A, phosphorylated the mitogen-activated protein kinase substrate ELK-1. This marked difference in substrate specificity between DYRK1A and ERK2 can be explained by the requirement for an arginine at the P -3 site of DYRK substrates and its presumed interaction with aspartate 247 conserved in all DYRKs.
Peripheral-blood mononuclear cell responses to recombinant hepatitis C virus antigens in patients with chronic hepatitis C (1993)

Peripheral blood mononuclear cell proliferative responses in vitro to recombinant yeast or Escherichia coli hepatitis C virus fusion proteins were evaluated in 20 patients with chronic hepatitis C who were reactive for antibody to hepatitis C virus (on enzyme immunoassay, version 2.0, and a four-antigen recombinant immunoblot assay). Twenty age-matched, healthy individuals negative for antibody to hepatitis C virus were used as a control group. Peripheral-blood mononuclear cells from all chronic hepatitis C patients with antibodies to hepatitis C virus antigens c22 and c100-3 proliferated in vitro in response to the corresponding recombinant hepatitis C virus fusion protein. Peripheral-blood mononuclear cells from 75% of patients infected with hepatitis C virus proliferated in response to cytidine monophosphate-keto-3-deoxyoctulosonic acid-core recombinant antigen but there was no proliferative response to cytidine monophosphate-keto-3-deoxyoctulosonic acid-EF (derived from the NS5 region). All hepatitis C virus-infected patients had 33c antibody, but peripheral-blood mononuclear cells from only 9 of 14 (64%) proliferated in vitro in response to 33c. Ninety-five percent of all hepatitis C virus-infected patients had peripheral-blood mononuclear cells that proliferated in response to at least one recombinant hepatitis C virus fusion protein. The numbers and percentages of CD3 T cells, CD19 B cells and natural killer cells from patients with chronic hepatitis C virus infection did not differ from those in the healthy control group. However, the number of non-major histocompatibility complex-restricted cytotoxic T cells (CD3-positive, CD56-positive, CD16-positive) was increased in patients with chronic hepatitis C virus infection (p < 0.05).
Prostate cancer progression, metastasis, and gene expression in transgenic mice. (1997)

We previously reported that a transgenic mouse line containing the fetal globin promoter linked to the SV40 T antigen (T Ag) viral oncogene (Ggamma/T-15) resulted in prostate tumors. In this study, we further explored tumor origin, frequency, invasiveness, androgen sensitivity, and gene expression pattern. T Ag was detected in adult but not fetal and neonatal prostates, suggesting a role for androgens in tumor progression. However, castration shortly after prostate morphogenesis did not prevent tumor development, suggesting an androgen-independent phenotype. Tumors originated within ventral or dorsal prostate lobes and involved intraepithelial neoplasia, rapid growth in the pelvic region, and metastasis to lymph nodes and distant sites. In addition, the primary cancers could be propagated in nude mice or nontransgenic mice. Seventy-five percent of hemizygous and 100% of homozygous transgenic males developed prostate tumors, suggesting a T Ag dosage effect. Biochemical characterization of advanced tumors revealed markers of both neuroendocrine and epithelial phenotypes; markers of terminal differentiation are lost early in tumorigenesis. Tumor suppressor genes (p53 and Rb), normally bound to T Ag, were up-regulated; bcl-2 proto-oncogene, which prevents apoptosis, was slightly up-regulated. Myc, a stimulus to cell cycle progression, was unchanged. We propose the Ggamma/T-15 transgenic line as a model of highly aggressive androgen-independent metastatic prostate carcinoma with features similar to end-stage prostate cancer in humans.
Spin transfer in nanomagnetic devices with perpendicular anisotropy (2006)

Spin momentum transfer in a nanomagnetic device with perpendicular magnetic anisotropy for both free and fixed magnetic layers is studied. The perpendicular anisotropy is induced by using CoFe∕Pt multilayer. The magnetoresistive loop shows that the perpendicular switching fields for the free and fixed layers are 170 and 380Oe, respectively, with ΔR∕R=0.47%. Resistance-current scanning clearly shows a full out-of-plane switching of the free layer magnetization under a sweeping current, which fully excludes the effect of switching by the magnetic field generated by the current. The critical current density is around 1.0×108A∕cm2, which could be tuned by changing the CoFe∕Pt multilayer structures.
Interaction between Myoglobin and Hyaluronic Acid in Their Layer-by-Layer Assembly:  Quartz Crystal Microbalance and Cyclic Voltammetry Studies (2006)

Myoglobin (Mb), with different net surface charges at different pH in buffers and negatively charged hyaluronic acid (HA) at pH 5.0 in solutions were alternately adsorbed onto various solid surfaces and successfully assembled into {Mb/HA}(n) layer-by-layer films. The Mb in {Mb/HA}(n) films showed a quasi-reversible cyclic voltammetry (CV) response for its heme Fe(III)/Fe(II) redox couple. Quartz crystal microbalance (QCM) and CV were used to confirm the film growth and characterize the films. The interaction between Mb and HA and the influencing factors for Mb adsorption on HA surface, such as pH, Mb concentration, and ionic strength, were investigated in detail. The assembly driving force for {Mb/HA}(n) films, especially for the films assembled with like-charged Mb and HA, was found to be of electrostatic origin, while the secondary interaction such as hydrophobic interaction also plays an important role in some circumstances. Although the growth of {Mb(pH 7.0)/HA}(n) and {Mb(pH 9.0)/HA}(n) films was linear with the adsorption step, the exponential growth of {Mb(pH 5.0)/HA}(n) films was observed, especially when the films became thick. This exponential increase of mass and thickness with deposition step for {Mb(pH 5.0)/HA}(n) films was most probably attributed to the diffusion mechanism in which some HA molecules could diffuse in to and out of the whole films during the film assembly. Atomic force microscopy (AFM) results supported this speculation. UV-vis and IR spectroscopies of {Mb/HA}(n) films, combined with the comparative CV experiments of {Mb/HA}(n) and {catalase/HA}(n) films, suggest that Mb in the {Mb/HA}(n) multilayer films retains its near-native structure.
Optical Magnetic Field Detection: Intracavity Phase Interferometry (2010)

A new approach to magnetometry is demonstrated. Using intracavity phase to frequency conversion a sensitivity of 10nT corresponding to a polarization rotation of 2×10−9rad can be achieved, using a short TGG crystal as sensing element.
Comparative investigation of the formation of polytetrafluoroethylene nanoparticles on different solid substrates through the adsorption of tetrafluoroethylene (2011)

Abstract The effects of different solid substrates, including carbon nanofibers (CNFs), activated carbon, alumina, silica, molecular sieves, and poly( N ‐vinylpyrrolidione) (PVP), were compared for the high‐pressure synthesis of polytetrafluoroethylene [PTFE or (CF 2 ) n ] nanoparticles via the adsorption of thermally synthesized tetrafluoroethylene (C 2 F 4 ) as the monomer. Scanning electron microscopy, Fourier transform infrared spectroscopy, and thermogravimetric analysis (TGA) were used for the characterization of the PTFE nanoparticles on different solid substrates. The results demonstrate that the average diameters of the PTFE nanoparticles were about 90 nm for the CNFs, 130 nm for PVP, 150 nm for alumina, and about 200 nm for silica. Also, TGA showed that the amounts of PTFE nanoparticles synthesized on each solid substrate were 3.53 ± 0.09% for CNFs, 2.31 ± 0.10% for PVP, 2.11 ± 0.12% for silica, and 0.97 ± 0.16% for alumina. Depending on the active surface area and the morphology of nanomaterials, such as CNFs, different capacities were evaluated for each solid support in the formation of the PTFE nanoparticles. The quantities and the size of the synthesized PTFE nanoparticles relied on the characteristics of the solid substrate. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Th1 and Th2 Cells in Health and Disease (1996)

Th1 and Th2 cells, representing extremely polarized modalities of the specific effector immune response, play an important role in both protection against exogenous insults and the induction of several immunopathological reactions. This book provides an authoritative update on the developments in this fast-moving field from both basic and clinical
Decreased expression of the C3b/C4b receptor (CR1) and the C3d receptor (CR2) on B lymphocytes and of CR1 on neutrophils of patients with systemic lupus erythematosus (1986)

Decreased numbers of complement receptor type 1 (CR1) have been observed on erythrocytes of patients with systemic lupus erythematosus (SLE) and on glomerular podocytes of patients having proliferative nephritis of SLE. In the present study, the analysis of the cellular expression of CR1 has been extended to include leukocytes. In addition, expression by B lymphocytes of the C3d receptor (CR2), which also serves as the receptor for the Epstein-Barr virus, was assessed. Receptor expression was measured by 2-color fluorescent flow cytometry of peripheral blood B cells, identified by the presence of the B1 antigen, that had also been stained with anti-CR1 or anti-CR2. B cells from 17 patients with SLE exhibited a mean relative fluorescence for CR1 that was 61% of that found in 17 normal individuals (P less than 0.001). The expression of CR2 by the patients' B cells (n = 14) was 62% of that of the B cells from normal subjects (n = 17) (P less than 0.001). The expression of CR1 correlated with that of CR2 among patients (r = 0.63; P less than 0.01) but not with the expression of CR2 among normal individuals (r = 0.36; P greater than 0.1). The mean CR1 content of the patients' neutrophils was only 59% of the normal mean (P less than 0.001). Thus, abnormalities of complement receptor expression occur on the leukocytes of patients with SLE. These deficiencies may be secondary to interaction of the cells with the products of complement activation, or, in some individuals, the deficiencies may be familial.
Optimal polyline tracking for artery motion compensation in coronary angiography (2002)

We propose a novel solution to the problem of motion compensation of coronary angiographs. As the heart is beating, it is difficult for the physician to observe closely a particular point (e.g. stenosis) on the artery tree. We propose, to rigidly compensate the sequence so that the area around the point of interest appears stable. This is a difficult problem because the arteries deform in a non-rigid manner and only their 2D X-ray projection is observed. Also, the lack of features around the selected point makes the matching subject to the aperture problem. The algorithm automatically extracts a section of the artery of interest, models it as a polyline, and tracks it. The problem is formulated as an energy minimization problem which is solved using a shortest path in a graph algorithm. The motion compensated sequence can be obtained by translating every pixel so that the point of interest remains stable. We have applied this algorithm to many examples in two sets of angiography data and have obtained excellent results.
Mitochondrial functionality in reproduction: from gonads and gametes to embryos and embryonic stem cells (2009)

Mitochondria-based events regulate different aspects of reproductive function, but these are not uniform throughout the several systems reviewed. Low mitochondrial activity seems a feature of 'stemness', being described in spermatogonia, early embryo, inner cell mass cells and embryonic stem cells.
Bright Light Resets the Human Circadian Pacemaker Independent of the Timing of the Sleep-Wake Cycle (1986)

Human circadian rhythms were once thought to be insensitive to light, with synchronization to the 24-hour day accomplished either through social contacts or the sleep-wake schedule. Yet the demonstration of an intensity-dependent neuroendocrine response to bright light has led to renewed consideration of light as a possible synchronizer of the human circadian pacemaker. In a laboratory study, the output of the circadian pacemaker of an elderly woman was monitored before and after exposure to 4 hours of bright light for seven consecutive evenings, and before and after a control study in ordinary room light while her sleep-wake schedule and social contacts remained unchanged. The exposure to bright light in the evening induced a 6-hour delay shift of her circadian pacemaker, as indicated by recordings of body temperature and cortisol secretion. The unexpected magnitude, rapidity, and stability of the shift challenge existing concepts regarding circadian phase-resetting capacity in man and suggest that exposure to bright light can indeed reset the human circadian pacemaker, which controls daily variations in physiologic, behavioral, and cognitive function.
Kinematics and Singularity Analysis of a Novel Type of 3-CRR 3-DOF Translational Parallel Manipulator (2002)

A new three-degrees-of-freedom (3-DOF) translational parallel manipulator (TPM) with linear actuators, i.e., 3-CRR TPM, is first proposed. The rotation singularity analysis, the inverse kinematics, the forward kinematics, and the kinematic singularity analysis of the 3-CRR TPM are then performed. The analysis shows that the proposed TPM has the following kinematic merits over previous TPMs. (1) The forward displacement analysis can be performed by solving a set of linear equations. (2) The Jacobian matrix of the TPM is constant. The inverse of the Jacobian matrix can be pre-calculated, and there is no need to calculate repeatedly the inverse of the Jacobian matrix in performing the forward displacement analysis and forward velocity analysis. (3) There is no rotation singularity. (4) There is no uncertainty singularity. (5) The TPM has a fewer number of links or joints. The geometric condition for a 3-CRR TPM to be isotropic is also revealed. Two additional kinematic merits exist for the isotropic 3-CRR TPM. The first is that an isotropic 3-CRR TPM is isotropic in its whole workspace. The second is that no calculation is needed in order to pre-determine the inverse of the Jacobian matrix. Finally, preliminary design considerations are presented.
Synthesis of sulfate esters of lithocholic acid, glycolithocholic acid, and taurolithocholic acid with sulfur trioxide-triethylamine (1977)

The facile synthesis of lithocholic acids sulfates by a procedure that produced the desired products in over 90% yield is described. Lithocholic acid sulfate and glycolithocholic acid sulfate were synthesized by reacting lithocholic acid or glycolithocholic acid with sulfur trioxide-triethylamine complex in dimethylformamide for 0.5-1 hr. Taurolithocholic acid sulfate was obtained by conjugating lithocholic acid sulfate with taurine in dimethylformamide at 90 degrees C for 0.5 hr. The one-pot synthesis of taurolithocholic acid sulfate starting from lithocholic acid is also described. This procedure, which generated lithocholic acid sulfate in situ, produced taurolithocholic acid sulfate in 98% yield, compared to an overall yield of less than 10% obtained by previously published procedures.
Mesothelin-Induced Pancreatic Cancer Cell Proliferation Involves Alteration of Cyclin E via Activation of Signal Transducer and Activator of Transcription Protein 3 (2008)

Mesothelin (MSLN) is a cell surface glycoprotein that is overexpressed in human pancreatic cancer. Although its value as a tumor marker for diagnosis and prognosis and as a preferred target of immunointervention has been evaluated, there is little information on the growth advantage of MSLN on tumor cells. In this study, we examined the effect of MSLN on pancreatic cancer cell proliferation, cell cycle progression, expression of cell cycle regulatory proteins, and signal transduction pathways in two pancreatic cancer cell lines, MIA-MSLN (overexpressing MSLN in MIA PaCa-2 cells) and BxPC-siMSLN (silencing MSLN in BxPC-3 cells). Increased cyclin E and cyclin-dependent kinase 2 expression found in MIA-MSLN cells correlated with significantly increased cell proliferation and faster cell cycle progression compared with control cells. BxPC-siMSLN cells showed slower proliferation and slower entry into the S phase than control cells. Signal transducer and activator of transcription protein 3 (Stat3) was constitutively activated in MIA-MSLN cells, but not in control cells. Inhibition of Stat3 activation in MIA-MSLN cells by the Janus-activated kinase-selective inhibitor tyrphostin AG490 was followed by a marked decrease in proliferation of the cells. Small interfering RNA against Stat3 significantly reduced the MIA-MSLN cell cycle progression with a concomitant decrease in cyclin E expression. Our data indicate that overexpression of MSLN in pancreatic cancer cells leads to constitutive activation of the transcription factor Stat3, which results in enhanced expression of cyclin E and cyclin E/cyclin-dependent kinase 2 complex formation as well as increased G(1)-S transition.
The Synthesis of Random Brush for Nanostructure of Block Copolymer (2007)

Abstract Polymer brush has been synthesized via conventional free radical polymerization to use a surface active material on the silicon substrate. The synthesized polymer brushes were successfully grafted onto the silicon oxide substrate and the hydrophilic silicon oxide substrate has been changed into the more hydrophobic one. The synthesized poly(styrene‐ ran ‐methyl methacrylate) brush grafted silicon substrate could provide poly(styrene‐ block ‐methyl methacrylate) with neutral surface.