gebhart/patrepeval huggingface dataset:
A complex between prostate-specific antigen and alpha 1-antichymotrypsin is the major form of prostate-specific antigen in serum of patients with prostatic cancer: assay of the complex improves clinical sensitivity for cancer. (1991)

We have studied the forms of prostate-specific antigen (PSA) in serum of patients with prostatic cancer and benign prostatic hyperplasia. Fractionation of serum by gel filtration and assay of the fractions for PSA showed that a considerable part of the PSA immunoreactivity in serum consisted of complexes that were larger than PSA. The complexes were assayed by time-resolved immunofluorometric assays based on an antibody against PSA on the solid phase and europium-labeled antibodies against various protease inhibitors as indicator antibodies. In addition to its monomeric form, PSA was found to occur in complex with alpha 1-antichymotrypsin. The proportion of the alpha 1-antichymotrypsin complex was a major form of PSA and it increased with increasing PSA concentrations, being over 85% at PSA levels exceeding 1000 micrograms/liter. A complex with alpha 1-protease inhibitor was also observed in serum of patients with prostatic cancer and very high levels of PSA. Complexes with alpha 2-macroglobulin and inter-alpha-trypsin inhibitor were detected, but their concentrations were low and similar in sera of cancer patients, normal men, and normal women, suggesting that they were not prostate derived. Commercial immunoradiometric assays for PSA were found to measure free PSA and its complexes with alpha 1-antichymotrypsin but not the complexes with alpha 2-macroglobulin and inter-alpha-trypsin inhibitor. The proportion of the PSA-alpha 1-antichymotrypsin complex was higher in patients with prostatic cancer than in those with benign hyperplasia. Therefore, assay of the complex had a higher sensitivity for cancer than assay of total PSA immunoreactivity.
OptiVol®fluid status monitoring with an implantable cardiac device: a heart failure management system (2007)

Early intervention and prevention of hospitalizations would reduce the burden of heart failure on the healthcare system while improving the quality of life of affected patients. Traditional methods of patient assessment, including physical examination and patient report of symptoms, have a low sensitivity for detecting elevations in left ventricular filling pressure, a major precursor of pulmonary congestion and heart failure decompensation. Intrathoracic fluid accumulation during pulmonary congestion leads to decreased impedance across the lung. The OptiVol system in the InSync Sentrycardiac resynchronization therapy-defibrillator, Concerto cardiac resynchronization therapy-defibrillator and Virtuoso implantable cardioverter-defibrillator devices monitors intrathoracic impedance and is intended to recognize early signs of volume accumulation before physical symptoms appear. Through a recent clinical trial, the default setting for the OptiVol system functioned as a predictor of hospitalization with 76.9% sensitivity. Intrathoracic impedance monitoring is not intended to replace careful frequent clinical evaluation of the heart failure patient, but instead aims to complement traditional heart failure management practices.
Fibroblast Growth‐Stimulatory Activity Released from Human Monocytes (1987)

Human monocytes release fibroblast growth-stimulatory activity. In this study tumour necrosis factor (TNF) has been identified as a major contributor to the monocyte-derived fibroblast growth-stimulatory activity. A neutralizing monoclonal antibody (MoAb) against recombinant TNF (rTNF) inhibited growth of FS-4 fibroblasts and skin biopsy fibroblasts induced by monocyte supernatants, indicating that TNF was involved in the stimulation. Optimal growth of FS-4 fibroblasts was induced by monocyte supernatants at dilutions which contained TNF at a concentration between 1.6 X 10(-6) and 4.0 X 10(-5) micrograms/ml, less growth being induced at higher TNF concentrations. Contrary to this, no optimal concentration interval was found for rTNF, since increasing rTNF concentrations always resulted in increased growth stimulation. It also appeared that natural TNF in the monocyte supernatants induced growth at a much lower concentration than rTNF tested in the absence of monocyte supernatant.
Chemical protein synthesis methods in drug discovery. (2001)

The applicability of chemical protein synthesis over the last five years has been greatly expanded by significant increases in the size (up to 600 amino acids) and variety of accessible proteins, including new classes of proteins such as phosphoproteins, glycoproteins and integral membrane proteins. Chemical protein synthesis has also produced novel high-throughput screening and biosensor technology, and exciting lead compounds for the generation of powerful synthetic protein pharmaceuticals.
Amplification of Padlock Probes for DNA Diagnostics by Cascade Rolling Circle Amplification or the Polymerase Chain Reaction (1999)

Abstract Context. —Padlock probes are highly specific reagents for DNA diagnostics that can discriminate gene sequences with single base mutations. When the 3′ and 5′ terminal regions of the oligonucleotide probes are juxtaposed on a target DNA sequence, they can be circularized by enzymatic ligation and become topologically locked to the target. However, to be useful in solution-based diagnostics, the sensitivity of padlock probes must be markedly enhanced. Objective. —To describe two methods for geometric amplification of circularized padlock probes. Design. —Cascade rolling circle amplification is an isothermal system that uses generic primers and a DNA polymerase with strong strand displacement activity to amplify circularized probes by a mechanism combining rolling circle replication and strand displacement synthesis. One of the primers was designed as an energy transfer–labeled primer, which generates a fluorescence signal only when incorporated into the amplified product, enabling a direct means of detection. Results. —Using pUC19 as a model target to circularize an 89-base probe, a 10 billion–fold amplification was achieved with Bst DNA polymerase (large fragment) within 1 hour starting with as few as 10 probe molecules. The polymerase chain reaction was also used to amplify ligated padlock probes in a rare target detection system. In mixing experiments containing both normal and mutant p53 or c-Ki-ras2 gene target sequences, mutant targets were easily detected in the presence of a 500-fold excess of normal target copies. Conclusion. —These results indicate that padlock probes can be amplified to the high levels required for solution-based DNA diagnostics.
Diagnostic Potential of Serum Proteomic Patterns in Prostate Cancer (2003)

These preliminary findings support recent observations that complex protein profiles have promising potential for the early detection of CaP and warrant future studies with streamlined technology. Furthermore, the combined effect of using 2 array types can greatly enhance the ability of protein profile patterns, suggesting the potential usefulness of alternative approaches to evaluate this new emerging technology.
Mercury Detection in Seawater Using a Mercaptoacetic Acid Modified Gold Microwire Electrode (2005)

Abstract It is demonstrated here that it is possible to determine mercury in chloride containing media like seawater by anodic stripping voltammetry using a modified electrode. A gold microwire electrode is modified using mercaptoacetic acid (MAA) to eliminate the problem of calomel formation, allowing the mercury to become fully removed from the electrode surface after each scan. In a synthetic salt solution of KNO 3 the sensitivity for mercury was found to be improved by the surface modification. In seawater the sensitivity was not significantly improved possibly because of complexation of the mercury by the abundant chloride; however, the MAA coating prevented the formation of calomel causing the background scan to be free of mercury. Measurements in seawater at various pH values demonstrated that mercury detection is possible at natural pH (around 8); however, best sensitivity was attained at pH 4.8 with a deposition time of 3 min. A peak for copper occurred at more negative potential but did not interfere at this pH. The calibration was linear between 0 and 37 nM mercury with a limit of detection of 1 nM mercury.
Characterization of RNA hairpin loop stability (1988)

Fifteen RNA hairpins that share the same stem sequence and have homopolymer loops of A, C and U residues which vary in length from three to nine nucleotides were synthesized and their thermal stabilities determined. Tm varies as a function of loop size but is almost independent of loop composition. Loops of four or five nucleotides are found to be the most stable loop size. This is consistent with the observation that four-membered loops are the most prevalent loop size in 16S-like RNAs. The contribution of each loop to hairpin stability was calculated by subtracting the known contribution of the helical stem. These data should be useful for predicting the stability of other hairpins.
Local Hyperthermia of the Prostate Gland for the Treatment of Benign Prostatic Hypertrophy and Urinary Retention (1990)

Local hyperthermia of the prostate was used to treat 72 patients who had an indwelling catheter because of urinary retention caused by benign prostatic hypertrophy. One month after completion of treatment 50% of patients were able to dispense with the catheter and 1 year later 40% remained catheter-free. The best results were achieved in patients who underwent 6 to 10 treatment sessions in conjunction with cyproterone acetate 50 mg tid administered during the treatment period only.
Complex Formation and Cooperation of Protein Kinase Cθ and Akt1/Protein Kinase Bα in the NF-κB Transactivation Cascade in Jurkat T Cells (2001)

Protein kinase C theta (PKC theta) is known to induce NF-kappa B, an essential transcriptional element in T cell receptor/CD28-mediated interleukin-2 production but also T cell survival. Here we provide evidence that PKC theta is physically and functionally coupled to Akt1 in this signaling pathway. First, T cell receptor/CD3 ligation was sufficient to induce activation as well as plasma membrane recruitment of PKC theta. Second, PKC theta selectively cooperated with Akt1, known to act downstream of CD28 co-receptor signaling, in activating a NF-kappa B reporter in T cells. Third, Akt1 function was shown to be required for PKC theta-mediated NF-kappa B transactivation. Fourth, PKC theta co-immunoprecipitated with Akt1; however, neither Akt1 nor PKC theta served as a prominent substrate for each other in vitro as well as in intact T cells. Finally, plasma membrane targeting of PKC theta and Akt1 exerted synergistic transactivation of the I-kappa B kinase beta/inhibitor of NF-kappa B/NF-kappa B signaling cascade independent of T cell activation. Taken together, these findings suggest a direct cross-talk between PKC theta and Akt1 in Jurkat T cells.
Platelet concentrates irradiated with ultraviolet light retain satisfactory in vitro storage characteristics and in vivo survival (1990)

We have previously reported that platelet concentrates (PC) may be irradiated with ultraviolet light (UVL) in a cryostorage pack such that mixed lymphocyte reactions (MLR) are abolished whilst satisfactory platelet function is retained during subsequent storage using Fenwal PL-1240 containers. We have now studied both platelet structure and function after irradiation in DuPont Stericell bags which are both UV-permeable and biocompatible. The irradiation dosage was 3000 Joules/m2 of UVL at a mean wavelength of 310 nm; a dose previously shown to abolish MLR. No detriment to platelet function was observed when compared to control as measured by aggregation responses to adenosine diphosphate (ADP), collagen and ristocetin, hypotonic shock response and pH during 5 d of storage. Lactate levels were significantly higher (P less than 0.01) and glucose levels lower (P less than 0.01) in UV-treated PC, although in the majority the lactate level did not exceed 20 mmol/l. Betathromboglobulin and platelet factor 4 levels were higher during storage in the UV group, the latter reaching significance (P less than 0.05). When whole platelets and platelet membranes were stained with Coomassie blue or Periodic Acid-Schiff's reagent after electrophoresis in polyacrylamide gels no obvious alterations to major membrane constituents were observed on days 1 and 5 of storage. Paired in vivo autologous studies in healthy volunteers using 111Indium-labelling were performed at the end of 5 d of storage. The UV-treated platelets gave satisfactory and equivalent results for recovery, half life and survival when compared to controls. We conclude that PC irradiated with UVL and stored for 5 d in DuPont Stericell containers appear suitable for transfusion and may prove to be nonimmunogenic. Further in vivo studies of haemostatic efficacy and recipient alloimmunization are now warranted.
DEAD-box helicase DP103 defines metastatic potential of human breast cancers (2014)

Despite advancement in breast cancer treatment, 30% of patients with early breast cancers experience relapse with distant metastasis. It is a challenge to identify patients at risk for relapse; therefore, the identification of markers and therapeutic targets for metastatic breast cancers is imperative. Here, we identified DP103 as a biomarker and metastasis-driving oncogene in human breast cancers and determined that DP103 elevates matrix metallopeptidase 9 (MMP9) levels, which are associated with metastasis and invasion through activation of NF-κB. In turn, NF-κB signaling positively activated DP103 expression. Furthermore, DP103 enhanced TGF-β-activated kinase-1 (TAK1) phosphorylation of NF-κB-activating IκB kinase 2 (IKK2), leading to increased NF-κB activity. Reduction of DP103 expression in invasive breast cancer cells reduced phosphorylation of IKK2, abrogated NF-κB-mediated MMP9 expression, and impeded metastasis in a murine xenograft model. In breast cancer patient tissues, elevated levels of DP103 correlated with enhanced MMP9, reduced overall survival, and reduced survival after relapse. Together, these data indicate that a positive DP103/NF-κB feedback loop promotes constitutive NF-κB activation in invasive breast cancers and activation of this pathway is linked to cancer progression and the acquisition of chemotherapy resistance. Furthermore, our results suggest that DP103 has potential as a therapeutic target for breast cancer treatment.
Biosynthetic Burden and Plasmid Burden Limit Expression of Chromosomally Integrated Heterologous Genes (pdc,adhB) in Escherichiacoli (1999)

Previous studies have shown an unexpectedly high nutrient requirement for efficient ethanol production by ethanologenic recombinants of Escherichia coli B such as LY01 which contain chromosomally integrated Zymomonas mobilis genes (pdc,adhB) encoding the ethanol pathway. The basis for this requirement has been identified as a media-dependent effect on the expression of the Z. mobilis genes rather than a nutritional limitation. Ethanol production was substantially increased without additional nutrients simply by increasing the level of pyruvate decarboxylase activity. This was accomplished by adding a multicopy plasmid containing pdc alone (but not adhB alone) to strain LY01, and by adding multicopy plasmids which express pdc and adhB from strong promoters. New strong promoters were isolated from random fragments of Z. mobilis DNA and characterized but were not used to construct integrated biocatalysts. These promoters contained regions resembling recognition sites for 3 different E. coli sigma factors: sigma(70), sigma(38), and sigma(28). The most effective plasmid-based promoters for fermentation were recognized by multiple sigma factors, expressed both pdc and adhB at high levels, and produced ethanol efficiently while allowing up to 80% reduction in complex nutrients as compared to LY01. The ability to utilize multiple sigma factors may be advantageous to maintain the high levels of PDC and ADH needed for efficient ethanol production throughout batch fermentation. From this work, we propose that the activation of biosynthetic genes in nutrient-poor media creates a biosynthetic burden that reduces the expression of chromosomal pdc and adhB by competing for transcriptional and translational machinery. This reduced expression can be viewed as analogous to the effect of plasmids (plasmid burden) on the expression of native chromosomal genes.
Caspase-mediated cleavage of the TIAM1 guanine nucleotide exchange factor during apoptosis. (2001)

Rho family GTPases Rac and Cdc42 are pivotal regulators of apoptosis in multiple cell types. However, little is known about the mechanism by which these GTPases are regulated in response to apoptotic stimuli. Here, we demonstrate that TIAM1, a Rac-specific guanine nucleotide exchange factor, is cleaved by caspases during apoptosis. TIAM1 cleavage occurs in multiple cell lines in response to diverse apoptotic stimuli such as ceramide, Fas, and serum deprivation. Processing occurs at residue 993 of TIAM1 and removes the NH(2)-terminal of TIAM's two pleckstrin homology domains, leaving a stable fragment containing the Dbl homology and COOH-terminal pleckstrin homology domains. This leads to functional inactivation of TIAM1, as determined by failure of the cleavage product to stimulate GTP loading of Rac in vivo. Furthermore, this product is defective in signaling to two independent Rac effectors, c-Jun NH(2)-terminal kinase and serum response factor. Finally, we demonstrate that in cells treated with ceramide, cleavage of TIAM1 coincided with the inactivation of endogenous Rac. These results reveal a novel mechanism for regulating guanine nucleotide exchange factor activity and GTPase-mediated signaling pathways.
Scheduling using behavioral templates (1995)

Article Scheduling using behavioral templates Share on Authors: Tai Ly Synopsys Inc., 700B E. Middlefield Road, Mountain View, CA Synopsys Inc., 700B E. Middlefield Road, Mountain View, CAView Profile , David Knapp Synopsys Inc., 700B E. Middlefield Road, Mountain View, CA Synopsys Inc., 700B E. Middlefield Road, Mountain View, CAView Profile , Ron Miller Synopsys Inc., 700B E. Middlefield Road, Mountain View, CA Synopsys Inc., 700B E. Middlefield Road, Mountain View, CAView Profile , Don MacMillen Synopsys Inc., 700B E. Middlefield Road, Mountain View, CA Synopsys Inc., 700B E. Middlefield Road, Mountain View, CAView Profile Authors Info & Claims DAC '95: Proceedings of the 32nd annual ACM/IEEE Design Automation ConferenceJanuary 1995 Pages 101–106https://doi.org/10.1145/217474.217514Published:01 January 1995 52citation351DownloadsMetricsTotal Citations52Total Downloads351Last 12 Months0Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
AC133, a Novel Marker for Human Hematopoietic Stem and Progenitor Cells (1997)

AC133 is one of a new panel of murine hybridoma lines producing monoclonal IgG antibodies (mAbs) to a novel stem cell glycoprotein antigen with a molecular weight of 120 kD. AC133 antigen is selectively expressed on CD34(bright) hematopoietic stem and progenitor cells (progenitors) derived from human fetal liver and bone marrow, and blood. It is not detectable on other blood cells, cultured human umbilical vein endothelial cells (HUVECs), fibroblast cell lines, or the myeloid leukemia cell line KG1a by standard flow cytometric procedures. All of the noncommitted CD34(+) cell population, as well as the majority of CD34(+) cells committed to the granulocytic/monocytic pathway, are stained with AC133 antibody. In vitro clonogenicity assays have demonstrated that the CD34(+)AC133(+) double-positive population from adult bone marrow contains the majority of the CFU-GM, a proportion of the CFU-Mix, and a minor population of BFU-E. The CD34(dim) and AC133(-) population has been shown to contain the remaining progenitor cells. AC133-selected cells engraft successfully in a fetal sheep transplantation model, and human cells harvested from chimeric fetal sheep bone marrow have been shown to successfully engraft secondary recipients, providing evidence for the long-term repopulating potential of AC133(+) cells. A cDNA coding for AC133 antigen has been isolated, which codes for a polypeptide consisting of 865 amino acids (aa) with a predicted size of 97 kD. This antigen is modeled as a 5-transmembrane molecule, a structure that is novel among known cell surface structures. AC133 antibody provides an alternative to CD34 for the selection and characterization of cells necessary for both short- and long-term engraftment, in transplant situations, for studies of ex vivo expansion strategies, and for gene therapy.
Adenoviruses in the immunocompromised host (1992)

Adenoviruses are among the many pathogens and opportunistic agents that cause serious infection in the congenitally immunocompromised, in patients undergoing immunosuppressive treatment for organ and tissue transplants and for cancers, and in human immunodeficiency virus-infected patients. Adenovirus infections in these patients tend to become disseminated and severe, and the serotypes involved are clustered according to the age of the patient and the nature of the immunosuppression. Over 300 adenovirus infections in immunocompromised patients, with an overall case fatality rate of 48%, are reviewed in this paper. Children with severe combined immunodeficiency syndrome and other primary immunodeficiencies are exposed to the serotypes of subgroups B and C that commonly infect young children, and thus their infections are due to types 1 to 7 and 31 of subgenus A. Children with bone marrow and liver transplants often have lung and liver adenovirus infections that are due to an expanded set of subgenus A, B, C, and E serotypes. Adults with kidney transplants have viruses of subgenus B, mostly types 11, 34, and 35, which cause cystitis. This review indicates that 11% of transplant recipients become infected with adenoviruses, with case fatality rates from 60% for bone marrow transplant patients to 18% for renal transplant patients. Patients with AIDS become infected with a diversity of serotypes of all subgenera because their adult age and life-style expose them to many adenoviruses, possibly resulting in antigenically intermediate strains that are not found elsewhere. Interestingly, isolates from the urine of AIDS patients are generally of subgenus B and comprise types 11, 21, 34, 35, and intermediate strains of these types, whereas isolates from stool are of subgenus D and comprise many rare, new, and intermediate strains that are untypeable for practical purposes. It has been estimated that adenoviruses cause active infection in 12% of AIDS patients and that 45% of these infections terminate in death within 2 months. In all immunocompromised patients, generalized illness involving the central nervous system, respiratory system, hepatitis, and gastroenteritis usually have a fulminant course and result in death. Treatments for adenovirus infections are of little proven value, although certain purine and pyrimidine analogs have shown beneficial effects in vitro and may be promising drugs.
A comparative study on the analgesic effect of tramadol, tramadol plus magnesium, and tramadol plus ketamine for postoperative pain management after major abdominal surgery (2002)

Adding magnesium or ketamine to tramadol improved analgesia and patient comfort and decreased the amount of tramadol required for postoperative pain management after major abdominal surgery.