gebhart/patrepeval huggingface dataset:
Correlation of Serum Immunoglobulin Free Light Chain Quantification with Urinary Bence Jones Protein in Light Chain Myeloma (2002)

Multiple myeloma is a malignant plasma cell dyscrasia characterized by bone marrow plasmacytosis (1). Malignant plasma cells produce an abnormal monoclonal immunoglobulin, the laboratory hallmark of the disease process, as well as cytokines, which stimulate cells of the bone marrow microenvironment (2)(3). The neoplastic clone and its products cause the dysfunction of several organs, including bone pain or fractures, renal failure, anemia, susceptibility to infection, hyperviscosity, and hypercalcemia (1). However, the most characteristic feature of multiple myeloma and other monoclonal gammopathies is the presence of a serum and/or urinary monoclonal (M) component on immunofixation (4). Approximately two-thirds of patients with a serum M component also have Bence Jones proteins (BJPs) in the urine. In almost 20% of myelomas, only immunoglobulin light chains are present in the serum and/or urine and are often designated as light chain multiple myeloma (LCMM).

Renal failure occurs in ∼25% of myeloma patients, and there is some renal pathology in more than one-half (1)(5)(6). The number of patients with renal disease varies considerably depending on the criteria used to define renal impairment. Serum creatinine concentrations remain in the reference interval until the glomerular filtration rate is reduced by almost 50%; therefore, the data obtained with blood creatinine concentrations most likely underestimate the incidence of renal involvement in myeloma. Data using the estimated creatinine clearance rate (7), which takes into account various variables, including patient age, weight, and gender, indicate that approximately one-half of patients have renal insufficiency at the time of diagnosis (5). The nature of the M component is also associated with the prevalence of renal disease (5)(8)(9). In light chain myeloma, 65% of patients have impaired renal function at the time of diagnosis when estimated creatinine clearance is used as the variable (5). The …
Synthetic Inhibitors of the Processing of Pretransfer RNA by the Ribonuclease P Ribozyme:  Enzyme Inhibitors Which Act by Binding to Substrate (2000)

2,2'-p-Phenylene bis[6-(4-methyl-1-piperazinyl)]benzimidazole, 2,2'-bis(3,5-dihydroxyphenyl)-6,6'-bis benzimidazole, and 2,2'-bis(4-hydroxyphenyl)-6,6'-bis benzimidazole are shown by UV-visible and fluorescence spectrophotometry to be strong ligands for tRNA, giving simple, hyperbolic binding isotherms with apparent dissociation constants in the micromolar range. Hydroxyl radical footprinting indicates that they may bind in the D and T loops. On the basis of this tRNA recognition as a rationale, they were tested as inhibitors of the processing of precursor tRNAs by the RNA subunit of Escherichia coli RNase P (M1 RNA). Preliminary studies show that inhibition of the processing of Drosophila tRNA precursor molecules by phosphodiester bond cleavage, releasing the extraneous 5'-portion of RNA and the mature tRNA molecule, was dependent on both the structure of the inhibitor and the structure of the particular tRNA precursor substrate for tRNA(Ala), tRNA(Val), and tRNA(His). In more detailed followup using the tRNA(His) precursor as the substrate, experiments to determine the concentration dependence of the reaction showed that inhibition took time to reach its maximum extent. I(50) values (concentrations for 50% inhibition) were between 5.3 and 20.8 microM, making these compounds among the strongest known inhibitors of this ribozyme, and the first inhibitors of it not based on natural products. These compounds effect their inhibition by binding to the substrate of the enzyme reaction, making them examples of an unusual class of enzyme inhibitors. They provide novel, small-molecule, inhibitor frameworks for this endoribonuclease ribozyme.
Synthesis and Evaluation of Novel Steroidal Oxime Inhibitors of P450 17 (17α-Hydroxylase/C17−20-Lyase) and 5α-Reductase Types 1 and 2 (2000)

17 alpha-Hydroxylase/C17-20-lyase (P450 17, CYP 17) and 5 alpha-reductase are the key enzymes in androgen biosynthesis and targets for the treatment of prostate cancer and benign prostatic hyperplasia. In the search of inhibitors for both enzymes, 23 pregnenolone- or progesterone-based steroids were synthesized bearing an oxime group connected directly or via a spacer to the steroidal D-ring. Tested for inhibition of human and rat P450 17, some pregnenolone (9, 11, 14) and a series of progesterone compounds (17-20) turned out to be highly active inhibitors of the human enzyme. The most active compound was Z-21-hydroxyiminopregna-5, 17(20)-dien-3 beta-ol (9) showing K(i) values of 44 and 3.4 nM for the human and rat enzymes, respectively, and a type II UV-difference spectrum indicating a coordinate bond between the oxime group and the heme iron. In contrast to the pregnenolones which showed no inhibition of 5 alpha-reductase isozymes 1 and 2, the progesterones 16, 17, 20, 21, and 23 showed marked inhibition, especially toward the type 2 enzyme. Compounds 17 and 20 were identified as potent dual inhibitors of both P450 17 and 5 alpha-reductase. Tested for selectivity, the most potent P450 17 inhibitors 9, 10, and 14 showed no or only marginal inhibition of P450 arom, P450 scc, and P450 TxA(2). Selected compounds were tested for inhibition of the target enzymes using whole-cell assays. Compounds 9-11 strongly inhibited P450 17 being coexpressed with NADPH-P450 reductase in E. coli cells, and 16, 20, and 23 markedly inhibited 5 alpha-reductase expressed in HEK 293 cells. Tested for in vivo activity, 9 (0.019 mmol/kg) decreased the plasma testosterone concentration in rats after 2 and 6 h by 57% and 44%.
A Monoclonal Antibody against COOH-terminal Peptide of Human Liver Manganese Superoxide Dismutase (1989)

Three stable hybridoma cell lines producing monoclonal antibodies specific for human liver manganese superoxide dismutase were established, and one monoclonal antibody, PG 11, was chosen for immunochemical studies. Immunoblotting demonstrated that the monoclonal antibody binds exclusively to the manganese superoxide dismutase. Immunohistochemical studies indicated that the enzyme is localized in the matrix of human liver mitochondria. To localize antibody-binding epitope, synthetic peptides of the NH2-terminal (residues 1-16) and COOH-terminal (residues 182-189, 190-196, and 182-196) parts of the enzyme were synthesized, and then their effects on the binding were studied using an enzyme-linked immunosorbent assay method. All of the above COOH-terminal peptides inhibited the binding whereas the NH2-terminal ones did not, indicating that PG 11 recognizes several peptides of COOH termini of manganese superoxide dismutase. This is the first report of monoclonal antibodies against human manganese superoxide dismutase with a distinct epitope and of the immunocytochemical demonstration of manganese superoxide dismutase.
Reconstitution of a High Affinity Binding Site for Type I Interferons (1995)

The type I interferon (IFN) receptor complex is assumed to be composed of multiple protein subunits. Recently, two proteins have been identified as potential receptor components, both of which share a high degree of structural homology with the immunoglobulin superfamily. One of these proteins, referred to as the human interferon alpha receptor (IFNAR), has been shown to be involved in interferon signal transduction, but it does not bind IFN with high affinity. A second putative receptor protein, named FLP40, has been cloned from human Daudi cells. Transfection of FLP40 into murine NIH 3T3 cells does not result in high affinity IFN binding. In this study, we demonstrate that when expressed in murine L929 cells neither IFNAR nor FLP40 by themselves are capable of binding human IFN-alpha 8. Co-expression of IFNAR and FLP40 results in cells capable of binding IFN-alpha 8 and IFN-alpha 2. Scatchard analysis of binding demonstrated the presence of high (KD 350 pM) and low (KD 4.0 nM) affinity binding sites. Binding of radiolabeled IFN-alpha 8 can be competed with either unlabeled IFN-alpha 8 or a recombinant form of human interferon beta, IFN-beta 1b, but not with IFN-gamma. Ligand binding of IFN-alpha 8 can be inhibited by antibodies directed against IFNAR providing further support for a role for this protein in the formation of a ligand binding site. This is the first demonstration indicating that two previously identified IFN receptor proteins, which individually do not bind type I IFN with high affinity, cooperate in the formation of a type I IFN receptor ligand binding complex.
Genetic Prodrug Activation Therapy for Breast Cancer: A Phase I Clinical Trial oferbB-2–Directed Suicide Gene Expression (1999)

The results of this study, the first targeted gene therapy for breast cancer and the first to use the cytosine deaminase system in human subjects, are encouraging for the development of genetic prodrug activation therapies that exploit the transcriptional profile of cancer cells.
Deoxycholic acid and the pathogenesis of gall stones. (1988)

Deoxycholic acid and the pathogenesis of gall stones That deoxycholic acid (DCA) may have a role in cholesterol gall stone formation has been discussed on several occasions'`but authoritative reviews of gall stone pathogenesis fail to mention this possibility.`" This may be because the evidence has never been comprehensively reviewed and so its strength is not widely appreciated. Perhaps, too, it is hard to believe that events in the colon can influence the fate of the gall bladder. But the facts suggest that this is indeed the case.
Trans geometric isomers of EPA decrease LXRα-induced cellular triacylglycerol via suppression of SREBP-1c and PGC-1β (2006)

Dietary mono- or di-trans fatty acids with chain lengths of 18-22 increase the risk of cardiovascular diseases because they increase LDL cholesterol and decrease HDL cholesterol in the plasma. However, the effects of trans isomers of PUFAs on lipid metabolism remain unknown. Dietary PUFAs, especially eicosapentaenoic acid (EPA) in marine oils, improve serum lipid profiles by suppressing liver X receptor alpha (LXRalpha) activity in the liver. In this study, we compared the effects of trans geometric isomers of eicosapentaenoic acid (TEPA) on triacylglycerol synthesis induced by a synthetic LXRalpha agonist (T0901317) with the effects of EPA in HepG2 cells. TEPA significantly decreased the amount of cellular triacylglycerol and the expression of mRNAs encoding fatty acid synthase, stearoyl-CoA desaturase-1, and glycerol-3-phosphate acyltransferase induced by T0901317 compared with EPA. However, there was no significant difference between the suppressive effect of TEPA or EPA on the expression of sterol-regulatory element binding protein-1c (SREBP-1c) induced by T0901317. We found that TEPA, but not EPA, decreased the mRNA expression of peroxisome proliferator-activated receptor gamma coactivator 1beta (PGC-1beta), which is a coactivator of both LXRalpha and SREBP-1. These results suggest that the hypolipidemic effect of TEPA can be attributed to a decrease not only in SREBP-1 but also in PGC-1beta expression.
Molecular characterization of human multiple myeloma cell lines by integrative genomics: Insights into the biology of the disease (2006)

To investigate the patterns of genetic lesions in a panel of 23 human multiple myeloma cell lines (HMCLs), we made a genomic integrative analysis involving FISH, and both gene expression and genome-wide profiling approaches. The expression profiles of the genes targeted by the main IGH translocations showed that the WHSC1/MMSET gene involved in t(4;14)(p16;q32) was expressed at different levels in all of the HMCLs, and that the expression of the MAF gene was not restricted to the HMCLs carrying t(14;16)(q32;q23). Supervised analyses identified a limited number of genes specifically associated with t(4;14) and involved in different biological processes. The signature related to MAF/MAFB expression included the known MAF target genes CCND2 and ITGB7, as well as genes controlling cell shape and cell adhesion. Genome-wide DNA profiling allowed the identification of a gain on chromosome arm 1q in 88% of the analyzed cell lines, together with recurrent gains on 8q, 18q, 7q, and 20q; the most frequent deletions affected 1p, 13q, 17p, and 14q; and almost all of the cell lines presented LOH on chromosome 13. Two hundred and twenty-two genes were found to be simultaneously overexpressed and amplified in our panel, including the BCL2 locus at 18q21.33. Our data further support the evidence of the genomic complexity of multiple myeloma and reinforce the role of an integrated genomic approach in improving our understanding of the molecular pathogenesis of the disease. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.
Electrophysiological correlates of the brain's intrinsic large-scale functional architecture (2008)

Spontaneous fluctuations in the blood-oxygen-level-dependent (BOLD) signals demonstrate consistent temporal correlations within large-scale brain networks associated with different functions. The neurophysiological correlates of this phenomenon remain elusive. Here, we show in humans that the slow cortical potentials recorded by electrocorticography demonstrate a correlation structure similar to that of spontaneous BOLD fluctuations across wakefulness, slow-wave sleep, and rapid-eye-movement sleep. Gamma frequency power also showed a similar correlation structure but only during wakefulness and rapid-eye-movement sleep. Our results provide an important bridge between the large-scale brain networks readily revealed by spontaneous BOLD signals and their underlying neurophysiology.
Accomplishments and challenges of computer stereo vision (2010)

Segmentation and grouping of image elements is required to proceed with image recognition. Due to the fact that the images are two dimensional (2D) representations of the real three dimensional (3D) scenes, the information of the third dimension, like geometrical relations between the objects that are important for reasonable segmentation and grouping, are lost in 2D image representations. Computer stereo vision implies on understanding information stored in 3D-scene. Techniques for stereo computation are observed in this paper. The methods for solving the correspondence problem in stereo image matching are presented. The process of 3D-scene reconstruction from stereo image pairs and extraction of parameters important for image understanding are described. Occluded and surrounding areas in stereo image pairs are stressed out as important for image understanding.
Analysis of E.Coli Pormoter sequences (1987)

We have compiled and analyzed 263 promoters with known transcriptional start points for E. coli genes. Promoter elements (-35 hexamer, -10 hexamer, and spacing between these regions) were aligned by a program which selects the arrangement consistent with the start point and statistically most homologous to a reference list of promoters. The initial reference list was that of Hawley and McClure (Nucl. Acids Res. 11, 2237-2255, 1983). Alignment of the complete list was used for reference until successive analyses did not alter the structure of the list. In the final compilation, all bases in the -35 (TTGACA) and -10 (TATAAT) hexamers were highly conserved, 92% of promoters had inter-region spacing of 17 +/- 1 bp, and 75% of the uniquely defined start points initiated 7 +/- 1 bases downstream of the -10 region. The consensus sequence of promoters with inter-region spacing of 16, 17 or 18 bp did not differ. This compilation and analysis should be useful for studies of promoter structure and function and for programs which identify potential promoter sequences.
The Apolipoprotein E-dependent Low Density Lipoprotein Cholesteryl Ester Selective Uptake Pathway in Murine Adrenocortical Cells Involves Chondroitin Sulfate Proteoglycans and an α2-Macroglobulin Receptor (2001)

Cells acquire lipoprotein cholesterol by receptor-mediated endocytosis and selective uptake pathways. In the latter case, lipoprotein cholesteryl ester (CE) is transferred to the plasma membrane without endocytosis and degradation of the lipoprotein particle. Previous studies with Y1/E/tet/2/3 murine adrenocortical cells that were engineered to express apolipoprotein (apo) E demonstrated that apoE expression enhances low density lipoprotein (LDL) CE uptake by both selective and endocytic pathways. The present experiments test the hypothesis that apoE-dependent LDL CE selective uptake is mediated by scavenger receptor, class B, type I (SR-BI). Surprisingly, SR-BI expression was not detected in the Y1/E/tet/2/3 clone of Y1 adrenocortical cells, indicating the presence of a distinct apoE-dependent pathway for LDL CE selective uptake. ApoE-dependent LDL CE selective uptake in Y1/E/tet/2/3 cells was inhibited by receptor-associated protein and by activated alpha(2)-macroglobulin (alpha(2)M), suggesting the participation of the LDL receptor-related protein/alpha(2)M receptor. Reagents that inhibited proteoglycan synthesis or removed cell surface chondroitin sulfate proteoglycan completely blocked apoE-dependent LDL CE selective uptake. None of these reagents inhibited SR-BI-mediated LDL CE selective uptake in the Y1-BS1 clone of Y1 cells in which LDL CE selective uptake is mediated by SR-BI. We conclude that LDL CE selective uptake in adrenocortical cells occurs via SR-BI-independent and SR-BI-dependent pathways. The SR-BI-independent pathway is an apoE-dependent process that involves both chondroitin sulfate proteoglycans and an alpha(2)M receptor.
Characterization of ERG , AR and PTEN Gene Status in Circulating Tumor Cells from Patients with Castration-Resistant Prostate Cancer (2009)

Hormone-driven expression of the ERG oncogene after fusion with TMPRSS2 occurs in 30% to 70% of therapy-naive prostate cancers. Its relevance in castration-resistant prostate cancer (CRPC) remains controversial as ERG is not expressed in some TMPRSS2-ERG androgen-independent xenograft models. However, unlike these models, CRPC patients have an increasing prostate-specific antigen, indicating active androgen receptor signaling. Here, we collected blood every month from 89 patients (54 chemotherapy-naive patients and 35 docetaxel-treated patients) treated in phase I/phase II clinical trials of an orally available, highly specific CYP17 inhibitor, abiraterone acetate, that ablates the synthesis of androgens and estrogens that drive TMPRSS2-ERG fusions. We isolated circulating tumor cells (CTC) by anti-epithelial cell adhesion molecule immunomagnetic selection followed by cytokeratin and CD45 immunofluorescence and 4',6-diamidino-2-phenylindole staining. We used multicolor fluorescence in situ hybridization to show that CRPC CTCs, metastases, and prostate tissue invariably had the same ERG gene status as therapy-naive tumors (n=31). We then used quantitative reverse transcription-PCR to show that ERG expression was maintained in CRPC. We also observed homogeneity in ERG gene rearrangement status in CTCs (n=48) in contrast to significant heterogeneity of AR copy number gain and PTEN loss, suggesting that rearrangement of ERG may be an earlier event in prostate carcinogenesis. We finally report a significant association between ERG rearrangements in therapy-naive tumors, CRPCs, and CTCs and magnitude of prostate-specific antigen decline (P=0.007) in CRPC patients treated with abiraterone acetate. These data confirm that CTCs are malignant in origin and indicate that hormone-regulated expression of ERG persists in CRPC.
Genetic Determinants of Autoimmune Disease and Coronary Vasculitis in the MRL- lpr/lpr Mouse Model of Systemic Lupus Erythematosus (1998)

MRL-lpr/lpr (MRL/lpr) mice are a model of human autoimmune disease. They exhibit a number of characteristics of systemic lupus erythematosus, including anti-DNA Abs, anti-cardiolipin Abs, immune complex-mediated vasculitis, lymphadenopathy, and severe glomerulonephritis. Although the autoimmune disorder is mediated primarily by mutation of the Fas gene (lpr), which interferes with lymphocyte apoptosis, MRL/lpr mice also have other predisposing genetic factors. In an effort to identify these additional factors, we have applied quantitative trait locus (QTL) mapping using an intercross between MRL/lpr mice and the nonautoimmune inbred strain BALB/cJ. A complete linkage map spanning the entire genome was constructed for 189 intercross progeny, and genetic loci contributing to features of the autoimmunity were identified using statistical analytic procedures. As expected, the primary genetic determinant of autoimmune disease in this cross was the Fas gene on mouse chromosome 19, exhibiting a lod score of 60. In addition, two novel loci, one on chromosome 2 (lod score, 4.3) and one on chromosome 11 (lod score, 3.1), were found to contribute to levels of anti-DNA Abs. Interestingly, the chromosome 19 and chromosome 11 QTLs, but not the chromosome 2 QTL, also exhibited associations with anti-cardiolipin Abs (lod scores, 38.4 and 2.6). We further examined the effects of these QTLs on the development of coronary vasculitis in the F2 mice. Our results indicate that the QTLs on chromosomes 11 and 19 also control the development of vasculitis, demonstrating common genetic determinants of autoantibody levels and vasculitis.
Conformational Diversity and Conformational Transitions of a Monoclonal Antibody Monitored by Circular Dichroism and Capillary Electrophoresis (1995)

Four major isoforms of the BR96 antibody were separated by micellar electrokinetic capillary chromatography. Heat-induced reversible isoform interconversions were observed at 70 degrees C, and after extended incubation at 80 degrees C, all species irreversibly transformed into a new single peak. In the presence of sodium dodecyl sulfate (1.0 mg/mL), the isoform transformations occurred at lower temperatures without altering the separation pattern. Size exclusion chromatography analysis detected no aggregation at temperatures below 80 degrees C. Parallel circular dichroism measurements indicated significant conformational changes at 70-80 degrees C. The parallelism between isoform transformations and secondary structure changes allows consideration of CE-separated isoforms of BR96 antibody as conformers, an equilibrium between which can be shifted by different physicochemical factors such as elevated temperatures and amphiphilic surfactants.
Biological Tissue Diagnostics Using Needle Biopsy and Spray Ionization Mass Spectrometry (2011)

Needle biopsy is a routine medical procedure for examining tissue or biofluids for the presence of disease using standard methods of pathology. In this work, spray ionization directly from tissue in the biopsy needle is shown to provide highly specific molecular information through mass spectrometry analysis. The data are available within a minute after the tissue biopsy, a time scale that allows immediate medical decisions to be made. This method has been performed for tissues in a variety of organs including brain, liver, kidney, adrenal gland, stomach, and spinal cord. Amino acids, hormones, fatty acids, anesthetics, and phospholipids are detected from the tissues and identified using exact mass measurement and tandem mass spectrometry. Lipid profiles are rich in information and, as in imaging MS methods, they have the potential to serve to distinguish diseased from healthy tissue. Needle biopsies allow a crude form of depth profiling that is demonstrated with the analysis of tissue samples taken by a needle inserted into a porcine kidney at various depths.