gebhart/patrepeval huggingface dataset:
Identical complementary deoxyribonucleic acids encode a human renal and bone parathyroid hormone (PTH)/PTH-related peptide receptor (1993)

Identical complementary DNAs (cDNAs) that encode a 593-amino acid human PTH (PTH)/PTH-related peptide (PTHrP) receptor were isolated by hybridization techniques from two cDNA libraries which had been constructed from human kidney and human osteoblast-like osteosarcoma cells (SaOS-2). Northern blot analysis of total RNA from human bone- and kidney-derived tissue revealed one single major messenger RNA species of about 2.5 kilobases in both tissues. The human PTH/PTHrP receptor has 91% and 81% identity, respectively, with the previously cloned rat and opossum receptors, indicating a high degree of conservation among mammals. Despite this striking degree of amino-acid conservation, the human PTH/PTHrP receptor has several unique biological properties when transiently expressed in COS-7 cells. The apparent dissociation constants for [Nle8,18,Tyr34] bovine PTH(1-34) amide [bPTH(1-34)] are similar for the human and the rat receptor (approximately 8 vs. approximately 15 nM) whereas [Tyr36]PTHrP(1-36) amide has a slightly lower affinity for the human (15-40 nM) than for the rat receptor (approximately 15 nM). Both ligands stimulate efficiently and with similar efficacy the accumulation of intracellular cAMP. The affinities for the antagonists [Nle8,18,Tyr34] bPTH(3.34) amide [bPTH(3-34)] and in particular for [Nle8,18,Tyr34] bPTH(7-34) amide [bPTH(7-34)] are considerably higher for the human receptor, e.g. approximately 8 nM vs. 30 nM for bPTH(3-34) and approximately 100 nM vs. 5000 nM for bPTH(7-34), respectively. Similar biological findings were previously attributed to differences in species- and/or organ-specific PTH/PTHrP receptors. The expression of the recombinant, highly homologous rat and human receptors in a uniform environment indicate that the moderate differences in the primary receptor structure have profound consequences for the receptor binding affinity of amino-terminally truncated PTH analogs. Furthermore, the molecular cloning of identical cDNAs encoding a human PTH/PTHrP receptor from the two major target organs for PTH, bone and kidney, provides strong evidence for one single PTH/PTHrP receptor in both organs, although additional and/or alternatively spliced receptors cannot be excluded.
Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. (1999)

Motivation: This article presents a method for assembling shotgun sequences which primarily uses high confidence regions whilst taking advantage of additional available information such as low confidence regions, quality values or repetitive region tags. Conflict situations are resolved with routines for analysing trace signals.
A Large Family of Genes That Share Homology withCLAVATA3 (2001)

The receptor kinase superfamily in plants includes a large number of genes, but very little is known about the ligands that bind to these receptors. In the Arabidopsis genome, for example, 340 receptor kinase genes have been identified ([The Arabidopsis Genome Initiative, 2000][1]). The proteins
Long survival of patients with small cell lung cancer after adjuvant treatment with the anti-idiotypic antibody BEC2 plus Bacillus Calmette-Guérin. (1999)

Despite active therapies for small cell lung cancer (SCLC), most patients relapse and die of the disease. The present study evaluates immunization using the anti-idiotypic antibody BEC2, which mimics the ganglioside GD3 expressed on the surface of most SCLC tumors, combined with Bacillus Calmette-Guérin (BCG) as an immune adjuvant. We hypothesized that active immunization could alter the natural history of the disease. Fifteen patients who had completed standard therapy for SCLC received a series of five intradermal immunizations consisting of 2.5 mg of BEC2 plus BCG over a 10-week period. Blood was collected for serological analysis, and outcome was monitored. All patients developed anti-BEC2 antibodies, despite having received chemotherapy with or without thoracic radiation. We detected anti-GD3 antibodies in five patients, including those with the longest relapse-free survival. The median relapse-free survival for patients with extensive stage disease is 11 months and has not been reached for patients with limited stage disease (>47 months), with only one of seven patients having relapsed after a median follow-up of 47 months. Immunization of patients with SCLC after standard therapy using BEC2 plus BCG can induce anti-GD3 antibodies and is safe. The survival and relapse-free survival in this group of patients are substantially better than those observed in a prior group of similar patients. A Phase III trial is being conducted to evaluate BEC2 plus BCG as adjuvant therapy after chemotherapy and irradiation.
Binding of Biliverdin, Bilirubin, and Thyroid Hormones to Lipocalin-Type Prostaglandin D Synthase (1999)

Lipocalin-type prostaglandin D synthase is a major protein of the cerebrospinal fluid and was originally known as beta-trace. We investigated the binding ability of prostaglandin D synthase toward bile pigments, thyroid hormones, steroid hormones, and fatty acids in this present study. We found that the recombinant enzyme binds bile pigments and thyroid hormones, resulting in quenching of the intrinsic tryptophan fluorescence, the appearance of induced circular dichroism of the lipophilic ligands, and a red shift of the absorption spectra of bilirubin and biliverdin. The binding of prostaglandin D synthase to lipophilic ligands was also demonstrated by the resonant mirror technique and surface plasmon resonance detection. The dissociation constants were calculated to be 33 nM, 37 nM, 660 nM, 820 nM, and 2.08 microM for biliverdin, bilirubin, L-thyroxine, 3,3',5'-triiodo-L-thyronine, and 3,3', 5-triiodo-L-thyronine, respectively. Biliverdin and bilirubin underwent a shift in their absorption peaks from 375 to 380 nm and from 439 to 446 nm, respectively, after binding to prostaglandin D synthase. Bilirubin bound to the enzyme showed a bisignate CD spectrum with a (-) Cotton effect at 422 nm and a (+) Cotton effect at 472 nm, indicating a right-handed chirality. The ligands also inhibited prostaglandin D synthase activity noncompetitively in a concentration-dependent manner, with IC50 values between 3.9 and 10. 9 microM. Epididymal retinoic acid-binding protein and beta-lactoglobulin, two other lipocalin proteins that bind retinoids such as prostaglandin D synthase, did not show any significant interaction with bile pigments or thyroid hormones. These results show that prostaglandin D synthase binds small lipophilic ligands with a specificity distinct from that of other lipocalins.
Targeting cell-extracellular matrix (ECM) interactions to enhance radiation efficacy for breast cancer treatment (2005)

Proc Amer Assoc Cancer Res, Volume 46, 2005

1659 

Background: Cell interactions with the extracellular matrix (ECM) have been shown to affect radiation response in several malignant cell lines, including breast cancer. β1 integrin is a critical mediator of cell-ECM interactions and has been implicated in multiple stages of cancer progression. β1 integrin mediated signaling has been shown to enhance cancer cell survival following radiation (Cordes, 2002). We have previously shown that ionizing radiation (IR) induces persistent and heritable changes in β1 integrin expression and distribution in human mammary epithelial cells cultured in a 3-dimensional laminin-rich culture (3D-rBM). To investigate how β1 integrin signaling modifies radiation response in the context of normal mammary epithelial cells and malignant cells, we tested the ability of β1 integrin inhibitory monoclonal antibody, AIIB2, to modify radiation effects in culture and in vivo. Methods: To model normal and malignant breast cells in their physiologic microenvironment, we propagated both non-malignant and tumorigenic breast cells in 3D-rBM. Non-malignant S1 cells form organized acinar structures while tumorigenic cell lines, T4-2, MDA-MB-231 and MCF-7 form disorganized, invasive colonies. To disrupt cell-ECM signaling via β1 integrin, β1 integrin inhibitory antibody, AIIB2 was added to cultures alone or 24 hours prior to a single administration of ionizing radiation at doses from 0-8 Gy. Cultures were assayed 48-72 hours after treatment for proliferation (by presence of Ki-67 nuclear antigen) and apoptosis (by TUNEL). To test the effects of these treatments in vivo, T4-2 xenografts were established in adult female nu -/- mice and given AIIB2 alone or in combination with single fractions of ionizing radiation (0-8 Gy). Tumors were evaluated for growth and for proliferation and apoptosis ex-vivo. Results: Inhibition of β1 integrin with monoclonal AIIB2 in combination with ionizing radiation increased the cytostatic effect in malignant tumors in 3D-rBM compared to antibody alone. In contrast, there was little effect on non-malignant cell line, S-1 in culture. In vivo, the combination of AIIB2 and IR had an increased cytostatic effect on T4-2 xenografts compared to AIIB2 alone with minimal toxicity. Conclusions: Malignant breast cell colonies are susceptible to decreased growth and increased apoptosis with β1 integrin inhibitory antibody and IR. In contrast, β1 integrin signaling in the context of normal tissue organization is refractory to β1 integrin inhibition and IR. The combination of β1 integrin inhibition using monoclonal antibody AIIB2 enhances the therapeutic efficacy of IR in malignant breast cancer and has potential for therapeutic clinical applications.
Identification and Quantification of Astaxanthin Esters in Shrimp (Pandalus borealis) and in a Microalga (Haematococcus pluvialis) by Liquid Chromatography−Mass Spectrometry Using Negative Ion Atmospheric Pressure Chemical Ionization (2004)

Negative ion liquid chromatography-atmospheric pressure chemical ionization mass spectrometry [negative ion LC-(APCI)MS] was used for the identification of astaxanthin esters in extracts of commercial shrimp (Pandalus borealis) and dried microalga (Haematococcus pluvialis) samples. A cleanup step using a normal phase solid phase extraction (SPE) cartridge was applied prior to analysis. Recovery experiments with astaxanthin oleate as model compound proved the applicability of this step (98.5 +/- 7.6%; n = 4). The assignment of astaxanthin esters in negative ion LC-(APCI)MS was based on the detection of the molecular ion (M*-) and the formation of characteristic fragment ions, resulting from the loss of one or two fatty acids. Quantification of individual astaxanthin esters was performed using an astaxanthin calibration curve, which was found to be linear over the required range (1-51 micromol/L; r2 = 0.9996). Detection limits, based on the intensity of M*-, a signal-to-noise ratio of 3:1, and an injection volume of 20 microL, were estimated to be 0.05 microg/mL (free astaxanthin), 0.28 microg/mL (astaxanthin-C16:0), and 0.78 microg/mL (astaxanthin-C16:0/C16:0), respectively. This LC-(APCI)MS method allows for the first time the characterization of native astaxanthin esters in P. borealis and H. pluvialis without using time-consuming isolation steps with subsequent gas chromatographic analyses of fatty acid methyl esters. The results suggest that the pattern of astaxanthin-bound polyunsaturated fatty acids of P. borealis does not reflect the respective fatty acid pattern found in triacylglycerides. Application of the presented LC-(APCI)MS technique in common astaxanthin ester analysis will forestall erroneous xanthophyll ester assignment in natural sources.
Detection of oxidant sensitive thiol proteins by fluorescence labeling and two-dimensional electrophoresis (2002)

Oxidants can activate signaling pathways and modulate a variety of cellular activities. Their action at a molecular level involves the post-translational modification of protein thiols. We have developed a proteomic method to monitor the reduction and oxidation of protein thiols, and identify those thiol proteins most sensitive to oxidation. Cells were disrupted in the presence of N-ethylmaleimide to block the reduced thiol proteins and dithiothreitol was added to reduce the oxidized thiol proteins before labeling with 5-iodoacetamidofluorescein. Two-dimensional (2-D) electrophoresis was used to resolve the labeled samples. We applied the method to Jurkat T lymphocytes and examined the effect of diamide on the oxidized and reduced thiol protein profiles. A small percentage of protein thiols were already oxidized in untreated cells. Exposure of cells to 2 mM diamide for ten minutes led to a dramatic increase in thiol protein oxidation as seen in the oxidized thiol protein map. However, it was difficult to detect any change in the pattern of reduced thiol proteins. Separation of proteins by 2-D electrophoresis revealed approximately 200 thiol proteins that were oxidized by diamide treatment. This method will be valuable in elucidating redox signaling pathways.
Further Genetic and Enzymological Characterization of the Three Bacillus subtilis Deoxyribonucleic Acid Polymerases (1973)

Bacillus subtilis has three DNA polymerases. Polymerase III is necessary for DNA replication while polymerase I is involved in DNA repair. Four independent mutations leading to loss of polymerase I activity were mapped by transformation between mdh and phoP. Since one of these mutant strains produces a heat-labile polymerase this locus is likely the polymerase I structural gene. Some polymerase III mutants fail to grow at elevated temperatures and have a greatly increased mutation rate. The structural genes for polymerases I and III are unlinked. Purified preparations of the three B. subtilis DNA polymerases have been characterized. Polymerases II and III catalyze a high rate of synthesis in the absence of a full deoxyribonucleoside triphosphate complement, the mechanism of which is probably a truncation of the normal synthetic process. Arabinosylcytosine triphosphate competitively inhibits polymerases II and III as well as DNA synthesis in toluene-treated cells. This analogue is incorporated by these polymerases. Single-stranded DNA is a potent inhibitor of polymerases II and III but not I. The B. subtilis polymerases are readily separable by column chromatography and respond differently to high ionic strength, heat, sulfhydryl reagents, arylazopyrimidines, and various templates. The differences and similarities of the three B. subtilis enzymes relative to the correspondingly numbered Escherichia coli enzymes are discussed.
Palliation of malignant ascites by the LeVeen peritoneo-venous shunt (1980)

A LeVeen peritoneo-venous shunt was placed in each of 5 patients under local anesthesia to relieve symptomatic malignant ascites. All patients had marked ascites due to histologically documented intraabdominal carcinomatosis, extensive hepatic neoplasm, or a combination of malignant ascites and severe parenchymal liver disease. Cases included metastatic breast carcinoma, pancreatic carcinoma, melanoma, and primary cholangiocarcinoma. Prompt relief of respiratory distress and discomfort associated with tense ascites was achieved in all patients; however, survival was short (one week to seven months) due to advanced disease. The LeVeen shunt can provide effective palliation of malignant ascites in carefully selected symptomatic patients.
Extracellular enzyme synthesis in a sporulation-deficient strain of Bacillus licheniformis (1995)

A deletion of the spoIIAC gene of Bacillus licheniformis was prepared in vitro by using the splicing-by-overlap-extension technique. This gene was introduced into B. licheniformis on a temperature-sensitive plasmid, and following integration and excision from the chromosome, a precisely located deletion on the chromosomal gene was prepared. The mutated bacterium was totally asporogenous and formed abortively disporic cells characterized by asymmetric septa at the poles of the cells. Qualitative plate tests revealed that the bacterium synthesized normal levels of DNase, polygalacturonate lyase, protease, RNase, and xylanase, but the hydrolysis zones due to beta-1,3-glucanase and carboxymethyl cellulase activity were smaller in the mutant than in the parent strain. The synthesis of alkaline protease was the same in batch cultures of the mutant and the parent during prolonged incubation for 72 h, but the alpha-amylase yields were reduced by about 30% by the mutation.
DNA Uptake in Bacteria (1999)

Natural competence is widespread among bacterial species. The mechanism of DNA uptake in both gram-positive and gram-negative bacteria is reviewed. The transformation pathways are discussed, with attention to the fate of donor DNA as it is processed by the competent cell. The proteins involved in mediating various steps in these pathways are described, and models for the transformation mechanisms are presented. Uptake of DNA across the inner membrane is probably similar in gram-positive and gram-negative bacteria, and at least some of the required proteins are orthologs. The initial transformation steps differ, as expected, from the presence of an outer membrane only in the gram-negative organisms. The similarity of certain essential competence proteins to those required for the assembly of type-4 pili and for type-2 protein secretion is discussed. Finally several hypotheses for the biological role of transformation are presented and evaluated.
Role of interleukin‐6 for left ventricular remodeling and survival after experimental myocardial infarction (2003)

Circulating levels of interleukin (IL)-6 are elevated after myocardial infarction (MI) and associated with increased morbidity and mortality. Its myocardial expression post-MI suggests a pathophysiological role in this condition. To explore the role of endogenous IL-6, we analyzed MI size, left ventricular (LV) remodeling, and mortality after permanent coronary ligation in IL-6 knockout mice (IL-6-/-) and wild-type controls (WT). Six weeks after MI, IL-6-/- and WT had similar mortality rates, MI sizes, LV remodeling, and LV dysfunction in vivo, determined by catheterization. Infarct size 24 h post-MI, shown by 2,3,5-triphenyltetrazolium chloride (TTC) staining, was similar at 24 h. Treatment with exogenous IL-6 did not alter MI size in WT. Infarction resulted in marked phosphorylation of STAT3, without differences between genotypes. Leukemia inhibitory factor (LIF) protein was increased 48 h post-MI in IL-6-/-, and angiotensin II and AT1 receptor (AT1R) protein were strongly increased in IL-6-/- baseline and post-MI, suggesting compensatory up-regulation. Lack of IL-6 does not affect long-term MI size or LV function, remodeling, and survival. In mice lacking IL-6, other members of the IL-6 family such as LIF and other factors signaling via JAK/STAT such as angiotensin may act in a compensatory manner to activate the JAK/STAT pathway, thereby maintaining STAT3 phosphorylation, which is crucial for the cellular effects of IL-6 cytokines.
Nanoscale Fourier-Transform Imaging with Magnetic Resonance Force Microscopy (2003)

We present a versatile method for Fourier encoding the spatial distribution of spins detected by magnetic resonance force microscopy. Shuttling a magnetic particle in synchrony with an rf pulse sequence causes spins in a constant-field slice near the particle to precess at a rate proportional to their x or y coordinate. A two-dimensional spin-density map is recovered by a linear Fourier transform of a set of integrated force signals. Performance of the rf sequence is demonstrated experimentally and numerical simulations show that the method can achieve nanoscale resolution. Our approach offers a new route to manipulating spin wave functions down to the atomic scale.
3D-TV: coding of disocclusions for 2D+depth representation of multi-view images (2008)

The 2D+depth (2D+D) format has recently emerged as a good candidate for the transmission of multi-view content in a 3D-TV broadcasting environment because it allows the rendering of new views with minimum processing requirements. Its main drawback is the appearance of disoccluded areas in the rendered views. We explore a way to encode these disoccluded areas as an enhancement layer in a 2D+D representation. We exploit the fact that the disocclusion is generally an extension to the farther side in a depth edge. We used an interpolating wavelet decomposition of the horizontal line formed by embedding the disoccluded area between the pixels defining the depth edge. This strategy preserves the value of pixels in the transmitted view. Our results show that the proposed method reduces the amount of information needed if compared to the simultaneous transmission of all views while improving the quality of the new views rendered from the 2D+D representation.
Reliable communication in the presence of failures (1987)

The design and correctness of a communication facility for a distributed computer system are reported on. The facility provides support for fault-tolerant process groups in the form of a family of reliable multicast protocols that can be used in both local- and wide-area networks. These protocols attain high levels of concurrency, while respecting application-specific delivery ordering constraints, and have varying cost and performance that depend on the degree of ordering desired. In particular, a protocol that enforces causal delivery orderings is introduced and shown to be a valuable alternative to conventional asynchronous communication protocols. The facility also ensures that the processes belonging to a fault-tolerant process group will observe consistent orderings of events affecting the group as a whole, including process failures, recoveries, migration, and dynamic changes to group properties like member rankings. A review of several uses for the protocols in the ISIS system, which supports fault-tolerant resilient objects and bulletin boards, illustrates the significant simplification of higher level algorithms made possible by our approach.
Acquisition using simultaneous sources (2008)

We present a technique in which two or more shots are acquired during the time it normally takes to acquire one shot. The two (or more) shots are fired in a near simultaneous manner with small random time delays between the component sources. A variety of processing techniques are applied to produce the same seismic images which would have resulted from firing the simultaneous shots separately. These processing techniques rely on coherency of the wavefield in the common-shot domain and unpredictability in the common-receiver, common-offset, and common-midpoint domains. We present results of its application on synthetic 2D, real 2D, and real 3D data from the Gulf of Mexico. These results demonstrate that, in deep water with modest water-bottom reflectivity, no special processing is required, whereas in shallower water with stronger water-bottom reflectivity, the use of shot-separation techniques is necessary. We conclude that this technique can be used robustly to improve source sampling and, for example, to acquire data from a range of azimuths simultaneously. This has important implications for the economics of wide-azimuth acquisition.