gebhart/patrepeval huggingface dataset:
Database Performance Tuning Handbook, with CD-ROM (1997)

From the Publisher:
Database administrators, programmers, system programmers, and technical specialist are responsible for optimizing database usage to improve system performance, but recent changes in database marketplace and the advent of Open Data Base Connectivity have forced them to learn and manage more than one database product.Fortunately, Jeffrey Allan Dunham's Database Performance Tuning Handbook covers all major database products and performance issues in one comprehensive volume.
Genetic and Antigenic Diversity ofEhrlichia chaffeensis:Comparative Analysis of a Novel Human Strain from Oklahoma and Previously Isolated Strains (1997)

A new Ehrlichia strain, designated as Ehrlichia chaffeensis, Sapulpa strain, was isolated from a patient from Oklahoma with severe ehrlichiosis. Isolation of the ehrlichial pathogen was achieved by inoculating patient blood onto HEL cells and DH82 cells. Antigenic properties of the new isolate were characterized with monoclonal antibodies, homologous patient serum, and polyclonal rabbit serum by Western immunoblotting. The results showed antigenic differences and protein size variation of Sapulpa strain compared with the other 2 strains of E. chaffeensis. Sequencing of the 16S rRNA gene showed 100% identity to that of E. chaffeensis, strain 91HE17. Polymerase chain reaction and sequencing of DNA homologous to the 120-kDa protein gene of E. chaffeensis, Arkansas strain, showed that this gene of Sapulpa strain was smaller than that of Arkansas strain and contained a repeat region with three tandem repeat units.
Chronic kidney disease: role of sympathetic nervous system activation and potential benefits of renal denervation (2013)

The prevalence of chronic kidney disease (CKD) and end-stage renal disease continues to increase worldwide. Hypertension and diabetes are recognised as two major factors contributing to further progression of CKD. Importantly, progressive renal impairment increases cardiovascular morbidity and mortality. Despite advances in pharmacological antihypertensive and anti-diabetic approaches, the alarming number of patients developing nephropathy indicates the failure of the available treatment strategies. The relevance of sympathetic activation for the development and progression of chronic kidney disease is well established. Likewise, progressive renal failure results in exaggerated sympathetic activation leading to a vicious cycle, providing the rationale for the use of renal denervation to modulate directly the mechanisms underlying disease progression. While initial data on the safety and effectiveness of the procedure to lower BP were obtained in patients with resistant hypertension and preserved renal function, there are now preliminary data to suggest that this approach can also be applied safely in patients with stage 3-4 CKD. Similarly, first reports applying renal denervation in patients with end-stage renal disease on dialysis demonstrate favourable effects. If appropriately designed clinical trials can confirm these initial observations, renal denervation may become a valuable new treatment option for the large cohort of patients with CKD.
Age-Related Nuclear Cataract: A Lens Transport Problem (2000)

Age-related nuclear cataract is a major cause of blindness. It is characterised by opacification and colouration in the centre of the lens and is accompanied by extensive protein oxidation. The reason for the onset of nuclear cataract is not known, but it is proposed here that the underlying cause is the development, with age, of a barrier to the transport of metabolites within the lens. Such a barrier may result in an increase in the half-lives of reactive molecules, such as UV filters, thus promoting posttranslational modification of proteins in the nucleus and may also act to prevent an adequate flux of antioxidants from reaching the lens interior and, as a consequence, allow oxidation of nuclear components. Further, this oxidation may take place even if the lens outer cortex and epithelium remain perfectly functional.
The MTT Tetrazolium Salt Assay Scrutinized: How to Use this Assay Reliably to Measure Metabolie Activity of Cell Cultures in vitro for the Assessment of Growth Characteristics, IC50-Values and Cell Survival (1995)

The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide (MTT) assay is widely used for in vitro measurement of the metabolic viability of cell cultures subjected to different culture conditions. This convenient assay, which is based on the ability of viable cells to produce formazan, can be affected significantly by a number of conditions. These conditions can be roughly divided into groups, firstly influences which affect the spectrum of the produced formazan and secondly influences which affect the amount of formazan produced per cell. We studied the various chemical and biochemical aspects involved in the MTT assay. Our data indicated that microscopical viewing of cell cultures before and after performing the assay, a medium renewal with a well-defined MTT-incubation medium at the end of the culture period and regular cell counting are essential steps to ensure a reliable performance of the MTT assay. In conclusion, providing the necessary precautions are taken, the MTT assay can be used reliably to measure metabolic activity of cell cultures in vitro for the assessment of growth characteristics, IC50-values and cell survival.
Antitumor efficacy, pharmacokinetics, and biodistribution of NX 211: a low-clearance liposomal formulation of lurtotecan. (2000)

Lurtotecan is a clinically active water-soluble camptothecin analogue that has been formulated into a low-clearance unilamellar liposome, NX 211. Comparative studies between free drug and NX 211 have been performed assessing pharmacokinetics in nude mice, tissue distribution in tumor-bearing mice, and antitumor efficacy in xenografts. Compared with lurtotecan, NX 211 demonstrated a significant increase in plasma residence time and a subsequent 1500-fold increase in the plasma area under the drug concentration curve. The volume of distribution was also greatly restricted, suggesting altered tissue distribution. Evaluation of tissues 24 h after administration of either [14C]NX 211 or [14C]lurtotecan to ES-2 tumor-bearing mice demonstrated a 40-fold increase in radiolabeled compound in the tumors of NX 211-treated mice compared with mice treated with lurtotecan. In single-dose efficacy studies, NX 211 produced a consistent 3-fold or greater increase in therapeutic index compared with lurtotecan in both the KB and ES-2 xenograft models. When compared at equitoxic levels in repeat-dose efficacy studies, NX 211 generated durable cures lasting >60 days and a 2-8-fold increase in log10 cell kill, compared with lurtotecan and topotecan, respectively. Together, these data demonstrate that NX 211 has significant therapeutic advantage over lurtotecan and that the improved antitumor activity is consistent with increased exposure and enhanced drug delivery to tumor sites.
Prognostic importance of c-erbB-2 expression in breast cancer. International (Ludwig) Breast Cancer Study Group. (1992)

We conclude that tumors with overexpression of the c-erbB-2 oncogene are less responsive to cyclophosphamide, methotrexate, and fluorouracil (CMF)-containing adjuvant therapy regimens than those with a normal amount of gene product.
Lymphoid and myeloid lineage commitment in multipotent hematopoietic progenitors (2010)

Summary: Hematopoietic stem cells (HSCs) continuously replenish all classes of blood cells through a series of lineage restriction steps that results in the progressive loss of differentiation potential to other cell lineages. This review focuses on the recent advances in understanding one of the earliest differentiation steps in HSC maturation, which involves the diversification of the lymphoid and myeloid cell lineages, the two major branches of hematopoietic cells. We discuss progress in the identification and characterization of progenitor populations downstream of HSCs, which has been a key to understanding the sequential biological events that take place along the course of differentiation into a certain hematopoietic cell type. We also discuss the importance of bone marrow microenvironment in lymphoid and myeloid lineage choice.
Effects of formoterol and budesonide on GM-CSF and IL-8 secretion by triggered human bronchial epithelial cells (2001)

The effect of formoterol, alone and in combination with budesonide, upon tumour necrosis factor-alpha stimulated (10 ng x mL(-1)) human bronchial epithelial cells was investigated. Addition of formoterol (> or = 10(-10) M) reduced granulocyte macrophage-colony stimulating factor (GM-CSF) levels, as assessed by enzyme-linked immunosorbent assay, by 40-50% and increased interleukin (IL)-8 levels by approximately 50%. The effects of formoterol were long lasting (23 h). Budesonide (10(-8) M) reduced the amounts of both cytokines (GM-CSF and IL-8) by 40%. Simultaneous addition of formoterol and budesonide reduced GM-CSF levels approximately 75%, while IL-8 levels were decreased approximately 40%, similar to the reduction obtained with budesonide alone. The glucocorticoid receptor (GR) antagonist RU486 did not influence the effect of formoterol, suggesting no involvement of the GR. Formoterol rapidly induced an elevation in intracellular cyclic adenosine monophosphate, which was reduced in the presence of propranolol. In addition, the alterations in cytokine secretion induced by formoterol could be fully blocked by propranolol, demonstrating that these effects are beta2-receptor mediated. In conclusion, the combination of budesonide and formoterol reduces the secretion of granulocyte macrophage-colony stimulating factor to basal levels and counteracts the capacity of formoterol alone to induce interleukin-8 production, modulations which may facilitate improved asthma control.
Suppression of acoustic noise in speech using spectral subtraction (1979)

A stand-alone noise suppression algorithm is presented for reducing the spectral effects of acoustically added noise in speech. Effective performance of digital speech processors operating in practical environments may require suppression of noise from the digital wave-form. Spectral subtraction offers a computationally efficient, processor-independent approach to effective digital speech analysis. The method, requiring about the same computation as high-speed convolution, suppresses stationary noise from speech by subtracting the spectral noise bias calculated during nonspeech activity. Secondary procedures are then applied to attenuate the residual noise left after subtraction. Since the algorithm resynthesizes a speech waveform, it can be used as a pre-processor to narrow-band voice communications systems, speech recognition systems, or speaker authentication systems.
Human cathepsin O. Molecular cloning from a breast carcinoma, production of the active enzyme in Escherichia coli, and expression analysis in human tissues. (1994)

A cDNA encoding a novel member of the cysteine proteinase family of proteins has been cloned from a human breast carcinoma cDNA library, by using a polymerase chain reaction-based cloning strategy. The isolated cDNA contains an open reading frame coding for a polypeptide of 321 amino acids that has been tentatively called cathepsin O. This protein presents all the structural features characteristic of the different cysteine proteinases identified to date, including the active site cysteine residue that is involved in covalent intermediate formation during peptide hydrolysis. The cathepsin O cDNA was expressed in Escherichia coli, and after purification and refolding, the recombinant protein was able to degrade the synthetic peptides benzyloxycarbonyl-Phe-Arg-7-amido-4- methylcoumarin and benzyloxycarbonyl-Arg-Arg-7-amido-4-methylcoumarin widely used as substrates for cysteine proteinases. Cathepsin O proteolytic activity was abolished by trans-epoxysuccinyl-L-leucylamido-(4-guanidino)butane (E-64), an inhibitor of this subclass of proteolytic enzymes, thus providing additional evidence that the isolated cDNA codes for an authentic cysteine proteinase. Northern blot analysis of poly(A)+ RNAs isolated from a variety of human tissues demonstrated that cathepsin O is expressed in all examined tissues, which is consistent with a putative role of this protein as a proteolytic enzyme involved in normal cellular protein degradation and turnover.
GT-1 Binding Site Confers Light Responsive Expression in Transgenic Tobacco (1990)

Light-dependent expression of rbcS, the gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase, which is the key enzyme involved in carbon fixation in higher plants, is regulated at the transcriptional level. Sequence analysis of the gene has uncovered a conserved GT motif in the -150 to -100 region of many rbcS promoters. This motif serves as the binding site of a nuclear factor, designated GT-1. Analysis of site-specific mutants of pea rbcS-3A promoter demonstrated that GT-1 binding in vitro is correlated with light-responsive expression of the rbcS promoter in transgenic plants. However, it is not known whether factors other than GT-1 might also be required for activation of transcription by light. A synthetic tetramer of box II (TGTGTGGTTAATATG), the GT-1 binding site located between -152 to -138 of the rbcS-3A promoter, inserted upstream of a truncated cauliflower mosaic virus 35S promoter is sufficient to confer expression in leaves of transgenic tobacco. This expression occurs principally in chloroplast-containing cells, is induced by light, and is correlated with the ability of box II to bind GT-1 in vitro. The data show that the binding site for GT-1 is likely to be a part of the molecular light switch for rbcS activation.
RAGE Activation by S100P in Colon Cancer Stimulates Growth, Migration, and Cell Signaling Pathways (2007)

These data indicate that S100P is expressed at greater levels in colon cancer than matched normal tissue and that S100P stimulates colon cancer cell growth, migration, Erk phosphorylation, and NFkappaB activation in vitro, suggesting that this ligand/receptor pair may be targeted for the development of new therapies.
Structural diversity in the Plasmodium falciparum merozoite surface antigen 2. (1991)

Antigens associated with the surface of merozoites of the malaria parasite Plasmodium falciparum are directly accessible to immune attack and therefore are prime vaccine candidates. We have previously shown that one of the two known merozoite surface antigens (merozoite surface antigen 2; MSA-2) exhibits considerable sequence and antigenic diversity in different isolates. The sequences of MSA-2 from three isolates revealed a central domain composed of repeats that vary in number, length, and sequence, flanked in turn by nonrepetitive variable sequences and by conserved N- and C-terminal domains. We report here the sequences of a further four MSA-2 alleles, containing repetitive sequences that are related but not identical to each other. The seven alleles of MSA-2 can be divided into two distinct allele families on the basis of nonrepetitive sequences. Hybridization studies with repeat probes indicated that all of the 44 P. falciparum isolates examined contained repeat regions similar to those defined in known MSA-2 sequences.
Impact of Drug Conjugation on Pharmacokinetics and Tissue Distribution of Anti-STEAP1 Antibody–Drug Conjugates in Rats (2011)

Antibody-drug conjugates (ADCs) are designed to combine the exquisite specificity of antibodies to target tumor antigens with the cytotoxic potency of chemotherapeutic drugs. In addition to the general chemical stability of the linker, a thorough understanding of the relationship between ADC composition and biological disposition is necessary to ensure that the therapeutic window is not compromised by altered pharmacokinetics (PK), tissue distribution, and/or potential organ toxicity. The six-transmembrane epithelial antigen of prostate 1 (STEAP1) is being pursued as a tumor antigen target. To assess the role of ADC composition in PK, we evaluated plasma and tissue PK profiles in rats, following a single dose, of a humanized anti-STEAP1 IgG1 antibody, a thio-anti-STEAP1 (ThioMab) variant, and two corresponding thioether-linked monomethylauristatin E (MMAE) drug conjugates modified through interchain disulfide cysteine residues (ADC) and engineered cysteines (TDC), respectively. Plasma PK of total antibody measured by enzyme-linked immunosorbent assay (ELISA) revealed ∼45% faster clearance for the ADC relative to the parent antibody, but no apparent difference in clearance between the TDC and unconjugated parent ThioMab. Total antibody clearances of the two unconjugated antibodies were similar, suggesting minimal effects on PK from cysteine mutation. An ELISA specific for MMAE-conjugated antibody indicated that the ADC cleared more rapidly than the TDC, but total antibody ELISA showed comparable clearance for the two drug conjugates. Furthermore, consistent with relative drug load, the ADC had a greater magnitude of drug deconjugation than the TDC in terms of free plasma MMAE levels. Antibody conjugation had a noticeable, albeit minor, impact on tissue distribution with a general trend toward increased hepatic uptake and reduced levels in other highly vascularized organs. Liver uptakes of ADC and TDC at 5 days postinjection were 2-fold and 1.3-fold higher, respectively, relative to the unmodified antibodies. Taken together, these results indicate that the degree of overall structural modification in anti-STEAP1-MMAE conjugates has a corresponding level of impact on both PK and tissue distribution.
Primary diffuse large B-cell lymphomas of the central nervous system are targeted by aberrant somatic hypermutation (2003)

We have addressed whether aberrant ongoing hypermutation can be detected in the proto-oncogenes PIM1, c-MYC, RhoH/TTF, PAX5, and the tumor-suppressor gene CD95 in primary central nervous system lymphomas (PCNSLs) derived from immunocompetent HIV-negative patients. Nine of 10 PCNSLs analyzed harbored somatic mutations in the PIM1, c-MYC, RhoH/TTF, and PAX5 genes, but not in the CD95 gene, with 8 tumors carrying alterations in at least 2 of these genes. Furthermore, ongoing aberrant mutation was evidenced in a subset of PCNSLs (2 of 3). Although most of the mutations corresponded to base pair substitutions, deletions were also present. The mean mutation frequency was approximately 60-fold lower for these genes compared with the values obtained for immunoglobulin genes in PCNSL. They were increased 2- to 5-fold compared with extracerebral diffuse large B-cell lymphoma (DLBCL). In summary, our data demonstrate aberrant somatic hypermutations at high frequency in the PIM1, PAX5, RhoH/TTF, and c-MYC genes in most PCNSLs. These findings may indicate a pathogenic role for aberrant somatic hypermutation in PCNSL development. In contrast, although mutations were detected in exon 9 of the CD95 gene, the lack of mutations in the 5' region provides no evidence for the CD95 gene as a target for aberrant somatic mutation.
Purification and Some Properties of Ribonuclease from Xenopus laevis Eggs. (1993)

A 122 kDa RNase from eggs of Xenopus laevis was purified by sequential chromatography on Sephadex G-75, DEAE-cellulose, heparin-Sepharose and TSK gel G3000SW columns, and gave a single 60 kDa band on SDS-polyacrylamide gel electrophoresis under reducing and nonreducing conditions. The RNase composed of two 60 kDa subunits is able to recognize pyrimidine bases specifically. The pH optimum of the RNase was 7.5 in Tris-HCl buffer. The enzyme activity was abolished by treatment at 80 degrees C for 5 min and pH 2 or 12 for 1 h. Since egg lectins with RNase activity obtained from Rana catesbeiana and R. japonica and bovine pancreatic RNase A show about 30% protein homology and these three proteins are 12-14 kDa heat-stable RNases, [K. Titani, K. Takio, M. Kuwada, K. Nitta, F. Sakakibara, H. Kawauchi, G. Takayanagi and S. Hakomori, Biochemistry, 26, 2189 (1987); Y: Kamiya, F. Oyama, R. Oyama, F. Sakakibara, K. Nitta, H. Kawauchi, Y. Takayanagi and K. Titani, J. Biochem. (Tokyo), 108, 139 (1990)], the data suggest that the X. laevis egg RNase is a unique protein compared with RNases from not only amphibians, but also mammals.
Differential Distribution and Expression of Panton-Valentine Leucocidin among Community-Acquired Methicillin-Resistant Staphylococcus aureus Strains (2005)

Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) is an emerging threat worldwide. CA-MRSA strains differ from hospital-acquired MRSA strains in their antibiotic susceptibilities and genetic backgrounds. Using several genotyping methods, we clearly define CA-MRSA at the genetic level and demonstrate that the prototypic CA-MRSA strain, MW2, has spread as a homogeneous clonal strain family that is distinct from other CA-MRSA strains. The Panton-Valentine leucocidin (PVL)-encoding genes, lukF and lukS, are prevalent among CA-MRSA strains and have previously been associated with CA-MRSA infections. To better elucidate the role of PVL in the pathogenesis of CA-MRSA, we first analyzed the distribution and expression of PVL among different CA-MRSA strains. Our data demonstrate that PVL genes are differentially distributed among CA-MRSA strains and, when they are present, are always transcribed, albeit with strain-to-strain variability of transcript levels. To directly test whether PVL is critical for the pathogenesis of CA-MRSA, we evaluated the lysis of human polymorphonuclear leukocytes (PMNs) during phagocytic interaction with PVL-positive and PVL-negative CA-MRSA strains. Unexpectedly, there was no correlation between PVL expression and PMN lysis, suggesting that additional virulence factors underlie leukotoxicity and, thus, the pathogenesis of CA-MRSA.
Broadband MIMO-OFDM wireless communications (2004)

Orthogonal frequency division multiplexing (OFDM) is a popular method for high data rate wireless transmission. OFDM may be combined with antenna arrays at the transmitter and receiver to increase the diversity gain and/or to enhance the system capacity on time-varying and frequency-selective channels, resulting in a multiple-input multiple-output (MIMO) configuration. The paper explores various physical layer research challenges in MIMO-OFDM system design, including physical channel measurements and modeling, analog beam forming techniques using adaptive antenna arrays, space-time techniques for MIMO-OFDM, error control coding techniques, OFDM preamble and packet design, and signal processing algorithms used to perform time and frequency synchronization, channel estimation, and channel tracking in MIMO-OFDM systems. Finally, the paper considers a software radio implementation of MIMO-OFDM.
Protease inhibitor variants in children and young adults with chronic asthma. (1979)

The results of systematic medical histories and pulmonary function tests on 26 children and young adults, 10 with Pi variant alpha1-antitrypsin phenotypes and 16 Pi normals, are reported. These subjects were selected from 57 consecutive patients who had chronic asthma. The incidence of Pi variants was 20.4% among 46 Caucasian subjects (ages seven to 21 years). The Pi variant patients required more bronchodilators and long-term corticosteroid therapy. Among the parents and siblings, 50% of those with abnormal Pi type had chronic obstructive lung disease. Grandparents of the Pi abnormal probands had greater incidence of chronic obstructive lung disease (P less than 0.05). Baseline specific airways conductance and maximal midexpiratory flow rates did not discriminat between the two groups. However, bronchodilator inhalation showed the Pi variant group to be significantly less responsive than the Pi normal group. Pi heterozygous state, particularly Pi MZ, should be considered when a young person with chronic asthma is unresponsive to adequate doses of bronchodilators and needs prolonged use of corticosteroids.