gebhart/patrepeval huggingface dataset:
Data Mining Using MLC a Machine Learning Library in C (1997)

Data mining algorithmsincluding machine learning, statistical analysis, and pattern recognition techniques can greatly improve our understanding of data warehouses that are now becoming more widespread. In this paper, we focus on classification algorithms and review the need for multiple classification algorithms. We describe a system called MLC++ , which was designed to help choose the appropriate classification algorithm for a given dataset by making it easy to compare the utility of different algorithms on a specific dataset of interest. MLC ++ not only provides a workbench for such comparisons, but also provides a library of C ++ classes to aid in the development of new algorithms, especially hybrid algorithms and multi-strategy algorithms. Such algorithms are generally hard to code from scratch. We discuss design issues, interfaces to other programs, and visualization of the resulting classifiers. 1 Introduction Data warehouses containing massive amounts of data have been b...
Principles and Practice of Immunoassay (1991)

Each chapter of this book aims to explore the basic physical and chemical principles involved in the immunoassay techniques discussed. The book also looks at the optimization and limitations of method
Partially-desulfated heparin improves survival inPseudomonaspneumonia by enhancing bacterial clearance and ameliorating lung injury (2013)

Nosocomial pneumonia (NP, or hospital-acquired pneumonia) is associated with infections originating from hospital-borne pathogens. Persistent microbial presence and acute lung injury are common features of these infections, contributing to the high mortality rates and excessive financial burden for these patients. Pseudomonas aeruginosa (PA), a gram-negative opportunistic pathogen, is one of the prominent pathogens associated with NP. PA pneumonia is characterized by excessive secretion of inflammatory cytokines, neutrophil infiltration, and subsequent lung damage. The persistent presence of PA along with overwhelming inflammatory response is suggestive of impairment in innate immunity. High mobility group box 1 (HMGB1), a recently discovered potent pro-inflammatory cytokine, plays an important role in PA lung infections by compromising innate immunity via impairing phagocyte function through toll-like receptors (TLR) TLR2 and TLR4. ODSH (2-O, 3-O-desulfated heparin), a heparin derivative with significant anti-inflammatory properties but minimal anti-coagulatory effects, has been shown to reduce neutrophilic lung injury in the absence of active microbial infections. This study examined the effects of ODSH on PA pneumonia. This study demonstrates that ODSH not only reduced PA-induced lung injury, but also significantly increased bacterial clearance. The ameliorated lung injury, together with the increased bacterial clearance, resulted in marked improvement in the survival of these animals. The resulting attenuation in lung injury and improvement in bacterial clearance were associated with decreased levels of airway HMGB1. Furthermore, binding of HMGB1 to its receptors TLR2 and TLR4 was blunted in the presence of ODSH. These data suggest that ODSH provides a potential novel approach in the adjunctive treatment of PA pneumonia.
Efficient depletion of alloreactive donor T lymphocytes based on expression of two activation‐induced antigens (CD25 and CD69) (2000)

T lymphocytes play an important role in allogeneic bone marrow/stem cell transplantation by supporting engraftment and immune recovery. Moreover, donor T cells have been shown to mediate the so-called graft-versus-leukaemia effect and are, therefore, increasingly used for adoptive immunotherapy. However, T-cell infusions are associated with the risk of a graft-versus-host reaction, which may lead to a life-threatening disease. To overcome this problem, we followed a new strategy for the exclusive depletion of alloreactive cells. We activated allogeneic T cells by cultivation on an adherent cell layer derived from peripheral blood. We then depleted activated cells based on the expression of CD25, CD69 or both activation-induced antigens using magnetic cell sorting. Mixed lymphocyte culture (MLC) reactions and helper T-lymphocyte precursor cell frequency (HTLP-f) assays demonstrated that this technique led to a significant decrease in alloreactivity of 'donor' cells, which at the same time preserved reactivity against third-party cells. The lowest level of alloreactivity was found when CD25 and CD69 antibodies were used together for depletion. This corresponds with our observation that expression of CD25 or CD69 may partially represent different activation pathways. We conclude that ex vivo depletion of CD25- and CD69-expressing alloreactive cells may help to overcome limitations of adoptive immunotherapy.
[Animal study of intravascular gene therapy based on polyurethane implantable devices]. (2006)

Site-specific intravascular delivery of adenoviral vectors for gene therapy can be achieved with these two kinds of polyurethane implants utilizing the antivector antibody tethering mechanism.
Mechanistic Studies and Methods To Prevent Aglycon Transfer of Thioglycosides (2006)

Thioglycosides have been employed extensively for the synthesis of complex oligosaccharides, carbohydrate libraries, and mimetics of O-glycosides. While very useful, aglycon transfer is a problematic side reaction with thioglycosides. In this paper, a series of mechanistic studies are described. The aglycon transfer process is shown to affect both armed and disarmed thioglycosides, cause anomerization of the carbon-sulfur bond of a thioglycoside, and destroy the product of a glycosylation reaction. The results indicate that the aglycon transfer process can be a major problem for a wide range of thioglycosides. This side reaction is especially important to consider when carrying out complex reactions such as solid-phase glycosylations, one-pot or orthogonal multicomponent glycosylations, and construction of carbohydrate libraries. To prevent transfer, a number of modified aglycons were examined. The 2,6-dimethylphenyl (DMP) aglycon was found to effectively block transfer in a variety of model studies and glycosylation reactions. The DMP group can be installed in one step from a commercially available thiol (2,6-dimethylthiophenol) and is useable as a glycosyl donor. On the basis of these features, the DMP group is proposed as a convenient and improved aglycon for thioglycosides.
Normalization of Striatal Tyrosine Hydroxylase and Reversal of Motor Impairment in Experimental Parkinsonism with Intravenous Nonviral Gene Therapy and a Brain-Specific Promoter (2004)

The goal of this work was to normalize striatal tyrosine hydroxylase (TH) activity with intravenous nonviral TH gene therapy and at the same time eliminate ectopic TH gene expression in peripheral organs such as liver in the rat. TH-expression plasmids, containing either the SV40 promoter or the glial fibrillary acidic protein (GFAP) gene promoter, were globally delivered to the brain across the blood-brain barrier (BBB) after intravenous administration of pegylated immunoliposomes (PILs). The GFAP-TH- or SV40-TH-expression plasmids were encapsulated in the interior of 85-nm PILs, which were targeted across both the BBB and the neuronal cell membrane with a monoclonal antibody (mAb) to the transferrin receptor (TfR). Striatal TH activity was 98% depleted with the unilateral intracerebral injection of 6-hydroxydopamine. TH in the striatum ipsilateral to the lesion was normalized 3 days after the intravenous injection of 10 microg per rat of either the SV40-TH or the GFAP-TH plasmid DNA. Whereas the SV40-TH gene caused a 10-fold increase in hepatic TH activity, there was no increase in liver TH with the GFAP-TH gene. The GFAP-TH gene therapy caused an 82% reduction in apomorphine-induced rotation in the lesioned rats. Confocal microscopy using antibodies to TH, GFAP, and neuronal nuclei (NeuN) showed the GFAP-TH gene was selectively expressed in nigra-striatal neurons, with no expression in either cortical neurons, or astrocytes. These studies demonstrate that global delivery of exogenous genes to the brain is possible with intravenous nonviral gene transfer, and that ectopic gene expression is eliminated with the use of brain-specific gene promoters.
Thyroxine 5′-Deiodinase Activity of Rat Kidney: Observations on Activation by Thiols and Inhibition by Propylthiouracil* (1978)

Enzymatic 5′-deiodination of T4 in various tissues is known to be stimulated by thiols and inhibited by propylthiouracil (PTU). Dithiothreitol (DTT) stimulation of rat kidney T4 5′-deiodinase followed saturation kinetics. Inhibition of the enzyme by PTU (10-5 M) was overcome in a concentration-dependent manner by DTT, methimazole (MMI), and thiourea. Pretreatment of catalytically active kidney microsomal preparations with PTU caused persistent inhibition of enzyme activity, assayed in the absence of PTU. Similarly, injection of PTU in rats in a dosage of 5 μg/100 g BW or greater significantly impaired T4 5′-deiodination in subsequently isolated kidney microsomal preparations. Reagents that cleave disulfide bonds (DTT and KCN), as well as the reductant, Na2S2O4, and the thioureylene, MMI, partially restored activity to PTU-inactivated enzyme in a time- and concentration-dependent way. These observations suggest that PTU inhibition of T4 5′-deiodinase results from an interaction of PTU with the enzyme, possibly via a PTU-enzyme disulfide which can be prevented or reversed by thiols or thioureylene agents, and raise the possibility that protein sulfhydryl groups may undergo oxidation during the reductive 5′-deiodination of L-T4.
Update on the Kelch-like (KLHL) gene family (2013)

The Kelch-like (KLHL) gene family encodes a group of proteins that generally possess a BTB/POZ domain, a BACK domain, and five to six Kelch motifs. BTB domains facilitate protein binding and dimerization. The BACK domain has no known function yet is of functional importance since mutations in this domain are associated with disease. Kelch domains form a tertiary structure of β-propellers that have a role in extracellular functions, morphology, and binding to other proteins. Presently, 42 KLHL genes have been classified by the HUGO Gene Nomenclature Committee (HGNC), and they are found across multiple human chromosomes. The KLHL family is conserved throughout evolution. Phylogenetic analysis of KLHL family members suggests that it can be subdivided into three subgroups with KLHL11 as the oldest member and KLHL9 as the youngest. Several KLHL proteins bind to the E3 ligase cullin 3 and are known to be involved in ubiquitination. KLHL genes are responsible for several Mendelian diseases and have been associated with cancer. Further investigation of this family of proteins will likely provide valuable insights into basic biology and human disease.
Sodium Bisulfite Protects Against Radiogenic and Chemically Induced Transformation in Hamster Embryo and Mouse C3H/10T-1/2 Cells (1985)

Pretreatment of hamster embryo cells or mouse C3H/10T-1/2 cells with sodium bisulfite (0.5, 2.5, 5.0 and 100 ppm) inhibits the oncogenic transformation of the cells following their exposure to x-rays or benzo(a)pyrene. The results suggest that low doses of bisulfite, a widely used food additive, can serve as a radioprotective and chemopreventive agent with anticarcinogenic potential.
CYP2D6 catalyzes tamoxifen 4-hydroxylation in human liver. (1997)

The major metabolites of tamoxifen (tam) formed by animal and human liver microsomes are mono-N-demethylated tam, 4-hydroxy-tam (4-OH-tam), and tam-N-oxide. The N-desmethylated-tam and 4-OH-tam are formed by P450s, whereas the N-oxide is primarily formed by flavin-containing monooxygenase. Because 4-OH-tam is a highly potent antiestrogen (and possibly is the active anticancer tam metabolite) and is on the path of formation of the reactive intermediate that binds covalently to proteins and DNA, it was of importance to identify the P450(s) catalyzing its formation. In the current study, three different preparations of expressed human P450s in Escherichia coli, lymphoblastoma cells, and insect cell line and livers from several human donors were used to identify the P450 isoform catalyzing the 4-hydroxylation (preliminary results were reported by Dehal et al., Eleventh International Symposium on Microsomes and Drug Oxidations, p. 71. Los Angeles, 1996). Tam metabolism was examined with human CYP2C8, 2C9, 2C18, 2C19, and 2D6 expressed in E. coli. These P450s were reconstituted with P450 reductase and lipid and were incubated with 50 microM [3H]tam and NADPH at 37 degrees C for 60 min. Essentially all of the recombinant P450s catalyzed the N-demethylation to various degrees; however, only 2D6 yielded detectable levels of 4-OH-tam. The inclusion of cytochrome b5 in the reconstituted system of 2D6 and 2C9 did not significantly affect the rate of 4-hydroxylation, indicating that b5 is not essential for this activity. Tam metabolism by CYP1A1, 1A2, 2A6, 2B6, 2C8, 2C9, 2D6, 2E1, and 3A4, expressed in lymphoblastoma cells, revealed that only 2D6 significantly catalyzed the 4-hydroxylation. Tam metabolism by CYP2D6 coexpressed with P450 reductase in a baculovirus infected insect cell line ("supersomes") exhibited marked tam 4-hydroxylation. In an experiment with human liver microsomes, the inclusion of quinidine, a specific 2D6 inhibitor, resulted in approximately 50% inhibition of tam 4-hydroxylation without affecting N-demethylation. Polyclonal antibodies raised against 2D6 moderately inhibited (approximately 30%) the 4-hydroxylation in human liver microsomes. These results demonstrate a significant contribution by CYP2D6 to the catalysis of tam-4-hydroxylation by human liver.
Deoxyribonucleic Acid Profiling Analysis of 40 Human Thyroid Cancer Cell Lines Reveals Cross-Contamination Resulting in Cell Line Redundancy and Misidentification (2008)

Many of these human cell lines have been widely used in the thyroid cancer field for the past 20 yr and are not only redundant, but not of thyroid origin. These results emphasize the importance of cell line integrity, and provide the short tandem repeat profiles for a panel of thyroid cancer cell lines that can be used as a reference for comparison of cell lines from other laboratories.
<title>High throughput screening using dynamic fluorescence</title> (1995)

Multifrequency phase-modulation data for fluorescence lifetime and anisotropy decay standards have been obtained for liquid samples in 96-well microtiter plates. We coupled the bifurcated fiber optic probe of a fluorescence plate reader to a phase and modulation time- resolving fluorometer. Laser excitation was used and multifrequency data could be acquired quickly over a range of modulation frequencies from 15 to greater than 150 MHz, at each well position, through the use of multiharmonic Fourier methods. We evaluated the system's performance for UV-excited fluorescence, with the goal of screening quality or properties of proteins or peptides by steady-state or dynamic intrinsic fluorescence intensity or anisotropy using the high throughput 96-well plate format.
Multi-MW peak power single-transverse mode operation of a 100 micron core diameter, Yb-doped photonic crystal rod amplifier (2007)

We developed a gain-staged master-oscillator/power-amplifier source featuring an Yb-doped, 100&mgr;m-core rod-like photonic crystal fiber (PCF) as the final amplifier. From this PCF, we obtained 1ns pulses of energy in excess of 4.3 mJ, peak/average power ~ 4.5 MW / 42W, and spectral width ~20 GHz. The PCF emitted a near-Gaussian, single-transversemode beam of M<sup>2</sup>~1.3.
Expression and function of a CD 5 cDNA in human and murine T cells (1988)

In order to define the function of the CD 5 (T1, Leu 1, Tp 67 in the human; Ly-1 in the mouse) molecule, a cDNA clone of human CD 5 was expressed in a CD5-deficient Jurkat cell line and in a murine T cell hybridoma. A Jurkat subclone (Jurkat 9.9) produced interleukin 2 (IL 2) in response to anti-CD 3 monoclonal antibody (mAb) cross-linked to solid support. IL 2 production was enhanced by co-culture with the anti-CD 5 mAb OKT 1. A CD 5-deficient mutant clone Jurkat 1.15 was generated by treatment with ethyl methanesulfonate followed by selection with anti-CD 5 mAb plus complement. Jurkat 1.15 did not demonstrate enhancement of IL 2 production by OKT 1 in the presence of cross-linked anti-CD 3 mAb. A cDNA encoding human CD 5 was introduced into a defective retrovirus which was used to infect Jurkat 1.15. A Jurkat clone stably expressing CD 5 was established. In response to OKT 1, a rise in intracellular calcium was observed in both the parent Jurkat 9.9 and the CD 5+ infectant but not in the CD 5- mutant or a G 418- resistant control. Furthermore, expression of CD 5 restored the augmentation of IL 2 production by OKT 1 in response to cross-linked anti-CD 3 mAb. A murine T cell hybridoma By 155.16 which produces IL 2 in response to HLA-DR antigens was also infected with the CD 5-recombinant retrovirus and three stable CD 5+ infectants were generated. These hybridomas showed enhancement of IL 2 production by stimulation with OKT 1 in the presence of suboptimal concentrations of soluble anti-murine CD 3 mAb. These results provide further evidence that CD 5 provides a co-stimulatory signal for T cell activation.
Phase I clinical trial of a monoclonal antibody against CD40-ligand (IDEC-131) in patients with systemic lupus erythematosus. (2001)

IDEC-131 (humanized Mab against CD40L) administered in a single intravenous infusion at doses of 0.05-15.0 mg/kg is safe and well tolerated in patients with SLE.
Finite element analysis of the lumbar spine with a new cage using a topology optimization method (2005)

In recent years, degenerative spinal instability has been effectively treated with a cage. However, little attention is focused on the design concept of the cage. The purpose of this study was to develop a new cage and evaluate its biomechanical function using a finite element method (FEM). This study employed topology optimization to design a new cage and analyze stress distribution of the lumbar spine from L1 to L3 with a new cage by using the commercial software ANSYS 6.0. A total of three finite element models, namely the intact lumbar spine, the spine with double RF cages, and with double new cages, were established. The loading conditions were that 10Nm flexion, extension, lateral bending, and torsion, respectively, were imposed on the superior surface of the L1 vertebral body. The bottom of the L3 vertebral body was constrained completely. The FEM estimated that the new cage not only could be reduced to 36% of the volume of the present RF cage but was also similar in biomechanical performance such as range of motion, stress of adjacent disc, and lower subsidence to the RF cage. The advantage of the new cage was that the increased space allowed more bone graft to be placed and the cage saved material. The disadvantage was that stress of the new cage was greater than that of the RF cage.
Cyclic strain induces reorganization of integrin α5β1 and α2β1 in human umbilical vein endothelial cells (1997)

Cyclic strain has been shown to modulate endothelial cell (EC) morphology, proliferation, and function. We have recently reported that the focal adhesion proteins focal adhesion kinase (pp125FAK) and paxillin, are tyrosine phosphorylated in EC exposed to strain and these events regulate the morphological change and migration induced by cyclic strain. Integrins are also localized on focal adhesion sites and have been reported to induce by tyrosine phosphorylation of pp125FAK under a variety of stimuli. To study the involvement of different integrins in signaling induced by cyclic strain, we first observed the redistribution of alpha and beta integrins in EC subjects to 4 h cyclic strain. Human umbilical vein endothelial cells (HUVEC) seeded on either fibronectin or collagen surfaces were subjected to 10% average strain at a frequency 60 cycles/min. Confocal microscopy revealed that beta 1 integrin reorganized in a linear pattern parallel with the long axis of the elongated cells creating a fusion of focal adhesion plaques in EC plated on either fibronectin (a ligand for alpha 5 beta 1) or collagen (a ligand for alpha 2 beta 1) coated after 4 h exposure to cyclic strain. beta 3 integrin, which is a vitronectin receptor, did not redistribute in EC exposed to cyclic strain. Cyclic strain also led to a reorganization of alpha 5 and alpha 2 integrins in a linear pattern in HUVEC seeded on fibronectin or collagen, respectively. The expression of integrins alpha 5, alpha 2, and beta 1 did not change even after 24 h exposure to strain when assessed by immunoprecipitation of these integrins. Cyclic strain-induced tyrosine phosphorylation of pp125FAK occurred concomitant with the reorganization of beta 1 integrin. We concluded that alpha 5 beta 1 and alpha 2 beta 1 integrins play an important role in transducing mechanical stimuli into intracellular signals.
Neoadjuvant Therapy in Pancreatic Cancer (2007)

Pancreatic cancer is the fourth leading cause of cancer deaths in the United States. Surgical resection offers the only hope of cure, though the addition of chemoradiation in the adjuvant setting has been shown to improve survival over surgery alone. Many patients are unable to receive adjuvant therapy due to prolonged postoperative recovery. For this reason, administration of chemoradiation preoperatively (neoadjuvant) has been proposed as an alternative to postoperative treatment. In patients with resectable disease, neoadjuvant therapy results in similar survivals compared to postoperative therapy, with a greater proportion of patients able to complete treatment. For selected patients with borderline or unresectable disease, neoadjuvant therapy offers the potential for tumor downstaging and increasing the likelihood of a margin-negative resection. This article reviews the use of neoadjuvant therapy in the treatment of pancreatic cancer.
SCID Mice: A Suitable Model for Experimental Studies of Urologic Malignancies (1991)

In vivo studies on human malignant tumors are limited because of a lack of suitable animal models. In this study, the usefulness of SCID (severe combined immunodeficiency) mice, deficient in functions of both T- and B-lymphocytes, was evaluated. Inbred SCID mice were kept in isolated cages and 2 x 10(7) cells of KU-7, an established bladder carcinoma cell line, were inoculated in the subcutaneous tissue of the flank region of six SCID mice. Athymic nude mice were inoculated by the same method and served as the controls. The KU-7 cells were taken within 14 days in the injected region in all six SCID mice, while in only five out of eight nude mice. Tumors subsequently formed at the site of inoculation in these mice were confirmed to be transitional cell carcinomas histologically and intra-abdominal metastases were noted in two SCID mice. We conclude that SCID mice provide an ideal in vivo model for experimental studies of human urologic malignant tumors.