gebhart/patrepeval huggingface dataset:
Enhanced inhibition of thymidylate synthase by methotrexate polyglutamates. (1985)

We have studied the effects of methotrexate (MTX-Glu1) and the polyglutamate derivatives of methotrexate (MTXPGs) with 2, 3, 4, and 5 glutamyl residues on the catalytic activity of thymidylate synthase purified from MCF-7 human breast cancer cells and on the kinetics of the ternary complex formation by 5-fluoro-2'-deoxyuridine 5'-monophosphate, folate cofactor, and thymidylate synthase. MTX-Glu1 exhibited uncompetitive inhibition of thymidylate synthase when reaction kinetics were analyzed by either double reciprocal plots or a computerized mathematical model based on nonlinear least-squares curve fitting. The Ki for MTX-Glu1 inhibition was 13 microM and the I50 was 22 microM, irrespective of the degree of polyglutamation of the folate. In contrast, the polyglutamated derivatives of MTX all acted as noncompetitive inhibitors. The MTXPGs had 75-300-fold greater potency than MTX-Glu1 as inhibitors of thymidylate synthase catalytic activity, with Ki values from 0.17 to 0.047 microM for MTX-Glu2 to MTX-Glu5, respectively. Neither MTX-Glu1 nor MTXPGs promoted the formation of a charcoal-stable ternary complex with thymidylate synthase and 5-fluoro-2'-deoxyuridine 5'-monophosphate. CH2-H4PteGlu5 (where PteGlu represents pteroylglutamic acid) was found to be 40-fold more potent than CH2-H4PteGlu1 in participating in the formation of a ternary complex, and 10 microM MTX-Glu5 significantly inhibited the formation of a ternary complex containing this folate as cofactor. The inhibition was determined to be due to a reduction in the kon. The potency of this inhibition was markedly greater in the presence of CH2-H4PteGlu1 as compared to CH2-H4PteGlu5. This finding suggests that the degree of interference with complex formation in intact cells would depend on the state of polyglutamation of available folate cofactor. Ternary complex formation with H2PteGlu5 as the folate cofactor was also investigated, and a 50% reduction in complex formation was found in the presence of a 2 microM concentration of MTX-Glu5. These findings have significant implications regarding the mechanism of action of MTX-Glu1 and contribute to an understanding of the complex interactions of MTX-Glu1 and 5-fluorouracil.
MLL -Rearranged B Lymphoblastic Leukemias Selectively Express the Immunoregulatory Carbohydrate-Binding Protein Galectin-1 (2010)

In B-ALL, Gal-1 is a highly sensitive and specific biomarker of MLL rearrangement that is likely induced by a MLL-dependent epigenetic modification.
[An experimental study on the reverse mechanism of PPAR-gamma agonist rosiglitazone in rats with non-alcoholic steatohepatitis]. (2007)

PPAR-gamma specific agonist rosiglitazone can play an anti-inflammatory role by IKK-beta/I kappa B/NF-kappa B/TNF alpha signal ways, and minimize inflammatory reaction at cellular and molecular levels. This may help to provide a new idea for treating NASH effectively.
Mechanism of human keratinocyte migration on fibronectin: Unique roles of RGD site and integrins (1992)

The migration of human keratinocytes over the wound bed plays an important role in the re-epithelialization of cutaneous wounds. Fibronectin, a large glycoprotein matrix component that is abundant within cutaneous wound beds, promotes keratinocyte migration. However, the mechanisms by which keratinocytes migrate over fibronectin are unknown. In this study, we sought to identify specific sites within the fibronectin molecule that induce keratinocyte locomotion and to characterize the cell surface receptors involved. The data show that the domain within the fibronectin molecule that induces human keratinocyte migration is the 120 kD cell-binding domain close to the carboxyl terminus. The 40 kD heparin-binding domain near the carboxyl terminus and the 45 kD gelatin-binding domain near the amino terminus did not promote keratinocyte migration. In addition, keratinocyte migration on both fibronectin and the 120 kD cell-binding domain was completely inhibited by the presence of GRGDSP peptide, suggesting that keratinocyte migration on fibronectin is mediated by recognizing the RGD sequence located within the cell-binding domain of fibronectin. Furthermore, keratinocytes were able to migrate directly on immobilized RGD substratum. Cell migration on fibronectin is mediated by the alpha 5 beta 1 integrin since antibodies blocking the alpha 5 and the beta 1 subunits completely inhibited keratinocyte migration on fibronectin. In addition, we demonstrate that human keratinocytes express alpha 5 beta 1 integrin in culture by flow cytometry.
Comparing Block Cipher Modes of Operation on MICAz Sensor Nodes (2009)

Wireless sensor networks are a key technology for "ubiquitous computing" applications. The challenges of securing such networks are tremendous. On the one side, sensor nodes are commonly deployed in potentially hostile environments, which requires additional protection in comparison to traditional computing systems. On the other side, the capabilities of sensor nodes in terms of computing power, memory, and available energy are severely limited, which makes it hard to adapt existing security solutions. In this paper, we examine different options for providing confidentiality and message authentication to sensor network communication. More specifically, we examine four modern block cipher modes of operation regarding their applicability in sensor networks. These are the offset codebook mode (OCB), the counter cipher feedback with header mode (CCFB+H), the EAX mode, and the Galois/Counter mode (GCM). Our practical evaluation targets the MICAz sensor node and accounts for the typically small packet size of sensor network traffic. Our results indicate that the CCFB+H mode is the best choice for a large range of applications.
A microfabricated flow chamber for optical measurements in fluids (2002)

The fabrication and initial testing of silicon micromachined flow chambers for applications in flow cytometry are reported. The flow chambers consist of a hexagonal flow duct with inlet and outlet ports, thin-film windows on the top and bottom of the duct, and integrated optical waveguides positioned to intercept the center of the duct within the visible area defined by the windows. An opening for a hypodermic needle allows injection of a suspension of microscopic particles into a liquid stream flowing through the duct. Each component of the device was tested individually, and good agreement between the experimental data and theoretical models was observed. Laminar flow was observed in several prototypes up to mean flow speeds of 3 m/s. No leaks were detected for inlet pressures as high as 30 psi.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An evaluation of fixation methods: Spatial and compositional cellular changes observed by Raman imaging (2016)

Although live cell imaging is desirable, it is not always feasible and in many situations cells are fixed in order to provide a ‘snapshot’ of the nature and distribution of molecules within a cell while minimising changes from cell movement, sample degradation etc. There is a wide range of fixation methods available that act via different mechanisms, and on different cell components. Each method has advantages and disadvantages and a choice of what fixation method to choose for a particular experiment needs to take these factors into consideration. Here we used Raman spectroscopic imaging of live cells, and compared with cells preserved with aldehyde, or organic solvent-based fixation methods to assess the chemical changes induced by each fixative, and their impact on the quality of images that can be obtained from fixed cells. Overall, aldehyde fixation methods performed significantly better than organic solvents with less severe loss of biochemical information. Aldehyde based fixatives show an altered biochemical content of the cells, attributed to adduct formation, but this can be minimised by optimising fixation temperature, or through removal of adduct formation by detergent-based permeabilization treatments as a second step (at the cost of the loss of other biochemical information). The results showed that organic solvents, on the other hand, lead to a severe loss of cell content, attributed to the loss of membrane integrity after the removal of lipids. Additionally, fixation with aldehydes prior to permeabilization with organic solvents does not provide adequate protection of cytoplasmic content. The use of Raman imaging is ideal for comparing groups of cells in terms of their molecular content, and the results show that aldehyde fixations methods are preferable for studies where the overall molecular content of the samples is important. Although there is no universal fixation method for every application, the results here allow us to provide a few general principles: where spectral similarity to live cells is important, fixation with paraformaldehyde at room temperature is preferable, at the cost of some blebbing and vacuole formation. Where preservation of cellular structure or biomolecular distribution is important, a mix of paraformaldehyde and glutaraldehyde would be more appropriate, but at the cost of some changes to spectral profile, particularly in DNA-related bands.
Human melanotransferrin (p97) has only one functional iron‐binding site (1992)

The iron-binding properties of melanotransferrin, the tumour-associated antigen also known as p97, have been investigated by UV/visible and fluorescence spectroscopy, amino acid sequence comparison, and modelling. These show that, in contrast to other transferrins, melanotransferrin binds only one Fe3+ ion per molecule. The binding properties of its N-terminal site are similar to other transferrins, but its C-terminal site does not bind iron at all. The differences can be related to specific amino acid changes in the C-terminal site.
Defining Features and Exploring Chemical Modifications to Manipulate RNAa Activity (2010)

RNA interference (RNAi) is an evolutionary conserved mechanism by which small double-stranded RNA (dsRNA)--termed small interfering RNA (siRNA)--inhibit translation or degrade complementary mRNA sequences. Identifying features and enzymatic components of the RNAi pathway have led to the design of highly-effective siRNA molecules for laboratory and therapeutic application. RNA activation (RNAa) is a newly discovered mechanism of gene induction also triggered by dsRNAs termed small activating RNA (saRNA). It offers similar benefits as RNA interference (RNAi), while representing a new method of gene overexpression. In the present study, we identify features of RNAa and explore chemical modifications to saRNAs that improve the applicability of RNAa. We evaluate the rate of RNAa activity in order to define an optimal window of gene induction, while comparing the kinetic differences between RNAa and RNAi. We identify Ago2 as a conserved enzymatic component of both RNAa and RNAi implicating that saRNA may tolerate modification based on Ago2 function. As such, we define chemical modifications to saRNAs that manipulate RNAa activity, as well as exploit their effects to design saRNAs with enhanced medicinal properties. These findings reveal functional features of RNAa that may be utilized to augment saRNA function for mechanistic studies or the development of RNAa-based drugs.
Role of Transforming Growth Factor-β1 in Invasion and Metastasis in Gastric Carcinoma (1999)

Transforming growth factor-beta1 is closely related to the invasion and metastasis of gastric cancer, and production of TGF-beta1 in the tumor does not contribute to the total amount of TGF-beta1 in the blood circulation. We interpret our observations to mean that in a tumor microenvironment, TGF-beta1 alters the biologic behavior of the tumor.
Structure of Recombinant Human Interleukin 5 Produced by Chinese Hamster Ovary Cells (1990)

The complete peptide map of purified recombinant human interleukin 5 (rhIL-5) was determined to verify its primary structure, glycosylation sites, and disulfide bonding structure. Each peptide fragment generated by Achromobacter protease I (API) digestion was purified and characterized by amino acid analysis and amino acid sequence analysis. After digestion with API, we could identify all the peptides which were expected from human IL-5 cDNA sequence. The analyses of sulfhydryl content in rhIL-5 molecule and disulfide-containing peptide obtained from API digestion indicated that active form of rhIL-5 existed as an antiparallel dimer linked by two pairs of Cys-44 and Cys-86. In addition, we concluded that Thr-3 and Asn-28 were glycosylated. The results indicate that primary structure of rhIL-5 is highly homogeneous and observed heterogeneity is due to the difference in the content of carbohydrate.
Adaptive antennas for mobile communications (1994)

Adaptive-antenna techniques offer the possibility of increasing the performance of mobile radio communication systems by maximising directional gain and enhancing the protection towards multipath conditions. The net effect of these techniques is to improve immunity to interference, extend the range of each cell and thus increase the system capacity. The paper presents the results of a two year research programme aimed at the development of practical adaptive-antenna signal-processing structures. Specifically, results obtained from a series of analysis and field trial activities undertaken with an adaptive antenna test bed and based around the DECT cordless standard are presented.
Multiple Type-B Response Regulators Mediate Cytokinin Signal Transduction in Arabidopsis (2005)

Type-B Arabidopsis thaliana response regulators (ARRs) are transcription factors that function in the final step of two-component signaling systems. To characterize their role in plant growth and development, we isolated T-DNA insertions within six of the genes (ARR1, ARR2, ARR10, ARR11, ARR12, and ARR18) from the largest subfamily of type-B ARRs and also constructed various double and triple combinations of these mutations. Higher order mutants revealed progressively decreased sensitivity to cytokinin, including effects on root elongation, lateral root formation, callus induction and greening, and induction of cytokinin primary response genes. The triple mutant arr1,10,12 showed almost complete insensitivity to cytokinin under many of the assay conditions used. By contrast, no significant change in the sensitivity to ethylene was found among the mutants examined. These results indicate that there is functional overlap among the type-B ARRs and that they act as positive regulators of cytokinin signal transduction.
Heterogeneity of therapeutic responses in asthma (2000)

Asthma is a complex clinical syndrome with multiple genetic and environmental factors contributing to its phenotypic expression. This aetiological heterogeneity adds to the complexity when addressing variation in the response to anti-asthma treatment. Currently, there are three main lines of treatment available: (i) inhaled glucocorticoids which have multiple mechanisms of action; (ii) beta 2-agonists which are very effective bronchodilators and act predominantly on airway smooth muscle; and (iii) cysteinyl-leukotriene inhibitors. Analysis of the repeatability (r) of the treatment response, defined as the fraction of the total population variance which results from among-individual differences, shows values of r between 60-80% indicating that a substantial fraction of the variance of the treatment response could be genetic in nature. Among the sources of variability that could contribute to the observed heterogeneity in the response to treatment are the degree of underlying inflammation, such as in glucocorticoid resistance, and polymorphisms in the genes encoding the drug target, such as beta 2-adrenoceptor and 5-lipoxygenase.
Zinc porphyrins: Potent inhibitors of hematopoieses in animal and human bone marrow (1997)

The effects of selected heme analogues on heme oxygenase activity in tissues and on human and rabbit bone marrow hematopoietic colony growth were examined. Zinc protoporphyrin (ZnPP) and zinc mesoporphyrin (ZnMP), at concentrations ranging between 1 and 20 microM, produced significant inhibition of human and rabbit bone marrow erythroid (CFU-E, BFU-E) and myeloid (CFU-GM) colony growth. The growth inhibition produced by ZnPP or ZnMP was not overcome with exposure of cultures to elevated levels of the growth factors erythropoietin and granulocyte-macrophage colony stimulating factor. In contrast, tin protoporphyrin and tin mesoporphyrin did not display any significant bone marrow toxicity when used at similar concentrations. In other studies, differential effects of tin mesoporphyrin and ZnMP administered intravenously on kidney heme oxygenase were demonstrated. Chromium mesoporphyrin administered intravenously proved lethal to animals. These results indicate that exposure of bone marrow to ZnPP and ZnMP can be deleterious to hematopoietic cells and raise the possibility that ZnPP, which is endogenously formed and found in high concentration in red blood cells in lead-poisoned children, may itself participate in the bone marrow toxicity produced by this metal.
Maspin, a Serpin with Tumor-Suppressing Activity in Human Mammary Epithelial Cells (1994)

A gene encoding a protein related to the serpin family of protease inhibitors was identified as a candidate tumor suppressor gene that may play a role in human breast cancer. The gene product, called maspin, is expressed in normal mammary epithelial cells but not in most mammary carcinoma cell lines. Transfection of MDA-MB-435 mammary carcinoma cells with the maspin gene did not alter the cells' growth properties in vitro, but reduced the cells' ability to induce tumors and metastasize in nude mice and to invade through a basement membrane matrix in vitro. Analysis of human breast cancer specimens revealed that loss of maspin expression occurred most frequently in advanced cancers. These results support the hypothesis that maspin functions as a tumor suppressor.
Kinetics of Hedgehog-Dependent Full-Length Gli3 Accumulation in Primary Cilia and Subsequent Degradation (2010)

Hedgehog (Hh) signaling in vertebrates depends on intraflagellar transport (IFT) within primary cilia. The Hh receptor Patched is found in cilia in the absence of Hh and is replaced by the signal transducer Smoothened within an hour of Hh stimulation. By generating antibodies capable of detecting endogenous pathway transcription factors Gli2 and Gli3, we monitored their kinetics of accumulation in cilia upon Hh stimulation. Localization occurs within minutes of Hh addition, making it the fastest reported readout of pathway activity, which permits more precise temporal and spatial localization of Hh signaling events. We show that the species of Gli3 that accumulates at cilium tips is full-length and likely not protein kinase A phosphorylated. We also confirmed that phosphorylation and βTrCP/Cul1 are required for endogenous Gli3 processing and that this is inhibited by Hh. Surprisingly, however, Hh-dependent inhibition of processing does not lead to accumulation of full-length Gli3, but instead renders it labile, leading to its proteasomal degradation via the SPOP/Cul3 complex. In fact, full-length Gli3 disappears with faster kinetics than the Gli3 repressor, the latter not requiring SPOP/Cul3 or βTrCP/Cul1. This may contribute to the increased Gli3 activator/repressor ratios found in IFT mutants.
Changes of serum anti-thyroid antibodies during and after pregnancy in autoimmune thyroid diseases. (1978)

Changes of serum anti-thyroglobulin haemagglutination antibodies (TGHA) and anti-thyroid microsomal haemagglutination antibodies (MCHA) were observed during pregnancy and after delivery in Graves' disease and autoimmune thyroiditis. Both TGHA and MCHA decreased as pregnancy progressed, and sometimes they became negative in late pregnancy. Transient increases of TGHA and MCHA were observed after delivery and the antibody titres reached peaks about 3-4 months post-partum in more than halft the patients. In some patients, antibodies developed after delivery. Similar transient increases of antibodies were observed after spontaneous and therapeutic abortion. These changes seem to be induced by physiological and immunological changes occurring during pregnancy and after delivery.
Mortality in patients with multiple sclerosis (2013)

Mortality in patients with multiple sclerosis (MS) is significantly increased compared with the general population. Many questions concerning survival in MS are still unanswered due to the difficulty of comparing information collected at different times and in different geographic areas. The increasing incidence of MS, the improvement in care of the chronically disabled, and different methodologies may explain the lack of coherence among studies' results. Reported times to death from birth and from disease onset/diagnosis are highly variable. Patients older at onset or with primary progressive course have shorter survival; however, data on sex and mortality are contradictory. Changes in sex ratio in MS over time represent one possible explanation. MS is the main cause of death in ≥50% of patients and the incidence of deaths not due to MS varies among countries. Particularly, suicide is substantially increased in patients with MS, and, despite its varying incidence, mainly due to "cultural bias," it should be considered an MS-related cause of death. Recent results of the long-term follow-up study of interferon-β-1b demonstrated a significant reduction of mortality among treated patients. Notwithstanding its long latency, mortality is therefore an unambiguously valid long-term outcome in randomized controlled trials. It usefully combines the net impact of treatment efficacy on longevity and adverse events, which may reduce it.
Identification of Inhibitors of Prohormone Convertases 1 and 2 Using a Peptide Combinatorial Library (1998)

A positional scanning synthetic peptide combinatorial library containing approximately 52 million hexapeptides was used to identify potential inhibitory peptides for recombinant mouse prohormone convertase 1 (PC1) and PC2 and to provide information on the specificity of these enzymes. The library surveys revealed that a P6 Leu, a P4 Arg, a P2 Lys, and a P1 Arg were most inhibitory against PC1, and a P6 Ile and a P4 Arg were most inhibitory against PC2. Using information derived from the library surveys, hexapeptide sets were synthesized and screened for inhibition of PC1 and PC2. The data obtained revealed the preference of both enzymes for a P3 Val. At P5, many substitutions were well tolerated. PC1 and PC2 proved to differ mainly in the selectivity of their S6 subsites. In PC1, this subsite displayed a strong preference toward occupation by Leu; the Ki value for peptide Ac-Leu-Leu-Arg-Val-Lys-Arg-NH2 was 28 times lower than that for peptide Ac-Ile-Ile-Arg-Val-Lys-Arg-NH2. In contrast, PC2 discriminated little between Leu and Ile at P6, as evidenced by the small (1.5-fold) difference in Ki values for these two peptides. Several hexapeptides synthesized as a result of the screen were found to represent potent inhibitors of PC2 (with Ki values in the submicromolar range) and, particularly, of PC1 (with Ki values in the low nanomolar range). The most potent inhibitor, Ac-Leu-Leu-Arg-Val-Lys-Arg-NH2, proved to be the same peptide for both enzymes and inhibited PC1 and PC2 in a competitive, fast-binding manner with Ki values of 3.2 and 360 nM, respectively. The four most potent peptide inhibitors of PC1 and PC2 were also tested against soluble human furin and found to exhibit a different rank order of inhibition; for example, Ac-Leu-Leu-Arg-Val-Lys-Arg-NH2 was 440-fold less potent against furin than against PC1, with a Ki of 1400 nM.