gebhart/patrepeval huggingface dataset:
Cartilage‐like gene expression in differentiated human stem cell spheroids: A comparison of bone marrow–derived and adipose tissue–derived stromal cells (2003)

Hypertrophy of chondrocytes and high matrix-remodeling activity in differentiated BMSC spheroids and in OA cartilage may be the basis for the strong similarities in gene expression profiles between these samples. Differentiated stem cell spheroids represent an attractive tool for use in drug development and identification of drug targets in OA cartilage-like tissue outside the human body. However, optimization of differentiation protocols to achieve the phenotype of healthy chondrocytes is desired for cell therapy and tissue engineering approaches.
(A,G)-Oligonucleotides Form Extraordinary Stable Triple Helices with a Critical R·Y Sequence of the Murine c-Ki-ras Promoter and Inhibit Transcription in Transfected NIH 3T3 Cells (1996)

The promoter of the murine c-Ki-ras proto-oncogene contains a critical homopurine-homopyrimidine sequence which is recognized by a protein factor and is a potential site for triplex-forming oligonucleotides (TFOs). The TFOs designed to bind this critical c-Ki-ras target have either an AG or a GT sequence motif. Of the two types, the first is found to form triplexes with extraordinarily high stability. For instance, both d(AGGGAGGGAGGAAGGGAGGG) (20AG) and d(GGGAGGGAGGGAAGGAGGGAGGGAGGGAGC) (30AG) are able to bind the c-Ki-ras target at 65 degrees C and to resist a polyacrylamide gel temperature of 55 degrees C. By contrast, the triplex formed by d(TGGGTGGGTGGTTGGGTGGG) (20GT) is largely dissociated at a gel temperature of 55 degrees C. The affinity constants of the TFOs at 37 degrees C, 50 mM Tris-HCl, pH 7.4, 50 mM NaCl, 5 mM MgCl2 (standard buffer) were determined through band-shift experiments and found to be respectively 1.0 x 10(6), 4.0 x 10(6), and 2.5 x 10(7) M-1 for 20GT, 30AG, and 20AG. The AG-triplexes exhibit in standard buffer monophasic melting profiles (Tm approximately 75 degrees C) and circular dichoroism spectra showing the typical negative ellipticity at 212 nm, which is a hallmark for triplex DNA. The rate at which the TFOs bind to the c-Ki-ras target at 37 degrees C was examined under pseudo-first-order conditions. When the TFOs are in excess over the target and in the micromolar concentration range, the kinetics of triplex formation are slow, characterized by association half-lives of about 1 h. The ability of the TFOs to act as artificial transcription repressors was examined in a cellular system employing transient transfection experiments. Cultured NIH 3T3 fibroblast cells were cotransfected with a DNA mixture composed by a TFO and plasmid pKRS-413 containing the chloramphenicol acetyltransferase (CAT) gene driven by the c-Ki-ras promoter. It was found that the CAT activity is specifically inhibited by the TFOs in a dose-dependent manner. As expected, stronger CAT repression is obtained with 20AG, the oligonucleotide which forms the more stable triplex. These data suggest that (A,G)-oligonucleotides may provide a valuable means for the selective repression of the c-Ki-ras gene expression.
Follicular dendritic cell-derived antigen and accessory activity in initiation of memory IgG responses in vitro (1996)

Follicular dendritic cells (FDC) release Ag in developing germinal centers in the form of immune complex-coated bodies (iccosomes). Iccosomes are endocytosed by B cells, and the B cells process and present the FDC-derived Ag to T cells. By 3 days after Ag challenge, Ab-forming cells producing IgG specific for the iccosomal Ag emerge from the developing germinal centers and home to the bone marrow, where most Ab in a secondary response are produced. In addition to providing Ag, FDC exhibit potent accessory activities that promote B cell proliferation. These observations prompted the hypothesis that both FDC-derived Ag and FDC-derived Ag-independent secondary signal(s) are essential for optimal secondary Ab responses. To test this hypothesis, methods were developed to separate Ag-bearing iccosomes from intact FDC, and we then examined the ability of isolated iccosomes to elicit secondary Ab responses in vitro in the presence and absence of intact FDC. In the absence of FDC, iccosomes bearing the appropriate Ag elicited only minimal levels of specific IgG. Proliferation studies revealed that iccosomes lacked the FDC accessory activity necessary to augment B cell proliferation. When a source of FDC lacking the relevant Ag but exhibiting accessory activity was added to the iccosomal/Ag/lymphocyte mixture, dramatic increases in IgG specific for the iccosomal Ag were obtained (increases were from low ng/ml to microg/ml levels of specific IgG). The results suggest the concept that Ag on FDC or on iccosomes signals B cells through B cell Ag receptor, the iccosome provides these B cells with Ag necessary to process and elicit T cell help, and a secondary signal(s) necessary to optimize the memory response is delivered to B cells by FDC in an Ag-nonspecific fashion.
Role of capecitabine (Xeloda®) in breast cancer (2003)

One rationale for the development of new treatment strategies for advanced breast cancer is to provide targeted antineoplastic therapy, while at the same time improving the quality of life of patients. One such drug, capecitabine (Xeloda), is an oral fluoropyrimidine 5-fluorouracil carbamate. Capecitabine is converted to 5-fluorouracil primarily in cancer tissue and it has been demonstrated to combine ease of administration, a manageable toxicity profile and potent antineoplastic activity. Capecitabine is widely used in metastatic breast cancer and offers symptom palliation and in combination with docetaxel (Taxotere) improved survival compared with docetaxel alone. Its toxicity profile includes hand-foot syndrome and stomatitis and diarrhea, whereas its hematologic side effects are mild. Capecitabine has been evaluated as a single agent in women with advanced breast cancer where it offers an overall response rate of 20-30%. Capecitabine is synergistic with other chemotherapeutic agents, such as the taxanes, where it increases the response rate to over 40%. This review will place the available data on the use of capecitabine in metastatic breast cancer as a single agent or as part of a combination regime in context.
Adding and Subtracting Eigenspaces (1999)

This paper provides two algorithms; one for adding eigenspaces, another for subtracting them, thus allowing for incremental updating and downdating of data models. Importantly, and unlike previous work, we keep an accurate track of the mean of the data, which allows our methods to be used in classification applications. The result of adding eigenspaces, each made from a set of data, is an approximation to that which would obtain were the sets of data taken together. Subtracting eigenspaces yields a result approximating that which would obtain were a subset of data used. Using our algorithms it is possible to perform “arithmetic” on eigenspaces without reference to the original data. We illustrate the use of our algorithms in three generic applications, including the dynamic construction of Gaussian mixture models.
High-Performance Air-Stable n-Channel Organic Thin Film Transistors Based on Halogenated Perylene Bisimide Semiconductors (2009)

The syntheses and comprehensive characterization of 14 organic semiconductors based on perylene bisimide (PBI) dyes that are equipped with up to four halogen substituents in the bay area of the perylene core and five different highly fluorinated imide substituents are described. The influence of the substituents on the LUMO level and the solid state packing of PBIs was examined by cyclic voltammetry and single crystal structure analyses of seven PBI derivatives, respectively. Top-contact/bottom-gate organic thin film transistor (OTFT) devices were constructed by vacuum deposition of these PBIs on SiO(2) gate dielectrics that had been pretreated with n-octadecyl triethoxysilane in vapor phase (OTS-V) or solution phase (OTS-S). The electrical characterization of all devices was accomplished in a nitrogen atmosphere as well as in air, and the structural features of thin films were explored by grazing incidence X-ray diffraction (GIXD) and atomic force microscopy (AFM). Several of those PBIs that bear only hydrogen or up to two fluorine substitutents at the concomitantly flat PBI core afforded excellent n-channel transistors, in particular, on OTS-S substrate and even in air (mu > 0.5 cm(2) V(-1) s(-1); I(on)/I(off) > 10(6)). The best OTFTs were obtained for 2,2,3,3,4,4,4-heptafluorobutyl-substituted PBI 1a ("PTCDI-C4F7") on OTS-S with n-channel field effect mobilities consistently >1 cm(2) V(-1) s(-1) and on-to-off current rations of 10(6) in a nitrogen atmosphere and in air. For distorted core-tetrahalogenated (fluorine, chlorine, or bromine) PBIs, less advantageous solid state packing properties were found and high performance OTFTs were obtained from only one tetrachlorinated derivative (2d on OTS-S). The excellent on-to-off current modulation combined with high mobility in air makes these PBIs suitable for a wide range of practical applications.
Epigenetic approaches for the detection of fetal DNA in maternal plasma (2010)

The presence of fetal DNA in the plasma of pregnant women has opened up new possibilities for noninvasive prenatal diagnosis. Over the past decades, different types of fetal markers have been developed, initially based on discriminative genetic markers such as male-specific signals or paternally-inherited polymorphisms, and gradually evolved to the detection of fetal-specific transcripts or epigenetic signatures. This development has extended the coverage of the application of cell-free fetal DNA to essentially all pregnancies, regardless of the gender of the fetus or its polymorphic status. In this review, we present an overview of the development of noninvasive prenatal diagnosis through epigenetics. We introduce the basis of how fetal DNA could be detected from a large background of maternal DNA in maternal plasma based on fetal-specific DNA methylation patterns. We evaluate the methodologies involved and discuss the factors that affect the robustness of the detection. We review the progress in adopting fetal epigenetic markers for noninvasive prenatal assessment of fetal chromosomal aneuploidies and pregnancy-associated disorders. We conclude with comments on the future directions regarding the search for new fetal epigenetic markers and the clinical implementation of epigenetic approaches for noninvasive prenatal diagnosis.
A Novel Yeast-Based Reporter Assay System for the Sensitive Detection of Genotoxic Agents Mediated by a DNA Damage–Inducible LexA-GAL4 Protein (2006)

Yeast-based genotoxicity testing systems can sensitively detect DNA damaging agents in the environment. We have developed a novel "indirect" reporter assay system based on a recombinant yeast containing both a sensor and a reporter plasmid. The sensor plasmid contains a gene encoding the artificial transcription factor of the Escherichia coli LexA DNA binding domain fused to the transcriptional activation domain of yeast Gal4p, which is regulated by the DNA damage-inducible RNR2 promoter. The reporter plasmid contains the E. coli lacZ gene with the LexA binding site in the 5'-upstream region, allowing transcriptional activation by the induced LexA-GAL4 protein. The activity of DNA damage-dependent beta-galactosidase (beta-gal) in the "indirect" reporter assay system was compared with that of a current yeast-based "direct" reporter system. The "indirect" system exhibited 1.5- to 5-fold greater beta-gal activity upon induction by alkylating agents or camptothecin. To increase the sensitivity of the new reporter system further, several deletion yeast strains were tested, and enhanced induction of reporter activity was observed in DNA repair-deficient mag1Delta cells. The "indirect" 96-well microtiter plate assay system is a potentially inexpensive and sensitive method for detecting genotoxic activities in a wide range of compounds, and in polluted environmental samples.
The Three-dimensional Structure of a Superantigen-like Protein, SET3, from a Pathogenicity Island of the Staphylococcus aureus Genome (2002)

The staphylococcal enterotoxin-like toxins (SETs) are a family of proteins encoded within the Staphylococcus aureus genome that were identified by their similarity to the well described bacterial superantigens. The first crystal structure of a member of the SET family, SET3, has been determined to 1.9 A (R = 0.205, R(free) = 0.240) and reveals a fold characteristic of the superantigen family but with significant differences. The SET proteins are secreted at varying levels by staphylococcal isolates, and seroconversion studies of normal individuals indicate that they are strongly antigenic to humans. Recombinant SETs do not exhibit any of the properties expected of superantigens such as major histocompatibility complex class II binding or broad T-cell activation, suggesting they have an entirely different function. The fact that the whole gene family is clustered within the pathogenicity island SaIn2 of the S. aureus genome suggests that they are involved in host/pathogen interactions.
Intermedin and tumor (2010)

Intermedin can promote tumor angiogenesis through a variety of signaling pathways. Hypoxia of tumor cells can induce an increased expression of intermedin. Recently, there have been a surge of researches on the relation between intermedin and tumor initiation, progression and metastasis. Intermedin may be a new target for tumor therapy.

Key words: 
Tumor; Angiogenesis; Hypoxia
Clinical significance of cathepsin E in pancreatic juice in the diagnosis of pancreatic ductal adenocarcinoma (2000)

Cathepsin E in the pancreatic juice is a novel marker for a definitive diagnosis of pancreatic ductal adenocarcinoma.
Oxidations Catalyzed by Metallocorroles (2004)

Abstract Metallocorroles, in particular those containing chromium, manganese, and iron, have been found to be efficient catalysts for oxidation reactions. This review deals with work on hydrocarbon oxidations after the 1999 advance made in corrole synthesis that sparked the Technion‐Caltech collaborative program.
Enterococcus faecalis Enhances Cell Proliferation through Hydrogen Peroxide-Mediated Epidermal Growth Factor Receptor Activation (2012)

Enterococcus faecalis is a member of the intestinal and oral microbiota that may affect the etiology of colorectal and oral cancers. The mechanisms by which E. faecalis may contribute to the initiation and progression of these cancers remain uncertain. Epidermal growth factor receptor (EGFR) signaling is postulated to play a crucial role in oral carcinogenesis. A link between E. faecalis and EGFR signaling in oral cancer has not been elucidated. The present study aimed to evaluate the association between E. faecalis and oral cancer and to determine the underlying mechanisms that link E. faecalis to EGFR signaling. We report the high frequency of E. faecalis infection in oral tumors and the clinical association with EGFR activation. Using human oral cancer cells, we support the clinical findings and demonstrate that E. faecalis can induce EGFR activation and cell proliferation. E. faecalis activates EGFR through production of H(2)O(2), a signaling molecule that activates several signaling pathways. Inhibitors of H(2)O(2) (catalase) and EGFR (gefitinib) significantly blocked E. faecalis-induced EGFR activation and cell proliferation. Therefore, E. faecalis infection of oral tumor tissues suggests a possible association between E. faecalis infection and oral carcinogenesis. Interaction of E. faecalis with host cells and production of H(2)O(2) increase EGFR activation, thereby contributing to cell proliferation.
Growth factor expression in aorta of normotensive and hypertensive rats. (1989)

Hypertension causes biochemical and morphological changes in the vessel wall by unknown mechanisms. Locally produced substances may have a role in mediating these vascular changes. We have studied the expression of platelet-derived growth factor (PDGF) B chain and PDGF A chain, insulin-like growth factor (IGF)-I and IGF-II, endothelial cell growth factor (ECGF), basic fibroblast growth factor (bFGF), and transforming growth factor-beta (TGF-beta) in aortic tissue from normotensive rats and rats made hypertensive by deoxycorticosterone (DOC)/salt treatment. Using Northern blotting, we found that genes for each of these growth factors were transcriptionally active in the aorta of both normotensive and hypertensive rats. TGF-beta aortic mRNA levels increased up to threefold as a result of DOC/salt hypertension. In contrast, no major changes in the expression of either PDGF chain, IGF-I or II, ECGF, or bFGF were detectable. The results indicate that at least seven genes coding for growth factors that were shown previously to influence growth and function of vascular cells in vitro, are expressed in rat aorta in vivo. These findings support the hypothesis that synthesis and release of growth factors in the arterial wall are involved in autocrine and/or paracrine regulatory mechanisms. In addition, the increased expression of TGF-beta in vivo may have a role in mediating the aortic changes induced by hypertension.
Enhancing immune responses to tumor-associated antigens (2009)

The goal of vaccine-based cancer immunotherapy is to induce a tumor-specific immune response that ultimately reduces tumor burden. However, the immune system is often tolerant to antigens presented by the tumor, as the cancer originates from within a patient and is therefore recognized as self. This article reviews selected clinical strategies for overcoming this immune tolerance, and approaches to enhance generation of immunity to tumor-associated antigens by activating innate immunity, potentiating adaptive immunity, reducing immunosuppression, and enhancing tumor immunogenicity. Success in the field of cancer vaccines has yet to be fully realized, but intelligent choice of immunomodulators, tumor antigens and patient populations will likely lead to clinically relevant uses for cancer vaccines.
Miniaturized 3D surface profilometer using digital fringe projection (2005)

Three-dimensional measurement systems of high precision have been widely applied in high-technology industries and bio-medical areas, especially for microscale accuracy measurement. However, due to their bulky volume, most of the current surface profilometers cannot perform 3D measurement within a space-restricted inspection environment. To overcome this drawback, a novel 3D surface profilometer with a miniaturized probe was developed according to the digital fringe projection (DFP) principle. Measurement of small objects within a limited space can be made by the profilometer which comprises a digital fringe projection system, coherent image fibres and optical lenses. Using phase shifting and an accurate calibration method, the proposed system can analyse the phase fringe and reconstruct clouds of surface points accurately. An example of 3D intra-oral dental measurement was provided to verify the feasibility and performance of the developed system and techniques. The experimental results indicate that the spatial and vertical measurement resolution can reach 25 µm and 5 µm, respectively, and the accuracy can be controlled within 25 µm, less than 1% of full measurement range.
Cationic palladium nitro complexes as catalysts for the oxygen-based oxidation of alkenes to ketones, and for the oxydehydrogenation of ketones and aldehydes to the α, β-unsaturated analogues (1989)

Cationic palladium nitro complexes permit more rapid and more selective oxidation of alkenes to ketones than existing metal nitro catalysts; they also oxidatively dehydrogenate ketones and aldehydes to the corresponding α, β-unsaturated analogues under extremely mild conditions.
Candidate locus approach for studying the genetics of asthma and atopy. (1997)

Insights into the complex genetic factors underlying asthma and atopy have arisen from investigating genes whose functions are likely to be involved in the pathogenesis of these disorders. Candidate genes have now been studied on 13 human autosomes, and genetic linkage analysis and association studies have identified potentially important genes on chromosomes 5, 6, 11 and 14. However, these four regions do not account for all the heritability of these disorders, and additional regions are now being identified by systematic searches of the whole genome.
Requirement of Voltage-Gated Calcium Channel β 4 Subunit for T Lymphocyte Functions (2005)

Calcium is known to play vital roles in diverse physiological processes, and it is known that voltage-gated calcium channels (Cav) mediate calcium influx in excitable cells. However, no consensus exists on the molecular identity of the calcium channels present in nonexcitable cells such as T lymphocytes. Here, we demonstrate that T lymphocytes express both regulatory beta4 and poreforming Cav1 alpha1 subunits of Cav channels. Cav beta4-mutant T lymphocytes fail to acquire normal functions and display impairment in the calcium response, activation of the transcription factor NFAT, and cytokine production. Although Cav1 channels of lymphocytes retain their voltage dependency, T cell receptor stimulation dramatically increases channel opening, providing a new mechanism for calcium entry in lymphocytes.
A manipulation environment of virtual and real objects using a magnetic metaphor (2002)

This paper describes a method for the consolidated manipulation of virtual and real objects using a "magnetic metaphor". The method reduces the behavioral differences between the virtual and real objects. A limited number of physical laws are selected and simulated for the virtual objects; at the same time, limitations are placed on the physical laws for the real objects. Accordingly, a compromise can be found between the physical laws that operate on virtual objects and those which operate on real objects. Therefore, a system with this method enables a user to manipulate virtual and real objects in a similar manner by expecting the same responses and behaviors according to the same physical laws. Experimental results show that the proposed method improves the task performance in the manipulation of virtual and real objects existing in the same environment simultaneously.
Development and Characterization of Murine Monoclonal Antibodies to the Latency-Associated Peptide of Transforming Growth Factor β 1 (1995)

Transforming growth factor beta (TGF-beta) is a multifunctional peptide that controls proliferation, differentiation, and other functions in a variety of cell types. Transforming growth factor beta activities have been implicated in a variety of diseased states including arthritis, prostate cancer, and AIDS, and in the repair of tissue injury caused by trauma, burns, and surgery. We describe the development and characterization of novel murine monoclonal antibodies (MAbs) to the latency-associated peptide (LAP) of TGF-beta 1, and the subsequent development of an ELISA for the detection and quantitation of TGF-beta 1-LAP in buffer and serum matrices. Fusion of immune splenocytes with myeloma cells yielded 576 hybridomas, 110 of which were antibody secreting. Five were selected for extensive characterization. Clinically, the MAbs described here should be valuable for studying potentially abnormal production and/or function of the LAP, and its relationship to TGF-beta.