gebhart/patrepeval huggingface dataset:
Quantitative PCR Protocols (1999)

In Quantitative PCR Protocols, Bernd Kochanowski and Udo Reischl assemble a significant collection of established and novel methods for the successful quantitation of nucleic acids. Each method has been refined and tested by its developer and proven to work in such problems as the analysis of eukaryotic gene expression, the quantitation of viral loads in clinical specimens, reporter gene expression, and quantitative oncogene analysis. Particular emphasis is placed on the underlying principles of the design of competitive or noncompetitive standards, as well as on the optimization of the amplification process. In important cases several methods are given for the same problem so that readers may set up test systems tailored to their specific practical needs. Quantitative PCR Protocols provides a collection of detailed methods that offers comprehensive and up-to-date information on how to control PCR to obtain reliable quantitation. With its step-by-step instructions researchers can really master the complexities of PCR and address otherwise inaccessible biological and diagnostic questions
The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation (2005)

Deciphering regulatory events that drive malignant transformation represents a major challenge for systems biology. Here we analyzed genome-wide transcription profiling of an in-vitro transformation process. We focused on a cluster of genes whose expression levels increased as a function of p53 and p16INK4A tumor suppressors inactivation. This cluster predominantly consists of cell cycle genes and constitutes a signature of a diversity of cancers. By linking expression profiles of the genes in the cluster with the dynamic behavior of p53 and p16INK4A, we identified a promoter architecture that integrates signals from the two tumor suppressive channels and that maps their activity onto distinct levels of expression of the cell cycle genes, which in turn, correspond to different cellular proliferation rates. Taking components of the mitotic spindle as an example, we experimentally verified our predictions that p53-mediated transcriptional repression of several of these novel targets is dependent on the activities of p21, NFY and E2F. Our study demonstrates how a well-controlled transformation process allows linking between gene expression, promoter architecture and activity of upstream signaling molecules.
Thalidomide in the treatment of chronic discoid lupus erythematosus (1982)

No abstract available.
Hepatocyte growth factor/scatter factor, a cytokine playing multiple and converse roles. (1997)

Hepatocyte growth factor (HGF), otherwise known as scatter factor (SF), is a recently identified cytokine which exerts a wide spectrum of biological functions on a variety of cell types. Its receptor is encoded by the c-met proto-oncogene. HGF/SF has been implicated in the regulation of mitogenesis, motogenesis, and morphogenesis. Over the past few years, the structure, function and signal transduction pathways of HGF/SF and its receptor have become clearer. The cytokine is now known to play important roles in the regulation of both normal physiological processes as well as pathological ones. This review summarises recent progress involving HGF/SF and its receptor and discusses their role in cell biology, organ regeneration, cancer and other processes. Hepatocyte growth factor (HGF) is a pleiotropic growth factor originally identified as a potent mitogen agent for rat hepatocytes. Subsequent studies have shown that it is mitogenic for a wide range of epithelial cells and not limited to hepatocytes. Its behaviour as a motogenic stimulator promoted its independent discovery and naming of scatter factor (SF). Analysis of cDNA and amino acid sequences have revealed that the two molecules are the same. A number of cytokine agents are known to stimulate cellular motility, however, it is the function of HGF/SF as a potent motogenic, mitogenic and morpho-regulatory agent on the diverse variety of cell types that makes the discovery of HGF/SF factor one of the most interesting stories in terms of identification of novel cytokines.
Genome Sequence of the Plant Pathogen and Biotechnology Agent Agrobacterium tumefaciens C58 (2001)

Agrobacterium tumefaciens is a plant pathogen capable of transferring a defined segment of DNA to a host plant, generating a gall tumor. Replacing the transferred tumor-inducing genes with exogenous DNA allows the introduction of any desired gene into the plant. Thus, A. tumefaciens has been critical for the development of modern plant genetics and agricultural biotechnology. Here we describe the genome of A. tumefaciens strain C58, which has an unusual structure consisting of one circular and one linear chromosome. We discuss genome architecture and evolution and additional genes potentially involved in virulence and metabolic parasitism of host plants.
Normalization of retinal vascular permeability in experimental diabetes with genistein. (2001)

Long-term oral administration of genistein significantly inhibits retinal vascular leakage in experimentally induced diabetic rats. Tyrosine kinase inhibition may be a useful pharmacological approach for the treatment of diabetic-induced retinal vascular leakage.
Predicted structural motif of IFNΤ (1994)

Ovine interferon tau (IFN tau) is a type I interferon that was originally identified as ovine trophoblast protein and is associated with the maternal recognition of pregnancy in sheep. Additionally, IFN tau possesses potent antiviral and antiproliferative activity without the corresponding toxicity found in known IFN alpha s. Structure-function studies with synthetic peptides have identified three discontinuous functional sites on the protein that are involved in receptor interaction and biological activity. However, the structural relationship of these regions is unknown. Therefore, a model relationship of these regions is unknown. Therefore, a model of the 3-D structure of IFN tau would be useful in interpretation of existing data and the design of future structure-function studies. Combining information from circular dichroism (CD) of both the full length recombinant IFN tau and synthetic peptides representing regions of the IFN tau molecule, with sequence homology of IFN tau to IFN beta, a protein of known 3-D structure, we have constructed a model of IFN tau using distance geometry and energy minimization methods. The most striking feature of this model is that functionally active domains of IFN tau, discontinuous in the primary structure, are localized to one side of the molecule and found to be spatially contiguous. This observation is consistent with multiple binding sites on IFN tau interacting simultaneously with the IFN tau receptor.
Investigation of deep dielectric charging and subsequent currents on geosynchronous spacecraft (1991)

Deep dielectric charging is the suspected mechanism for formation of potential barriers aboard the ISEE 1 spacecraft. Energetic electron distribution functions in the plasmasheet were examined for both surface and deep dielectric charging. Surface charging was found to be dependent on whether the satellite surfaces were in shadow. The surface potential is regulated by photoelectric emission, and is two orders of magnitude higher than other mechanisms. Deep dielectric charging deposits charge within dielectrics, and is independent of surface effects, such as photoemission and radiation-induced conductivity. Deposition of electrons into solar array cover cells begins at approximately 10 keV.
Cytokeratin expression patterns in normal and malignant urothelium: a review of the biological and diagnostic implications. (1999)

The cytokeratins are the intermediate filament proteins characteristic of epithelial cells. In human cells, some 20 different cytokeratin isotypes have been identified. Epithelial cells express between two and ten cytokeratin isotypes and the consequent profile which reflects both epithelial type and differentiation status may be useful in tumour diagnosis. The transitional epithelium or urothelium of the urinary tract shows alterations in the expression and configuration of cytokeratin isotypes related to stratification and differentiation. In transitional cell carcinoma, changes in cytokeratin profile may provide information of potential diagnostic and prognostic significance. The intensification of immunolabelling with some CK8 and CK18 antibodies may underly an active role in tumour invasion and foci of CK17-positive cells may represent proliferating populations. Loss of CK13 is a marker of grade and stage and de novo expression of CK14 is indicative of squamous differentiation and an unfavourable prognosis. However, perhaps the most important recent finding is the demonstration that a normal CK20 expression pattern is predictive of tumour non-recurrence and can be used to make an objective differential diagnosis between transitional cell papilloma and carcinoma. This review will consider cytokeratin expression in urothelium and discuss the application of cytokeratin typing to the diagnosis and prognosis of patients with TCC.
Respiratory Care Controversies II (2010)

Despite a plethora of publications on the art and science of respiratory care, a number of basic issues remain unanswered. These clinical controversies are often settled by expert opinion and personal bias. By definition, a controversy has compelling arguments for each side of the issue. This Respiratory Care Journal Conference addressed 12 clinical controversies, ranging from spirometry screening for chronic lung disease to the timing of tracheostomy. This paper is a concise synopsis of the salient points of each side of each argument and provides the points of consensus and points of contention. When appropriate, further research is suggested to address still unanswered questions.
Protein glycosylation analysis by HILIC‐LC‐MS of Proteinase K‐generated N‐ and O‐glycopeptides (2010)

Analysis of protein glycosylation is essential in order to correlate certain disease types with oligosaccharide structures on proteins. Here, a method for the MS characterization of site-specific protein glycosylation is presented. Using asialofetuin and fetuin as model substances, a protocol for glycopeptide dissection was developed based on unspecific proteolysis by Proteinase K. The resulting glycopeptides were then resolved by nanoscale hydrophilic interaction liquid chromatography-electrospray multistage MS. The early elution range of O-glycopeptides was clearly separated from the late elution range of N-glycopeptides. Glycopeptides were analyzed by ion trap-MS/MS, which revealed fragmentations of glycosidic linkages and some peptide backbone cleavages; MS(3) spectra predominantly exhibited cleavages of the peptide backbone and provided essential information on the peptide sequence. The previously reported N- and O-glycan attachment sites of fetuin could be confirmed; moreover using our method, the occupation of a new, additional O-glycosylation site serine 296 was found. In conclusion, this approach appears to be a valuable technique for in-depth analysis of the site-specific N-glycosylation and O-glycosylation of individual glycoproteins.
In vitro activities of two glycylcyclines against gram-positive bacteria (1994)

The glycylcyclines designated CL 329,998 and CL 331,002 are N,N-dimethylglycylamido derivatives of minocycline and 6-demethyl-6-deoxytetracycline, respectively. In vitro activities of these two antimicrobial agents were compared with those of tetracycline, minocycline, and seven other antimicrobial agents against 412 gram-positive organisms. Both new drugs were significantly more active than minocycline against methicillin-resistant Staphylococcus aureus (MICs for 90% of isolates tested, 0.25 and 0.5 microgram/ml versus 4 micrograms/ml). CL 329,998 inhibited all streptococci, lactobacilli, and Leuconostoc spp. at concentrations of < or = 0.5 microgram/ml, with CL 331,002 slightly less active against some species. All enterococci, including minocycline-resistant and multidrug-resistant isolates, were inhibited at < or = 0.5- and < or = 1.0-microgram/ml concentrations of the new drugs, respectively. Only bacteriostatic activity was evident by time-kill curves. The two glycylcyclines demonstrated activities in vitro that were superior to those of minocycline against several gram-positive bacterial species, and at relatively low concentrations, they inhibited isolates resistant to both tetracycline and minocycline.
Sequences of the bovine and yeast ADP-ribosylation factor and comparison to other GTP-binding proteins. (1988)

The ADP-ribosylation factor (ARF) is a 21-kDa GTP-binding protein that serves as the cofactor in the cholera toxin-catalyzed activation of the stimulatory guanine nucleotide-binding protein of adenylate cyclase (Gs). An oligonucleotide probe based on the partial amino acid sequence was used to clone ARF from a bovine adrenal chromaffin cDNA library. The yeast (Saccharomyces cerevisiae) ARF gene was then cloned from a YCp50 genomic library by cross-species hybridization by using the coding region of the bovine gene. RNA gel blots of poly(A)+ RNA indicate that only one ARF message size (900 and 2000 base pairs) is present in yeast and cows, respectively. Comparison of the cDNA-derived amino acid sequences of ARF to other GTP-binding proteins reveals a structural relationship between ARF and the ras family of proteins. A slightly better structural relationship is detected when ARF is compared to the alpha subunits of the trimeric GTP-binding proteins, including Gs alpha. All of the biochemical characteristics of the purified ARF, including the lack of GTPase activity and the posttranslational myristoylation, are consistent with the derived sequences. Comparison of the ARF sequences to that of the chicken processed pseudogene (CPS-1), previously reported as a ras homologue, reveals that CPS-1 is actually an ARF-derived gene. These results demonstrate that ARF is a GTP-binding protein with structural features of both the ras and the trimeric GTP-binding protein families.
Epoxyquinol B, a Naturally Occurring Pentaketide Dimer, Inhibits NF-κB Signaling by Crosslinking TAK1 (2008)

Several epoxyquinoids interfere with NF-kappaB signaling by targeting IKKbeta or NF-kappaB. We report that epoxyquinol B (EPQB), classified as an epoxyquiniod, inhibits NF-kappaB signaling through inhibition of the TAK1 complex, a factor upstream of IKKbeta and NF-kappaB. cDNA microarray analysis revealed that EPQB decreased TNF-alpha-induced expression of NF-kappaB target genes. EPQB covalently bound to a recombinant TAK1-TAB1 fusion protein in vitro, and inhibited its kinase activity. Furthermore, in vitro/in situ treatment with EPQB resulted in a ladder-like hypershift of TAK1 protein bands. We reported recently that EPQB crosslinks proteins via cysteine residues by opening its two epoxides, and our current results suggest that EPQB inhibits NF-kappaB signaling by crosslinking TAK1 itself or TAK1 through other proteins.
SHED: Stem cells from human exfoliated deciduous teeth (2003)

To isolate high-quality human postnatal stem cells from accessible resources is an important goal for stem-cell research. In this study we found that exfoliated human deciduous tooth contains multipotent stem cells [stem cells from human exfoliated deciduous teeth (SHED)]. SHED were identified to be a population of highly proliferative, clonogenic cells capable of differentiating into a variety of cell types including neural cells, adipocytes, and odontoblasts. After in vivo transplantation, SHED were found to be able to induce bone formation, generate dentin, and survive in mouse brain along with expression of neural markers. Here we show that a naturally exfoliated human organ contains a population of stem cells that are completely different from previously identified stem cells. SHED are not only derived from a very accessible tissue resource but are also capable of providing enough cells for potential clinical application. Thus, exfoliated teeth may be an unexpected unique resource for stem-cell therapies including autologous stem-cell transplantation and tissue engineering.
Personalized X-Ray 3-D Reconstruction of the Scoliotic Spine From Hybrid Statistical and Image-Based Models (2009)

This paper presents a novel 3-D reconstruction method of the scoliotic spine using prior vertebra models with image-based information taken from biplanar X-ray images. We first propose a global modeling approach by exploiting the 3-D scoliotic curve reconstructed from a coronal and sagittal X-ray image in order to generate an approximate statistical model from a 3-D database of scoliotic patients based on a transformation algorithm which incorporates intuitive geometrical properties. The personalized 3-D reconstruction of the spine is then achieved with a novel segmentation method which takes into account the variable appearance of scoliotic vertebrae (rotation, wedging) from standard quality images in order to segment and isolate individual vertebrae on the radiographic planes. More specifically, it uses prior 3-D models regulated from 2-D image level set functionals to identify and match corresponding bone structures on the biplanar X-rays. An iterative optimization procedure integrating similarity measures such as deformable vertebral contours regulated from high-level anatomical primitives, morphological knowledge and epipolar constraints is then applied to globally refine the 3-D anatomical landmarks on each vertebra level of the spine. This method was validated on twenty scoliotic patients by comparing results to a standard manual approach. The qualitative evaluation of the retro-projection of the vertebral contours confirms that the proposed method can achieve better consistency to the X-ray image's natural content. A comparison to synthetic models and real patient data also yields good accuracy on the localization of low-level primitives such as anatomical landmarks identified by an expert on each vertebra. The experiments reported in this paper demonstrate that the proposed method offers a better matching accuracy on a set of landmarks from biplanar views when compared to a manual technique for each evaluated cases, and its precision is comparable to 3-D models generated from magnetic resonance images, thus suitable for routine 3-D clinical assessment of spinal deformities.
Ultrafast compound doppler imaging: A new approach of doppler flow analysis (2010)

This work applies the concept of compounded plane wave transmissions at very high frames rates of some KHz for ultrafast Doppler analysis over a large region of interest. As this compound imaging method has a similar quality to the standard focusing method but is 10 times faster, it is possible to generate fast Doppler images at frame rates of 300Hz. This frame rate is able to visualize transient phenomena and to display duplex modes with simultaneous color and spectrum analysis for each pixel of the image. The interest of the method is not restricted to high velocity flows; by optimizing the quality of the ultrasonic compounded image, it is possible to image very small velocity flows. This method is applied to a functional imaging of the rat brain by detecting changes in the flow after a drug injection.
Hydrogenation and Hydrocarbonation and Etching of Single-Walled Carbon Nanotubes (2006)

We present a systematic experimental investigation of the reactions between hydrogen plasma and single-walled carbon nanotubes (SWNTs) at various temperatures. Microscopy, infrared (IR) and Raman spectroscopy, and electrical transport measurements are carried out to investigate the properties of SWNTs after hydrogenation. Structural deformations, drastically reduced electrical conductance, and an increased semiconducting nature of SWNTs upon sidewall hydrogenation are observed. These changes are reversible upon thermal annealing at 500 degrees C via dehydrogenation. Harsh plasma or high temperature reactions lead to etching of nanotubes likely via hydrocarbonation. Smaller SWNTs are markedly less stable against hydrocarbonation than larger tubes. The results are fundamental and may have implications to basic and practical applications including hydrogen storage, sensing, band gap engineering for novel electronics, and new methods of manipulation, functionalization, and etching of nanotubes.
Nuclear localization signal(s) required for nuclear targeting of the maize regulatory protein Opaque-2. (1992)

The maize regulatory protein Opaque-2 (O2) localizes to the nucleus in both maize and tobacco cells. Here we show that in-frame carboxy- and amino-terminal fusions of O2 to reporter protein beta-glucuronidase (GUS) were sufficient to direct GUS to the nucleus in transgenic tobacco plants and in transiently transformed onion cells. Two independent regions of O2 containing 135 and 149 amino acids were identified that were able to redirect GUS to the nucleus in both systems. A quantitative biochemical analysis of GUS in nuclei isolated from transgenic tobacco plants revealed that the second region was more efficient than the first one. The precise location of nuclear localization signals (NLSs) was determined using an onion transformation system. The first NLS was located between residues 101 and 135 and had the structure of a simian virus 40 NLS. The second NLS was located in the basic, DNA binding domain (between residues 223 and 254) and had a bipartite structure. The presence of one of the O2 NLSs in the basic domain is in complete agreement with similar findings of NLSs in the basic domain of three other basic/leucine zipper proteins, suggesting that this domain may be bifunctional. The effect of amino- versus carboxy-terminal GUS fusions is discussed.
Protective Effect of a Single Interleukin-12 (IL-12) Predose Against the Toxicity of Subsequent Chronic IL-12 in Mice: Role of Cytokines and Glucocorticoids (1997)

The mechanisms of interleukin-12 (IL-12) toxicity were studied in mice using a schedule (murine rIL-12, 400 ng/mouse, intraperitoneally [IP] once daily for 5 days) that markedly reduced body weight and food intake. On day 5, IL-12–treated mice had elevated serum and spleen IFN-γ and tumor necrosis factor (TNF). Serum sTNFR-P75 and corticosterone (CS) were also elevated. IL-12 toxicity was partially prevented by anti–IFN-γ antibodies or dexamethasone (DEX). A pre-dose of IL-12 (200 ng/mouse on day −14) completely prevented the toxicity of subsequent IL-12. The IL-12 predose also inhibited IL-12–induced IFN-γ levels, but did not modify IL-12–induced CS, TNF or sTNFR-P75. A protective effect was observed with a predose of lipopolysaccharide (LPS) or murine recombinant (r)IL-10. The protective effect of the IL-12 predose was reduced by coadministration of anti–IFN-γ, but a predose of murine rIFN-γ was not protective, suggesting that IFN-γ is necessary but not sufficient for the protective effect of IL-12. The IL-12 predose specifically protected against IL-12 toxicity and did not modify LPS toxicity. These data indicate that IL-12 can induce tolerance to its own toxicity, probably through a downregulation of IL-12–induced IFN-γ but independently of endogenous glucocorticoids. IFN-γ, and possibly IL-10, might be important in this tolerance.