gebhart/patrepeval huggingface dataset:
DNA extraction from paraffin-embedded tissues using a salting-out procedure: a reliable method for PCR amplification of archival material. (1997)

Many techniques have been described for the extraction of DNA from paraffin-embedded tissues. Numerous efforts have been directed at simplification of these methods for rapid analysis using PCR. One disadvantage to some of the simpler procedures is inefficient PCR amplification, and for more involved ones using phenol/chloroform extraction, reduction in the yield of DNA. In the present study we report the use of a novel salting-out procedure that was utilized to extract DNA from 259 separate microdissection specimens of formalin-fixed, paraffin-embedded tissue sections. These sections were derived from 97 patients with tumors of the ampulla of Vater resected between 1965 and 1995 at our institution. The mean DNA yield was 22.75 micrograms (median 13.2 +/- 30.25) and the mean 260/280 absorbance ratio was 1.68 (median 1.70 +/- 0.25). All specimens (259/259) were successfully used to amplify K-ras exon 1 by a nested PCR technique. These results indicate that this DNA extraction method produces good yields of quality DNA, even from specimens several decades old.
Prediction of prostate cancer from prostate biopsy in Chinese men using a genetic score derived from 24 prostate cancer risk-associated SNPs (2013)

A genetic score based on PCa risk-associated SNPs is an independent predictor of prostate biopsy outcomes in Chinese men and may be helpful to determine the need for prostate biopsy among patients within a "gray zone" of PCa risk.
Ion energy distributions and sheath voltages in a radio-frequency-biased, inductively coupled, high-density plasma reactor (1999)

Ion energy distributions were measured at a grounded surface in an inductively coupled, high-density plasma reactor for pure argon, argon–helium, and argon–xenon discharges at 1.33 Pa (10 mTorr), as a function of radio-frequency (rf) bias amplitude, rf bias frequency, radial position, inductive source power, and ion mass. The ground sheath voltage which accelerates the ions was also determined using capacitive probe measurements and Langmuir probe data. Together, the measurements provide a complete characterization of ion dynamics in the sheath, allowing ion transit time effects to be distinguished from sheath impedance effects. Models are presented which describe both effects and explain why they are observed in the same range of rf bias frequency.
Two New Species of Deep-Water Corallimorpharia (Cnidaria: Anthozoa) from the Northeast Pacific, Corallimorphus denhartogi and C. pilatus (2002)

Corallimorpharia is currently considered an order of hexacorallian anthozoans. Being skeletonless, its members are sometimes referred to as sea anemones, but they are morphologically more similar to members of Scleractinia than to members of Actiniaria. We describe two new species of corallimorpharians from deep water off the west coast of North America as Corallimorphus denhartogi, n. sp. and Corallimorphus pilatus, n. sp. The former occurs at depths of 2550-4300 m from Oregon to Baja California, and the latter at depths of 198-900 m from British Columbia to southernmost California. The average size of individuals of C. denhartogi is greater than that of C. pilatus, and tentacles of the latter are more densely arrayed and relatively longer than those of the former. The distribution and sizes of their cnidae distinguish them from one another as well as from their four congeners, which are widely distributed in the world's oceans. In the collections we examined, specimens of C. denhartogi are more common than those of C. pilatus.
Performance assessment of time-domain optical brain imagers, part 1: basic instrumental performance protocol (2014)

Performance assessment of instruments devised for clinical applications is of key importance for validation and quality assurance. Two new protocols were developed and applied to facilitate the design and optimization of instruments for time-domain optical brain imaging within the European project nEUROPt. Here, we present the "Basic Instrumental Performance" protocol for direct measurement of relevant characteristics. Two tests are discussed in detail. First, the responsivity of the detection system is a measure of the overall efficiency to detect light emerging from tissue. For the related test, dedicated solid slab phantoms were developed and quantitatively spectrally characterized to provide sources of known radiance with nearly Lambertian angular characteristics. The responsivity of four time-domain optical brain imagers was found to be of the order of 0.1 m² sr. The relevance of the responsivity measure is demonstrated by simulations of diffuse reflectance as a function of source-detector separation and optical properties. Second, the temporal instrument response function (IRF) is a critically important factor in determining the performance of time-domain systems. Measurements of the IRF for various instruments were combined with simulations to illustrate the impact of the width and shape of the IRF on contrast for a deep absorption change mimicking brain activation.
Functional Differences of Two Distinct Catalases in Mesorhizobium loti MAFF303099 under Free-Living and Symbiotic Conditions (2008)

Protection against reactive oxygen species (ROS) is important for legume-nodulating rhizobia during the establishment and maintenance of symbiosis, as well as under free-living conditions, because legume hosts might assail incoming microbes with ROS and because nitrogenase is extremely sensitive to ROS. We generated mutants of two potential catalase genes in Mesorhizobium loti MAFF303099 to investigate their physiological significance. Biochemical results indicated that genes with the locus tags mlr2101 and mlr6940 encoded a monofunctional catalase and a bifunctional catalase-peroxidase, respectively, that were named katE and katG. Under free-living conditions, the katG mutant demonstrated an extended generation time and elevated sensitivity to exogenous H(2)O(2), whereas the katE mutant exhibited no generation time extension and only a slight increase in sensitivity to exogenous H(2)O(2). However, the katE mutant showed a marked decrease in its survival rate during the stationary phase. With regard to symbiotic capacities with Lotus japonicus, the katG mutant was indistinguishable from the wild type; nevertheless, the mutants with disrupted katE formed nodules with decreased nitrogen fixation capacities (about 50 to 60%) compared to those formed by the wild type. These mutant phenotypes agreed with the expression profiles showing that transcription of katG, but not katE, was high during the exponential growth phase and that transcription levels of katE versus sigA were elevated during stationary phase and were approximately fourfold higher in bacteroids than mid-exponential-phase cells. Our results revealed functional separation of the two catalases, as well as the importance of KatE under conditions of strong growth limitation.
Regulation of Receptor Tyrosine Kinase Signaling by Endocytic Trafficking (2001)

Activated receptor tyrosine kinase (RTK) receptors are rapidly internalized and eventually delivered to the lysosomes. Although ligand-induced endocytosis was originally thought to be a mechanism of receptor inactivation, many studies suggest that receptors remain active within endosomes. This review discusses the role that internalized signaling complexes may play in different RTK systems including recent data on how ubiquitination may regulate this process. In general, it appears that some receptor systems have evolved to enhance endosomal signaling, as is the case for TrkA and NGF. In contrast, the insulin receptor system appears to limit the extent of endosomal signaling. The EGFR system is the intermediate example. In this case, some signals are specifically generated from the cell surface while others appear to be generated from within endosomes. This may act as a mechanism to produce ligand-specific signals. Thus, trafficking could play diverse roles in receptor signaling, depending on the specific cell and tissue type.
Gallium arsenide and other compound semiconductors on silicon (1990)

The physics of the growth mechanisms, characterization of epitaxial structures and device properties of GaAs and other compound semiconductors on Si are reviewed in this paper. The nontrivial problems associated with the heteroepitaxial growth schemes and methods that are generally applied in the growth of lattice mismatched and polar on nonpolar material systems are described in detail. The properties of devices fabricated in GaAs and other compound semiconductors grown on Si substrates are discussed in comparison with those grown on GaAs substrates. The advantages of GaAs and other compound semiconductors on Si, namely, the low cost, superior mechanical strength, and thermal conductivity, increased wafer area, and the possibility of monolithic integration of electronic and optical devices are also discussed.
ChemInform Abstract: Fuel Cells (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Rapid Identification of Bio-Molecules Applied for Detection of Biosecurity Agents Using Rolling Circle Amplification (2012)

Detection and identification of pathogens in environmental samples for biosecurity applications are challenging due to the strict requirements on specificity, sensitivity and time. We have developed a concept for quick, specific and sensitive pathogen identification in environmental samples. Target identification is realized by padlock- and proximity probing, and reacted probes are amplified by RCA (rolling-circle amplification). The individual RCA products are labeled by fluorescence and enumerated by an instrument, developed for sensitive and rapid digital analysis. The concept is demonstrated by identification of simili biowarfare agents for bacteria (Escherichia coli and Pantoea agglomerans) and spores (Bacillus atrophaeus) released in field.
Photophysical Properties of a Rhodium Tetraphenylporphyrin-tin Corrole Dyad. The First Example of a Through Metal–Metal Bond Energy Transfer† (2005)

The luminescence spectroscopy study and the determination of the photophysical parameters for the M-M'-bonded rhodium meso-tetraphenylporphyrin-tin(2,3,7,13,17,18-hexamethyl-8,12-diethylcorrole) complex, (TPP)Rh-Sn(Me6Et2Cor) 1, was investigated. The emission bands as well as the lifetimes (tau(e)) and the quantum yields (Phi(e); at 77 K using 2MeTHF as solvent) were compared with those of (TPP)RhI 2 (TPP = tetraphenylporphyrin) and (Me6Et2Cor)SnCl 3 (Me6Et2Cor = 2,3,7,13,17,18-hexamethyl-8,12-diethylcorrole) which are the two chemical precursors of 1. The energy diagram has been established from the absorption, fluorescence and phosphorescence spectra. The Rh(TPP) and Sn(Me6Et2Cor) chromophores are the energy donor (D) and acceptor (A), respectively. The total absence of fluorescence in 1 (while fluorescence is observed in the tin derivative 3) indicates efficient excited state deactivation, presumably due to heavy atom effect and intramolecular energy transfer (ET). The large decreases in tau(P) and Phi(P) of the Rh(TPP) chromophore going from 2 to 1 indicate a significant intramolecular ET in the triplet states of 1 with an estimated rate ranging between 10(6) and 10(8) s(-1). Based on the comparison of transfer rates with other related dyads that exhibit similar D-A separations and no M-M' bond, and for which slower through space ET processes (10(2)-10(3) s(-1)) operate, a through M-M' bond ET has been unambiguously assigned to 1.
Compilation and Characterization of Arabiopsis thaliana Response Regulators Implicated in His-Asp Phosphorelay Signal Transduction (1999)

His-Asp phosphorelays are evolutionary-conserved powerful biological tactics for intracellular signal transduction. Such a phosphorelay is generally made up of "sensor histidine (His)-kinases", "response regulators", and "histidine-containing (HPt) phosphotransmitters". In the higher plant, Arabidopsis thaliana, results from recent intensive studies suggested that His-Asp phosphorelays may be widely used for propagating environmental stimuli, such as phytohormones (e.g., ethylene and cytokinin). In this study, we first inspected extensively the occurrence of Arabidopsis response regulators in order to compile and characterize them. The results showed that this higher plant has, at least, 14 members of the family of response regulators that can be classified into two distinct subtypes (type-A and type-B), as judged from their structural designs, biochemical properties, and expression profiles. Comparative studies were conducted for each representative (ARR3 and ARR4 for type-A, and ARR10 for type-B). It was suggested that expression of the type-A response regulator is cytokinin-inducible, while that of the type-B response regulator appears to be not. Results from yeast two-hybrid analyses suggested that the type-B response regulator may have an ability to stably interact with a set of HPt phosphotransmitters (AHPs). These and other results will be discussed with special reference to the His-Asp phosphorelay signaling network in Arabidopsis thaliana.
The Yeast Split-Ubiquitin Membrane Protein Two-Hybrid Screen Identifies BAP31 as a Regulator of the Turnover of Endoplasmic Reticulum-Associated Protein Tyrosine Phosphatase-Like B (2004)

In the past decade, traditional yeast two-hybrid techniques have identified a plethora of interactions among soluble proteins operating within diverse cellular pathways. The discovery of associations between membrane proteins by genetic approaches, on the other hand, is less well established due to technical limitations. Recently, a split-ubiquitin system was developed to overcome this barrier, but so far, this system has been limited to the analysis of known membrane protein interactions. Here, we constructed unique split-ubiquitin-linked cDNA libraries and provide details for implementing this system to screen for binding partners of a bait protein, in this case BAP31. BAP31 is a resident integral protein of the endoplasmic reticulum, where it operates as a chaperone or cargo receptor and regulator of apoptosis. Here we describe a novel human member of the protein tyrosine phosphatase-like B (PTPLB) family, an integral protein of the endoplasmic reticulum membrane with four membrane-spanning alpha helices, as a BAP31-interacting protein. PTPLB turns over rapidly through degradation by the proteasome system. Comparisons of mouse cells with a deletion of Bap31 or reconstituted with human BAP31 indicate that BAP31 is required to maintain PTPLB, consistent with a chaperone or quality control function for BAP31 in the endoplasmic reticulum membrane.
Process Considerations for Scale-up of Liquid Chromatography and Electrophoresis (1986)

Chromatography is an important preparative and industrial process. Scale-up of chromatographic processes requires computation of mass transfer characteristics as a function of column area, support particle size and feed volume. In this context, an analytical solution for longitudinal diffusion in packed beds, developed by Lapidus and Amundson, is used to demonstrate the characteristics of a typical size exclusion separation of proteins, including estimation of maximum sample size as allowed by support properties. Electrophoresis is also a powerful fractionation technique for proteins, but is subject to many microscopic effects. These include electric double layers, hydrodynamic drag, and electrical relaxation. In addition, macroscopic effects, such as electroosmosis and thermal gradients, also impact separation efficiency. These effects are discussed in relation to elution processes using selected examples. The combination of an electric field with a chromatographic process has recently been proposed to extend the power of electrophoresis separations. Analysis of such a process, referred to as electrochromatography, is also presented.
Further biochemical characterization of the human thymocyte differentiation antigen T6. (1982)

Charge heterogeneity of the human thymocyte antigen T6 was studied by isoelectric focusing and two-dimensional gel electrophoresis. The larger subunit of T6 (a 49,000 m.w. glycoprotein) contained several oligosaccharide side chains bearing up to 12 terminal sialic acids. When T6 antigens from 19 individual thymuses were analyzed, no differences in the isoelectric focusing patterns of the larger subunit could be detected. The larger subunit of the T6 antigen from MOLT-4 cells (52,000 m.w.) contained an extra oligosaccharide if compared with the T6 antigen from thymus or three other T leukemic cell lines. Two types of small subunits of T6 were found. In addition to a protein of m.w. 12,000, pI 5.5 identified as beta 2-microglobulin, a (m.w. 12,000, pI 7.0) nonglycosylated protein, was detected on two dimensional gels. This protein does not cross-react with beta 2-microglobulin, and its amount varied in different T6 preparations. The tissue distribution, the m.w. the association with beta 2-microglobulin, and the limited structural heterogeneity of T6 support the idea that T6 is the human homologue of the murine thymus leukemia antigen (TL).
The rendering architecture of the DN10000VS (1990)

The Appollo DN10000VS treats graphics as an integral part of the system architecture. Graphics requirements influence the entire system design. All floating-point computations for graphics are performed by the CPU(s), while rasterizing is handled by simplified hardware having no microcode. We decided to support alpha buffering, quadratic interpolation, and texture mapping directly in hardware. This partitioning reduces the cost of a high-end workstation, without sacrificing high rendering quality and performance. This paper describes some of the design trade-offs which led to the final system design.
Elucidation of the Structural Features of Heparan Sulfate Important for Interaction with the Hep-2 Domain of Fibronectin (2000)

The interaction of fibronectin with cell surface heparan sulfate proteoglycans is important biologically in inducing reorganization of the cytoskeleton and the assembly of focal adhesions. The major heparan sulfate-binding site in fibronectin, which is also implicated in these morphological events, is the COOH-terminal Hep-2 domain. We describe the first extensive study of the structural determinants required for the interaction between heparan sulfate/heparin and Hep-2. It is clear that, in heparan sulfate, there is a very prominent role for N-sulfate groups, as opposed to a relatively small apparent contribution from carboxyl groups. Furthermore, a minimal octasaccharide binding sequence appeared to contain at least two 2-O-sulfated iduronate residues, but no 6-O-sulfate groups. However, affinity was enhanced by the presence of 6-O-sulfates, and the interaction with Hep-2 also increased progressively with oligosaccharide size up to a maximum length of a tetradecasaccharide. This overall specificity is compatible with recent information on the structure of Hep-2 (Sharma, A., Askari, J. A., Humphries, M. J., Jones, E. Y., and Stuart, D. I. (1999) EMBO J. 18, 1468-1479) in which two separate, positively charged clusters, involving up to 11 basic amino acid residues (mostly arginines with their preferential ability to co-ordinate sulfate groups), could form a single extended binding site.
Animal models for chronic lymphocytic leukemia (2006)

B-cell chronic lymphocytic leukemia (B-CLL), the most common leukemia in the Western world, results from an expansion of a rare population of CD5+ mature B-lymphocytes. Although clinical features and genomic abnormalities in B-CLL have been studied in considerable detail, the molecular mechanisms underlying disease development has remained unclear until recently. In the last 4 years, several transgenic mouse models for B-CLL were generated. Investigations of these mouse models revealed that deregulation of three pathways, Tcl1-Akt pathway, TNF-NF-kB pathway, and Bcl2-mediated anti-apoptotic pathway, result in the development of B-CLL. While deregulation of TCL1 alone caused a B-CLL phenotype in mice, overexpression of Bcl2 required aberrantly activated TNF-NF-kB pathway signaling to yield the disease phenotype. In this article, we present what has been learned from mice with B-CLL phenotype and how these mouse models of B-CLL were used to test therapeutic treatments for this common leukemia.
Solvatochromic Fluorescent Probes for Monitoring the Photopolymerization of Dimethacrylates (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolvatochromic Fluorescent Probes for Monitoring the Photopolymerization of DimethacrylatesWolter F. Jager, Andries A. Volkers, and D. C. NeckersCite this: Macromolecules 1995, 28, 24, 8153–8158Publication Date (Print):November 1, 1995Publication History Published online1 May 2002Published inissue 1 November 1995https://pubs.acs.org/doi/10.1021/ma00128a027https://doi.org/10.1021/ma00128a027research-articleACS PublicationsRequest reuse permissionsArticle Views491Altmetric-Citations83LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Mediation of Poly(ADP-Ribose) Polymerase-1-Dependent Cell Death by Apoptosis-Inducing Factor (2002)

Poly(ADP-ribose) polymerase-1 (PARP-1) protects the genome by functioning in the DNA damage surveillance network. PARP-1 is also a mediator of cell death after ischemia-reperfusion injury, glutamate excitotoxicity, and various inflammatory processes. We show that PARP-1 activation is required for translocation of apoptosis-inducing factor (AIF) from the mitochondria to the nucleus and that AIF is necessary for PARP-1-dependent cell death. N-methyl-N'-nitro-N-nitrosoguanidine, H2O2, and N-methyl-d-aspartate induce AIF translocation and cell death, which is prevented by PARP inhibitors or genetic knockout of PARP-1, but is caspase independent. Microinjection of an antibody to AIF protects against PARP-1-dependent cytotoxicity. These data support a model in which PARP-1 activation signals AIF release from mitochondria, resulting in a caspase-independent pathway of programmed cell death.