gebhart/patrepeval huggingface dataset:
Alterations in Cell Cycle Genes in Early Stage Lung Adenocarcinoma Identified by Expression Profiling (2003)

In normal lung epithelial cells, cellular division is an ordered, tightly regulated process involving multiple checkpoints that assess extracellular growth signals, cell size, and DNA integrity. In contrast, neoplastic lung cells develop the ability to bypass several of these checkpoints, particularly at the G1/S and G2/M boundaries. We used genomic profiling to compare gene expression levels in early stage lung adenocarcinomas and non-neoplastic pulmonary tissue in order to comprehensively identify alterations in the process of cell cycling. RNA extracted from node negative, poorly differentiated lung adenocarcinomas (15 patients) and non-neoplastic pulmonary tissue (5 patients) was hybridized to oligonu-cleotide microarray filters containing 44,363 genes. Ontological classification was used to extract genes involved with cell cycle progression. Further analysis discovered a subset of differentially expressed genes for further study. Of the 624 cell cycle genes on the microarray filters, 40 genes were predicted to be differentially expressed in lung adeno-carcinomas. Alterations in several genes (i.e., cyclin B1, cyclin D1, p21, MDM2) are consistent with published data in the literature. We also identified 19 novel genes that have neither been described in non-small cell lung cancer (i.e., cdc2, cullin 4A, ZAC, p57, DP-1, GADD45, PISSLRE, cdc20) nor in any other tumors (i.e., cyclin F, cullin 5, p34). These results identified several potential cell cycle genes altered in lung cancer.
CCK-2/gastrin receptor-targeted tumor imaging with (99m)Tc-labeled minigastrin analogs. (2005)

The promising characteristics of [(99m)Tc]Demogastrin 1-3 both in vitro and in animal models illustrate their suitability for CCK-2/gastrin-R-targeted tumor imaging. These qualities could be confirmed for [(99m)Tc]Demogastrin 2, which provided excellent delineation of tumor deposits in a first patient with metastatic medullary thyroid cancer.
High Km glucose-phosphorylating (glucokinase) activities in a range of tumor cell lines and inhibition of rates of tumor growth by the specific enzyme inhibitor mannoheptulose. (1995)

Differences in modes of control of glycolysis in tumor cells, compared with normal cells, have suggested that phosphofructokinase may not catalyse the rate-controlling step. Instead, hexokinase activity may assume a more important regulatory role. Hexokinase activities are consistently lower than those of phosphofructokinase in tumor cells, and the former enzyme may be saturated with its substrate (M. Board et al., Biochem. J. 265: 503-509, 1990). The present work has focused on the glucose-phosphorylation step in tumor cell glycolysis. A range of eight human tumor cell-lines, one human tumor tissue, and four rat tumor cell lines were found to have an additional glucose-phosphorylating activity, with properties similar to hepatic glucokinase. Maximal activities range from 1.1-20 nmol/min/mg cell protein, and the activity is consistently absent from any untransformed cell line or tissue tested, except rat liver tissue (18 nmol/min/mg cell protein). Tumor cell glucokinase activity has been characterized by its high Km for glucose (8-11.8 mM); inhibition by the specific glucokinase inhibitor, mannoheptulose (I50, 12.5 mM); and lack of inhibition by 10 mM glucose-6-phosphate. Mannoheptulose also causes inhibition of glucose uptake by tumor cells (25-75% at 30 mM mannoheptulose) and inhibition of rates of growth of cultured tumor cell lines (I50, 21.4 mM). Rates of growth of human tumors in experimental animals are dramatically reduced (by 65-79%) by a dose of 1.7 mg/g mannoheptulose daily for 5 days. The potential of the naturally occurring sugar, mannoheptulose (which is purified from avocados and is assumed to be of low toxicity), as a cancer treatment is discussed.
Nickel-based Enzyme Systems (2009)

Of the eight known nickel enzymes, all but glyoxylase I catalyze the use and/or production of gases central to the global carbon, nitrogen, and oxygen cycles. Nickel appears to have been selected for its plasticity in coordination and redox chemistry and is able to cycle through three redox states (1+, 2+, 3+) and to catalyze reactions spanning approximately 1.5 V. This minireview focuses on the catalytic mechanisms of nickel enzymes, with an emphasis on the role(s) of the metal center. The metal centers vary from mononuclear to complex metal clusters and catalyze simple hydrolytic to multistep redox reactions.
A facile kit for F-18 radiolabeling of peptides for PET (2011)

1489 Objectives The aim of this study was to develop a rapid, one-step, kit to radiolabel peptides with F-18, at high specific activity. Methods A new 2-(4-(carboxymethyl)-7-{[4-(carboxymethyl)phenyl]methyl}-1,4,7-triazacyclononan-1-yl)acetic acid (NODA-MPAA) ligand was attached to peptides for pretargeting and receptor targeting. The peptides were formulated in lyophilized kits containing Al3+, ascorbic acid, and a bulking agent. The peptide kits were radiolabeled in one step by adding F-18 in saline, heating briefly, and then purifying rapidly by solid phase extraction (SPE). The kits were optimized by examining the effects of pH, different bulking agents, Al3+/peptide ratios and the addition of a co-solvent and an antioxidant. Results An optimized kit containing 20 nmol of a NODA-MPAA-peptide for pretargeting was labeled with F-18 in a single step with a specific activity up to 153 GBq/μmol (4135 Ci/mmol) in high isolated yield (58-93%) after a simple SPE purification. The total reaction and purification time was about 30 min. Optimal kit labeling yield was observed at pH 4.0±0.2, with 0.1 mg of ascorbic acid. A 1:1 ratio of F-18 in saline to ethanol was used for the radiolabeling and an Al:NODA-MPAA-peptide ratio was optimal at about 0.6:1. Similar labeling results were obtained with octreotide and bombesin peptides. An acceptable lypohilized cake was prepared using α,α-trehalose as a bulking agent; 2.5% to as much as 50%/wt did not affect the radiolabeling yield. Conclusions An optimized, facile kit containing 20 nmol of a NODA-MPAA-peptide for pretargeting was radiolabeled with F-18 in saline/ethanol 1:1, heated to 100°C briefly and then purified by SPE to produce the F-18-labeled peptide in a single step and in high yield. The peptide kits have been F-18-labeled with specific activities as high as 153 GBq/μmol (4135 Ci/mmol). This labeling technique appears to be generally useful, since the receptor targeting peptide kits labeled with the same efficiency as the pretargeting peptide kit. Research Support Supported in part by NIH Grant# 5R44RR028018
The aetiological significance of Bordetella bronchiseptica and Pasteurella multocida in atrophic rhinitis of swine. (1981)

Experimental infection with either pure culture of Bordetella bronchiseptica or B. bronchiseptica and a toxin-producing strain of Pasteurella multocida was studied in newborn piglets from 26 sows. Pigs inoculated with B. bronchiseptica alone got mild lesions, whereas pigs inoculated with both organisms showed clinical and pathological signs of atrophic rhinitis, corresponding to the progressive natural diseases. The effect of vaccinating sows against B bronchiseptica during pregnancy was studied.
Pyrazines and Related Compounds. I. A New Synthesis of Hydroxypyrazines (1949)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPyrazines and Related Compounds. I. A New Synthesis of HydroxypyrazinesReuben G. JonesCite this: J. Am. Chem. Soc. 1949, 71, 1, 78–81Publication Date (Print):January 1, 1949Publication History Published online1 May 2002Published inissue 1 January 1949https://pubs.acs.org/doi/10.1021/ja01169a023https://doi.org/10.1021/ja01169a023research-articleACS PublicationsRequest reuse permissionsArticle Views1113Altmetric-Citations65LEARN 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
A Portable Scatterometer For Optical Shop Use (1985)

The scattering of optical components has become a more and more critical issue in modern sensor systems. This is a result of improved performance capabilities on the part of detectors and of optical elements themselves, as well as an increased awareness of the effects of scatter on system performance. There are several programs that evaluate scatter in complicated optical trains, the best known of which are APART and GUERAP (Arizona Paraxial Analysis of Radiative Transfer and General Unwanted Energy Radiation Analysis Program). These programs require component scatter data as inputs for the analysis and even the beginning design approaches. These data have generally been generated with laboratory instruments that were essentially goniometric radiometers. The data have been difficult to obtain and usually obtained for small representative samples of the real surfaces. If, in the process of manufacture of the parts a measurement of the scatter was made, it was done with a relatively crude jerry-rigged apparatus. Sometimes the measurements made this way were quite accurate, but they were never easy.
Molecular Cloning of cDNA for Matriptase, a Matrix-degrading Serine Protease with Trypsin-like Activity (1999)

A major protease from human breast cancer cells was previously detected by gelatin zymography and proposed to play a role in breast cancer invasion and metastasis. To structurally characterize the enzyme, we isolated a cDNA encoding the protease. Analysis of the cDNA reveals three sequence motifs: a carboxyl-terminal region with similarity to the trypsin-like serine proteases, four tandem cysteine-rich repeats homologous to the low density lipoprotein receptor, and two copies of tandem repeats originally found in the complement subcomponents C1r and C1s. By comparison with other serine proteases, the active-site triad was identified as His-484, Asp-539, and Ser-633. The protease contains a characteristic Arg-Val-Val-Gly-Gly motif that may serve as a proteolytic activation site. The bottom of the substrate specificity pocket was identified to be Asp-627 by comparison with other trypsin-like serine proteases. In addition, this protease exhibits trypsin-like activity as defined by cleavage of synthetic substrates with Arg or Lys as the P1 site. Thus, the protease is a mosaic protein with broad spectrum cleavage activity and two potential regulatory modules. Given its ability to degrade extracellular matrix and its trypsin-like activity, the name matriptase is proposed for the protease.
Minireview: the herpes simplex virus amplicon--a versatile defective virus vector. (1994)

The Herpes simplex virus (HSV) amplicon was designed in our laboratory, as a defective virus vector, capable of shuttle delivery of DNA sequences and genes from prokaryotic to eukaryotic cells, tissues or organs. The HSV vector was termed "amplicon" to delineate the fact that it carried the cloned sequences of interest, within amplified concatemeric defective genomes, packaged in HSV virions. Employing the replication functions of their helper virus, the amplicons are wide tropic vectors, capable of entry, replication, and gene expression in varied types of cells, both in vitro, and in vivo. In this brief review, the amplicons will be revisited, beginning with studies of the naturally occurring defective genomes, where many of the virologic aspects of the system were established. Properties of the amplicon system and its components, will be enlightened. The cis acting functions required for amplicon propagation will be briefly described. This will follow with examples of our studies of prokaryotic, viral and eukaryotic DNA sequences, which were amplified and expressed within HSV defective genomes. Studies designed to examine the involvement of helper viruses will be described, including our analyses of host shutoff mutant helper viruses. Finally, recent studies of other laboratories will be reviewed, with emphasis on what appears to be the use of amplicons as neurotropic vectors, towards potential gene therapy.
Far-infrared light generation at semiconductor surfaces and its spectroscopic applications (1992)

Femtosecond pulses of far-infrared (FIR) radiation can be generated in the depletion field near semiconductor surfaces under optical excitation via the inverse Franz-Keldysh effect or electric-field-induced optical rectification. This coherent mechanism differs from previously proposed incoherent mechanisms and is expected to dominate for nonresonant excitation as well as for resonant excitation with optical fields. Two femtosecond time-resolved spectroscopic applications using a visible excitation pulse and a FIR probe pulse are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Best practice for implementing a data warehouse: a review for strategic alignment. (2003)

A review of literature pertaining to data warehouse implementations over the last eight years has been undertaken. It was found that the views of data warehouse practitioners in particular have changed over the period&amp;apos;s pre and post 2000, to the extent that fewer authors place any emphasis on the need for a clear business purpose before embarking on a data warehouse project. Notably, pre 2000, there was no reference to the need to deliver a return on data warehouse investment, but today it appears to be critical that data warehouses prove their financial value. However, data warehouses do have strategic and therefore long term value for an organization. The case study review in this paper supports the notion of strategic alignment but it is the mapping of their experiences to the configuration school of strategic management that explains the degree of success.
Dense Packing and Symmetry in Small Clusters of Microspheres (2003)

When small numbers of colloidal microspheres are attached to the surfaces of liquid emulsion droplets, removing fluid from the droplets leads to packings of spheres that minimize the second moment of the mass distribution. The structures of the packings range from sphere doublets, triangles, and tetrahedra to exotic polyhedra not found in infinite lattice packings, molecules, or minimum-potential energy clusters. The emulsion system presents a route to produce new colloidal structures and a means to study how different physical constraints affect symmetry in small parcels of matter.
Identification of Human Intestinal Alkaline Sphingomyelinase as a Novel Ecto-enzyme Related to the Nucleotide Phosphodiesterase Family (2003)

Alkaline sphingomyelinase (alk-SMase) hydrolyzes dietary sphingomyelin and generates sphingolipid messengers in the gut. In the present study, we purified the enzyme, identified a part of the amino acid sequence, and found a cDNA in the GenBank coding for the protein. The cDNA contains 1841 bp, and the open reading frame encodes 458 amino acids. Transient expression of the cDNA linked to a Myc tag in COS-7 cells increased alk-SMase activity in the cell extract by 689-fold and in the medium by 27-fold. High activity was also identified in the anti-Myc immunoprecipitated proteins and the proteins cross-reacted with anti-human alk-SMase. Northern blotting of human intestinal tissues found high levels of alk-SMase mRNA in the intestine and liver. The amino acid sequence shared no similarity with acid and neutral SMases but was related to the ecto-nucleotide phosphodiesterase (NPP) family with 30-36% identity to human NPPs. Alk-SMase has a predicted signal peptide domain at the N terminus and a signal anchor domain at the C terminus. The ion-binding sites and the catalytic residue of NPPs were conserved, but the substrate specificity domain was modified. Alk-SMase had no detectable nucleotidase activity, but its activity against sphingomyelin could be inhibited by orthovanadate, imidazole, and ATP. In contrast to NPPs, alk-SMase activity was not stimulated by divalent metal ions but inhibited by Zn2+. Differing from NPP2, the alk-SMase cleaved phosphocholine but not choline from lysophosphatidylcholine. Phylogenetic tree indicated that the enzyme is a new branch derived from the NPP family. Two cDNA sequences of mouse and rat that shared 83% identity to human alk-SMase were identified in the GenBank. In conclusion, we identified the amino acid and cDNA sequences of human intestinal alk-SMase, and found that it is a novel ecto-enzyme related to the NPP family with specific features essential for its SMase activity.
Relationship between genotype and function of the human CYP1A1 gene (1993)

A comparative study of human CYP1A1 genotypes and enzymatic activity was performed in a racially diverse population in order to determine frequencies of CYP1A1 genetic polymorphisms and the relationship between CYP1A1 genotype and function. Restriction fragment length polymorphism analyses revealed significantly higher frequencies of a variant Msp1 polymorphism in Asians versus European-Americans, while African-American CYP1A1 genotypic frequencies more closely approximated those of Asians. Comparison of CYP1A1 genotypes at the Msp1 locus to a polymorphic site in exon 7 of the gene revealed a higher frequency of variant genotypes at the Msp1 site. Measurement of lymphocyte CYP1A1 enzyme activity by the ethoxyresorufin O-deethylase assay revealed significantly elevated levels of inducible enzyme activity among variant exon 7 genotypes when compared to wild-type genotypic individuals. These results demonstrate racially distinct patterns of CYP1A1 genotypes, and suggest a functional link between genotype and catalytic activity of the cytochrome P-450 protein responsible for the metabolism of many carcinogenic polycyclic aromatic hydrocarbons.
A 45nm SOI CMOS Class-D mm-Wave PA with &#x003E;10V<inf>pp</inf> differential swing (2012)

The ever-increasing demand for low-cost portable communication devices pushes for higher integration of wireless transceivers in deeply-scaled silicon technologies. Given the overwhelming digital content of a mobile platform, ideally, the RF components should be realized with topologies that allow for their seamless scaling into 22nm and 14nm CMOS technologies. The Power Amplifier (PA) remains one of the most challenging circuit blocks to implement in nanoscale CMOS due to the strict requirements for output power, efficiency and linearity imposed by wireless communication standards. The low breakdown voltage of nanoscale MOSFETs limits the maximum drain voltage swing and the maximum achievable output power. In order to circumvent this problem, a typical approach is to increase the device size and use a reactive matching network to transform the load resistance to a value significantly lower than 50Ω. Nevertheless, due to the typically low-Q passive components that can be manufactured in a nanoscale CMOS process, and because of the high impedance transformation ratio involved, most of the additional output power that would be gained by increasing the device size is wasted in resistive losses in the matching networks, resulting in poor efficiency. This problem is exacerbated at mm-Wave frequencies where the loss of the passive components is even higher, and using lower f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> /f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MAX</sub> thicker oxide or extended drain MOS devices [1] is not viable.
A Two-Level Load/Store Queue Based on Execution Locality (2008)

Multicore processors have emerged as a powerful platform on which to efficiently exploit thread-level parallelism (TLP). However, due to Amdahl’s Law, such designs will be increasingly limited by the remaining sequential components of applications. To overcome this limitation it is necessary to design processors with many lower–performance cores for TLP and some high-performance cores designed to execute sequential algorithms. Such cores will need to address the memory-wall by implementing kilo-instruction windows. Large window processors require large Load/Store Queues that would be too slow if implemented using current CAMbased designs. This paper proposes an Epoch-based Load Store Queue (ELSQ), a new design based on Execution Locality. It is integrated into a large-window processor that has a fast, out-of-order core operating only on L1/L2 cache hits and N slower cores that process L2 misses and their dependent instructions. The large LSQ is coupled with the slow cores and is partitioned into N small and local LSQs, one per core. We evaluate ELSQ in a large-window environment, finding that it enables high performance at low power. By exploiting locality among loads and stores, ELSQ outperforms even an idealized central LSQ when implemented on top of a decoupled processor design.
Evidence that the red cell skeleton protein 4.2 interacts with the Rh membrane complex member CD47 (2002)

Rh(null) red cells are characteristically stomato-spherocytic. This and other evidence suggest that the Rh complex represents a major attachment site between the membrane lipid bilayer and the erythroid skeleton. As an attempt to identify the linking protein(s) between the red cell skeleton and the Rh complex, we analyzed the expression of Rh, RhAG, CD47, LW, and glycophorin B proteins in red cells from patients with hereditary spherocytosis associated with complete protein 4.2 deficiency but normal band 3 (4.2(-)HS). Flow cytometric and immunoblotting analysis revealed a severe reduction of CD47 (up to 80%) and a slower mobility of RhAG on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, possibly reflecting an overglycosylation state. Unexpectedly, 4.2(-/-) mice, which are anemic, displayed a normal red cell expression of CD47 and RhAG. These results suggest that human protein 4.2, through interaction with CD47, is involved in the skeleton linkage and/or membrane translocation of the Rh complex. However, these potential role(s) of protein 4.2 might be not conserved across species. Finally, the absence or low expression of red cell CD47 in CD47(-/-) mice and in some humans carrying RHCE gene variants (D--, D., and R(N)), respectively, had no detectable effect on protein 4.2 and RhAG expression. Since these cells are morphologically normal with no sign of hemolysis, it is assumed that CD47 deficiency per se is not responsible for the cell shape abnormalities and for the compensated hemolytic anemia typical of 4.2(-) and Rh(null) red cells.