gebhart/patrepeval huggingface dataset:
Rapid screening of genetic polymorphisms using buccal cell DNA with detection by matrix‐assisted laser desorption/ionization mass spectrometry (1995)

A new approach is developed for the rapid and cost-effective detection of human genetic polymorphisms based on matrix-assisted laser description/ionization mass spectrometric (MALDI MS) detection using a nitrocellulose film substrate. This method employs polymerase chain reaction (PCR) amplification using DNA extracted from buccal cells as templates, followed by direct digestion with restriction enzymes and subsequent analysis by MALDI MS. The extraction of DNA from buccal cells provides a rapid and convenient means for sampling PCR-based diagnostic analysis. The amount of DNA was sufficient as the template for both normal PCR amplifications, and amplifications involving the use of mismatched primers and multiple primers. The MALDI MS methodology has been successfully used for the analysis of such PCR products where restriction fragments generated directly in PCR reactions have been used for detection of carbonic anhydrase and cystic fibrosis transmembrane conductance regulator as model genes. The detection of genetic polymorphisms following routine biological and clinical procedures with the MALDI MS method is demonstrated. The results from MALDI MS analysis are shown to be comparable to those obtained from gel electrophoresis but the MALDI MS method is several orders of magnitude faster than gel electrophoretic techniques. The method described herein should also be readily extended to other areas involving DNA screening and testing.
OFDMA: A Broadband Wireless Access Technology (2006)

In this note, we review the design philosophies for uplink and downlink of OFDMA systems and demonstrate that OFDMA is a superior access technology for broadband wireless data network compared with traditional access technologies such as TDMA and CDMA. The main advantages of OFDMA over TDMA/CDMA stem from the scalability of OFDMA, the uplink orthogonality of OFDMA and the ability of OFDMA to take advantage of the frequency selectivity of the channel. Other advantages of OFDMA include its MIMO-friendliness and ability to provide superior quality of service (QoS).
Possible common biological and immunological properties for detecting encapsulated strains of Staphylococcus epidermidis (1988)

Twenty strains of capsular type II Staphylococcus epidermidis, determined by the method of Ichiman, were obtained from clinical specimens. Among them, 5, 5, and 10 strains were 4+, 3+, and 2+ in the intensities of their reactions against fluorescent antibody, respectively. Strains exhibiting 4+ and 3+ intensities were mouse virulent and phage nontypable, while 2+ strains were mouse avirulent and phage typable. When three strains randomly selected from each of the mouse-virulent and mouse-avirulent strains were compared in terms of their cell volume indices, all mouse-virulent strains had significantly higher indices (average, 1.86 times) than the mouse-avirulent strains. With intraperitoneal injection of the strains into mice, strains with higher cell volume indices resisted ingestion by peritoneal cells, while strains with low cell volume indices were sensitive to phagocytosis. When the capacity to absorb a definite amount of passive protective activity in rabbit antiserum prepared with capsular type II strains was compared among these strains, 10 to 20 mg of mouse-virulent strains was capable of completely absorbing the passive protective activity, whereas more than 80 mg of the cells was required for similar absorption by mouse-avirulent strains. In ultra-thin sections of three mouse-virulent strains stained with ferritin-conjugated rabbit antiserum, well-defined capsules were detected around cell walls; however, no capsule was seen around the walls of three mouse-avirulent strains.
Peptidotriazoles on Solid Phase:  [1,2,3]-Triazoles by Regiospecific Copper(I)-Catalyzed 1,3-Dipolar Cycloadditions of Terminal Alkynes to Azides (2002)

The cycloaddition of azides to alkynes is one of the most important synthetic routes to 1H-[1,2,3]-triazoles. Here a novel regiospecific copper(I)-catalyzed 1,3-dipolar cycloaddition of terminal alkynes to azides on solid-phase is reported. Primary, secondary, and tertiary alkyl azides, aryl azides, and an azido sugar were used successfully in the copper(I)-catalyzed cycloaddition producing diversely 1,4-substituted [1,2,3]-triazoles in peptide backbones or side chains. The reaction conditions were fully compatible with solid-phase peptide synthesis on polar supports. The copper(I) catalysis is mild and efficient (>95% conversion and purity in most cases) and furthermore, the X-ray structure of 2-azido-2-methylpropanoic acid has been solved, to yield structural information on the 1,3-dipoles entering the reaction. Novel Fmoc-protected amino azides derived from Fmoc-amino alcohols were prepared by the Mitsunobu reaction.
Preterm birth prevention by 17 alpha-hydroxyprogesterone caproate vs. daily nursing surveillance. (2009)

There was no difference in recurrent SPTD between women treated with 17P and those receiving dPNS.
Interactions Between SAN 582H and Selected Safeners on Grain Sorghum (Sorghum bicolor) and Corn (Zea mays) (1996)

The efficacy of the safeners naphthalic anhydride (NA), CGA-92194, and CGA-133205 as protectants of grain sorghum and of NA, R-29148, CGA-154281, and dichlormid as protectants of corn against injury from the chloroacetamide herbicide, SAN 582H, was evaluated under greenhouse conditions. SAN 582H applied alone reduced the shoot growth of ‘Funk G522DR’ and ‘Funk G623’ sorghum, but had no effect on the growth of the ‘GP-10’ genotype of sorghum. Corn (‘Northrup-King 9283’ hybrid) was considerably more tolerant than grain sorghum to SAN 582H. The rate of SAN 582H causing 50% reduction of corn shoot height (GR 50 ) was 5.1 kg/ha as compared to 1.1 kg/ha for grain sorghum. NA applied as seed dressing at 5 or 10 g/kg seed, provided moderate protection to ‘G522DR’ and ‘G623’ sorghum and no protection to corn against SAN 582H injury. Dressing of sorghum seeds with CGA-133205 provided moderate protection to G522DR sorghum, whereas seed-applied CGA-92194 provided moderate protection to G623 sorghum against SAN 582H. The dichloroacetamide safeners R-29148, dichlormid, and CGA-154281 were all effective as protectants of corn against SAN 582H injury. These results demonstrate that, as with other chloroacetamide herbicides, the tolerance of corn and grain sorghum to SAN 582H can be enhanced with the use of safeners of the dichloroacetamide type and oxime ether type, respectively.
Transplantation of Human Embryonic Stem Cell-Derived Cells to a Rat Model of Parkinson's Disease: Effect of In Vitro Differentiation on Graft Survival and Teratoma Formation (2006)

Human embryonic stem cells (hESCs) have been proposed as a source of dopamine (DA) neurons for transplantation in Parkinson's disease (PD). We have investigated the effect of in vitro predifferentiation on in vivo survival and differentiation of hESCs implanted into the 6-OHDA (6-hydroxydopamine)-lesion rat model of PD. The hESCs were cocultured with PA6 cells for 16, 20, or 23 days, leading to the in vitro differentiation into DA neurons. Grafted hESC-derived cells survived well and expressed neuronal markers. However, very few exhibited a DA neuron phenotype. Reversal of lesion-induced motor deficits was not observed. Rats grafted with hESCs predifferentiated in vitro for 16 days developed severe teratomas, whereas most rats grafted with hESCs predifferentiated for 20 and 23 days remained healthy until the end of the experiment. This indicates that prolonged in vitro differentiation of hESCs is essential for preventing formation of teratomas.
DNA repair in prokaryotes and lower eukaryotes (1998)

Overview of DNA Damage and Repair, P. Hanawalt. Part I. Prokaryotic Responses to DNA Damage. Nucleotide Excision Repair in Escherichia coli , L. Grossman, C.-L. Lin, and Y. Ahn. Prokaryotic Base Excision Repair D. M. Wilson III, B. P. Engelward, and L. Samson. Oxidative DNA Damage and Mutagenesis, T. G. Newcomb and L. A. Loeb. Regulation of Endonuclease IV as Part of an Oxidative Stress Response in Escherichia coli, B. Weiss. The 'GO' System in Escherichia coli, J. H. Miller. The SOS Response, W. H. Koch and R. Woodgate. DNA Double-Strand Break Repair and Recombination in Escherichia coli, G. R. Smith. Transcription Repair Coupling in Escherichia coli , R. Bockrath. Branched DNA Resolving Enzymes (X-Solvases), B. Kemper. Dam-Directed DNA Mismatch Repair, Lene Juel Rasmussen, L. Samson, and M. G. Marinus. Translesion DNA Synthesis, Z. Hatahet and S. S. Wallace . DNA Repair and Mutagenesis in Streptococcus pneumoniae, S. A. Lacks. DNA Repair in Deinococcus radiodurans, J. R. Battista. Part II. DNA Repair in Lower Eukaryotes. The Genetics and Biochemistry of the Repair of UV-Induced DNA Damage in Saccharomyces cerevisiae, W. Siede. Double-Strand Break and Recombinational Repair in Saccharomyces cerevisiae, J. A. Nickoloff and M. F. Hoekstra. Pathways and Puzzles in DNA Replication and Damage Checkpoints in Yeast, T. Weinert and D. Lydal. Regulatory Networks That Control DNA Damage-Inducible Genes in Saccharomyces cerevisiae J. B. Bachant and S. J. Elledge. Mismatch Repair Systems in Saccharomyces cerevisiae, Gray F. Crouse. DNA Repair in Schizosaccharomyces pombe, D. J. F. Griffiths and A. M. Carr. Toward Repair Pathways in Aspergillus nidulans, E. Kafer and G. S. May. DNA Repair in Neurospora, A. L. Schroeder, H. Inoue, and M. S. Sachs. Pathways of DNA Repair in Ustilago maydis, W. K. Holloman, R. L. Bennett, A. Cole-Strauss, D. O. Ferguson, K. Onel, M. H. Rendi, M. L. Rice, M. P. Thelen, and E. B. Kmiec. Processing of DNA Damage in the Nematode Caenorhabditis elegans, P. S. Hartman and G. Nelson. DNA Repair in Higher Plants, A. B. Britt. Modes of DNA Repair in Xenopus Oocytes, Eggs, and Extracts, D. Carroll. Index.
PAX6 expression identifies progenitor cells for corneal keratocytes (2005)

Keratocytes of the corneal stroma produce a transparent extracellular matrix required for vision. During wound-healing and in vitro, keratocytes proliferate, becoming fibroblastic, and lose biosynthesis of unique corneal matrix components. This study sought identification of cells in the corneal stroma capable of assuming a keratocyte phenotype after extensive proliferation. About 3% of freshly isolated bovine stromal cells exhibited clonal growth. In low-mitogen media, selected clonal cultures displayed dendritic morphology and expressed high levels of keratan sulfate, aldehyde dehydrogenase 3A1, and keratocan, molecular markers of keratocyte phenotype. In protein-free media, both primary keratocytes and selected clonal cells aggregated to form attachment-independent spheroids expressing elevated levels of those marker molecules. The selected clonal cells exhibited normal karyotype and underwent replicative senescence after 65-70 population doublings; however, they continued expression of keratocyte phenotypic markers throughout their replicative life span. The progenitor cells expressed elevated mRNA for several genes characteristic of stem cells and also for genes expressed during ocular development PAX6, Six2, and Six3. PAX6 protein was detected in the cultured progenitor cells and a small number of stromal cells in intact tissue but was absent in cultured keratocytes and fibroblasts. Cytometry demonstrated PAX6 protein in 4% of freshly isolated stromal cells. These results demonstrate the presence of a previously unrecognized population of PAX6-positive cells in adult corneal stroma that maintain the potential to assume a keratocyte phenotype even after extensive replication. The presence of such progenitor cells has implications for corneal biology and for cell-based therapies targeting corneal scarring.
The fine structure of oogonia and oocytes in human ovaries (1967)

ABSTRACT Twenty-eight foetal and post-natal human ovaries (6 weeks post conception to 11 years post partum) have been examined with the electron microscope. Stages in the normal differentiation of germ cells (oogonia; oocytes at the pre-leptotene, leptotene, zygotene, pachytene, and diplotene stages of meiotic prophase) were identified by comparison with (a) corresponding cells in histological and squash preparations, and (b) similar cells in the rat ovary. Atretic cells (oogonia in mitosis ; oocytes at pachytene and diplotene) were also examined. The nuclei of oogonia contain an evenly dispersed fibrillar matrix which becomes organized into irregular strands in oocytes at pre-leptotene. At leptotene these strands become the sheaths surrounding unpaired, electron-dense axial threads or ‘cores’, which become associated in pairs during the transitory zygotene stage, and tend to be polarized within the nucleus. Single and paired threads are replaced by ‘tripartite ribbons’ (synaptinemal complexes) at pachytene; longitudinal subdivision of the lateral components of the ribbon is observed in some nuclei and may represent a later stage. At diplotene, essentially unpaired cores are observed as at leptotene, although they are thicker and more intimately related to the surrounding fibrillar sheath. The latter is also more highly organized than at earlier stages. This chromosomal structure is retained in oocytes in promordial follicles in post-natal ovaries. The dictyate stage observed in rat ovaries is not found in man. The organization of the cytoplasm does not change markedly as oogenesis advances, although organelles become more numerous, and the internal structure more complex, as the cells enlarge towards the diplotene stage. Oogonia degenerating during mitosis differ from normal cells in that the chromosomes become fused to form an irregular mass. Abnormal membrane-bound areas are also observed in the cytoplasm. Atretic oocytes at pachytene coalesce to form ‘pools’ of cytoplasm containing several nuclei in various stages of pyknosis. Atretic cells at diplotene may contain grossly swollen cytoplasmic organelles and clumped, homogeneous chromosomes. The ‘atretic divisions’ appear to be phagocytosed by somatic cells, but the means of elimination of degenerating meiocytes was not determined.
Primary structures of human protein kinase C βI and βII differ only in their C‐terminal sequences (1987)

Two types of cDNA clones encoding human protein kinase C (PKC) were isolated from a spleen cDNA library using rabbit protein kinase C beta I/beta II cDNA as a hybridization probe. Nucleotide sequence analyses of these cDNA inserts revealed complete primary structures of two distinct types of human protein kinase C beta I and beta II which differ only in their C-terminal 50 or 52 amino acid residues. It was concluded that there exist four distinct types of PKC, PKC alpha, beta I, beta II and gamma, in human as well as rabbit, and that the corresponding sequences are strictly conserved among mammalian species.
Anionic Surfactant Phospholipids Inhibit Lipopolysaccaride‐induced Inflammation from Alveolar Macrophages and U937 Cells (2006)

Lipopolysaccharide (LPS), derived from Gram‐negative bacteria, is a potent pro‐inflammatory toxin and causes lethal disorders including acute lung injury and acute respiratory distress syndrome. Pulmonary surfactant is secreted as a complex mixture of lipids and proteins by alveolar type II cells. Surfactant phospholipids are essential in reducing surface tension at the air‐liquid interface. In the present study, we determined palmitoyloleoyl‐phosphatidylglycerol (POPG) and phosphatidylinositol (PtdIns), which are minor components of surfactant, regulated the inflammatory response of alveolar macrophages. POPG and PtdIns significantly inhibited LPS‐induced nitric oxide and tumor necrosis factor (TNF)‐α production from rat and human alveolar macrophages and U937 cell lines. POPG reduced LPS‐elicited phosphorylation of p38 MAPK , ERK and Iκ Bα and mitogen‐activated protein kinase phosphatase (MKP)‐1 expression. POPG and PtdIns strongly bind to CD14 and appear to block the toll‐like receptor 4 signaling by interfering with direct binding of LPS to CD14. POPG administered intratracheally to mice inhibited the LPS‐induced neutrophil infiltration and TNF‐α production in the pulmonary compartment. POPG was also effective when administered intravenously. Our data clearly identify the anti‐inflammatory properties of surfactant phospholipids at the environmental interface of the lung. NIH PO1‐HL073907.
The dynamics of a hybrid system based on the NV center in spin bath (2015)

Hybrid system based on nuclear spins coupled to defect electron spin in solid has been proposed as an appealing strategy to manipulate qubits for quantum information processing. While universal quantum control and the time optimal control have been arrived, the influence of environment on the system has been ignored. We studied the dynamics of the hybrid system under the surrounding environment using the quantum master equation approach. The quantum master equation and the mean-value equations of the dynamical variables have been derived. Here we focus on a special platform based on the Nitrogen-Vacancy center electronic spin in diamond and nearby carbon-13 nuclear spins.
Noise estimation by minima controlled recursive averaging for robust speech enhancement (2002)

In this letter, we introduce a minima controlled recursive averaging (MCRA) approach for noise estimation. The noise estimate is given by averaging past spectral power values and using a smoothing parameter that is adjusted by the signal presence probability in subbands. The presence of speech in subbands is determined by the ratio between the local energy of the noisy speech and its minimum within a specified time window. The noise estimate is computationally efficient, robust with respect to the input signal-to-noise ratio (SNR) and type of underlying additive noise, and characterized by the ability to quickly follow abrupt changes in the noise spectrum.
The red flour beetle's large nose: An expanded odorant receptor gene family in Tribolium castaneum (2007)

The Tribolium castaneum genome sequence reveals a large number of odorant receptor (Or) genes compared to those found in other insects whose olfactory genomes have been studied-341 Or genes and pseudogenes, encoding 259 intact odorant receptor proteins. An RT-PCR study of larvae and adults revealed that only 145 (64%) of 233 genes with successful genomic DNA amplifications were expressed. No expression of the other 87 genes was detected at any age, suggesting either that these genes are not expressed in this particular strain, or that they are induced only in certain environmental or developmental conditions. TcOR1, the ortholog of the Drosophila Or83b (DmOr83b) gene, which is required for the function of olfactory receptor proteins in Drosophila, was expressed in extracts from adult and larval heads and in extracts from adult bodies. Expression of 41 TcOr genes was detected in extracts from larval head tissue and 111 in extracts from adult head tissue (both figures exclude TcOr1). Twenty-eight TcOrs were detected only in adult bodies. Beetle pupae were injected with TcOr1 dsRNA; unlike sham-injected and control beetles, these knock-down beetles showed no significant response to the Tribolium aggregation pheromone, supporting the hypothesis that TcOr1 plays a similar decisive role in olfaction to DmOr83b. The substantial number of Ors poses the question of why Tribolium has such a large olfactory receptor repertoire, and underlines the need for more studies of the natural history of this species.
Replication of the base pair 6-thioguanine/5-methyl-2-pyrimidinone with the large Klenow fragment of Escherichia coli DNA polymerase I (1993)

The kinetics and the fidelity of replication of the base pair 6-thioguanine (Gs)/5-methyl-2-pyrimidinone (Th) have been determined by using defined oligomers with the large Klenow fragment of Escherichia coli DNA polymerase I. The insertion efficiency, Vmax/Km (min-1 microM-1), of Th opposite Gs is 1.5 and the insertion efficiency of Gs opposite Th is 0.7. By comparison, the insertion efficiencies of C opposite G and G opposite C are 0.5 and 1.5. The insertion efficiency of the next base, A opposite T, is 2 times greater after the base pair Gs/Th than after G/C. The fidelity of replication with respect to thymine and adenine has misinsertion frequencies, or ratios of the insertion efficiency of the "wrong" base to the "right" base, of 7 x 10(-4) for T opposite Gs (T/Gs), 4 x 10(-6) for T/Th, and a maximum stable misinsertion frequency of 4 x 10(-4) for A/Th. No detectable elongation occurs after an A is inserted opposite a Gs. These values are similar to the misinsertion frequencies of G and C with T and A. The maximum stable misinsertion frequencies with G and C are 4 x 10(-2) for G/Th, 3 x 10(-2) -7 x 10(-3) for Gs/C, and 2.6 x 10(-1) for C/Gs, and the misinsertion frequency is < 1 x 10(-3) for Th/G. The kinetics results and molecular modeling suggest modifications to the Gs/Th base pair that may provide higher levels of fidelity of replication with respect to C and G.
Tip-induced anodization of titanium surfaces by scanning tunneling microscopy: A humidity effect on nanolithography (1993)

A scanning tunneling microscope was employed for tip-induced anodization of titanium (Ti) surfaces. Spatial resolution of fabricated patterns was remarkably affected by the tip shape and humidity in the atmosphere. The amount of adsorbed water on the Ti surface determined by humidity has a key role in controlling the resolution, and the resolution becomes worse with increasing humidity. Under the optimized conditions, tip-induced anodization of Ti was successfully achieved with a spatial resolution of 30 nm.
Human immunodeficiency virus reverse transcriptase. General properties and its interactions with nucleoside triphosphate analogs. (1987)

Using affinity purified human immunodeficiency virus (HIV) reverse transcriptase the reaction assay conditions were determined. The optimum incorporation of dTMP into the (rA)n(dT)10 template with HIV reverse transcriptase required 6 mM MgCl2 and 80 mM KCl. The template specificity of HIV reverse transcriptase is quite different from those of the human gamma-polymerase-associated reverse transcriptase or avian virus reverse transcriptase. The preferential inhibition of HIV reverse transcriptase as compared to human gamma-reverse transcriptase was observed with several nucleoside analog triphosphates. The Ki values for thymidine triphosphate analogs with HIV reverse transcriptase ranged from 5 to 13 nM with decreasing effectiveness for 3'-fluoro greater than 3'-amino greater than 2',3'-dideoxy greater than 3'-azido groups. This study provides information on the structure activity relationships of the triphosphate analogs inhibitory effects on HIV reverse transcriptase versus human gamma-polymerase-associated reverse transcriptase, and the possible mechanisms of action of 3' azido thymidine and the 2',3'-dideoxynucleosides, and also identifies other nucleoside analogs for possible development as inhibitors of HIV.