bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human papilloma virus detection in neoplastic and non-neoplastic nasopharyngeal tissues in Taiwan
Authors: Huang Cheng-Chih , Hsiao Jenn-Ren , Yang Ming-Wei , Wu Yuan-Hua , Hsu Keng-Fu , Chang Yao , Chen Chaio-Wei , Tsai Sen-Tien , Wei Hsuan-Pei , Jin Ying-Tai 
Published: April 2011

BackgroundHuman papilloma virus (HPV) has been implicated in the carcinogenesis and prognosis of certain head and neck cancers. Whether it also has a role in the pathogenesis of nasopharyngeal carcinoma (NPC) in Taiwan is unclear.MethodsDetection and genotyping of HPVs were performed in 43 primary NPCs (one WHO-I and 42 WHO-II/III) and 40 nasopharyngeal controls using PCR-based HPV genotyping arrays. Localisation of high-risk HPV and Epstein–Barr virus genomes was performed in another 46 primary NPCs (five WHO-I and 41 WHO-II/III) and seven paired metastatic WHO-II/III NPCs using in situ hybridisation.ResultsIn the HPV genotyping cohort, oncogenic HPVs were detected equally in WHO-II/III NPCs (31%, 13/42) and nasopharyngeal controls (35%, 14/40). Tumour high-risk HPV status did not correlate with the prognosis of patients with NPC. In the high-risk HPV in situ hybridisation cohort, 14 (88%) of the 16 oncogenic HPV-positive WHO-II/III NPCs showed a unique cytoplasmic/perinuclear staining pattern, which is distinct from the typical dot/punctate nuclear staining pattern indicating HPV genome integration. In addition, oncogenic HPVs were not always retained in NPC cells during the process of metastasis.ConclusionsThis study does not support an association between oncogenic HPV and the carcinogenesis or prognosis of WHO-II/III NPCs in Taiwan.
Molecular cloning of DNA complementary to Drosophila melanogaster α-amylase mRNA
Authors: Benkel Bernhard F. , Abukashawa Sumaia , Boer Poppo H. , Hickey Donal A. 
Published: April 2011

Several lambda clones containing cDNAs from Drosophila melanogaster were identified in a lambda cDNA bank using two different approaches: (i) cross-species hybridization using a mouse amylase cDNA probe, and (ii) probing with a differential probe, generated from Drosophila RNA. An amylase cDNA fragment was used, in turn, for the isolation and characterization of amylase genomic clones. The size of the Drosophila amylase mRNA was estimated at 1650 b. This is comparable with the size of the murine amylase messenger that encodes a protein of similar molecular weight. In Drosophila larvae, amylase mRNA can account for as little as 0.01% of the poly(A)+ RNA under conditions of dietary glucose repression or greater than 1% of poly(A)+ RNA under derepressing dietary conditions. Key words: Drosophila, amylase cDNA, genomic clones.
Hordeum chilense (2n = 14) computer-assisted Giemsa karyotypes
Authors: Armstrong K. C. , Craig Iris L. , Merritt C. 
Published: April 2011

The Giemsa karyotype of three accessions of Hordeum chilense Roem. and Schult were studied in detail. The idiograms were developed using a computer-assisted software program that contained the ability to straighten and measure chromosomes. Distinctive banding patterns were formed on each of the seven chromosome pairs, which in conjunction with length and arm ratio allowed the identification of each chromosome. Some differences in the banding patterns of the accessions were noted. Key words: Hordeum, chromosome banding.
The phylogeny of the polyploid wheats Triticum aestivum (bread wheat) and Triticum turgidum (macaroni wheat)
Authors: Kerby K. , Kuspira J. 
Published: April 2011

The phylogeny of the polyploid wheats has been the subject of intense research and speculation during the past 70 years. Various experimental approaches have been employed to ascertain the diploid progenitors of these wheats. The species having donated the D genome to Triticum aestivum has been unequivocally identified as Aegilops squarrosa. On the basis of evidence from many studies, Triticum monococcum has been implicated as the source of the A genome in both Triticum turgidum and Triticum aestivum. However, numerous studies since 1968 have shown that Triticum urartu is very closely related to Triticum monococcum and that it also carries the A genome. These studies have prompted the speculation that Triticum urartu may be the donor of this chromosome set to the polyploid wheats. The donor of the B genome to Triticum turgidum and Triticum aestivum remains equivocal and controversial. Six different diploid species have been implicated as putative B genome donors: Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Aegilops speltoides, and Triticum urartu. Until recently, evidence presented by different researchers had not permitted an unequivocal identification of the progenitor of the B genome in polyploid wheats. Recent studies, involving all diploid and polyploid wheats and putative B genome donors, lead to the conclusion that Aegilops speltoides and Triticum urartu can be excluded as B genome donors and that Aegilops searsii is the most likely source of this chromosome set. The possibility of the B genome having arisen from an AAAA autotetraploid or having a polyphyletic origin is discussed. Key words: phylogeny; Triticum aestivum; Triticum turgidum; A, B, and D genomes.
Genetic variation in three subspecies of Melanoplus sanguinipes (F.). I. Morphometric traits
Authors: Chapco William 
Published: April 2011

Samples of three subspecies of Melanoplus sanguinipes (M. s. sanguinipes, M. s. vulturnus, and M. s. defectus), raised under the same laboratory conditions, differ significantly in a number of morphometric traits. The heritable nature of these differences was explored by performing intersubspecific crosses, hybrid crosses, and backcrosses. On the whole, the genetics underlying each trait was complex, with the presence or absence of heterosis, of genic interaction, and of maternal effects being dependent on the strains compared and the sex of the insects. Key words: Melanoplus sanguinipes, Acrididae, quantitative genetics, morphometric traits.
Topographical changes in rye chromosome ultrastructure caused by the C-banding procedure
Authors: Dille J. E. , Gustafson J. P. , Brown Jr. M. , Appels R. , Craig S. 
Published: April 2011

The changes in the surface features of rye chromosome 1 induced by the C-banding procedure was investigated using the scanning electron microscope. Each step in the procedure produced significant changes in the surface topography of the chromosome and minor differences in its general morphology. The most noticeable alteration, chromosomes flattened and smooth, occurred when they were incubated in phosphate buffer without Leishman's stain. Since chromosomes not treated with barium hydroxide were uniformly stained, it seems probable that this alkali removes chromatin unselectively and that the C-bands produced here are due to a differential affinity of the heterochromatin to the stain. Key words: rye, heterochromatin, C-banding.
Genetic variants in progeny of regenerated maize plants
Authors: Lee Michael , Phillips R. L. 
Published: April 2011

Tissue culture has been shown to be a method of generating genetic variation in regenerated plants and their progeny for several maize (Zea mays L.) genotypes. The objectives of this study were to (i) estimate the frequency and types of variants arising from maize tissue cultures, (ii) investigate the effect of culture age on the frequency of variants per regenerated plant, and (iii) estimate the frequency of sectoring among regenerated plants of an F3 from Oh43/A188 genetic background that had not been examined previously for genetic stability in culture. Organogenic callus cultures were initiated from immature F3 embryos for several Oh43ms isoline × A188 crosses. Plants were regenerated either 3 to 4 or 8 to 9 months after culture initiation. Progenies of 248 plants regenerated from 74 cultures were scored for kernel, seedling, and other sporophytic variants following one or two generations of self-pollination. The frequency of variants per regenerated plants increased from 0.5 after 3 to 4 months of culture to 1.3 after 8 to 9 months. A total of 44 variant phenotypes were observed. Defective kernels were the most frequent variant. Most variants were inherited as single-gene recessives. Segregation patterns suggested that the ear and tassel of several (40 of 80) self-pollinated, regenerated plants were genetically discordant. Key words: Zea mays L., tissue culture, somaclonal variation, chimera, qualitative variation.
Inheritance of organelle DNA in barley and Hordeum × Secale intergeneric hybrids
Authors: Soliman K. , Fedak G. , Allard R. W. 
Published: April 2011

Four reciprocal hybrids of Hordeum vulgare (deficiens type) and seven nonreciprocal hybrids resulting from controlled pollination between two Hordeum and three Secale species were assayed for variation in their organelle DNA. The chloroplast and mitochondrial DNAs of these hybrids were distinct. Genetic variability exists within species of the genus Hordeum with organelle transmission being strictly maternal. On the other hand, biparental inheritance was obtained in the intergeneric hybrids involving Hordeum and Secale. There was selective transmission of Secale bands and the number of gene copies transmitted through the pollen was under genetic control. No recombination occurred between the two parental genomes. Key words: DNA, organelle, intergeneric hybrids, Hordeum Secale.
Site-specific independent double labeling of proteins with reporter atoms
Authors: Wallace Carmichael JA , Clark-Lewis Ian 
Published: April 2011

Many types of physical, spectroscopic, and biological studies of proteins and other macromolecules are facilitated by the incorporation of reporter groups. In many cases these are single atom substitutes, for example isotopes (13C for C), or light (F for H) and heavy (Se for S) atom homologs. In some circumstances the incorporation of two different labels in the same molecule would be greatly desirable. Commonly used protein engineering methods for incorporating them can rarely cope with differential double labeling, and have other limitations such as universal, non-specific, or random incorporation. Although de novo peptide synthesis has the power to achieve highly specific labeling, the difficulties inherent in creating long sequences lead us to propose protein semisynthesis as the most practical approach. By ligating combinations of natural and labeled synthetic fragments to reform holoproteins, we can overcome any of the limitations discussed. Using cytochrome c as a model protein we show that two reporter atoms, selenium and bromine, can be simultaneously and site-specifically incorporated without significant consequences to structure and (or) function. This capability opens up the prospect of advances in a number of areas in structural biology.Key words: semisynthesis, peptide synthesis, reporter groups, cytochrome c, structural biology.
Expression of purinergic P2X2 receptor-channels and their role in calcium signaling in pituitary cells
Authors: Stojilkovic Stanko S , Tomic Melanija , Goor Fredrick Van , Koshimizu Taka-aki 
Published: April 2011

Pituitary cells express purinergic receptor-channels (P2XR), the activation of which by ATP is associated with the facilitation of Ca2+ influx. Pharmacological, RT-PCR, and nucleotide sequence analyses confirm the presence of a wild type P2X2aR and a spliced isoform P2X2bR, which lacks a portion of carboxyl terminal amino acids. Wild type and spliced isoform receptors have a similar EC50 for ATP and time-course for activation, but the spliced isoform exhibits rapid and complete desensitization, whereas the wild type channel desensitizes slowly and incompletely. Deletion and insertion studies have revealed that a 6 residue sequence located in carboxyl tail (Arg371-Pro376) is required for sustained Ca2+ influx through wild type receptors. When co-expressed, the wild type and spliced channels form functional heteropolymeric channels. The patterns of Ca2+ signaling in the majority of pituitary cells expressing ATP-gated receptor-channels are highly comparable to those observed in cells co-transfected with P2X2aR and P2X2bR. ATP-induced [Ca2+]i response in pituitary cells is partially inhibited by nifedipine, a blocker of voltage-gated L-type Ca2+ channels, suggesting that P2X2R not only drive Ca2+ into the cell, but also activate voltage-gated Ca2+ entry. Our results indicate that ATP represents a paracrine and (or) autocrine factor in the regulation of Ca2+ signaling, and that its actions are mediated in part by heteropolymeric P2X2R. Key words: ATP-gated channels, gonadotrophs, lactotrophs, somatotrophs.
Association of DNAse sensitive chromatin domains with the nuclear periphery in 3T3 cells in vitro
Authors: Chan Jonathan KL , Park Paul C , Boni Umberto De 
Published: April 2011

DNAse sensitive chromatin, putative transcriptionally competent sequences, exists either as pan-nuclear speckles in cells with nuclei which exhibit a flat geometry, or as a shell apposed to the nuclear envelope in cells with spheroidal nuclei. To test the hypothesis that DNAse sensitive chromatin is similarly associated with the nuclear periphery in cell types with a very flat geometry such as 3T3 fibroblasts, cells were subjected to hypotonic expansion to change their nuclei from a flat ellipsoid to a spheriod. This was based on the assumption that such a spatial association is not resolvable due to the interdigitation at the nuclear midplane of DNAse sensitive chromatin associated with the upper and lower nuclear surfaces. In situ nick translation was used to visualize the distribution of DNAse sensitive chromatin as a function of nuclear geometry. Both unexpanded and expanded cells exhibit DNAse sensitive chromatin as a dome at the apical side of the nucleus, i.e., that aspect of the cell facing the culture medium. The results argue for a polarized association of DNAse sensitive chromatin with the nuclear envelope and indicate that the nuclear periphery may function as a compartment for the spatial coupling of transcription and nucleo-cytoplasmic transport.Key words: nuclear organization, DNAse sensitive chromatin, hypotonic expansion, 3T3 cells.
Caractéristiques géotechniques du secteur du Parc Olympique, Montréal
Authors: Ballivy Gerard , Loiselle André , Durand Marc , Poirier Michel 
Published: April 2011

Under natural conditions, the western limit of the Olympic Park site along Sherbrooke Street is formed by a terrace of marine clay deposited in the Champlain Sea. This terrace has an average height of 60 ft (18 m) and overlies shallow fine grained deposits of fluvio–glacial or glacial origin, which are encountered at ground surface in the eastern part of the site. The bedrock, of Ordovician age, is part of a monoclinal structure which dips at 3° to 5° towards the northeast; bedding planes and vertical fractures form the main planes of discontinuity. The surficial part of the bedrock has been strongly disturbed by the action of glaciers during the Wisconsin glaciation: a displaced rock slab now covers the main part of the site and has greatly affected the design of the foundations for the various structures.Geotechnical investigations carried out by the City of Montreal on or near the site for earlier tunneling projects were used to establish a geotechnical map of the Olympic Park site. Based on this map, the foundation elevations for the different buildings, the type of earth supporting structures, and the geometry of cut slopes could be selected. Along Sherbrooke Street, 70 ft (21 m) deep excavations were necessary in an area where lateral movements could not be tolerated. Consequently a program for monitoring the cast-in-place diaphragm retaining wall and the slopes was carried out by the City of Montreal with the participation of the Ecole Polytechnique de Montréal. [Journal translation]
The kinematic behaviour of drag anchors in sand
Authors: Neubecker S R , Randolph M F 
Published: April 2011

The kinematic behaviour of drag achors during embedment in sand is examined in this paper. A series of centrifuge model anchor tests has been performed in silica and calcareous sands in which both force and kinematic data were obtained during the course of anchor embedment. In this paper, the kinematic data have been examined to determine general rules for the kinematic behaviour of a drag anchor during embedment. These rules provide an essential step towards a theoretical simulation of a complete anchor embedment history and hence a predictive tool for the ultimate holding capacity of a drag anchor. Key words: drag anchor, kinematics, sand, limit equilibrium, ultimate holding capacity.
On the estimation of frost loads
Authors: Rajani B , Zhan C 
Published: April 2011

Frost load is an important loading condition to consider for the design of buried pipes. Though frost loads can be much greater than earth loads, it is not presently possible to estimate frost loads except using heuristic arguments. This paper describes the development of simplified methods to estimate frost load. Important variables are identified that can explain how the effects of frost loading can be mitigated. Sensitivity analyses are presented to highlight the importance of the different variables involved in the simplified methods. Frost loads measured in a field case study are compared with calculated frost loads in trenches with clay and sand backfills. Key words: frost load, frost depth, buried pipe, trench backfills, trench width.
Measurement of hydraulic conductivity in oil sand tailings slurries
Authors: Suthaker Nagula N , Scott J Don 
Published: April 2011

Fine tails, the resulting fine waste from oil sand processing, undergoes large-strain consolidation in tailings ponds. Its consolidation behaviour must be analyzed using a large-strain consolidation theory, which requires the determination of the relationship between the void ratio and hydraulic conductivity. Conventional measurement techniques are not suitable for fine tails, and a special slurry consolidometer, with a clamping device to prevent seepage-induced consolidation, was designed to determine the hydraulic conductivity of the fine tails and nonsegregating fine tails  sand slurries. The hydraulic conductivity of slurries is not constant but decreases with time to a steady-state value. Hydraulic conductivity is also influenced by the hydraulic gradient and bitumen content. It is shown that a low hydraulic gradient, less than 0.2, is necessary to counteract the effect of the bitumen and to represent tailings pond conditions. The hydraulic conductivity of fine tails  sand mixes is controlled by the fines void ratio, hence, fines content. The hydraulic conductivity of chemically amended nonsegregating tailings can be lower than that of fine tails. However, acidlime or acid  fly ash amended nonsegregating tailings have similar hydraulic conductivity values in terms of fines void ratio. The hydraulic conductivity of nonsegregating tailings appears to be governed by fines content and by the nature of the fines aggregation caused by the chemical additive. Key words: tailings, slurries, hydraulic conductivity, slurry consolidometer, nonsegregating tailings, oil sands.
Synthesis and decarboxylation of Δ2-cephem-4,4-dicarboxylic acids
Authors: Wolfe Saul , Ro Stephen , Kim Chan-Kyung , Shi Zheng 
Published: April 2011

Penicillin V was converted in 14 steps into Δ2-cephems having hydrogen at C-3, hydrogen or ethyl at C-2, and two methoxycarbonyl, two benzyloxycarbonyl, or one methoxycarbonyl and one benzyloxycarbonyl substituent at C-4. Deprotection of these Δ2-cephem-4,4-dicarboxylic acid esters by alkaline hydrolysis (in the case of methyl esters) or hydrogenolysis (in the case of benzyl esters) led in all cases to rapid decarboxylation of the Δ2-cephem-4,4-dicarboxylic acid or Δ2-cephem-4,4-dicarboxylic acid monoester. With hydrogen at C-2, hydrolysis of the dimethyl ester with 1 equiv of base produced a Δ2-cephem. With 2 equiv of base, and with all compounds having methyl at C-2, hydrolysis or hydrogenolysis afforded 4α-substituted-Δ2-cephems.In contrast, simpler benzyl or methyl acetamidomalonates could be deprotected without difficulty to afford stable malonic acids. Reasons for the differences in ease of decarboxylation were examined using semiempirical (AM1) and ab initio (3-21G) molecular orbital calculations. The decarboxylation barriers of unionized cephem or acetamido malonic acids were found to be high (3540 kcal mol1). Although the monoanion of acetamidomalonic acid retained a high barrier, the epimeric monoanions of a Δ2-cephem malonic acid decarboxylated with barriers of only 2 kcal mol1.Key words: mercaptoazetidinone, bromomalonate esters, MO calculations, sulfoxides, hydrogenolysis.
Tripodal trisamides based on nicotinic and picolinic acid derivatives
Authors: Hoveyda H R , Karunaratne Veranja , Nichols Christopher J , Rettig Steven J , Stephens Ashley KW , Orvig Chris 
Published: April 2011

A number of polydentate arylamide ligands have been prepared by coupling various acyclic tripodal or linear polyamines with derivatives of nicotinic and picolinic acids. Two synthetic procedures were utilized; tris{[(2-hydroxynicotinyl)carbonyl]-2-aminoethyl}amine (H3NICTREN) was prepared by Method A, the HOSu/DCC method, and the other arylamides in this study were prepared by Method B, the CDI method. Method A involved the reaction of N-hydroxysuccinimide with 2-hydroxynicotinic acid (in the presence of dicyclohexylcarbodiimide (DCC) as a dehydrative coupling reagent) to form the succinimide ester, followed by reaction with TREN to yield H3NICTREN. Method B involved reaction of a carboxylic acid (2-hydroxynicotinic, 3-hydroxypicolinic, nicotinic, or picolinic acids) with carbonyldiimidazole (CDI) to form the N-acylimidazolide, followed by reaction with the amine (TREN, TAME, spermidine, or TRPN) to yield the desired arylamide. The X-ray structure of 1,1,1-tris{[(3-hydroxypicolinyl)carbonyl]-2-aminomethyl}ethane (H3PICTAME) was determined; crystals of H3PICTAME are monoclinic, a = 10.257(2), b = 15.572(3), c = 15.208(2) Å, β = 96.124(15)°, Z = 4, space group P21/a. The structure was solved by direct methods and refined by full-matrix least-squares procedures to R = 0.041 and Rw = 0.038 for 2506 reflections with I >= 3 sigma (I). In the solid state, H3PICTAME contains an extensive hydrogen-bonding network, with eight intra- and one intermolecular H-bonds per molecule; the ligand is partially preorganized for metal ion chelation. The acid dissociation constants of H3NICTREN and those of 1,1,1-tris{[(2-hydroxynicotinyl)carbonyl]-2- aminomethyl}ethane (H3NICTAME) have been determined; pKa1 = 11.2 (10.68), pKa2 = 10.7 (10.58), pKa3 = 10.0 (9.71), and pKa4 = 6.25 for H3NICTREN (H3NICTAME); the high phenolic pKa's are consistent with the hydrogen bonding observed in the solid state.Key words: arylamide, hydrogen bonding, preorganization.