bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Native Status of Sea Lampreys in Lake Champlain Based on Mitochondrial DNA Sequencing Analysis
Authors: Waldman John R. , Grunwald Cheryl , Wirgin Isaac 
Published: July 2006

AbstractAdult sea lampreys Petromyzon marinus parasitize a variety of recreationally, commercially, and ecologically important fishes in the north temperate Atlantic Ocean and some inland waters of North America, including the Great Lakes and Lake Champlain. This has resulted in the development of international, provincial, and state programs to suppress their abundance in some of these waters. This effort, in part, emanates from the nonnative status afforded sea lampreys in these lakes by management agencies. However, whether the sea lamprey is native to Lake Champlain has long been debated, and the outcome of this debate may impact the intensity of efforts to suppress their abundance there. We addressed this issue by using sequence analysis of the mitochondrial DNA control region. Resultant haplotype frequencies of sea lampreys from the Lake Champlain watershed were compared among sea lamprey collections made in multiple drainages within the Lake Ontario and Lake Superior watersheds and Atlantic coast rivers. We found no evidence of population structuring among tributaries within any of these four systems, but we did find highly significant genetic differentiation between systems. Haplotype diversity was low in the collections from the two Great Lakes and even more so in those from Lake Champlain compared with that in Atlantic coast rivers. Our genetic results are most consistent with the hypothesis that sea lampreys are native to Lake Champlain, having colonized the lake postglacially by one of several zoogeographic corridors.
A Long‐Term Program for Validation and Verification of Dentaries for Age Estimation in the Yellowstone–Sakakawea Paddlefish Stock
Authors: Scarnecchia Dennis L. , Ryckman L. Fred , Lim Youngtaik , Power Greg , Schmitz Brad , Riggs Vic 
Published: July 2006

AbstractAn approach is described to assess the accuracy and precision of age estimates for paddlefish Polyodon spathula of the Yellowstone–Sakakawea stock in Montana and North Dakota. Twenty‐five of 30 fish tagged with coded wire tags as age‐0 fish in 1995 and recaptured over the period 2002–2005 were independently aged correctly with dentaries (lower jaw bones); estimates for the other five fish deviated from actual ages by 1 year. For fish older than age 10, estimated ages based on dentaries collected from 1991 to 2004 were compared with the estimated minimum expected ages of recovered fish that were jaw‐tagged during 1964–2004. Of 323 fish, 300 (93%) had estimated ages that were the minimum expected age or older. The ages for the remaining 23 fish were less than the minimum expected ages, mostly by three or fewer years; these fish spanned a range of ages but tended to be older. Precision estimates (mean coefficient of variation) for age determination ranged from 3.6% for female fish from Montana in 2003 to 7.1% for male fish from North Dakota in 2003. The results indicate that estimating ages from Yellowstone–Sakakawea paddlefish dentaries is generally a repeatable, straightforward process with sufficient accuracy and precision to be useful for stock assessment. Validation studies should be conducted on other paddlefish stocks because the ease of interpreting dentaries varies with locality.
Influence of Beaver Activity on Summer Growth and Condition of Age‐2 Atlantic Salmon Parr
Authors: Sigourney Douglas B. , Letcher Benjamin H. , Cunjak Richard A. 
Published: July 2006

AbstractThe activity of beavers Castor canadensis in freshwater environments can have considerable localized impacts on the physical and biological components of riparian ecosystems. By changing the habitat of a stream, beaver dams can cause spatial variation in growth opportunity that may have direct consequences for the growth of resident fish. In a small stream in eastern Canada, we studied the effects of an ephemeral beaver pond on the growth and maturity of age‐2 Atlantic salmon Salmo salar parr tagged with passive integrated transponder tags. Water temperature remained relatively uniform throughout the study site. We found very little movement of recaptured fish in the study site. Fish that were recaptured in the beaver pond displayed faster summer growth rates in both length and mass than fish that were recaptured immediately above or below the pond. We also found that parr in the pond maintained relatively high condition factors, whereas fish above and below the pond appeared to decrease in condition factor throughout the summer. In addition to growth, the maturation rates of age‐2 males were higher above the dam than below. This study demonstrates the effect a beaver dam can have on individual growth rates. By influencing growth during sensitive periods, the beaver pond may also influence individual life history pathways. This information could be an important component in ecosystem models that predict the effect of beaver population dynamics on the growth of individual salmonids at the landscape scale.
Survey of the Peace Economics Literature: Recent Key Contributions and a Comprehensive Coverage Up to 1992 (Part II)
Authors: Isard Walter , Anderton Charles H. 
Published: July 2006

In this part we wish to present a short, but compact survey of the main strands of thought in the literature on peace economics up to 1992. A more detailed and thorough survey requires a book-length manuscript currently being written.
There are many ways in which this survey can be organized. One way would address first the question of why there is conflict, proceed to the identification of specific economic factors generating or lying behind conflicts, hone into the consequent phenomena of military expenditures and arms races, perhaps then investigate the interplay of economic factors in specific conflicts (including those leading to major unrest, wars, revolutions and terrorism), examine the basis for arms control, and finally at all stages probe into the manifold direct and indirect effects (the impact) of arms escalation, control and disarmament.
To proceed in this way, however, is not very useful. The literature on peace economics is "helter skelter," appearing in diverse journals and books without adhering to any semblance of organization. Hence we choose to present first some general conceptual materials to help identify the myriad of forces and problems that have been encountered. Then we proceed to survey the literature, for the most part on operational models and hypothesis testing, following the four approaches suggested by economic reasoning that Arrow (chapter 2) uses in treating the economic effects of arms reduction. These are: standard resource allocation theory, macroeconomic stability analysis, modern growth theory, and political economy thinking. We find examination of the literature in this manner at least as good if not better than any other that has been proposed. However, we discuss writings on arms race models and arms control which are the outgrowth of the standard resource allocation problem in a separate section. Also since there are extensive writings on sectoral and regional impacts of military expenditures which employ models derived from both standard resource allocation theory and macroeconomic stability analysis, we add a section on these impacts after the discussion of macroeconomic stability analysis. Finally, we end up with a section on conflict management analysis and procedures, a topic of concern to all social sciences and many professions, and one on which economists have made notable contributions.
Sequencing peptides by electrospray ion-trap mass spectrometry: A useful tool in synthesis of Axinastatin 3
Authors: Jia Chenxi , Qi Wei , He Zhimin , Qiao Bin 
Published: July 2006

Abstract
Axinastatin 3 as a potential anticancer agent was synthesized by chemical methods. In an electrospray ion-trap mass spectrometer, using one stage of tandem mass spectrometry (MS/MS), the linear peptide intermediate was sequenced via the complementarities of y and b ions. Then, using multistep MS/MS (to MS6), the cyclic peptide was sequenced through sequentially removing one amino acid residue in each stage of MS/MS. The difference of the fragmentation mechanisms and the sequencing approaches between them is discussed.
Studies on genetic changes in rye samples (Secale cereale L.) maintained in a seed bank
Authors: Chwedorzewska Katarzyna , Bednarek Piotr , Lewandowska Renata , Krajewski Paweł , Puchalski Jerzy 
Published: July 2006

AbstractThe aim of this study was to identify genetic changes in rye seeds induced by natural ageing during long-term storage and consecutive regeneration cycles under gene bank conditions. Genomic DNA from four rye samples varying in their initial viability after one and three cycles of reproduction was analyzed by AFLP (amplified fragment length polymorphism) fingerprinting. Seven EcoRI/MseI primer combinations defined 663 fragments, and seven PstI/MseI primer combinations defined 551 fragments. The variation in the frequency of the seventy-four EcoRI/MseI bands was statistically significant between samples. These changes could be attributed to genetic changes occurring during storage and regeneration. However, the PstI/MseI fragments appeared to be uninfluenced by seed ageing, regeneration and propagation. A combined Principle Coordinate Analysis revealed differences between samples with different initial viability. We showed that materials with low initial viability differ in their response from highly viable ones, and that the changes exhibited in the former case are preserved through regeneration cycles.
Genotyping of recombinant Pichia pastoris strains
Authors: Viader-Salvadó José , Cab-Barrera Eddy , Galán-Wong Luis , Guerrero-Olazarán Martha 
Published: July 2006

AbstractA simplified amplified-fragment length polymorphism (AFLP) method was used to genotype Pichia pastoris strains obtained by transformation of P. pastoris strain GS115 with a single integration vector. A total of 14 transformants and 3 control strains were analyzed, which generated 16 different band patterns. A clonal variation was obtained after the transformation process due to genetic differences generated during the transformation event of the host strain. Furthermore, the cluster analysis showed that the transformants with lesser genetic differences with respect to the P. pastoris host strain are the recombinant strains with the highest level of recombinant protein production.
The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.)
Authors: Kasprzak Andrzej , Šafář Jan , Janda Jaroslav , Doležel Jaroslav , Wolko Bogdan , Naganowska Barbara 
Published: July 2006

AbstractThe narrow-leafed lupin possesses valuable traits for environment-friendly agriculture and for the production of unconventional agricultural products. Despite various genetic and environmental studies, the breeding of improved cultivars has been slow due to the limited knowledge of its genomic structure. Further advances in genomics require, among other things, the availability of a genomic DNA library with large inserts. We report here on the construction of the first DNA library cloned in a BAC (bacterial artificial chromosome) vector from diploid Lupinus angustifolius L. cv. Sonet. The high molecular weight DNA used for its preparation was isolated from interphase nuclei that were purified by flow cytometry. The library comprises 55,296 clones and is ordered in 144×384-well microtitre plates. With an average insert size of 100 kb, the library represents six haploid genome equivalents. Thanks to the purification of the nuclei by flow cytometry, contamination with chloroplast DNA and mitochondrial DNA was negligible. The availability of a BAC library opens avenues for the development of a physical contig map and positional gene cloning, as well as for the analysis of the plant’s genome structure and evolution.
Impact of linkage disequilibrium on multipoint linkage analysis
Authors: Amos Christopher I. , Huang Qiqing 
Published: July 2006

AbstractIn this chapter we describe the impact that an inaccurate assumption of linkage equilibrium has upon linkage methods. Most multipoint linkage analysis programs assume linkage equilibrium among tightly linked markers. Violation of this assumption leads to biased evidence for linkage when analyzing affected sib‐pairs and an excess probability of falsely detecting evidence for linkage. Including the parents in the analysis or additional unaffected siblings reduces or eliminates this bias. Procedures for removing markers in strong linkage disequilibrium (LD) or for treating linked markers as sets of alleles at a single locus have been developed. Some parametric linkage methods can perform analysis incorporating haplotype frequencies among tightly linked markers, but these approaches are awkward to implement for dense multipoint mapping.
Functional prediction through phylogenetic inference and structural classification of proteins
Authors: Sjölander Kimmen , Specht Chelsea 
Published: July 2006

AbstractComputational prediction of gene function is an essential tool for modern biologists. The primary method of function prediction used today is based on homology, involving the transfer of annotation from the top hit in a database search to the gene of interest. However, homology‐based methods of function prediction have been shown to be prone to systematic errors stemming from gene duplication, domain shuffling, and existing database errors. In recent years, methods of gene function prediction have focused on inclusion of information from evolutionary studies and structural analysis, and the success of these methods in inferring function from sequence data is very encouraging. In this paper, we present a perspective on the use of phylogenetic and structural analyses for improving the inference of protein function.
BioPAX– biological pathway data exchange format
Authors: Bader Gary D. , Cary Michael P. , Sander Chris 
Published: July 2006

AbstractPathway information is vital for successful modeling of cellular systems. The over 215 on‐line pathway databases vary widely in representation and coverage of biological processes, making their combined use extremely difficult. Future pathway information systems for querying, visualization, and analysis must support standard exchange formats to successfully integrate data on a large scale. BioPAX (www.biopax.org) is a data exchange format for biological pathways developed by pathway databases, such as BioCyc, WIT, Kyoto Encyclopedia of Genes and Genomes (KEGG), aMAZE, Integrating Network Objects with Hierarchies (INOH), PATIKA, Reactome, Biomolecular Interaction Database (BIND), and others. Level 1 supports metabolic pathways. Level 2 adds support for molecular interactions. Level 3 will add additional support for signal transduction and genetic regulatory networks. The ultimate goal of BioPAX is to enable seamless collection and use of pathway information so that it may be efficiently applied to answer biological questions.
Cover Picture: Colloidal Synthesis of Hollow Cobalt Sulfide Nanocrystals (Adv. Funct. Mater. 11/2006)
Authors: Yin Y. , Erdonmez C. K. , Cabot A. , Hughes S. , Alivisatos A. P. 
Published: July 2006

AbstractHollow nanocrystals have been synthesized through a mechanism analogous to the Kirkendall Effect. When a cobalt nanocrystal reacts with sulfur in solution, the outward diffusion of cobalt atoms is faster than the inward diffusion of sulfur atoms through the sulfide shell. The dominating outward diffusion of cobalt cations produces vacancies that can condense into a single void in the center of the nanocrystal at high temperatures. This process provides a general route to the synthesis of hollow nanostructures of a large number of compounds and is described in the Full Paper by A. P. Alivisatos and co‐workers on p. 1389.Formation of cobalt sulfide hollow nanocrystals through a mechanism similar to the Kirkendall Effect has been investigated in detail. It is found that performing the reaction at > 120 °C leads to fast formation of a single void inside each shell, whereas at room temperature multiple voids are formed within each shell, which can be attributed to strongly temperature‐dependent diffusivities for vacancies. The void formation process is dominated by outward diffusion of cobalt cations; still, the occurrence of significant inward transport of sulfur anions can be inferred as the final voids are smaller in diameter than the original cobalt nanocrystals. Comparison of volume distributions for initial and final nanostructures indicates excess apparent volume in shells, implying significant porosity and/or a defective structure. Indirect evidence for fracture of shells during growth at lower temperatures was observed in shell‐size statistics and transmission electron microscopy images of as‐grown shells. An idealized model of the diffusional process imposes two minimal requirements on material parameters for shell growth to be obtainable within a specific synthetic system.
Complete trisomy 17p syndrome in a girl with der(14)t(14;17)(p11.2;p11.2)
Authors: Mikhail Fady M. , McIlvried Dawn , Holt R. Lynn , Messiaen Ludwine , Descartes Maria D. , Carroll Andrew J. 
Published: July 2006

AbstractWe report on an 8‐year‐old girl with near‐complete trisomy 17p syndrome due to a de novo unbalanced t(14;17)(p11.2;p11.2). She has features consistent with the previously described cases with complete trisomy 17p, including pre‐ and post‐natal growth retardation, motor and mental retardation, skeletal anomalies, clinodactyly of the 5th finger, hypertrichosis, as well as facial characteristics including microcephaly, receding forehead, ptosis, low‐set malformed ears, smooth philtrum, high‐arched palate, and a short broad neck. Fluorescence in situ hybridization showed that the breakpoints were p11.2 for both chromosome 14 and 17. Microsatellite analysis showed that the duplicated 17p was of paternal origin, and indicated that the breakpoint involving 17p11.2 is most likely located within the ∼1‐Mb segment from the centromere, and not involving the proximal Smith–Magenis syndrome (SMS) low copy repeat. We compare the clinical features of our patient with those previously reported to further delineate the phenotype of complete trisomy 17p syndrome. © 2006 Wiley‐Liss, Inc.
Comprehensive genetic analysis of relevant four genes in 49 patients with Marfan syndrome or Marfan‐related phenotypes
Authors: Sakai Haruya , Visser Remco , Ikegawa Shiro , Ito Etsuro , Numabe Hironao , Watanabe Yoriko , Mikami Haruo , Kondoh Tatsuro , Kitoh Hiroshi , Sugiyama Ryusuke , Okamoto Nobuhiko , Ogata Tsutomu , Fodde Riccardo , Mizuno Seiji , Takamura Kyoko , Egashira Masayuki , Sasaki Nozomu , Watanabe Sachiro , Nishimaki Shigeru , Takada Fumio , Nagai Toshiro , Okada Yasushi , Aoka Yoshikazu , Yasuda Kazushi , Iwasa Mitsuji , Kogaki Shigetoyo , Harada Naoki , Mizuguchi Takeshi , Matsumoto Naomichi 
Published: July 2006

AbstractIn order to evaluate the contribution of FBN1, FBN2, TGFBR1, and TGFBR2 mutations to the Marfan syndrome (MFS) phenotype, the four genes were analyzed by direct sequencing in 49 patients with MFS or suspected MFS as a cohort study. A total of 27 FBN1 mutations (22 novel) in 27 patients (55%, 27/49), 1 novel TGFBR1 mutation in 1 (2%, 1/49), and 2 recurrent TGFBR2 mutations in 2 (4%, 2/49) were identified. No FBN2 mutation was found. Three patients with either TGFBR1 or TGFBR2 abnormality did not fulfill the Ghent criteria, but expressed some overlapping features of MFS and Loeys–Dietz syndrome (LDS). In the remaining 19 patients, either of the genes did not show any abnormalities. This study indicated that FBN1 mutations were predominant in MFS but TGFBRs defects may account for approximately 5–10% of patients with the syndrome. © 2006 Wiley‐Liss, Inc.
Pharmacokinetics and Stability Properties of Catalase Modified with Water‐Soluble Polysaccharides
Authors: Valdivia Aymara , Pérez Yunel , Gómez Leissy , Ramírez Hector L. , Schacht Etienne H. , Villalonga Reynaldo 
Published: July 2006

AbstractBovine liver catalase (EC 1.11.1.6) was chemically modified with mannan, carboxymethylcellulose, and carboxymethylchitin. The enzyme retained about 48–97% of the initial specific activity after glycosidation with the polysaccharides. The prepared neoglycoenzyme was 1.9–5.7 fold more stable against the thermal inactivation processes at 55°C, in comparison with the native counterpart. Also, the modified enzyme was more resistant to proteolytic degradation with trypsin. Pharmacokinetics studies revealed higher plasma half‐life time for all the enzyme‐polymer preparations, but better results were achieved for the enzyme modified with the anionic macromolecules.
A Dodecalanthanide Wheel Supported by p‐tert‐Butylsulfonylcalix[4]arene
Authors: Kajiwara Takashi , Katagiri Kensuke , Takaishi Shinya , Yamashita Masahiro , Iki Nobuhiko 
Published: July 2006

AbstractA dodecaholmium wheel of [Ho12(L)6(mal)4(AcO)4(H2O)14] (1; mal=malonate) was synthesized by using p‐tert‐butylsulfonylcalix[4]arene (H4L) as a cluster‐forming ligand. The wheel consists of three fragments of mononuclear A3− ([Ho(L)(mal)(H2O)]3−), trinuclear B3− ([Ho(H2O)2(mal)(Ho(L)(AcO))2]3−), and C3+ ([Ho(H2O)2]3+), and an alternate arrangement of these fragments (A3−C3+B3−C3+A3−C3+B3−C3+) results in a wheel structure. The longest and shortest diameters of the core were estimated to be 17.7562(16) and 13.6810(13) Å, respectively, and the saddle‐shaped molecule possesses a pocketlike cavity inside.
Maximum Likelihood Estimation of Marginal Pairwise Associations with Multiple Source Predictors
Authors: O'Brien Liam M. , Fitzmaurice Garrett M. , Horton Nicholas J. 
Published: July 2006

AbstractResearchers interested in the association of a predictor with an outcome will often collect information about that predictor from more than one source. Standard multiple regression methods allow estimation of the effect of each predictor on the outcome while controlling for the remaining predictors. The resulting regression coefficient for each predictor has an interpretation that is conditional on all other predictors. In settings in which interest is in comparison of the marginal pairwise relationships between each predictor and the outcome separately (e.g., studies in psychiatry with multiple informants or comparison of the predictive values of diagnostic tests), standard regression methods are not appropriate. Instead, the generalized estimating equations (GEE) approach can be used to simultaneously estimate, and make comparisons among, the separate pairwise marginal associations. In this paper, we consider maximum likelihood (ML) estimation of these marginal relationships when the outcome is binary. ML enjoys benefits over GEE methods in that it is asymptotically efficient, can accommodate missing data that are ignorable, and allows likelihood‐based inferences about the pairwise marginal relationships. We also explore the asymptotic relative efficiency of ML and GEE methods in this setting. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)