bluuebunny/crossref_metadata_2025_split huggingface dataset:
BAPS 2: enhanced possibilities for the analysis of genetic population structure
Authors: Corander Jukka , Waldmann Patrik , Marttinen Pekka , Sillanpää Mikko J. 
Published: April 2004

Abstract
Summary: Bayesian statistical methods based on simulation techniques have recently been shown to provide powerful tools for the analysis of genetic population structure. We have previously developed a Markov chain Monte Carlo (MCMC) algorithm for characterizing genetically divergent groups based on molecular markers and geographical sampling design of the dataset. However, for large-scale datasets such algorithms may get stuck to local maxima in the parameter space. Therefore, we have modified our earlier algorithm to support multiple parallel MCMC chains, with enhanced features that enable considerably faster and more reliable estimation compared to the earlier version of the algorithm. We consider also a hierarchical tree representation, from which a Bayesian model-averaged structure estimate can be extracted. The algorithm is implemented in a computer program that features a user-friendly interface and built-in graphics. The enhanced features are illustrated by analyses of simulated data and an extensive human molecular dataset.
Availability: Freely available at http://www.rni.helsinki.fi/~jic/bapspage.html
Data mining in bioinformatics using Weka
Authors: Frank Eibe , Hall Mark , Trigg Len , Holmes Geoffrey , Witten Ian H. 
Published: April 2004

Abstract
Summary: The Weka machine learning workbench provides a general-purpose environment for automatic classification, regression, clustering and feature selection—common data mining problems in bioinformatics research. It contains an extensive collection of machine learning algorithms and data pre-processing methods complemented by graphical user interfaces for data exploration and the experimental comparison of different machine learning techniques on the same problem. Weka can process data given in the form of a single relational table. Its main objectives are to (a) assist users in extracting useful information from data and (b) enable them to easily identify a suitable algorithm for generating an accurate predictive model from it.
Availability: http://www.cs.waikato.ac.nz/ml/weka
Direct measurement of protein osmotic second virial cross coefficients by cross‐interaction chromatography
Authors: Tessier Peter M. , Sandler Stanley I. , Lenhoff Abraham M. 
Published: April 2004

AbstractThe importance of weak protein interactions, such as protein self‐association, is widely recognized in a variety of biological and technological processes. Although protein self‐association has been studied extensively, much less attention has been devoted to weak protein cross‐association, mainly due to the difficulties in measuring weak interactions between different proteins in solution. Here a framework is presented for quantifying the osmotic second virial cross coefficient directly using a modified form of self‐interaction chromatography called cross‐interaction chromatography. A theoretical relationship is developed between the virial cross coefficient and the chromatographic retention using statistical mechanics. Measurements of bovine serum albumin (BSA)/lysozyme cross‐association using cross‐interaction chromatography agree well with the few osmometry measurements available in the literature. Lysozyme/α‐chymotrypsinogen interactions were also measured over a wide range of solution conditions, and some counterintuitive trends were observed that may provide new insight into the molecular origins of weak protein interactions. The virial cross coefficients presented in this work may also provide insight into separation processes that are influenced by protein cross‐interactions, such as crystallization, precipitation, and ultrafiltration.
Conformational analysis of HAMLET, the folding variant of human α‐lactalbumin associated with apoptosis
Authors: Casbarra Annarita , Birolo Leila , Infusini Giuseppe , Dal Piaz Fabrizio , Svensson Malin , Pucci Piero , Svanborg Catharina , Marino Gennaro 
Published: April 2004

AbstractA combination of hydrogen/deuterium (H/D) exchange and limited proteolysis experiments coupled to mass spectrometry analysis was used to depict the conformation in solution of HAMLET, the folding variant of human α‐lactalbumin, complexed to oleic acid, that induces apoptosis in tumor and immature cells. Although near‐ and far‐UV CD and fluorescence spectroscopy were not able to discriminate between HAMLET and apo‐α‐lactalbumin, H/D exchange experiments clearly showed that they correspond to two distinct conformational states, with HAMLET incorporating a greater number of deuterium atoms than the apo and holo forms. Complementary proteolysis experiments revealed that HAMLET and apo are both accessible to proteases in the β‐domain but showed substantial differences in accessibility to proteases at specific sites. The overall results indicated that the conformational changes associated with the release of Ca2+ are not sufficient to induce the HAMLET conformation. Metal depletion might represent the first event to produce a partial unfolding in the β‐domain of α‐lactalbumin, but some more unfolding is needed to generate the active conformation HAMLET, very likely allowing the protein to bind the C18:1 fatty acid moiety. On the basis of these data, a putative binding site of the oleic acid, which stabilizes the HAMLET conformation, is proposed.
Identification and analysis of polyserine linker domains in prokaryotic proteins with emphasis on the marine bacterium Microbulbifer degradans
Authors: Howard Michael B. , Ekborg Nathan A. , Taylor Larry E. , Hutcheson Steven W. , Weiner Ronald M. 
Published: April 2004

AbstractPolyserine linkers (PSLs) are interdomain, serine‐rich sequences found in modular proteins. Though common among eukaryotes, their presence in prokaryotic enzymes is limited. We identified 46 extracellular proteins involved in complex carbohydrate degradation from Microbulbifer degradans that contain PSLs that separate carbohydrate‐binding domains or catalytic domains from other binding domains. In nine M. degradans proteins, PSLs also separated amino‐terminal lipoprotein acylation sites from the remainder of the polypeptide. Furthermore, among the 76 PSL proteins identified in sequence repositories, 65 are annotated as proteins involved in complex carbohydrate degradation. We discuss the notion that PSLs are flexible, disordered spacer regions that enhance substrate accessibility.
Structure of fosfomycin resistance protein FosA from transposon Tn2921
Authors: Pakhomova Svetlana , Rife Chris L. , Armstrong Richard N. , Newcomer Marcia E. 
Published: April 2004

AbstractThe crystal structure of fosfomycin resistance protein FosA from transposon Tn2921 has been established at a resolution of 2.5 Å. The protein crystallized without bound Mn(II) and K+, ions crucial for efficient catalysis, providing a structure of the apo enzyme. The protein maintains the three‐dimensional domain‐swapped arrangement of the paired βαβββ‐motifs observed in the genomically encoded homologous enzyme from Pseudomonas aeruginosa (PA1129). The basic architecture of the active site is also maintained, despite the absence of the catalytically essential Mn(II). However, the absence of K+, which has been shown to enhance enzymatic activity, appears to contribute to conformational heterogeneity in the K+‐binding loops.
A comparison between clearing and radiographic techniques in the study of the root‐canal anatomy of maxillary first and second molars
Authors: Omer O. E. , Al Shalabi R. M. , Jennings M. , Glennon J. , Claffey N. M. 
Published: April 2004

AbstractAim  To compare a clearing technique with conventional radiography in studying certain features of the root‐canal system of maxillary right first and second molars. A secondary aim was to assess interexaminer agreement for these features using radiographs.Methodology  Eighty‐three recently extracted permanent maxillary right first molars and 40 recently extracted maxillary right second molars from an Irish population were included. Standard periapical radiographs were taken from a buccolingual and mesiodistal direction. The specimens were then decoronated, demineralized in 10% hydrochloric acid for 8 days and then cleared using methyl salicylate. The cleared teeth were examined using a dissecting microscope (×20), and data relating to number of roots, canal type following Vertucci's classification, presence of lateral canals, presence of transverse anastomoses and position/number of apical foramina were collected. The radiographs were examined by two independent trained endodontists using an X‐ray viewer and a magnifying lens (×2) in a dark room for the same features studied using the clearing technique.Results  The Kappa values for the agreement between the radiographic examiners A and B and the clearing technique and between the two examiners for the number of roots were 0.60, 0.64 and 0.53; for the root‐canal type, 0.37, 0.41 and 0.42; for the number of roots with lateral canals, 0.21, 0.18 and 0.14; and for the transverse anastomoses, 0.29 for radiographic Examiner A. Radiographic Examiner B did not feel capable of accurately recognizing transverse anastomoses from the radiographs. For the position/number of apical foramina, the Kappa values were 0.33 and 0.24, respectively. In general, the Kappa values were low to modest for all comparisons.Conclusions  It is concluded that the agreement between the two radiographic examiners and the agreement between either radiographic examiner and the clearing technique were poor to moderate, indicating the limited value of radiographs alone when studying certain aspects of the root‐canal system.
In vitroevaluation of the effectiveness of irrigants and intracanal medicaments on microorganisms within root canals
Authors: Menezes M. M. , Valera M. C. , Jorge A. O. C. , Koga‐Ito C. Y. , Camargo C. H. R. , Mancini M. N. G. 
Published: April 2004

AbstractAim To evaluatein vitrothe effectiveness of sodium hypochlorite (NaOCl), chlorhexidine (CHX) and five intracanal medicaments on microorganisms within root canals.Methodology Ninety‐six human single‐rooted extracted teeth were used. After removing the crowns, canal preparation was completed and the external root surfaces were coated with epoxy resin. Following sterilization, the teeth were contaminated withCandida albicansandEnterococcus faecalis, and were incubated at 37 ± 1 °C for 7 days. The teeth were divided according to the irrigant solution or intracanal medicament: group 1, sterile physiologic solution (SPS) and calcium hydroxide (Ca(OH)2) paste; group 2, SPS and camphorated paramonochlorophenol (CPMC); group 3, SPS and tricresol formalin; group 4, SPS and CaOH2 + CPMC paste; group 5, SPS and PMC furacin; group 6, 2.5% NaOCl without intracanal medication; group 7, 2.0% CHX without intracanal medication and group 8, SPS without intracanal medication (control group). Microbiological samples were collected with sterile paper points, and bacterial growth was determined. The data were submitted to the analysis of variance (anova,P = 0.05).Results ForC. albicans, groups 3 and 8 were statistically less effective than groups 1, 2, 4 and 5 (Kruskal–Wallis (K–W) = 65.241; gl = 7;P = 0.001). ForE. faecalis, groups 6 and 8 were statistically less effective than groups 1–4 and 7 (K–W = 61.048; gl = 7;P = 0.001).Conclusions Ca(OH)2 + CPMC paste was the most effective intracanal medicament for the elimination of the two microorganisms; 2.0% CHX solution was more effective than 2.5% NaOCl againstE. faecalis.
Who Benefits from Deregulating the Separation of Banking Activities? Differential Effects on Commercial Bank, Investment Bank, and Thrift Stock Returns
Authors: Czyrnik Kathy , Klein Linda Schmid 
Published: April 2004

AbstractWe analyze the deregulation impact on commercial banks, investment banks, and thrifts associated with four major events progressively integrating commercial and investment banking activities in the United States during the 1990s. We find that commercial banks are the only group to react favorably to Federal Reserve announcements relaxing firewalls and easing restrictions on commercial bank revenues from investment banking activities. These regulations primarily benefit large banks. The Bankers Trust acquisition announcement of investment bank Alex Brown is associated with increased wealth for each of the three types of financial service institutions. At the eventual deregulation of the financial services industry, with the passage of the Financial Services Modernization Act in 1999, the values of commercial banks and investment banks increase significantly although thrifts are not affected.
‘Do not attempt resuscitation’ decision‐making: a study exploring the attitudes and experiences of nurses
Authors: Giles Helen , Moule Pam 
Published: April 2004

Summary• At the time of the research being undertaken, a policy regarding resuscitation decisions did not exist at a local hospital. However, it was proposed that a new ‘do not attempt resuscitation’ policy should be implemented• Nurses' attitudes to, and experiences of, the communication involved in ‘do not attempt resuscitation’ decision‐making were explored and compared with five variables (nurses' age, nurses' grade, years of nursing, area of nursing practice and length of nursing experience on current ward)• Seventy‐eight qualified nurses, who made up a convenience sample, participated in the study. An adapted questionnaire was used to explore nurses' attitudes to, and experiences of, ‘do not attempt resuscitation’ decision‐making• The findings suggested that nurses' attitudes did generally concur with the guidelines outlined in the new policy. However, in practice, there were many disparities between nurses' experiences of current ‘do not attempt resuscitation’ decision‐making and the policy's guidelines• There were no significant differences between nurses' attitudes to current ‘do not attempt resuscitation’ decision‐making and the five variables. However, there was one significant difference identified between nurses' experiences and the area of nursing practice (p = 0·008)• To adhere to the principles of the forthcoming ‘do not attempt resuscitation’ policy at the local hospital, the research findings have suggested that changes need to occur to both nurses' attitudes to and nurses' experiences of current ‘do not attempt resuscitation’ decision‐making
TNF‐α hyperpolarizes membrane potential and potentiates the response to nicotinic receptor stimulation in cultured rat myenteric neurones
Authors: Rehn M. , Hübschle T. , Diener M. 
Published: April 2004

AbstractAims:
Tumour necrosis factor‐α (TNF‐α) plays a central role in the pathophysiology of inflammatory bowel disease. The present experiments were designed to characterize the action of this cytokine on enteric neurones.Methods:  Myenteric ganglia from newborn rats were treated for 20 h with TNF‐α (100 ng mL−1) and studied with the patch‐clamp technique.Results:  Control neurones showed a membrane potential of −34.6 ± 2.2 mV (n = 22), whereas TNF‐α‐treated cells exhibited a membrane potential of −50.8 ± 3.5 mV (n = 25). The depolarization evoked by carbachol (50 μm) was potentiated from 5.2 ± 0.7 mV (n = 6) in control neurones to 27.5 ± 2.0 mV (n = 10) in TNF‐α‐treated cells. This effect was mimicked by 1,1‐dimethyl‐4‐phenylpiperazinium iodide, but not by bethanechol. The changes in basal membrane potential and in the nicotinic receptor response were suppressed by the non‐selective cyclooxygenase (COX) inhibitor indomethacin (10 μm), and the COX II‐specific inhibitor, nimesulide (100 μm), whereas the COX‐I selective inhibitor SC‐560 (5 μm) and the proteintyrosinekinase inhibitor genistein (50 μm) only partially inhibited the action of TNF‐α. Staining of the ganglionic cells with an antibody against the transcription factor STAT5 revealed that TNF‐α induced a nuclear translocation of STAT5 in non‐neuronal cells.Conclusion:  TNF‐α changes the electrophysiological properties of myenteric neurones via cyclooxygenase metabolites and protein tyrosine phosphorylation; the cells primarily responding to the cytokine seem to be non‐neuronal cells in the ganglion culture, which respond with a nuclear STAT5 translocation suggesting an action on gene transcription.
Constitutive expression of inducible Hsp70 is linked to natural shifts in skeletal muscle phenotype
Authors: O'Neill D. E. T. , Noble E. G. 
Published: April 2004

AbstractAim:  Constitutive expression of heat shock protein 70 (Hsp70) is elevated in frequently recruited, metabolically efficient rodent striated muscle. We aimed to assess the relative importance of muscle phenotype vs. increased contractile activity on this pattern of expression using the rat diaphragm, which undergoes a dramatic and sustained increase in recruitment with parturition and development.Methods:  Diaphragms were collected from rats of various ages (20 day fetus, 1 and 3 days, and 1, 3, 6 and 12 weeks postpartum; PP), and assessed for changes in oxidative capacity, Hsp70 and Type I myosin heavy chain (MHCI) (used as a marker of muscle phenotype changes).Results:  Oxidative capacity of the diaphragm (as indicated by citrate synthase activity) and whole body growth rate (% increase in body weight per week), factors thought to require chaperone activity, increased rapidly, peaked at 3–6 weeks PP and declined late in development. In contrast, at 1 week PP, increased contractile activity in the diaphragm had not altered the expression of Hsp70 protein or mRNA from fetal levels. Significant increases in Hsp70 were not observed until between 1 and 3 weeks, achieving their highest levels at 12 weeks PP. Both MHC I protein (r = 0.69, P = 0.001) and mRNA (r = 0.76, P = 0.001) were significantly correlated with their Hsp70 counterparts.Conclusions:  Expression of Hsp70 in the developing diaphragm represents an adaptation associated with a shift towards a slower, more metabolically efficient adult phenotype rather than simply a response to contractile stress.
New model for kinetic studies of HDL metabolism in humans
Authors: Chétiveaux M. , Ouguerram K. , Zair Y. , Maugère P. , Falconi I. , Nazih H. , Krempf M. 
Published: April 2004

AbstractBackground   The aim of the study was to develop a new model for kinetic studies of Apolipoprotein A‐I of HDL (Apo A‐I‐HDL) labelled with stable isotope by using HDL subclasses isolated with fast protein liquid chromatography (FPLC).Materials and methods  Apo A‐I‐HDL kinetics were studied by infusing [5.5.5–2H3]‐leucine for 14 h in six healthy subjects. Preβ1 and αHDL were separated by FPLC and total HDL by ultracentrifugation (HDL‐UC).Results  The tracer‐to‐tracee ratios were higher in preβ1 HDL than in HDL‐UC or αHDL. Leucine enrichments found in HDL‐UC were higher compared with αHDL, suggesting that HDL‐UC were composed of a mixture of Apo A‐I‐αHDL and Apo A‐I‐preβ1 HDL. Kinetic analysis of data obtained from FPLC was achieved using a multicompartmental model, including a conversion between preβ1 and αHDL compartments. The production rate of preβ1 HDL was 7·72 ± 2·86 mg kg−1 d−1 (mean ± SD). Preβ1 HDL were converted to αHDL at a rate of 96·24 ± 42·99 pool d−1, and the synthesis rate of preβ1 HDL from αHDL was 10‐fold slower: 7·09 ± 4·51 pool d−1. Apo A‐I‐FCR of HDL‐UC was estimated using a one‐compartment model (0·165 ± 0·074 pool d−1), and was higher but not significantly compared with FCR of Apo A‐I‐αHDL (0·112 ± 0·026 pool d−1) calculated with the new model.Conclusions  This study reports for the first time a model involving enrichments of Apo A‐I in preβ1 and αHDL which allowed the measure of Apo A‐I cycling within HDL fraction and will aid better understanding of kinetics of HDL in humans.
Are the long‐term fluctuations in Atlantic bluefin tuna (Thunnus thynnus) population related to environmental changes?
Authors: Ravier Christelle , Fromentin Jean‐Marc 
Published: April 2004

AbstractWe tested whether synchronous, long‐term fluctuations in Atlantic bluefin tuna (Thunnus thynnus) trap catches, collected from the ancestral Mediterranean and Atlantic trap fishery, might be related to large‐scale environmental change. Nine time series of trap catches of more than 80 yr long were compared with long time series of three preselected environmental variables, i.e. the North Atlantic Oscillation (NAO), the Length of the Day Index (LOD, a proxy of the atmospheric circulation index) and the temperature. Spectral analyses of trap catches, LOD and temperature displayed similar spectra with peaks at low frequencies, whereas those of the NAO exhibited a broad band spectrum. Regression analyses and tests of correlation did not reveal any clear relationship between trap catches on the one hand and NAO and LOD on the other hand. In contrast, long‐term fluctuations in trap catches appear to be closely and negatively related to long‐term trends in temperature. Underlying processes that could explain such a relationship are discussed, with special focus on changes in migration patterns of the Atlantic bluefin tuna.
Change in feeding ecology and trophic dynamics of Pacific salmon (Oncorhynchus spp.) in the central Gulf of Alaska in relation to climate events
Authors: Kaeriyama M. , Nakamura M. , Edpalina R. , Bower J. R. , Yamaguchi H. , Walker R. V. , Myers K. W. 
Published: April 2004

AbstractThe effects of climate events on the feeding ecology and trophic dynamics of Pacific salmon (Oncorhynchus spp.) in offshore waters of the central Gulf of Alaska were investigated during early summers (1994–2000), based on analyses of stomach contents, and carbon and nitrogen stable isotopes (δ13C and δ15N). Gonatid squids (mainly Berryteuthis anonychus) were the dominant prey of all salmon species except for chum salmon (O. keta). During the 1997 El Niño event and the 1999 La Niña event, squids decreased sharply in the diets of all Pacific salmon except coho salmon (O. kisutch) in the Subarctic Current, and chum salmon diets changed from gelatinous zooplankton (1995–97) to a more diverse array of zooplankton species. A δ13C and δ15N analysis indicated that all salmon species occupied the same branch of the food web in 1999–2000. We hypothesize that high‐seas salmon adapt to climate‐induced changes in their prey resources by switching their diets either within or between trophic levels. To understand the effects of climate change on Pacific salmon in the Gulf of Alaska, biological oceanographic research on B. anonychus and other important prey resources is needed.
Assumed and inferred spatial structure of populations: the Scandinavian brown bears revisited
Authors: Manel S. , Bellemain E. , Swenson J. E. , François O. 
Published: April 2004

AbstractWe reanalysed the spatial structure of the Scandinavian brown bear (Ursus arctos) population based on multilocus genotypes. We used data from a former study that had presumed a priori a specific population subdivision based on four subpopulations. Using two independent methods (neighbour‐joining trees and Bayesian assignment tests), we analysed the data without any prior presumption about the spatial structure. A subdivision of the population into three subpopulations emerged from our study. The genetic pattern of these subpopulations matched the three geographical clusters of individuals present in the population. We recommend considering the Scandinavian brown bear population as consisting of three (instead of four) subpopulations. Our results underline the importance of determining genetic structure from the data, without presupposing a structure, even when there seems to be good reason to do so.