bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pedicle preservation in a Silurian rhynchonelliformean brachiopod from Herefordshire, England: soft-tissue or an artefact of interpretation?—A Reply
Authors: Sutton Mark D. , Briggs Derek E. G. , Siveter David J. , Siveter Derek J. 
Published: August 2008

ABSTRACTWe consider the reinterpretation of Bethia by Bassett et al. (2008) to be flawed in several regards. Details of the pedicle rootlets and wrinkles strongly imply a soft-tissue structure rather than calcified sheath. The ornament is unusual, but equally so under either an orthide or a plectambonitoidean model. The reinterpretation of the ‘deltial plates’ as ‘chilidial plates’ is likely correct, but argues against a plectambonitoidean affinity by implying that the pedicle emerges between the valves. Other arguments presented in favour of a plectambonitoidean affinity are also discussed; we consider them unpersuasive. Finally, we contend that Bethia is sufficiently well characterised to deserve a taxonomic name.
Diversity analysis of the Early Ordovician Sinorthis Fauna (Brachiopoda) from the Meitan Formation of Zunyi, northern Guizhou, South China
Authors: Zhan Renbin , Jin Jisuo 
Published: August 2008

ABSTRACTThe lower Meitan Formation (Floian, upper Lower Ordovician) at the Dajiaosi section, Zunyi District, northern Guizhou Province of South China, contains a moderately rich and diverse Sinorthis Fauna, with 22 species attributable separately to 15 families and seven orders of brachiopods. The fauna can be differentiated into three associations: the Paralenorthis serica, the Sinorthis typica, and the Tarfaya intercalare associations. These occupied a relatively wide palaeoecological range from lower BA3 to upper BA2 settings and from silty to clay substrate conditions. In South China, the Early Ordovician brachiopod radiation was marked by the diversification of the orthide-dominated Sinorthis Fauna, which first appeared and diversified in the middle part (relatively deep water) of the Upper Yangtze Platform in the Didymograptellus eobifidus Biozone, but rapidly declined in the succeeding Corymbograptus deflexus and basal Azygograptus suecicus biozones. During the latest Floian and early Dapingian, it expanded into comparatively shallow-water settings in the onshore direction (Changning area, southern Sichuan), offshore carbonate platform (Yichang, Hubei), and areas adjacent to the submergent Qianzhong Arch (such as the Zunyi area). The first appearance datum of the Sinorthis Fauna in shallower-water settings generally postdates that in the deeper-water environment in the central Upper Yangtze Platform, probably as a result of the fauna tracking a favoured BA3 setting during a gradual marine transgression.
Co-existence of interarea and palintrope: contribution of a new pentameride brachiopod from the Upper Ordovician of Sweden
Authors: Wright Anthony D. , Jia-Yu Rong 
Published: August 2008

ABSTRACTA new genus of pentameride brachiopod, Costilamnulella, described herein from the middle Ashgill of Sweden, is particularly interesting in that the ventral valve possesses both an interarea and a palintrope. Brachiopods normally have one or the other, but both structures do occur amongst the pentamerides, e.g. in Clorinda, Anastrophia and Brevilamnulella. The presence of these structures in three separate pentameride families indicates the persistence of the more primitive condition of an interarea whilst the more advanced palintrope is becoming established. Costilamnulella is interpreted as a restricted side line of the main development of the more widely occurring Brevilamnulella, which survived the end-Ordovician event and may have shared its ancestry with the ubiquitous Clorinda.
Gyrothyris williamsi sp. nov. and inter-relationships of some taxa from waters around New Zealand and the southern oceans (Rhynchonelliformea: Terebratelloidea)
Authors: Bitner Maria Aleksandra , Cohen Bernard L. , Long Sarah. L. , Richer de Forges Bertrand , Saito Michiko 
Published: August 2008

ABSTRACTThis paper describes a terebratelloid articulate brachiopod, Gyrothyris williamsi sp. nov., based on 95 specimens from seamounts on the Lord Howe Rise, Coral Sea, SW Pacific Ocean. The new species is attributed to Gyrothyris on the basis of (a) morphological and growth trajectory similarities; (b) phylogenetic analyses of an alignment of DNA sequence (∼2900-sites) obtained from nuclear-encoded small- and large-subunit ribosomal RNA genes (SSU and LSU); and (c) the presence of a distinctive, two-part deletion in the LSU gene. It is distinguished morphologically from Gyrothyris mawsoni and its subspecies by both internal and external morphology and by its isolated geographical distribution, which extends the patchy, known range of this genus to an area some 2000 km north of its previous northern limit around New Zealand. Phylogenetic analyses of the rDNAs and of mitochondrial cox1 gene sequences (663 sites) confirm previous indications that the New Zealand endemic terebratelloid genera form a clade (Neothyris (Calloria, Gyrothyris, Terebratella), but the position of Terebratella with respect to Calloria and Gyrothyris remains weakly established. These sequences disagree inexplicably about the closeness of the relationship between Neothyris parva and N. lenticularis. Analyses of the first sequences from Calloria variegata, a species restricted to the Hauraki Gulf, New Zealand, are consistent with the possibility that it originated locally, and recently, from C. inconspicua. Magellania venosa from S. America/Falklands joins with Antarctic Magellania fragilis and M. joubini to form an rDNA clade that excludes Terebratalia as the putative sister-group of the New Zealand terebratelloid clade. The cox1 (but not the rDNA) sequences of the New Zealand clade pass a test for clock-like rates of evolution, and maximum likelihood pairwise distances suggest that if genetic isolation between the ancestor of Antarctic Magellania and the last common ancestor of the New Zealand terebratelloid clade was initiated by separation of the Antarctic and New Zealand plates ∼90 Mya, isolation from M. venosa was initiated earlier, perhaps ∼145 Mya. However, in the simple phylogenetic reconstruction presented here from cox1 sequences, S. American and Antarctic Magellania spp. do not yield a well-supported clade, perhaps because of differences in base composition.
AMP hydrolysis in soluble and microsomal rat cardiac cell fractions: kinetic characterization and molecular identification of 5′-nucleotidase
Authors: Pochmann Daniela , Innocente Adrine M. , Cotomacci Guilherme , Barreto-Chaves Maria Luiza M. , Sarkis João J. F. 
Published: August 2008

The present study describes the enzymatic properties and molecular identification of 5′-nucleotidase in soluble and microsomal fractions from rat cardiac ventricles. Using AMP as a substrate, the results showed that the cation and the concentration required for maximal activity in the two fractions was magnesium at a final concentration of 1 mM. The pH optimum for both fractions was 9.5. The apparent Km (Michaelis constant) values calculated from the Eadie–Hofstee plot were 59.7±10.4 μM and 134.8±32.1 μM, with Vmax values of 6.7±0.4 and 143.8±23.8 nmol Pi/min/mg of protein (means±S.D., n=4) from soluble and microsomal fractions respectively. Western blotting analysis of ecto-5′-nucleotidase revealed a 70 kDa protein in both fractions, with the major proportion present in the microsomal fraction. The presence of these enzymes in the heart probably has a physiological function in adenosine signalling. Furthermore, the presence of ecto-5′-nucleotidase in the microsomal fraction could have a role in the modulation of the excitation–contraction-coupling process through involvement of the Ca2+ influx into the sarcoplasmic reticulum. The measurement of maximal enzyme activities in the two fractions highlights the potential capacity of the different pathways of purine metabolism in the heart.
Surveillance of Healthcare-Acquired Infections in Queensland, Australia: Data and Lessons From the First 5 Years
Authors: Morton Anthony P. , Clements Archie C. A. , Doidge Shane R. , Stackelroth Jenny , Curtis Merrilyn , Whitby Michael 
Published: August 2008

Objective.To present healthcare-acquired infection surveillance data for 2001-2005 in Queensland, Australia.Design.Observational prospective cohort study.Setting.Twenty-three public hospitals in Queensland.Methods.We used computer-assisted surveillance to identify episodes of surgical site infection (SSI) in surgical patients. The risk-adjusted incidence of SSI was calculated by means of a risk-adjustment score modified from that of the US National Nosocomial Infections Surveillance System, and the incidence of inpatient bloodstream infection (BSI) was adjusted for risk on the basis of hospital level (level 1, tertiary referral center; level 2, large general hospital; level 3, small general hospital). Funnel and Bayesian shrinkage plots were used for between-hospital comparisons.Patients.A total of 49,804 surgical patients and 4,663 patients who experienced healthcare-associated BSI.Results.The overall cumulative incidence of in-hospital SSI ranged from 0.28% (95% confidence interval [CI], 0%–1.54%) for radical mastectomies to 6.15% (95% CI, 3.22%–10.50%) for femoropopliteal bypass procedures. The incidence of inpatient BSI was 0.80,0.28, and 0.22 episodes per 1,000 occupied bed-days in level 1, 2, and 3 hospitals, respectively.Staphylococcus aureuswas the most commonly isolated microorganism for SSI and BSI. Funnel and shrinkage plots showed at least 1 hospital with a signal indicating a possible higher-than-expected rate of S. aureus-associated BSI.Conclusions.Comparisons between hospitals should be viewed with caution because of imperfect risk adjustment. It is our view that the data should be used to improve healthcare-acquired infection control practices using evidence-based systems rather than to judge institutions.
Fast and accurate search for non-coding RNA pseudoknot structures in genomes
Authors: Huang Zhibin , Wu Yong , Robertson Joseph , Feng Liang , Malmberg Russell L. , Cai Liming 
Published: August 2008

Abstract
Motivation: Searching genomes for non-coding RNAs (ncRNAs) by their secondary structure has become an important goal for bioinformatics. For pseudoknot-free structures, ncRNA search can be effective based on the covariance model and CYK-type dynamic programming. However, the computational difficulty in aligning an RNA sequence to a pseudoknot has prohibited fast and accurate search of arbitrary RNA structures. Our previous work introduced a graph model for RNA pseudoknots and proposed to solve the structure–sequence alignment by graph optimization. Given k candidate regions in the target sequence for each of the n stems in the structure, we could compute a best alignment in time O(ktn) based upon a tree width t decomposition of the structure graph. However, to implement this method to programs that can routinely perform fast yet accurate RNA pseudoknot searches, we need novel heuristics to ensure that, without degrading the accuracy, only a small number of stem candidates need to be examined and a tree decomposition of a small tree width can always be found for the structure graph.
Results: The current work builds on the previous one with newly developed preprocessing algorithms to reduce the values for parameters k and t and to implement the search method into a practical program, called RNATOPS, for RNA pseudoknot search. In particular, we introduce techniques, based on probabilistic profiling and distance penalty functions, which can identify for every stem just a small number k (e.g. k ≤ 10) of plausible regions in the target sequence to which the stem needs to align. We also devised a specialized tree decomposition algorithm that can yield tree decomposition of small tree width t (e.g. t ≤ 4) for almost all RNA structure graphs. Our experiments show that with RNATOPS it is possible to routinely search prokaryotic and eukaryotic genomes for specific RNA structures of medium to large sizes, including pseudoknots, with high sensitivity and high specificity, and in a reasonable amount of time.
Availability: The source code in C++ for RNATOPS is available at www.uga.edu/RNA-Informatics/software/rnatops/
Contact: cai@cs.uga.edu
Supplementary information: The online Supplementary Material contains all illustrative figures and tables referenced by this article.
Peptide Finder: mapping measured molecular masses to peptides and proteins
Authors: Alexandridou Anastasia , Tsangaris George Th. , Vougas Konstantinos , Nikita Konstantina , Spyrou George 
Published: August 2008

AbstractSummary: The identification of unknown amino acid sequences of peptides as well as protein identification is of great significance in proteomics. Here, we present a publicly available web application that facilitates a high resolution mapping of measured molecular masses to peptides and proteins, irrespectively of the enzyme/digestion method used. Furthermore, multi-filtering may be applied in terms of measured mass tolerance, molecular mass and isoelectric point range as well as pattern matching to refine the results. This approach serves complementary to the existing solutions for protein identification and gives insights in novel peptides discovery and protein identification at the cases where the identification scores from the other approaches may be below significance threshold. Peptide Finder has been proven useful in proteomics procedures with experimental data from MALDI-TOF.Availability: Peptide Finder web-application is available at http://bioserver-1.bioacademy.gr/Bioserver/PeptideFinder/.Contact: gspyrou@bioacademy.gr
Establishment and molecular profiling of a novel human pancreatic cancer panel for 5‐FU
Authors: Yanagihara Kazuyoshi , Takigahira Misato , Tanaka Hiromi , Arao Tokuzo , Aoyagi Yasuyuki , Oda Tatsuya , Ochiai Atsushi , Nishio Kazuto 
Published: August 2008

Ten novel human pancreatic carcinoma cell lines (Sui65 through Sui74) were established from a transplantable pancreatic carcinoma cell line. All the cell lines resembled the original clinical carcinoma in terms of the morphological and biological features, presenting with genetic alterations such as point mutations of K‐ras and p53, attenuation or lack of SMAD4 and p16 and other relevant cellular characteristics. Using this panel, we evaluated the effects of 5‐FU in suppressing the proliferation of pancreatic carcinoma cells. When tested in vitro, although Sui72 was highly susceptible to 5‐FU, the other cell lines were found to be resistant to the drug. When Sui72 and Sui70 were implanted subcutaneously in SCID mice followed by treatment with 5‐FU, the drug was found to be effective against Sui72 but not Sui70, consistent with the results in vitro. In order to identify the molecular determinant for high sensitivity of Sui72 to 5‐FU, we examined the mRNA expression levels of the metabolic enzymes of 5‐FU. Decreased expression of DPYD was observed in Sui72 as compared with other cell lines (0.1 versus 0.6 ± 0.5, 0.1‐fold).It is believed that the novel cell lines established in the present study will be useful for analyzing the pattern of progression of pancreatic cancer and for evaluating the efficacy of anticancer agents. (Cancer Sci 2008; 99: 1859–1864)
Physicochemical and sensory optimisation of a low glycemic index ice cream formulation
Authors: Whelan Anthony P. , Vega Cesar , Kerry Joseph P. , Goff H. Douglas 
Published: August 2008

SummaryThe development of a low glycemic index ice cream with as close as possible physicochemical properties and sensory quality compared with a sucrose‐sweetened ice cream was investigated. Three relatively new novel commercial sweeteners – tagatose, erythritol and trehalose – were studied, along with maltitol and polydextrose. Once the freezing curves were matched, other physicochemical properties also were found to match. Sweetness and sweet taste could then be adjusted for sensory optimisation with a combination of these sugars and supplementation with sucralose to boost the sweetness as necessary.
Effect of glutamate and inosinate on sensory and instrumental texture of extruded products
Authors: Cassar Renata , Sardinha Fátima A. , Arêas José A. G. 
Published: August 2008

SummaryExpanded products have been developed by extrusion of non‐conventional highly nutritious raw materials such as amaranth and chickpea blended with bovine lung. As sensory acceptance of these snacks is restricted, this study aimed at improving their texture, through the addition of monosodium glutamate (MSG) and disodium inosinate (IMP) flavor enhancers to the feeding material, or to the flavor added after the extrusion. Sensory and mechanical analyses showed that both enhancers affected texture, assessed by sensory and instrumental methods. Addition of IMP together with MSG to the chickpea‐based snacks presented the best results. This beneficial effect was not observed in the amaranth‐based snack, suggesting that IMP and MSG can favorably impact texture of extruded products depending on the amount and type of protein present.
Physicochemical and sensory characteristics of cookies containing residue from king palm (Archontophoenix alexandrae) processing
Authors: Vieira Manoela A. , Tramonte Karina C. , Podestá Rossana , Avancini Sandra R. P. , Amboni Renata D. de M. C. , Amante Edna R. 
Published: August 2008

SummaryThe aim of this study was to evaluate the chemical properties of the flours prepared with residues from organic king palm processing, and also to determine the cookie‐making performance of residue blends from organic king palm processing and wheat flour, as well as the effect of the blends on the consumers’ acceptance and purchase intent of high‐fibre cookies. The king palm flours (PFs) contained high contents of total dietary fibre and total ash. Blends containing 0%, 10%, 15%, 20% and 25% of either PF or sieved king‐palm flour (SPF) replacing wheat flour were prepared. The total dietary fibre content of the cookies ranged from 4 to 7 g (100 g)−1on a dry‐matter basis. The level of these components improved with increased amounts of PF and SPF in the blends. All the cookies were acceptable and approved in relation to purchase intent.
Impact of ripening stages of banana flour on the quality of extruded products
Authors: Gamlath Shirani 
Published: August 2008

SummaryThe study investigated the physical, nutritional and sensory properties of different ripening stages of banana during extrusion processing in combination with rice flour to develop quality snack products. Dehydrated banana flours at ripening stages 4, 5 and 6 (peel colour) were mixed separately at 40% banana to 60% rice flour levels. The mixtures were extruded through a twin‐screw extruder at 120 °C barrel temperature, 220 and 260 r.p.m, screw speed and 12% feed moisture. Increase in ripeness indicated negative effect on expansion and water absorption capacity while increasing the water solubility index and moisture retention (wet basis) of the products. Protein and mineral (except for zinc and copper) content of the products were significantly different (P < 0.05) from 4 to 6 of the ripening stages. Most of the essential amino acids in the extruded products increased significantly (P < 0.05) at the ripening stage of 6. All the products were within the acceptable range in the 9‐point Hedonic scale showing the best texture and flavour scores for stage 4 and 6, respectively. The extruded products show potential as snack products because of their nutritional quality and sensory acceptability.
Probiotic potential and sensory properties of coconut flan supplemented with Lactobacillus paracasei and Bifidobacterium lactis
Authors: Corrêa Sabrina B. M. , Castro Inar A. , Saad Susana M. I. 
Published: August 2008

SummaryThe effect of probiotic cultures on sensory performance of coconut flan during storage at 5 °C and the viability of these micro organisms for up to 28 days were investigated. Sensory analyses of the product were performed after 7, 14 and 21 days of storage. Coconut flans were produced with no addition of cultures (T1, control), or supplemented with Bifidobacterium lactis (T2), Lactobacillus paracasei (T3) and B. lactis + L. paracasei (T4). Populations of L. paracasei and B. lactis as single or in co‐culture remained above 7 log CFU g−1 during the entire storage period. Viability of L. paracasei was higher for T3. All products were well accepted and no significant differences (P > 0.05) were detected between the coconut flans studied. The addition of L. paracasei and B. lactis to coconut flan resulted in its having great potential as a functional food, which has high sensory acceptability.
Aromatic profiles of spray‐dried encapsulated orange flavours: influence of matrix composition on the aroma retention evaluated by sensory analysis and electronic nose techniques
Authors: Galmarini M. V , Zamora M. C. , Baby R. , Chirife J. , Mesina V. 
Published: August 2008

AbstractSpray‐dried orange flavour encapsulated in different amorphous matrices composed of maltodextrin (MD) and different combinations with; sucrose, trehalose, lactose, modified starch and gum arabic (ga); were evaluated by sensory analysis and electronic nose (e‐nose). With both techniques the flavours encapsulated in MD‐sucrose and MD‐lactose–sucrose were perceived as similar. However, the e‐nose did not detect any differences among the other matrices (MD‐trehalose, MD, MD‐sucrose at a different concentration and MD‐ga). On the contrary, sensory analysis was able to group MD‐trehalose and MD describing them by: woody, marmalade, syrup, citrus terpenes, and Vitamin C; MD‐sucrose at 40% and 10% concentration and MD‐lactose–sucrose were grouped and represented by powder juice, tangerine and pungency, while MD‐ga was differentiated from the rest by the attributes peely, plastic, solvent and green. In this way, it was shown that matrix composition determines the aromatic profile of spray‐dried encapsulated orange flavours.
Probiotic foods: consumer perception and attitudes
Authors: Viana Julia V. , Da Cruz Adriano G. , Zoellner Sidney S. , Silva Ramon , Batista Aline L. D. 
Published: August 2008

SummaryThe objective of this study was to evaluate the perception and the attitudes towards probiotic foods of the population in the city of Rio de Janeiro, Brazil. Four hundred and twenty (100.0%) people were interviewed in small‐, medium‐ and large‐sized supermarkets located in various parts of the city of Rio de Janeiro. One hundred and twenty‐two (29.05%) people defined probiotic foods correctly. Ninety‐one (21.67%) were unable to mention a single example of a probiotic food. The results of this study indicate the need for an elementary easy‐to‐understand educational programme using accessible language in order to fix the concepts related to these products.
Sensory shelf life of butterhead lettuce leaves in active and passive modified atmosphere packages
Authors: Ares Gastón , Lareo Claudia , Lema Patricia 
Published: August 2008

SummaryThe objective of the present work was to study the influence of both passive and active modified atmosphere packaging on sensory shelf life of butterhead lettuce leaves, stored at 5 and 10 °C. Results showed that the efficacy of active modified atmosphere with respect to passive modified atmosphere depended on the storage temperature considered. When stored at 10 °C, despite being subjected to different package atmosphere composition, lettuce leaves in active and passive modified atmosphere showed the same sensory deterioration rate and sensory shelf life. On the contrary, when stored at 5 °C, lettuce leaves in active modified atmosphere packages showed lower deterioration rate and higher sensory shelf life than those in passive modified atmosphere. Sensory shelf life of lettuce in modified atmosphere packages was estimated using criteria determined according to consumers’ rejection to purchase percentage, which consisted on an improvement over more arbitrary criteria presented in most studies.