bluuebunny/crossref_metadata_2025_split huggingface dataset:
CressExpress: A Tool For Large-Scale Mining of Expression Data from Arabidopsis
Authors: Srinivasasainagendra Vinodh , Page Grier P. , Mehta Tapan , Coulibaly Issa , Loraine Ann E. 
Published: May 2008

AbstractCressExpress is a user-friendly, online, coexpression analysis tool for Arabidopsis (Arabidopsis thaliana) microarray expression data that computes patterns of correlated expression between user-entered query genes and the rest of the genes in the genome. Unlike other coexpression tools, CressExpress allows characterization of tissue-specific coexpression networks through user-driven filtering of input data based on sample tissue type. CressExpress also performs pathway-level coexpression analysis on each set of query genes, identifying and ranking genes based on their common connections with two or more query genes. This allows identification of novel candidates for involvement in common processes and functions represented by the query group. Users launch experiments using an easy-to-use Web-based interface and then receive the full complement of results, along with a record of tool settings and parameters, via an e-mail link to the CressExpress Web site. Data sets featured in CressExpress are strictly versioned and include expression data from MAS5, GCRMA, and RMA array processing algorithms. To demonstrate applications for CressExpress, we present coexpression analyses of cellulose synthase genes, indolic glucosinolate biosynthesis, and flowering. We show that subselecting sample types produces a richer network for genes involved in flowering in Arabidopsis. CressExpress provides direct access to expression values via an easy-to-use URL-based Web service, allowing users to determine quickly if their query genes are coexpressed with each other and likely to yield informative pathway-level coexpression results. The tool is available at http://www.cressexpress.org.
Functional Analysis of a Predicted Flavonol Synthase Gene Family in Arabidopsis
Authors: Owens Daniel K. , Alerding Anne B. , Crosby Kevin C. , Bandara Aloka B. , Westwood James H. , Winkel Brenda S.J. 
Published: May 2008

AbstractThe genome of Arabidopsis (Arabidopsis thaliana) contains five sequences with high similarity to FLAVONOL SYNTHASE1 (AtFLS1), a previously characterized flavonol synthase gene that plays a central role in flavonoid metabolism. This apparent redundancy suggests the possibility that Arabidopsis uses multiple isoforms of FLS with different substrate specificities to mediate the production of the flavonols, quercetin and kaempferol, in a tissue-specific and inducible manner. However, biochemical and genetic analysis of the six AtFLS sequences indicates that, although several of the members are expressed, only AtFLS1 encodes a catalytically competent protein. AtFLS1 also appears to be the only member of this group that influences flavonoid levels and the root gravitropic response in seedlings under nonstressed conditions. This study showed that the other expressed AtFLS sequences have tissue- and cell type-specific promoter activities that overlap with those of AtFLS1 and encode proteins that interact with other flavonoid enzymes in yeast two-hybrid assays. Thus, it is possible that these “pseudogenes” have alternative, noncatalytic functions that have not yet been uncovered.
Effect of a new non‐cleavable substrate analog on wild‐type and serine mutants in the signature sequence of adenylosuccinate lyase of Bacillus subtilis and Homo sapiens
Authors: Sivendran Sharmila , Colman Roberta F. 
Published: May 2008

AbstractAdenylosuccinate lyase (ASL) catalyzes two β‐elimination reactions in purine biosynthesis, leading to the question of whether the two substrates occupy the same or different active sites. Kinetic studies of Bacillus subtilis and human ASL with a new substrate analog, adenosine phosphonobutyric acid, 2′(3′), 5′‐diphosphate (APBADP), show that it acts as a competitive inhibitor with respect to either substrate (KI ∼ 0.1 μM), indicating that the two substrates occupy the same active site. Binding studies show that both the B. subtilis and human ASLs bind up to 4 mol of APBADP per mole of enzyme tetramer and that both enzymes exhibit cooperativity: negative for B. subtilis ASL and positive for human ASL. Mutant B. subtilis ASLs, with replacements for residues previously identified as critical for catalysis, bind the substrate analog similarly to wild‐type ASL. Two serines in a flexible loop of ASL have been proposed to play roles in catalysis because they are close to the substrate in the crystal structure of Escherichia coli ASL. We have now mutated the corresponding serines to alanines in B. subtilis and human ASL to evaluate their involvement in enzyme function. Kinetic data reveal that human Ser289 and B. subtilis Ser262 and Ser263 are essential for catalysis, while the ability of these Ser mutants to bind APBADP suggests that they do not contribute to substrate affinity. Although these serines are not visible in the crystal structure of human adenylosuccinate lyase complexed with substrate or products (PDB #2VD6), they may be interacting with the active sites.
Decreasing delays in urgent and expedited surgery in a university teaching hospital through audit and communication between peri‐operative and surgical directorates
Authors: Cosgrove J. F. , Gaughan M. , Snowden C. P. , Lees T. 
Published: May 2008

SummaryNational Confidential Enquiry into Patient Outcome and Death guidelines for urgent surgery recommend a fully staffed emergency operating theatre and restriction of ‘after‐midnight’ operating to immediate life‐, limb‐ or organ‐threatening conditions. Audit performed in our institution demonstrated significant decreases in waiting times for urgent surgery and an increased seniority of medical care associated with overnight pre‐operative assessment of patients by anaesthetic trainees. Nevertheless, urgent cases continued to be delayed unnecessarily. A classification of delays was developed from existing guidelines and their incidence was audited. The results were disseminated to involved directorates. A repeat of the audit demonstrated a significant decrease in delays (p = 0.001), a significant increase in the availability of surgeons (p = 0.001) and a significant decrease in the median waiting time for urgent surgery compared to the first audit cycle and a previous standard (p < 0.01). We conclude that auditing delays and disseminating the results of the audit significantly decreases delays and median waiting times for urgent surgery because of improved surgical availability.
A survey of inhalational anaesthetic abuse in anaesthesia training programmes*
Authors: Wilson J. E. , Kiselanova N. , Stevens Q. , Lutz R. , Mandler T. , Tran Z. V. , Wischmeyer P. E. 
Published: May 2008

SummaryThis study aims to assess the prevalence and outcomes of inhalational anaesthetic abuse among anaesthesia training programmes. Online surveys were completed by chairpersons of academic anaesthesia training programmes in the United States. The response rate was 84% (106/126 programmes). Twenty‐two percent of the departments had had at least one incident of inhalational anaesthetic abuse. Forty‐eight percent (15/31) of the persons abusing inhalational anaesthetics were sent for rehabilitation. Only 22% (7/31) of those found to be abusing inhalational anaesthetics were ultimately able to return successfully to anaesthesia practice with sustained recovery. The mortality rate among individuals found abusing inhalational anaesthetics was 26% (8/31). The majority of the anaesthesia departments (97/104, 93%) did not have any pharmacy accounting of inhalational anaesthetics. This is the first published survey of inhalational anaesthesia abuse. Inhalational anaesthetic abuse should be considered in at‐risk individuals or those with a history of substance abuse. The concern about substance abuse is not unique to American anaesthetists. Countries around the world deal with similar substance abuse issues.
The natural history of conditional transcranial Doppler flow velocities in children with sickle cell anaemia
Authors: Hankins Jane S. , Fortner Gail L. , McCarville M. Beth , Smeltzer Matthew P. , Wang Winfred C. , Li Chin‐Shang , Ware Russell E. 
Published: May 2008

SummaryChildren with sickle cell anaemia (SCA) and conditional transcranial Doppler (TCD) [time‐averaged mean velocity (TAMV) 170–199 cm/s] have increased risk of primary stroke, but receive no specific therapy. Some will convert to abnormal velocities (TAMV ≥200 cm/s) with further increase in stroke risk. In 2003, our centre initiated universal TCD screening, targeting all children (aged 2–16 years) with SCA. TCD examinations were repeated at intervals based on initial results. To determine rates and risk factors for TCD conversion, we reviewed all examinations since 2003, excluding patients receiving hydroxycarbamide (hydroxyurea) or transfusions. Of the eligible population, 274 children (98%) were screened at a median age of 7·1 years (range 1·7–18·2). Fifty‐four patients (20%) had conditional TAMV either on initial screening or a subsequent examination. The 18‐month cumulative incidence of conversion from conditional to abnormal TAMV was 23%. Age, initial TAMV, laboratory values, blood pressure and oxygen saturation were not significantly associated with conversion. Our cohort provides systematic longitudinal evaluation of an unselected paediatric population universally screened and retested at regular intervals. Our data document a high conversion rate to abnormal velocities among untreated children with SCA. Therapy should be considered for the prevention of conversion to abnormal TCD velocities.
Impact of maternal atopy and probiotic supplementation during pregnancy on infant sensitization: a double‐blind placebo‐controlled study
Authors: Huurre A. , Laitinen K. , Rautava S. , Korkeamäki M. , Isolauri E. 
Published: May 2008

SummaryBackground
The effects of breastfeeding and probiotics on infant sensitization still remain discrepant.Objective
To explore probable explanatory factors in infant sensitization and the protective effect of probiotics.Methods
Altogether 171 mother–infant pairs from an ongoing placebo‐controlled double‐blind study with nutrition modulation by dietary counselling and probiotic supplementation were studied. Skin prick testing was done in infants at 6 and 12 months and in mothers at third trimester of pregnancy. The breast milk concentrations of cytokines TGF‐β2, soluble CD14, IFN‐γ, TNF‐α, IL‐10, IL‐6, IL‐4 and IL‐2 were measured.Results
The risk of sensitization increased in infants with allergic mothers breastfeeding over 6 months [odds ratio (OR=4.83, P=0.005)], or exclusively breastfeeding over 2.5 months (OR=3.4, P=0.018). Probiotic supplementation had a protective effect against sensitization in infants with a high hereditary risk due to maternal sensitization (OR=0.3, P=0.023). The concentration of TGF‐β2 tended to be higher in the colostrum of the mothers in the probiotic group as compared with those on placebo (probiotic/placebo ratio=1.50, P=0.073). A similar result was obtained in the subgroup of allergic mothers (probiotic/placebo ratio=1.56, P=0.094).Conclusion
Infants of atopic mothers, specifically when breastfed exclusively over 2.5 months or totally over 6 months, had a higher risk of sensitization at the age of 12 months. This risk could be reduced by the use of probiotics during pregnancy and lactation, partly by resulting in a beneficial composition of the breast milk.
Functional consequences of viral impacts on bacterial communities: a food‐web model analysis
Authors: MIKI TAKESHI , NAKAZAWA TAKEFUMI , YOKOKAWA TAICHI , NAGATA TOSHI 
Published: May 2008

Summary1. Viruses in aquatic ecosystems can alter the abundance of bacteria and influence organic matter flows and bacterial community composition, but the combined effects of the multiple processes involved in the bacteria‐mediated carbon cycle are not entirely clear.2. We developed a new conceptual model that incorporates a fundamental but neglected aspect of bacteria–organic matter interactions: that different bacterial groups utilize different kinds of organic matter. In addition, the model incorporates several other realistic features of microbial food webs, including the presence of lysogenic viruses, bacterial resistance to viral infection and dependence of protozoan grazing rate on viral infection.3. Our model analysis indicates that a ‘viral shunt’ view (i.e. viruses enhance bacterial utilization of organic carbon through regeneration of organic matter but diminish carbon flow to higher trophic levels) is robust, regardless of the specific situations we examined by either incorporating or ignoring various features of microbial food webs.4. We also found that host‐specific mortality induced by viral infection changes the bacterial utilization of different types of organic matter, which was attributable to diminished ‘apparent competition’ between predator‐sharing bacterial groups that use different carbon sources. This mechanism can facilitate transformation to carbon dioxide of diverse types of carbon sources (e.g. organic matter of algal and terrestrial origin, methane or xenobiotics) and extends the previously recognized roles of viruses in microbial food webs.
Characterization of temperate cyanophages active against freshwater phycocyanin‐rich Synechococcus species
Authors: DILLON AMANDA , PARRY JACQUELINE D. 
Published: May 2008

Summary1. This study addressed the prevalence of lysogeny within 19 strains of freshwater Synechococcus sp. rich in phycocyanin (PC) that were isolated from a temperate lake or obtained, in four cases, from a culture collection.2. Lysis of 16 Synechococcus strains (84%) was inducible with mitomycin C, but the required concentration (20 μg mL−1) was higher than in other studies. Mitomycin C induction yielded burst sizes of 3.5–23.7 phages per cell.3. Transmission Electron Microscopy of the resultant temperate phages showed that all belonged to the family Siphoviridae with capsid diameters ranging from 40.3 to 53.5 nm and tail lengths from 129 to 186 nm. None of the cyanophages could be maintained in the lytic cycle using the three non‐lysogenic strains, or any of the other 16 lysogenic strains of Synechococcus.4.These results suggest a potentially high level of lysogeny within PC‐rich Synechococcus species in natural freshwaters, but that the presence of these temperate cyanosiphoviruses may go undetected with the lower mitomycin C concentrations commonly used.
Estimates of bacterial and phytoplankton mortality caused by viral lysis and microzooplankton grazing in a shallow eutrophic lake
Authors: TIJDENS MARJOLIJN , VAN DE WAAL DEDMER B. , SLOVACKOVA HANA , HOOGVELD HANS L. , GONS HERMAN J. 
Published: May 2008

Summary1. Since viral lysis and zooplankton grazing differ in their impact on the aquatic food web, it is important to assess the relative importance of both mortality factors. In this study, an adapted version of the dilution technique was applied to simultaneously estimate the impact of both viral lysis and zooplankton grazing on the mortality of heterotrophic bacteria, eukaryotic algae, unicellular cyanobacteria, prochlorophytes and especially filamentous cyanobacteria in a shallow eutrophic lake.2. Four dilution experiments were performed in December 2004, January 2005, and March and April 2006. Viral and heterotrophic bacterial abundances were obtained by epifluorescence microscopy and abundances of different phytoplankton groups by flow cytometry and light microscopy.3. Viral lysis was identified as the main mortality cause during the December 2004 and January 2005 experiments, apparently removing between 84% and 97% of the potential filamentous cyanobacterial production and up to 101% of the potential heterotrophic bacterial production. Microzooplankton grazing was estimated to remove between 90% and 99% of the potential unicellular cyanobacterial production and up to 46% of the potential heterotrophic bacterial production during the spring 2006 experiments.4. In some cases, no significant impact of viral lysis or zooplankton grazing was detected. Contrary to expectations, the apparent growth rate of filamentous cyanobacteria was even sometimes observed to decrease significantly upon dilution of microzooplankton.5. The dilution technique can give valuable insight into the impact of zooplankton grazing and viral lysis on the mortality of different plankton groups but require some caveats require special care to be taken when comparing and interpreting results.
Variable importance of viral‐induced bacterial mortality along gradients of trophic status and humic content in lakes
Authors: LYMER DAVID , LINDSTRÖM EVA S. , VREDE KATARINA 
Published: May 2008

Summary1. The goals of this study were to assess which environmental gradients can be important in predicting viral abundance (VA), the frequency of virus‐infected cells (FVIC) and burst size (BS), and to assess which lake characters favour viral‐induced bacterial mortality (VBM) as opposed to potential grazer‐induced bacterial mortality (PGBM).2. The epilimnion and hypolimnion of 21 lakes differing in trophic status and humic content were investigated. Samples were obtained for viral and bacterial abundance, the FVIC and burst size, flagellate and ciliate abundances and water chemistry. The potential importance of VBM in relation to PGBM was calculated based on data on FVIC and flagellate and ciliate abundance.3. Partial least squares regression (PLS) analysis showed that VA as well as the ratio between viral and bacterial abundance were positively related to inorganic nutrient concentrations, dissolved organic carbon concentration, chlorophyll‐a concentration and bacterial production.4. The PLS model also revealed that FVIC decreased with increasing trophic status whereas BS increased. Furthermore, potential grazing was positively related to increasing trophic status and decreasing humic content. PGBM appeared to be dominating over VBM in the majority of lakes sampled, especially in the epilimnion.5. Thus, the relative importance of viruses for bacterial mortality was potentially highest in humic lakes of medium trophic status and it was also greater in the hypolimnion than in the epilimnion.
Molecular characterization of the major hemelipoglycoprotein in ixodid ticks
Authors: Donohue K. V. , Khalil S. M. S. , Mitchell R. D. , Sonenshine D. E. , Michael Roe R. 
Published: May 2008

AbstractThe major hemelipoglyco‐carrier protein (CP) found throughout the development of male and female adult American dog ticks, Dermacentor variabilis (Say) was sequenced. DvCP is a single transcript coding for two protein subunits that together contain three motifs: (1) a lipoprotein n‐terminal domain that is a common attribute of proteins that bind lipids, carbohydrates and metals; (2) a domain of unknown function characteristic of proteins with several large open beta sheets; and (3) a von Willebrand factor type D domain near the carboxy‐terminus apparently important for multimerization. These motifs, which are also found in tick vitellogenin, are not shared by heme‐binding proteins studied thus far in other hematophagous insects. DvCP message was highest in fat body and salivary gland but was also found in midgut and ovary tissue. Expression was initiated by blood feeding in virgin females and not by mating, as is typical of tick vitellogenin; and the message was found in fed males at levels similar to part fed, virgin females. CP appears to be highly conserved among the Ixodida. The closest match by BlastP to DvCP is vitellogenin from Caenorhabditis elegans (AAC04423), suggesting that CP is a novel protein. The role of CP in heme sequestration, the evolution of hematophagy and host complementation are discussed.
Corn and rice waste: a comparative and critical presentation of methods and current and potential uses of treated waste
Authors: Arvanitoyannis Ioannis S. , Tserkezou Persefoni 
Published: May 2008

SummaryAlthough corn and rice waste can be hardly classified among the most hazardous waste, their treatment is very important in view of the great volume of waste materials involved. In this review article, an update is provided for most of the waste treatment techniques (composting, pyrolysis, gasification, combustion) used to alter the physical, chemical or biological character of the waste, to reduce its volume and/or toxicity and to make the waste safer for disposal. Furthermore, all current and potential uses of treated corn and rice waste such as fertilisers, biomass and biogas/biofuel are summarised. Four comprehensive tables and six figures provide a thorough presentation of both waste treatment methods (characteristics, advantages and disadvantages) and uses of treated corn and rice waste.
Inhibition effects of grape seed extracts on melanosis formation in shrimp (Parapenaeus longirostris)
Authors: Gokoglu Nalan , Yerlikaya Pinar 
Published: May 2008

SummaryThe aim of this study was to investigate the effects of grape seed extracts on inhibition of melanosis in shrimp. Defatted grape seed powder was extracted using ethanol. Dipping solutions in five different concentrations (0, 2.5, 5.0, 10 and 15 g L−1) were prepared using grape seed extract and distilled water. The shrimps were dipped into the solutions and stored at 4 °C. Melanosis was investigated by sensory analysis and lightness, redness and yellowness values were measured by chromometer during the storage for 3 days. According to the results, grape seed extracts showed inhibition effect on the formation of melanosis. The best results were obtained with the solution of 15 g L−1.
Evolution of available lysine and lactose contents in supplemented microencapsulated fish oil infant formula powder during storage
Authors: Chávez‐Servín Jorge Luis , Castellote Ana Isabel , López‐Sabater M. Carmen 
Published: May 2008

SummaryIn this work we report the evolution of available lysine, lactose and lipid hydroperoxide contents as indicators of food quality and stability of two types of infant formula powder stored at 25° and 37 °C for 12 months. The first type was supplemented with microencapsulated fish oil (MFO), made of little powder particles in a food starch‐coated matrix of caseinate and saccharose to prevent the oxidation of polyunsaturated fatty acid (PUFA). The second type was not supplemented and was used for reference. MFO might not be stable during storage and affect negatively the quality of the formula in two ways: by oxidation of PUFA, which may also easily react with lysine upon oxidation, blocking lysine, or by hydrolysis of saccharose, producing reducing sugars and increasing the Maillard reaction. Slight changes were observed in lysine and lactose evolution. By comparing the two formulae, this study shows that the MFO material did not negatively affect the studied parameters, indicating therefore acceptable stability in the conditions tested.