bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stress Ulcer Prophylaxis and Ventilation Pneumonia Prevention by Antibacterial Cytoprotective Agents?
Authors: Daschner F. , Kappstein I. , Engels I. , Reuschenbach K. , Pfisterer J. , Krieg N. , Vogel W. 
Published: September 2009

AbstractThe gastric and tracheal flora of 142 consecutive patients receiving stress ulcer prophylaxis were investigated, identifying identical isolates by typing. Furthermore, the growth pattern of normal respiratory bacteria and organisms causing ventilation pneumonia at different pH values and the in vitro effect of sucralfate and bismuth subsalicylate on these bacteria in simulated gastric fluid were studied. The results obtained were as follows: (1) with rising gastric pH bacterial counts in gastric aspirates, especially gram-negatives, increased significantly; (2) in 45 (31.7%) of the patients identical organisms were first isolated in gastric samples and one to two days later in tracheal secretions; (3) ventilation pneumonia was significantly more frequent in patients with high gastric pH; (4) pathogens causing ventilation pneumonia grew well in simulated gastric fluid at higher pH values, unlike normal respiratory organisms; and (5) sucralfate and bismuth subsalicylate showed antibacterial activity against frequent causative organisms of ventilation pneumonia.
Statistical Analysis of Stratified 2X2 Tables
Authors: Davis Charles S. 
Published: September 2009

Previous papers in this series have discussed design and analysis issues for epidemiologic data that can be presented in a 2 × 2 table.‘” the primary focus was on methods for determining the extent of association between a dichotomous disease state and a dichotomous risk factor. methods appropriate for cross-sectional, prospective, and retrospective studies using matched or unmatched samples were described.In order to study the association between disease status and a dichotomous risk factor, it is often necessary to take into account other variables that may influence either the disease status or the risk factor. For example, Hemming, Overall, and Britt studied the association between the occurrence of nosocomial infections (risk factor) and mortality (disease status) in a large cohort of infants in a newborn intensive care unit. these authors analyzed the data using methods for summarizing the results from a single 2 × 2 table. However, because very low birth weight is associated strongly with both the acquisition of nosocomial infection and mortality, it may be more appropriate to control or adjust for the effects of birthweight.
Misleading the masses: detection of mislabelled and substituted frozen fish products in South Africa
Authors: von der Heyden Sophie , Barendse Jaco , Seebregts Anthony J. , Matthee Conrad A. 
Published: August 2009

Abstract
von der Heyden, S., Barendse, J., Seebregts, A. J., and Matthee, C. A. 2010. Misleading the masses: detection of mislabelled and substituted frozen fish products in South Africa. – ICES Journal of Marine Science, 67: 176–185. Mislabelling poses a threat to the sustainability of seafood supply chains and, when frequent, can significantly affect conservation efforts. Here we identify the most popular fish in the South African market through consumer and retailer surveys and data gathered by a sustainable seafood campaign. Of these species, we tested a number of widely available and generally high-market priced fish, utilizing mtDNA 16S rRNA sequencing. Tests of 178 samples revealed that about half of all fillets are mislabelled. Most problematic was kob, Argyrosomus spp., for which some 84% of fillets provided belonged to other species, including mackerel, croaker, and warehou. Phylogenetic analyses provided strong support that the fillets sold as barracuda and wahoo were probably king mackerel and that red snapper fillets included fillets of river snapper, Lutjanus argentimaculatus, which is a species prohibited for sale in South Africa. We also discovered substitution of yellowtail for dorado. From preliminary population genetic comparisons, some 30% of kingklip samples probably had their origin in New Zealand, rather than southern Africa. The research revealed a market conducive to mislabelling through poor consumer and retailer awareness, and highlighted the value of sustainable seafood campaigns to draw attention to this.
Symptomatology of Iris yellow spot virus in Selected Indicator Hosts
Authors: Bag Sudeep , Pappu H. R. 
Published: August 2009

Thrips-transmitted Iris yellow spot virus is an economically important pathogen of onion bulb and seed crops. To better understand the biological diversity of IYSV, several plant species were evaluated for their response to mechanical inoculation with IYSV under controlled greenhouse conditions. Accepted for publication 3 June 2009. Published 24 August 2009.
Extraction of RNA from Amphioxus Embryos or Adult Amphioxus Tissue
Authors: Yu J.K. Sky , Holland Linda Z. 
Published: September 2009

INTRODUCTIONThis protocol describes how to isolate total RNA from amphioxus using a patented TRI reagent that is commercially available from several sources. The protocol can be applied to both adult tissues and embryos, although we recommend different sample pretreatment methods for adults and embryos. After the samples are prepared, they are homogenized in TRI reagent, which disrupts the cells and maintains the integrity of RNA. After the addition of chloroform and phase separation, RNA is extracted in the aqueous phase and subsequently recovered by precipitation with isopropyl alcohol. The resulting RNA can be used for gel blotting (Northern analysis), selection of polyadenylated RNA, or for synthesizing cDNA with reverse transcriptase PCR (RT-PCR).
Fluorescent In Situ Hybridization (FISH) on Diploid Nuclei and Mitotic Chromosomes from Drosophila melanogaster Larval Tissues
Authors: Blattes Roxane , Käs Emmanuel 
Published: September 2009

INTRODUCTIONThis protocol adapts the multicolor fluorescent in situ hybridization (FISH) method for use with interphase nuclei and mitotic chromosomes of neuroblasts from dissected Drosophila melanogaster larval brains. It is suitable for the simultaneous detection of two or more target sequences, is readily applicable to heterochromatin sequences, and provides the specificity and sensitivity needed to covisualize single-copy and repeated sequences. It is equally successful for detecting other sequences, such as single-copy euchromatin genes. This is made possible chiefly through the use of fixation procedures adjusted to suit the nature of the hybridization targets (e.g., condensed heterochromatin sequences), as well as the use of a mild chemical treatment to denature DNA instead of heat. Also, omitting mitotic blockers such as colchicine yields chromosomes with well-preserved morphology and permits detailed mapping of detected sequences. Most importantly, using this technique on diploid mitotic chromosomes and interphase nuclei allows the unambiguous localization of under-replicated heterochromatin sequences that cannot be resolved within the chromocenter of polytene chromosomes.
Tissue Sampling and Genomic DNA Purification from the Western Clawed Frog Xenopus tropicalis: Figure 1.
Authors: Showell Chris , Conlon Frank L. 
Published: September 2009

INTRODUCTIONThe extraction of genomic DNA from Western clawed frog (Xenopus tropicalis) tissue samples is an essential step for genotyping known mutations, identifying live animals carrying nonfluorescent transgenes, and reverse genetic screening techniques. We describe here a method for sampling tail tissue from X. tropicalis tadpoles at stage 48 and later. This method of tissue sampling allows a significant amount of genomic DNA to be obtained from tadpoles without killing them. In both Xenopus laevis and X. tropicalis, the tip of the tail is able to regenerate following surgery and its removal does not have a significant effect on the survival of the tadpole when performed carefully. Genomic DNA purification can be carried out in “deep-well” 96-well plates, making it amenable to high-throughput applications. Typically, the DNA yield is sufficient for more than 100 standard 50-μL polymerase chain reactions (PCRs) (using 1-5 μL of DNA per reaction), so it can be used for genetic screening and mapping studies.
Evaluation of the capacity of three halophytes to desalinize their rhizosphere as grown on saline soils under nonleaching conditions
Authors: Rabhi Mokded , Hafsi Chokri , Lakhdar Abdelbasset , Hajji Saïd , Barhoumi Zouhaier , Hamrouni Mohamed Hédi , Abdelly Chedly , Smaoui Abderrazak 
Published: August 2009

AbstractIn the sabkha of Soliman (N‐E Tunisia), soil samples of the upper 20 cm were taken during the driest period of the year (July–August) from inside and outside tufts of two perennial halophytes: Arthrocnemum indicum (Willd.) Moq. and Suaeda fruticosa Forssk., both from family Chenopodiaceae. Samples were analysed for electrical conductivity of the saturation paste extract (ECe) and soluble sodium (Na+) content. Then, tufts were divided into three size categories and their shoot biomass production and Na+ content were determined. Our results showed a considerable contribution of shoot Na+ accumulation to rhizosphere desalination. The capacity of the two native halophytes A. indicum. and S. fruticosa to desalinize saline soils was compared with that of an introduced halophyte, Sesuvium portulacastrum L. (Aizoaceae). Seedlings were grown under greenhouse conditions in pots containing 8 kg of saline soil each. Pots were irrigated with tap water during 170 days without leaching. Our results confirmed the contribution of shoot Na+ accumulation to soil desalination. They showed also that among the three studied species, Sesuvium portulacastrum L. seems to be the most convenient to be used for this purpose in arid and semi‐arid regions where precipitation is too low to leach salts from rhizosphere.
The structure and status of forest fragments outside protected areas in central Uganda
Authors: Baranga Deborah , Chapman Colin A. , Kasenene John M. 
Published: August 2009

AbstractGiven the extent of tropical forest deforestation and as a number of conservation programmes and local communities rely on forest fragments, it has become important to understand how fragment exploitation by local communities affects forest structure and function. The effects of forest exploitation on forest structure and status of forest fragments were investigated in 20 nonreserved forest fragments in central Uganda. Enumeration of plots showed that tree species composition of the forest fragments was 60.0%, 23.7% and 6.3% for under‐storey, middle and top canopy trees respectively. The major activity was fuel wood extraction (65%), followed by brick making (10%), cultivation and livestock paddocks (10%), charcoal burning (5%), local brew distillation and others (5%). These extractive processes caused drastic structural changes, habitat degradation and destruction. Tree stumps enumeration indicated that under storey trees formed the highest proportion for wood extraction. There was no significant difference in the level of forest exploitation (basal area loss) among forest patches of varying sizes.
The ecological impacts of a migratory bat aggregation on its seasonal roost in Kasanka National Park, Zambia
Authors: Byng James W. , Racey Paul A. , Swaine Mike D. 
Published: August 2009

AbstractThe ecological impacts of migratory species on their seasonal environments are poorly known. The effects of several million straw‐coloured fruit bats (Eidolon helvum), which migrate seasonally to Kasanka National Park, Zambia each year, on the small area of mushitu‘swamp’ forest in which they roost, were investigated. The structure of the mushitu forest was profoundly altered by the presence of E. helvum, with increased roost tree mortality, lowering and opening of the forest canopy and a decrease in tree basal area. Eidolon helvum are also thought to increase the severity of fires within their roost site because the structural changes result in a drier microclimate. The effects of increased nitrogen and phosphorous input were less apparent. These findings suggest that the ecological impact of this migratory bat species on its seasonal environment could ultimately threaten the long‐term viability of its seasonal roost.
Environmental parameters and anthropogenic effects predicting the spatial distribution of wild ungulates in the Akagera savannah ecosystem
Authors: Averbeck Christiane , Apio Ann , Plath Martin , Wronski Torsten 
Published: August 2009

AbstractSavannah areas affected by human activities such as livestock keeping and agriculture are often characterized by shifts in landscape structuring, with a predominance of few(er) habitat types. This is typically accompanied by pronounced changes in the communities of ungulates. The aim of this study was to find out whether shifts in ungulate communities in Lake Mburo National Park (LMNP) are primarily predicted by an alteration in the composition of the preferred habitat types or if more complex interactions between habitat changes and the prevalence of ungulates occur. Monthly road counts were used to establish the number of eleven ungulate species in LMNP and adjacent unprotected Ankole Ranching Scheme. The common duiker (Sylvicapra grimmia campbelliae Gray, 1843) was found in more abundance in disturbed areas, while showing a significant change in habitat use. Common duiker tended to use the vegetation type otherwise used by the bushbuck (Tragelaphus scriptus dama Neumann, 1902). Our results support the claim that the occurrence of ungulates is not only directly affected by the availability of ‘suitable’ habitats, but behavioural plasticity and competitive exclusion also need to be considered.
Space use of the spotted sand lizard (Pedioplanis l. lineoocellata) under different degradation states
Authors: Wasiolka Bernd , Jeltsch Florian , Henschel Joh , Blaum Niels 
Published: August 2009

AbstractAlthough the effects of grazing‐induced savannah degradation on animal diversity are well documented, knowledge of how they affect space use or responding behaviour remains poor. In this study, we analysed space use of the spotted sand lizard (Pedioplanis l. lineoocellata) in degraded versus nondegraded habitats of southern Kalahari savannah habitats. Lizards were radio tracked, daily movement distances recorded and home range sizes calculated. In degraded Kalahari savannah habitats where plant diversity and perennial grass cover are low but shrub cover high, P. lineoocellata moves larger distances (40.88 ± 6.42 m versus 27.43 ± 5.08 m) and occupies larger home ranges (646.64 ± 244.84 m2 versus 209.15 ± 109.84 m2) than in nondegraded habitats (high plant diversity, high perennial grass cover and low shrub cover). We assume that this increase in daily movement distances and home range sizes is a behavioural plasticity to limited food resources in degraded savannah habitats. Although P. lineoocellata is able to adjust to resource‐poor savannah habitats, the increase in the lizard’s movement activities is likely to result in a higher predation risk. This is supported by the lower availability of protective vegetation i.e. perennial grass cover. Hence, we conclude that despite behavioural plasticity of P. lineoocellata, overgrazing has a severe negative impact on the space use of P. lineoocellata.
Effect of polymorphisms in the FASN, OLR1, PPARGC1A, PRL and STAT5A genes on bovine milk‐fat composition
Authors: Schennink A. , Bovenhuis H. , Léon‐Kloosterziel K. M. , Van Arendonk J. A. M. , Visker M. H. P. W. 
Published: August 2009

SummaryThe aim of our study was to estimate effects of polymorphisms in the ATP‐binding cassette G2 (ABCG2), fatty acid synthase (FASN), oxidized low‐density lipoprotein receptor 1 (OLR1), peroxysome proliferator‐activated receptor‐γ coactivator‐1α (PPARGC1A), prolactin (PRL) and signal transducer and activator of transcription 5A (STAT5A) genes on milk production traits and detailed milk‐fat composition. Milk‐fat composition phenotypes were available for 1905 Dutch Holstein–Friesian cows. First, the presence of each SNP in the Dutch Holstein–Friesian population was evaluated by direct sequencing of the PCR product surrounding the SNP in 22 proven Dutch Holstein–Friesian bulls. The ABCG2 SNP did not segregate in the bull population. Second, we genotyped the cows for the FASNg.16024G>A, FASNg.17924A>G, OLR1g.8232C>A, PPARGC1Ac.1790+514G>A, PPARGC1Ac.1892+19G>A, PRLg.8398G>A and STAT5Ag.9501G>A polymorphisms, and estimated genotype effects on milk production traits and milk‐fat composition. FASNg.17924A>G and OLRg.8232C>A had a significant effect (P < 0.05) on milk‐fat percentage. However, we were not able to confirm results reported in the literature that showed effects of all evaluated polymorphisms on milk‐fat percentage or milk‐fat yield. All polymorphisms showed significant effects (P < 0.05) on milk‐fat composition. The polymorphisms in FASN and STAT5A, which had an effect on C14:0 and were located on chromosome 19, could not fully explain the quantitative trait locus for C14:0 that was previously detected on chromosome 19 in a genome‐wide scan using linkage analysis.
Phospho‐STAT5 and phospho‐Akt expression in chronic myeloproliferative neoplasms
Authors: Grimwade Lizz F. , Happerfield Lisa , Tristram Colin , McIntosh Gary , Rees Mark , Bench Anthony J. , Boyd Elaine M. , Hall Marie , Quinn Amy , Piggott Nigel , Scorer Paul , Scott Mike A. , Erber Wendy N. 
Published: August 2009

SummaryThe majority of Myeloproliferative Neoplasms (MPNs) are characterised by mutations in genes encoding molecules or receptors involved in cell signalling, the most common being the JAK2 V617F mutation. This mutation leads to ligand‐independent activation of downstream signalling pathways by constitutive phosphorylation. The signalling pathways affected include the Janus kinase‐signal transducers and activators of transcription (JAK‐STAT) and phosphotidylinositide‐3 kinase (PI3K) pathways, which regulate cell survival and apoptosis respectively. Monoclonal antibodies to phospho‐STAT5 and phospho‐Akt were generated and assessed by immunocytochemistry on bone marrow biopsies of MPN patients with JAK2 V617F, JAK2 exon 12, MPL exon 10 and KIT D816V mutations. JAK2 V617F mutation was associated with significantly increased levels of phosphorylated STAT5 and Akt in haemopoietic cells, most marked in megakaryocytes. In contrast, JAK2 exon 12 and MPL exon 10 mutations did not affect the level of phosphorylation. In systemic mastocytosis with KIT D618V mutation there was significantly increased expression of phosphorylated STAT5 and Akt in neoplastic mast cells although there was no change in the expression in other haemopoietic cells. JAK2 V617F is associated with upregulated phosphorylation of STAT5 and Akt in megakaryocytes, and to a lesser extent in other haemopoietic cells. Immunocytochemistry of bone marrow trephines for these phospho‐proteins can be used as a supplementary diagnostic test with a high negative predictive value.
Absence of VOD in paediatric thalassaemic HSCT recipients using defibrotide prophylaxis and intravenous Busulphan
Authors: Cappelli Barbara , Chiesa Robert , Evangelio Costanza , Biffi Alessandra , Roccia Tito , Frugnoli Ilaria , Biral Erika , Noè Anna , Fossati Marco , Finizio Valentina , Miniero Roberto , Napolitano Sara , Ferrua Francesca , Soliman Clara , Ciceri Fabio , Roncarolo Maria G. , Marktel Sarah 
Published: August 2009

SummaryHepatic veno‐occlusive disease (VOD) is a common complication of haematopoietic stem cell transplantation (HSCT), with reported incidences of 5–40% in children. Recently, defibrotide (DF) has been successfully used as prophylaxis and treatment of VOD. This study reports data on 63 human leucocyte antigen‐matched HSCT performed in 57 children affected by beta thalassemia at very high risk for developing VOD (liver fibrosis, iron overload, hepatitis C virus infections, busulphan‐based conditioning, methotraexate + ciclosporine). All patients received a busulphan‐based conditioning regimen, either orally (four HSCT) or intravenously (59 HSCT). All patients received oral DF (40 mg/kg per day, final dose) as VOD prophylaxis from median day −9 to median day +29. In order to overcome the lack of oral paediatric formulations, a galenic formulation was administered. DF was well tolerated. Only one patient fulfilled Seattle Criteria for VOD diagnosis. This patient had discontinued DF 6 d prior to VOD onset, due to high risk of haemorrhage. We concluded that oral defibrotide prophylaxis and i.v. busulphan safely abated VOD incidence in high‐risk patients who had undergone HSCT. A galenic preparation of oral DF also permits this treatment in low‐weight patients. Costs of DF prophylaxis are acceptable considering the reduced incidence of VOD.
Association studies of erythoid α‐spectrin at the tetramerization site
Authors: Lam Vinh Q. , Antoniou Chloe , Rolius Ramunas , Fung Leslie W.‐M. 
Published: August 2009

SummaryThe functional roles of residues 21–43 and 55–59 in the α‐spectrin N‐terminal region in forming tetramers were determined by the introduction of mutations at each of these positions. We measured association affinities for tetramer formation (Kd), which can be used to predict clinical severity, of these mutants. A total of nine residues critical for association with β‐spectrin were found. The mutations of six of these residues have already been known to cause hereditary elliptocytosis or hereditary pyropoikilocytosis. Clinical symptoms associated with three mutations of residues 23, 57 and 58 have not yet been reported. We suggest that these mutations may also introduce abnormalities to erythrocytes.
Phase II study of the histone deacetylase inhibitor MGCD0103 in patients with previously treated chronic lymphocytic leukaemia
Authors: Blum Kristie A. , Advani Anjani , Fernandez Louis , Van Der Jagt Richard , Brandwein Joseph , Kambhampati Suman , Kassis Jeannine , Davis Melanie , Bonfils Claire , Dubay Marja , Dumouchel Julie , Drouin Michel , Lucas David M. , Martell Robert E. , Byrd John C. 
Published: August 2009

SummaryMGCD0103, an orally available class I histone deacetylase (HDAC) inhibitor, was examined for pre‐clinical activity in chronic lymphocytic leukaemia (CLL). A phase II clinical trial was performed, starting at a dose of 85 mg/d, three times per week. Dose escalation to 110 mg or the addition of rituximab was permitted in patients without a response after two or more cycles. MGCD0103 demonstrated pre‐clinical activity against CLL cells with a LC50 (concentration lethal to 50%) of 0·23 μmol/l and increased acetylation of the HDAC class I specific target histone H3. Twenty‐one patients received a median of two cycles of MGCD0103 (range, 0–12). All patients had previously received fludarabine, 33% were fludarabine refractory, and 71% had del(11q22·3) or del(17p13·1). No responses according to the National Cancer Institutes 1996 criteria were observed. Three patients received 110 mg and four patients received concomitant rituximab, with no improvement in response. Grade 3–4 toxicity consisted of infections, thrombocytopenia, anaemia, diarrhoea, and fatigue. HDAC inhibition was observed in six out of nine patients on day 8. Limited activity was observed with single agent MGCD0103 in high risk patients with CLL. Future investigations in CLL should focus on broad HDAC inhibition, combination strategies, and approaches to diminish constitutional symptoms associated with this class of drugs.