bluuebunny/crossref_metadata_2025 huggingface dataset:
PREDA: an R-package to identify regional variations in genomic data
Authors: Ferrari Francesco , Solari Aldo , Battaglia Cristina , Bicciato Silvio
Published: July 2011

Summary: Chromosomal patterns of genomic signals represent molecular fingerprints that may reveal how the local structural organization of a genome impacts the functional control mechanisms. Thus, the integrative analysis of multiple sources of genomic data and information deepens the resolution and enhances the interpretation of stand-alone high-throughput data. In this note, we present PREDA (Position RElated Data Analysis), an R package for detecting regional variations in genomics data. PREDA identifies relevant chromosomal patterns in high-throughput data using a smoothing approach that accounts for distance and density variability of genomics features. Custom-designed data structures allow efficiently managing diverse signals in different genomes. A variety of smoothing functions and statistics empower flexible and robust workflows. The modularity of package design allows an easy deployment of custom analytical pipelines. Tabular and graphical representations facilitate downstream biological interpretation of results.

Availability:  PREDA is available in Bioconductor and at http://www.xlab.unimo.it/PREDA.

Contact:  silvio.bicciato@unimore.it

Supplementary information:  Supplementary information is available at Bioinformatics online.
DivBayes and SubT: exploring species diversification using Bayesian statistics
Authors: Ryberg Martin , Nilsson R. Henrik , Matheny P. Brandon
Published: July 2011

Summary: DivBayes is a program to estimate diversification rates from species richness and ages of a set of clades. SubT estimates diversification rates from node heights within a clade. Both programs implement Bayesian statistics and provide the ability to account for uncertainty in the ages of taxa in the underlying data, an improvement over more commonly used maximum likelihood methods.

Availability: DivBayes and SubT are released as C++ source code under the GNU GPL v. 3 software license in Supplementary information 1 and Supplementary Data, respectively, and at http://web.utk.edu/~kryberg/. They have been successfully compiled on various Linux, MacOS X and Windows systems.

Contact:  kryberg@utk.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Nearshore, seasonally persistent fronts in sea surface temperature on Red Sea tropical reefs
Authors: Blythe Jonathan N. , da Silva José C. B. , Pineda Jesús
Published: July 2011

Blythe, J. N., da Silva, J. C. B., and Pineda. J. 2011. Nearshore, seasonally persistent fronts in sea surface temperature on Red Sea tropical reefs. – ICES Journal of Marine Science, 68: 1827–1832. Temperature variability was studied on tropical reefs off the coast of Saudi Arabia in the Red Sea using remote sensing from Aqua and Terra satellites. Cross-shore gradients in sea surface temperature (SST) were observed, including cold fronts (colder inshore) during winter and warm fronts (warmer inshore) during summer. Fronts persisted over synoptic and seasonal time-scales and had a periodic annual cycle over a 10-year time-series. Measurements of cross-shore SST variability were conducted at the scale of tens of kilometres, which encompassed temperature over shallow tropical reef complexes and the continental slope. Two tropical reefs that had similar reef geomorphology and offshore continental slope topography had identical cold fronts, although they were separated by 100 km along the Red Sea coast of Saudi Arabia. Satellite SST gradients across contours of topography of tropical reefs can be used as an index to flag areas potentially exposed to temperature stress.
Assessing the Acute Red Eye in Older People
Authors: Schroeder Knut
Published: July 2011

A70-year-old woman comes to see you in surgery because she has developed a red and sore eye. Which issues do you need to consider as part of a focused clinical assessment?
Chronic Fatigue Syndrome
Authors: Gibson Jeremy C. , Smith Bozena , Ward Christopher D.
Published: July 2011

In this article, we outline GP management of chronic fatigue syndrome (CFS), the condition also known colloquially in the UK as ‘ME’. The paper is based on National Institute for Health and Clinical Excellence (NICE) guidelines and also incorporates evidence-based strategies available to specialist services. GPs are well placed to make an early diagnosis of CFS and give patients helpful advice to manage their fatigue, hopefully avoiding multiple inappropriate referrals to specialist medical clinics.
Azospirillum formosense sp. nov., a diazotroph from agricultural soil
Authors: Lin Shih-Yao , Shen Fo-Ting , Young Li-Sen , Zhu Zhi-Long , Chen Wen-Ming , Young Chiu-Chung
Published: July 2011

A Gram-negative, spiral or rod-shaped, non-spore-forming diazotrophic bacterium, designated CC-Nfb-7T, was isolated from agricultural soil in Yunlin County, Taiwan. 16S rRNA gene sequence analysis showed that strain CC-Nfb-7T was most closely related to

Azospirillum brasilense

DSM 1690T (97.4 % 16S rRNA gene sequence similarity),

Azospirillum rugosum

IMMIB AFH-6T (96.8 %) and

Azospirillum oryzae

JCM 21588T (96.6 %); <96.5 % 16S rRNA gene sequence similarity was found with all other members of the genus

Azospirillum

. DNA–DNA relatedness between strain CC-Nfb-7T and

A. brasilense

DSM 1690T,

A. rugosum

DSM 19657T and

A. oryzae

JCM 21588T was 38.9, 30.1 and 31.8 %, respectively. The respiratory quinone was ubiquinone Q-10. The major fatty acids were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (consisting of C16 : 1ω7c and/or C16 : 1ω6c), summed feature 2 (consisting of C14 : 0 3-OH and/or iso-C16 : 1 I), C16 : 0, C18 : 0 2-OH and C16 : 0 3-OH. The polar lipids consisted mainly of phosphatidylglycerol, phosphatidylcholine and one unidentified phospholipid. Furthermore, moderate amounts of phosphatidylethanolamine, phosphatidyldimethylethanolamine and one unidentified aminophospholipid were also detected. Strain CC-Nfb-7T could be distinguished from members of phylogenetically related species by differences in phenotypic properties. On the basis of morphological, chemotaxonomic and phylogenetic data, strain CC-Nfb-7T represents a novel species within the genus

Azospirillum

, for which we propose the name Azospirillum formosense sp. nov. The type strain is CC-Nfb-7T ( = BCRC 80273T = JCM 17639T = DSM 24137T).
Nocardia goodfellowii sp. nov. and Nocardia thraciensis sp. nov., isolated from soil
Authors: Sazak Anil , Sahin Nevzat , Camas Mustafa
Published: July 2011

The taxonomic position of two soil actinomycetes, strains A2012T and A2019T, isolated from Turkish soils, was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the strains belonged to the family

Nocardiaceae

. Strains A2012T and A2019T were most closely related to

Nocardia caishijiensis

DSM 44831T (98.9 %) and

Nocardia mexicana

CIP 108295T (98.6 %), respectively; similarity to other type strains of the genus

Nocardia

ranged from 96.9 to 97.9 %. However, DNA–DNA relatedness and phenotypic data demonstrated that strains A2012T and A2019T could be clearly distinguished from members of the most closely related

Nocardia

species. It is evident from the genotypic and phenotypic data that the two isolates represent two novel species of the genus

Nocardia

. It is proposed, therefore, that strains A2012T and A2019T be classified in the genus

Nocardia

as representatives of Nocardia goodfellowii sp. nov. (type strain A2012T = DSM 45516T = NRRL B-24833T = KCTC 19986T) and Nocardia thraciensis sp. nov. (type strain A2019T = DSM 45517T = NRRL B-24834T = KCTC 19985T), respectively.
Reclassification of

Rhizobium tropici

type A strains as Rhizobium leucaenae sp. nov.
Authors: Ribeiro Renan Augusto , Rogel Marco A. , López-López Aline , Ormeño-Orrillo Ernesto , Barcellos Fernando Gomes , Martínez Julio , Thompson Fabiano Lopes , Martínez-Romero Esperanza , Hungria Mariangela
Published: July 2011

Rhizobium tropici

is a well-studied legume symbiont characterized by high genetic stability of the symbiotic plasmid and tolerance to tropical environmental stresses such as high temperature and low soil pH. However, high phenetic and genetic variabilities among

R. tropici

strains have been largely reported, with two subgroups, designated type A and B, already defined within the species. A polyphasic study comprising multilocus sequence analysis, phenotypic and genotypic characterizations, including DNA–DNA hybridization, strongly supported the reclassification of

R. tropici

type A strains as a novel species. Type A strains formed a well-differentiated clade that grouped with

R. tropici

,

Rhizobium multihospitium

,

Rhizobium miluonense

,

Rhizobium lusitanum

and

Rhizobium rhizogenes

in the phylogenies of the 16S rRNA, recA, gltA, rpoA, glnII and rpoB genes. Several phenotypic traits differentiated type A strains from all related taxa. The novel species, for which the name Rhizobium leucaenae sp. nov. is proposed, is a broad host range rhizobium being able to establish effective root-nodule symbioses with Leucaena leucocephala, Leucaena esculenta, common beans (Phaseolus vulgaris) and Gliricidia sepium. Strain CFN 299T ( = USDA 9039T = LMG 9517T = CECT 4844T = JCM 21088T = IAM 14230T = SEMIA 4083T = CENA 183T = UMR1026T = CNPSo 141T) is designated the type strain of Rhizobium leucaenae sp. nov.
Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant
Authors: Woo Sung-Geun , Srinivasan Sathiyaraj , Yang Jihoon , Jung Yong-An , Kim Myung Kyum , Lee Myungjin
Published: July 2011

Strain MJ31T, a Gram-reaction-positive, aerobic, rod-shaped, non-motile bacterium, was isolated from a sludge sample collected at the Daejeon sewage-disposal plant, in South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MJ31T belonged to the genus

Nocardioides

, appearing most closely related to

Nocardioides dubius

KSL-104T (98.6 % sequence similarity),

Nocardioides jensenii

DSM 20641T (97.6 %),

Nocardioides daedukensis

MDN22T (97.2 %) and

Nocardioides mesophilus

MSL-22T (97.0 %). The chemotaxonomic properties of strain MJ31T were consistent with those of the genus

Nocardioides

: MK-8(H4) was the predominant menaquinone, iso-C16 : 0, iso-C17 : 0 and C18 : 1ω9c were the predominant cellular fatty acids, and the cell-wall peptidoglycan was based on ll-2,6-diaminopimelic acid. The genomic DNA G+C content of strain MJ31T was 71.2 mol%. Some differential phenotypic properties and low DNA–DNA relatedness values (<28 %) with the type strains of closely related species indicated that strain MJ31T represents a novel species, for which the name Nocardioides daejeonensis sp. nov. is proposed. The type strain is MJ31T ( = KCTC 19772T = JCM 16922T).
Mycobacterium litorale sp. nov., a rapidly growing mycobacterium from soil
Authors: Zhang Yabo , Zhang Jianli , Fang Caiyuan , Pang Huancheng , Fan Jinping
Published: July 2011

A Gram-positive, acid-fast and rapidly growing rod, designated F4T, was isolated from a soil sample of Haikou in China. The isolate shared 98.2 % 16S rRNA gene sequence similarity with

Mycobacterium monacense

B9-21-178T, 96.2 % hsp65 sequence similarity with

M. monacense

FI-05352 and 79.6 % 16S–23S rRNA internal transcribed spacer sequence similarity with

M. monacense

B9-21-178T. DNA–DNA relatedness between the isolate and

M. monacense

DSM 44395T was 43.5 %. The morphological analysis and physiological tests also showed that the isolate differed from any strain reported to date. The mycolic acid profile and the cellular fatty acid composition were also determined. On the basis of phenotypic and chemotaxonomic characteristics and phylogenetic data, it was concluded that strain F4T ( = CGMCC 4.5724T = JCM 17423T) merited classification as the type strain of a novel species, for which the name Mycobacterium litorale sp. nov. is proposed.
Sphingomonas polyaromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from an oil port water sample
Authors: Luo Yuan-Rong , Tian Yun , Huang Xu , Kwon Kaekyoung , Yang Sung-Hyun , Seo Hyun-Seok , Kim Sang-Jin , Zheng Tian-Ling
Published: July 2011

A bacterial strain (B2-7T) capable of degrading a wide range of polycyclic aromatic hydrocarbon compounds (2–4 rings) was isolated from a water sample taken from Botan Oil Port in Xiamen, China. The isolate was Gram-negative, short-rod-shaped, aerobic, non-motile and formed yellow-pigmented colonies on LB medium. Cells of strain B2-7T were catalase-positive and oxidase-negative. Optimal growth of strain B2-7T was observed at pH 7.0, at 26 °C and in 0.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain B2-7T grouped with members of the genus

Sphingomonas

and it showed 16S rRNA gene sequence similarity of 95.40 % to

Sphingomonas yunnanensis

YIM 003T. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. Q-10 and sym-homospermidine were the predominant ubiquinone and polyamine components, respectively. The major fatty acids were C18 : 1ω7c (67.2 %), C14 : 0 2-OH (10.0 %) and C16 : 0 (9.6 %). The G+C content of the genomic DNA was 61.8 mol%. Based on phenotypic properties, and phylogenetic and genomic data, strain B2-7T represents a novel species of the genus

Sphingomonas

within the class

Alphaproteobacteria

, for which the name Sphingomonas polyaromaticivorans sp. nov. is proposed. The type strain is B2-7T ( = KCCM 42951T = JCM 16711T).
Sandaracinus amylolyticus gen. nov., sp. nov., a starch-degrading soil myxobacterium, and description of Sandaracinaceae fam. nov.
Authors: Mohr Kathrin I. , Garcia Ronald O. , Gerth Klaus , Irschik Herbert , Müller Rolf
Published: July 2011

A novel starch-degrading myxobacterium designated NOSO-4T (new organism of the

Sorangiineae

strain 4) was isolated in 1995 from a soil sample containing plant residues, collected in Lucknow, Uttar Pradesh, India. The novel bacterium shows typical myxobacterial characteristics such as Gram-negative, rod-shaped vegetative cells, swarming colonies, fruiting body-like aggregates and bacteriolytic activity. The strain is mesophilic, strictly aerobic and chemoheterotrophic. Based on 16S rRNA gene sequences, NOSO-4T shows highest similarity (96.2 %) with the unidentified bacterial strain O29 (accession no. FN554397), isolated from leek (Allium porrum) rhizosphere, and to the myxobacteria

Jahnella thaxteri

(88.9 %) and

Chondromyces pediculatus

(88.5 %). Major fatty acids are C17 : 1 2-OH, C20 : 4ω6 (arachidonic acid), and the straight-chain fatty acids C17 : 0, C15 : 0 and C16 : 0. The genomic DNA G+C content of the novel isolate is 66.8 mol%. It is proposed that strain NOSO-4T represents a novel species in a new genus, i.e. Sandaracinus amylolyticus gen. nov., sp. nov., but also belongs to a new family, Sandaracinaceae fam. nov. The type strain of the type species, S. amylolyticus sp. nov., is NOSO-4T ( = DSM 53668T = NCCB 100362T).
The ROOT DETERMINED NODULATION1 Gene Regulates Nodule Number in Roots of Medicago truncatula and Defines a Highly Conserved, Uncharacterized Plant Gene Family
Authors: Schnabel Elise L. , Kassaw Tessema K. , Smith Lucinda S. , Marsh John F. , Oldroyd Giles E. , Long Sharon R. , Frugoli Julia A.
Published: July 2011

The formation of nitrogen-fixing nodules in legumes is tightly controlled by a long-distance signaling system in which nodulating roots signal to shoot tissues to suppress further nodulation. A screen for supernodulating Medicago truncatula mutants defective in this regulatory behavior yielded loss-of-function alleles of a gene designated ROOT DETERMINED NODULATION1 (RDN1). Grafting experiments demonstrated that RDN1 regulatory function occurs in the roots, not the shoots, and is essential for normal nodule number regulation. The RDN1 gene, Medtr5g089520, was identified by genetic mapping, transcript profiling, and phenotypic rescue by expression of the wild-type gene in rdn1 mutants. A mutation in a putative RDN1 ortholog was also identified in the supernodulating nod3 mutant of pea (Pisum sativum). RDN1 is predicted to encode a 357-amino acid protein of unknown function. The RDN1 promoter drives expression in the vascular cylinder, suggesting RDN1 may be involved in initiating, responding to, or transporting vascular signals. RDN1 is a member of a small, uncharacterized, highly conserved gene family unique to green plants, including algae, that we have named the RDN family.
Genotype‐directed, dose‐finding study of irinotecan in cancer patients with UGT1A1*28 and/or UGT1A1*6 polymorphisms
Authors: Satoh Taroh , Ura Takashi , Yamada Yasuhide , Yamazaki Kentaro , Tsujinaka Toshimasa , Munakata Masaki , Nishina Tomohiro , Okamura Shu , Esaki Taito , Sasaki Yasutsuna , Koizumi Wasaburo , Kakeji Yoshihiro , Ishizuka Naoki , Hyodo Ichinosuke , Sakata Yuh
Published: July 2011

Irinotecan‐induced severe neutropenia is associated with homozygosity for the UGT1A1*28 or UGT1A1*6 alleles. In this study, we determined the maximum‐tolerated dose (MTD) of irinotecan in patients with UGT1A1 polymorphisms. Patients who had received chemotherapy other than irinotecan for metastatic gastrointestinal cancer were enrolled. Patients were divided into three groups according to UGT1A1 genotypes: wild‐type (*1/*1); heterozygous (*28/*1, *6/*1); or homozygous (*28/*28, *6/*6, *28/*6). Irinotecan was given every 2 weeks for two cycles. The wild‐type group received a fixed dose of irinotecan (150 mg/m2) to serve as a reference. The MTD was guided from 75 to 150 mg/m2 by the continual reassessment method in the heterozygous and homozygous groups. Dose‐limiting toxicity (DLT) and pharmacokinetics were evaluated during cycle 1. Of 82 patients enrolled, DLT was assessable in 79 patients (wild‐type, 40; heterozygous, 20; and homozygous, 19). Dose‐limiting toxicity occurred in one patient in the wild‐type group, none in the heterozygous group, and six patients (grade 4 neutropenia) in the homozygous group. In the homozygous group, the MTD was 150 mg/m2 and the probability of DLT was 37.4%. The second cycle was delayed because of neutropenia in 56.3% of the patients given the MTD. The AUC0–24 h of SN‐38 was significantly greater (P < 0.001) and more widely distributed in the homozygous group. Patients homozygous for the UGT1A1*28 or UGT1A1*6 allele can receive irinotecan in a starting dose of 150 mg/m2, but many required dose reductions or delayed treatment in subsequent cycles. UMIN Clinical Trial Registration number: UMIN000000618. (Cancer Sci 2011; 102: 1868–1873)
IKZF1 deletions predict a poor prognosis in children with B‐cell progenitor acute lymphoblastic leukemia: A multicenter analysis in Taiwan
Authors: Yang Yung‐Li , Hung Chia‐Cheng , Chen Jiann‐Shiuh , Lin Kai‐Hsin , Jou Shiann‐Tarng , Hsiao Chih‐Cheng , Sheen Jiunn‐Ming , Cheng Chao‐Neng , Wu Kang‐Hsi , Lin Shu‐Rung , Yu Sung‐Liang , Chen Hsuan‐Yu , Lu Meng‐Yao , Wang Shih‐Chung , Chang Hsiu‐Hao , Lin Shu‐Wha , Su Yi‐Ning , Lin Dong‐Tsamn
Published: July 2011

Despite current risk‐directed therapy, approximately 15–20% of pediatric patients with acute lymphoblastic leukemia (ALL) have relapses. Recent genome‐wide analyses have identified that an alteration of IKZF1 is associated with very poor outcomes in B‐cell progenitor ALL. In this study, we determined the prognostic significance of IKZF1 deletions in patients with childhood ALL. This study analyzed 242 pediatric B‐cell progenitor ALL patients in Taiwan. We developed a simple yet sensitive multiplex quantitative PCR coupled with capillary electrophoresis to accurately determine the allele dose of IKZF1, and high resolution melting was used for mutation screening for all coding exons of IKZF1. Twenty‐six (10.7%) pediatric B‐cell progenitor ALL patients were found to harbor these deletions. Most of the deletions were broader deletions that encompassed exon 3 to exon 6, consistent with previous reports. Genomic sequencing of IKZF1 was carried out in all cases and no point mutations were identified. Patients with IKZF1 deletions had inferior event‐free survival (P < 0.001), and overall survival (P = 0.0016). The association between IKZF1 deletions and event‐free survival was independent of age, leukocyte count at presentation, and cytogenetic subtype by multivariate Cox analysis (P = 0.003, hazard ratio = 2.45). This study indicates that detection of IKZF1 deletions upon diagnosis of B‐cell progenitor ALL may help to identify patients at risk of treatment failure. IKZF1 deletions could be incorporated as a new high‐risk prognostic factor in future treatment protocols. To the best of our knowledge, this is the first study to examine the poor prognosis of IKZF1 deletions in an Asian population. (Cancer Sci 2011; 102: 1874–1881)
Shear wave elastography in the diagnosis of thyroid nodules: feasibility in the case of coexistent chronic autoimmune Hashimoto’s thyroiditis
Authors: Magri Flavia , Chytiris Spyridon , Capelli Valentina , Alessi Sarah , Nalon Elisa , Rotondi Mario , Cassibba Sara , Calliada Fabrizio , Chiovato Luca
Published: July 2011

Objective  ShearWave™ Elastography (SWE) is real‐time, quantitative and user‐independent technique, recently introduced in the diagnostic work‐up of thyroid nodules. Hashimoto’s thyroiditis (HT), characterized by variable degrees of lymphocytic infiltration and fibrosis, might affect shear wave propagation. The aim of this study was to assess the feasibility of SWE in cytologically benign thyroid nodules within both Hashimoto’s and nonautoimmune thyroid glands. The effect of autoimmunity on the gland stiffness was also evaluated.

Design  longitudinal study in a single centre.

Patients  SWE was performed in 75 patients with a benign thyroid nodule at cytology: 33 with Hashimoto’s thyroiditis (HT group) and 42 with uni‐ or multi‐nodular goitre, negative for thyroid autoimmunity (non‐HT group).

Results  The elasticity index (EI) of the extra‐nodular tissue was greater, though not statistically significant, in the HT than in the non‐HT group (24·0 ± 10·5 kPa vs 20·8 ± 10·4 kPa; P = 0·206). However, the EI of extra‐nodular tissue was related to the TPOAb titre in the HT group (P = 0·02) and was significantly higher in patients with HT receiving L‐thyroxine than in the euthyroid subjects (P = 0·02). The EI of thyroid nodules was similar in HT and non‐HT groups. In both groups, the stiffness of nodules was significantly higher than that of the embedding tissue.

Conclusions  Our data indicate that SWE correctly defines the elasticity of thyroid nodules independently from the coexistence of autoimmune thyroiditis, always being able to differentiate nodular tissue from the surrounding parenchyma. In HT, the stiffness of extra‐nodular tissue increases in relation to both the thyroid antibody titre and the degree of impairment of thyroid function.
The impact of sea‐level rise onSnowyPlovers inFlorida: integrating geomorphological, habitat, and metapopulation models
Authors: Aiello‐Lammens Matthew E. , Chu‐Agor Ma. Librada , Convertino Matteo , Fischer Richard A. , Linkov Igor , Resit Akçakaya H.
Published: July 2011

Sea‐level rise (SLR) is a projected consequence of global climate change that will result in complex changes in coastal ecosystems. These changes will cause transitions among coastal habitat types, which will be compounded by human‐made barriers to the gradual inland migration of these habitat types. The effect of these changes on the future viability of coastal species will depend on the habitat requirements and population dynamics of these species. Thus, realistic assessments of the impact ofSLRrequire linking geomorphological models with habitat and population models. In this study, we implemented a framework that allows this linkage, and demonstrated its feasibility to assess the effect ofSLRon the viability of theSnowyPlover population inFlorida. The results indicate thatSLRwill cause a decline in suitable habitat and carrying capacity for this species, and an increase in the risk of its extinction and decline. The model projected that the population size will decline faster than the area of habitat or carrying capacity, demonstrating the necessity of incorporating population dynamics in assessing the impacts ofSLRon coastal species. The results were most sensitive to uncertainties in survival rate and fecundity, and suggested that future studies on this species should focus on the average and variability of these demographic rates and their dependence on population density. The effect ofSLRon this species’ viability was qualitatively similar with most alternative models that used the extreme values of each uncertain parameter, indicating that the results are robust to uncertainties in the model.
Inter‐observer reproducibility and analysis of gastric volume measurements and gastric emptying assessed with magnetic resonance imaging
Authors: Fruehauf H. , Menne D. , Kwiatek M. A. , Forras‐Kaufman Z. , Kaufman E. , Goetze O. , Fried M. , Schwizer W. , Fox M.
Published: July 2011

Background  Magnetic resonance (MR) imaging provides direct, non‐invasive measurements of gastric function and emptying. The inter‐observer variability (IOV) of MR volume measurements and the most appropriate analysis of MR data have not been established. To assess IOV of total gastric volume (TGV) and gastric content volume (GCV) measurements from MR images and the ability of standard power exponential (PowExp), and a novel linear exponential (LinExp) model to describe MR data.

Methods  Ten healthy volunteers received three different volumes of a liquid nutrient test meal (200–800 mL) on 3 days in a randomized order. Magnetic resonance scans were acquired using a 1.5T system every 1–5 min for 60 min. Total gastric volume and GCV were measured independently by three observers. Volume data were fitted by PowExp and LinExp models to assess postprandial volume change and gastric emptying half time (T50).

Key Results  An initial rise in GCV and TGV was often observed after meal ingestion, thereafter GCV and TGV decreased in an approximately linear fashion. Inter‐observer variability decreased with greater volumes from 12% at 200 mL to 6% at 600 and 800 mL. Inter‐observer variability for T50 was <5%. PowExp and LinExp models provided comparable estimates of T50; however, only LinExp described dynamic volume change in the early postprandial period.

Conclusions & Inferences  Gastric MR provides quantitative measurements of postprandial volume change with low IOV, unless the stomach is nearly empty. The novel LinExp model describes the dynamic volume changes in the early postprandial period more accurately than the PowExp model used in existing gastric emptying studies.
Effects of dietary fat levels on nutrient digestibility and production performance of growing‐furring blue foxes (Alopex lagopus)
Authors: Geng Y.Y. , Yang F. H. , Xing X.M. , Gao X.H.
Published: July 2011

The objective of this study was to determine whether nutrient digestibility and production performance of growing‐furring blue foxes (Alopex lagopus) are affected by different dietary fat levels. Sixty‐four young animals were randomly assigned to four groups (A, B, C, D) provided with diets containing approximately 12%, 26%, 40%, 54% fat in the dry matter respectively. When dietary fat level was increased, the apparent digestibility of main nutrients except for crude carbohydrates, and gross energy were improved (p < 0.0001). The amount of nitrogen excreted was reduced and the biological value of protein was enhanced (p < 0.0001). Over the experimental phase, the efficiency of metabolizable energy (ME) used for gain in group B (26% fat content) was higher than that in other groups. When diets with 12–26% fat content were fed, there was an increasing tendency in skin size. But it had negative effects on skin size and fur quality when the amount of fat content was over 40%. In conclusion, the experiment showed that dietary fat could significantly improve some nutrient utilization and significantly reduce feed/gain ratio as a main energy source. The most preferable fur quality and efficiency of ME used for gain were obtained when diet contained 26% fat level in growing‐furring period.
The effect of depurinized milk draught diet on rat serum uric acid, lipid status and haematological parameters
Authors: Kocic G. , Pavlovic R. , Nikolic G. , Stojanovic D. , Jevtovic T. , Sokolovic D. , Cencic A. , Stojanovic S. , Jelic M. , Zivanovic S.
Published: July 2011

Hyperuricaemia and gout are closely related, but hyperuricaemia is an independent risk factor for endothelial damage, autoinflammation and haemodynamic abnormalities. Milk, generally known as a ‘purine‐free diet’, is an essential protein source for patients suffering from hyperuricaemia and gout. As milk still contains different purine ribonucleotides, the new product, depurinized milk, almost free of purine nucleotides and uric acid, was produced. The potential effect of depurinized milk diet on serum uric acid (SUA) level, lipid parameters and blood haematological parameters was explored in rats after 72 h and 15 days, in relation to standard laboratory chow or the untreated milk diet. The beneficial effect on SUA was achieved when depurinized milk draught was given instead of standard chow for 72 h [28.39 ± 4.76 μm; p < 0.001 vs. standard diet (STD) 47.6 ± 6.12, vs. untreated milk diet 31.55 ± 8.50; p < 0.05] or as a supplement for STD for 15 days experiment (35.38 ± 6.40 μm; p < 0.05 vs. STD only 48.05 ± 4.32; vs. untreated milk + STD 46.02 ± 9.48). Depurinized milk diet significantly decreased the low density lipoproteins/high density lipoproteins (LDL/HDL) ratio (p < 0.001), triglycerides (p < 0.05) and leucocyte count (p < 0.001), while both milk draughts enhanced haemoglobin concentration (p < 0.01). In conclusion, considering the detrimental effect of persisting hyperuricaemia, the depurinized milk draught may meet the demand of healthy dairy product for population under hyperuricaemic risk.
Deconstructing child and adolescent mental health: questioning the‘taken‐for‐granted’…
Authors: Bradley Stephen K , Carter Bernie
Published: July 2011

BRADLEY SK and CARTER B. Nursing Inquiry 2011; 18: 303–312 Deconstructing child and adolescent mental health: questioning the ‘taken‐for‐granted’…

We present a critical deconstructive reading, seeking to problematise ‘taken‐for‐granted’ assumptions in child and adolescent mental health (CAMH). The start point for this critical reading is conventional ‘history‐telling’ within CAMH. The aim is not to take issue with the detail in such histories but to critically examine the texts, so as to highlight constructions that structure the presentation of conventional histories and possible purposes that such constructions may serve. The argument is that such conventional histories leave key questions not just unanswered, but unconsidered – a tendency that can be seen throughout the CAMH literature more generally. Therefore, we then pursue critical discussion of how ‘taken‐for‐granted’ constructions of CAMH enabled psychiatry to successfully expand its power and influence to establish hegemony over ‘problem children’. We do not claim any closure to this critical reading; that is, we do not claim that our critical deconstructive reading is the only reading possible. Similarly, it is not presented in any sense as ‘final word’. Rather our hope for this work is that it might stimulate readers to question the ‘taken‐for‐granteds’ that we present, and indeed others that they might identify themselves. In so doing, it is our hope that creative dialogue might ensue.
Rules and reality: quantifying the practice of apprenticeship in early modern England1
Authors: MINNS CHRIS , WALLIS PATRICK
Published: July 2011

This article uses recently digitized samples of apprentices and masters in London and Bristol to quantify the practice of apprenticeship in the late seventeenth century. Apprenticeship appears much more fluid than is traditionally understood. Many apprentices did not complete their terms of indenture; late arrival and early departure from the master's household were widespread. Other apprentices appear to have been absent temporarily, returning to the master shortly before the end of their indenture. Regression analysis indicates that the patterns of presence and absence broadly reflect the resources and external opportunities available to apprentices.
Accuracy of Two Stereolithographic Surgical Templates: A Retrospective Study
Authors: Cassetta Michele , Giansanti Matteo , Di Mambro Alfonso , Calasso Sabrina , Barbato Ersilia
Published: July 2011

Background: The use of computer software and stereolithography for dental implant therapy has significantly increased during the last few years. The aim of this study was to evaluate and compare the mean accuracy and maximum deviations values of dental implant placement using two stereolithographic (SLA) guide systems.

Materials and Methods: Twenty patients were selected and 227 implants were inserted using bone‐, tooth‐ and mucosa‐supported SLA surgical guides. Thirty‐one guides, both single‐ and multiple‐type, were used. Some of the single‐type surgical guides were fixed with osteosynthesis screws. A postoperative computer tomography (CT) was performed and an iterative closest point algorithm was used to match the jaw of the CT preoperative with the jaw of the postoperative CT. Quantitative data of each group were described. The t‐test was used to determine the influence of the utilization of the different types of SLA on accuracy values.

Results: t‐Test demonstrated a better accuracy of the multiple‐type guides in almost all deviation values when the mucosa‐supported guides were considered. Regarding the bone‐supported template, the single‐type fixed group showed a better accuracy while the highest values of deviation were registered by the multiple‐type guides. The single‐type group showed a better accuracy when the tooth support was considered.

Conclusions: The results of the present study indicated best accuracy of the single‐type guide using a bone or tooth support. The multiple‐type guide recorded the best accuracy data when the mucosa support was considered comparing either a fixed and a not‐fixed single‐type guide.
The N‐terminal region of the bacterial DNA polymerase PolC features a pair of domains, both distantly related to domain V of the DNA polymerase III τ subunit
Authors: Timinskas Kęstutis , Venclovas Česlovas
Published: July 2011

PolC is one of two essential replicative DNA polymerases in Bacillus subtilis and other Gram‐positive bacteria. The 3D structure of PolC has recently been solved, yet it lacks the N‐terminal region. For this PolC region of ∼ 230 residues, both the structure and function are unknown. In the present study, using sensitive homology detection and comparative protein structure modeling, we identified, in this enigmatic region, two consecutive globular domains, PolC‐NI and PolC‐NII, which are followed by an apparently unstructured linker. Unexpectedly, we found that both domains are related to domain V of the τ subunit, which is part of the bacterial DNA polymerase III holoenzyme. Despite their common homology to τ, PolC‐NI and PolC‐NII exhibit very little sequence similarity to each other. This observation argues against simple tandem duplication within PolC as the origin of the two‐domain structure. Using the derived structural models, we analyzed residue conservation and the surface properties of both PolC N‐terminal domains. We detected a surface patch of positive electrostatic potential in PolC‐NI and a hydrophobic surface patch in PolC‐NII, suggesting their possible involvement in nucleic acid and protein binding, respectively. PolC is known to interact with the τ subunit, however, the region responsible for this interaction is unknown. We propose that the PolC N‐terminus is involved in mediating the PolC‐τ interaction and possibly also in binding DNA.
The ins and outs of pertussis toxin
Authors: Locht Camille , Coutte Loic , Mielcarek Nathalie
Published: July 2011

Pertussis toxin, produced and secreted by the whooping cough agent Bordetella pertussis, is one of the most complex soluble bacterial proteins. It is actively secreted through the B. pertussis cell envelope by the Ptl secretion system, a member of the widespread type IV secretion systems. The toxin is composed of five subunits (named S1 to S5 according to their decreasing molecular weights) arranged in an A–B structure. The A protomer is composed of the enzymatically active S1 subunit, which catalyzes ADP‐ribosylation of the α subunit of trimeric G proteins, thereby disturbing the metabolic functions of the target cells, leading to a variety of biological activities. The B oligomer is composed of 1S2:1S3:2S4:1S5 and is responsible for binding of the toxin to the target cell receptors and for intracellular trafficking via receptor‐mediated endocytosis and retrograde transport. The toxin is one of the most important virulence factors of B. pertussis and is a component of all current vaccines against whooping cough.
Carboxylate and aromatic active‐site residues are determinants of high‐affinity binding of ω‐aminoaldehydes to plant aminoaldehyde dehydrogenases
Authors: Kopečný David , Tylichová Martina , Snegaroff Jacques , Popelková Hana , Šebela Marek
Published: July 2011

The crystal structures of both isoforms of the aminoaldehyde dehydrogenase from pea (PsAMADH) have been solved recently [Tylichováet al. (2010) J Mol Biol396, 870–882]. The characterization of the PsAMADH2 proteins, altered here by site‐directed mutagenesis, suggests that the D110 and D113 residues at the entrance to the substrate channel are required for high‐affinity binding of ω‐aminoaldehydes to PsAMADH2 and for enzyme activity, whereas N162, near catalytic C294, contributes mainly to the enzyme’s catalytic rate. Inside the substrate cavity, W170 and Y163, and, to a certain extent, L166 and M167 probably preserve the optimal overall geometry of the substrate channel that allows for the appropriate orientation of the substrate. Unconserved W288 appears to affect the affinity of the enzyme for the substrate amino group through control of the substrate channel diameter without affecting the reaction rate. Therefore, W288 may be a key determinant of the differences in substrate specificity found among plant AMADH isoforms when they interact with naturally occurring substrates such as 3‐aminopropionaldehyde and 4‐aminobutyraldehyde.
Detection of continuum radio emission associated with Geminga
Authors: Pellizzoni A. , Govoni F. , Esposito P. , Murgia M. , Possenti A.
Published: July 2011

A deep Very Large Array observation of the Geminga pulsar field led to the discovery, at a higher than 10σ significance level, of radio emission trailing the neutron star proper motion. This ∼10 arcsec long radio feature, detected with a flux of ∼0.4 mJy at 4.8 GHz, is marginally displaced (2.7 ± 1.8 arcsec) from the pulsar (which, at any rate, is unlikely to contribute with magnetospheric pulsed emission more than 15 per cent to the total observed radio luminosity, ∼1026 erg s−1) and positionally coincident with the X-ray axial tail recently discovered by Chandra and ascribed to the pulsar wind nebula (PWN). Overall, the Geminga radio tail is compatible with the scenario of a synchrotron-emitting PWN, but the present data do not allow us to discriminate between different (and not always necessarily mutually exclusive) possible processes for producing that. If this radio feature results not from intrinsic peculiarities of Geminga, but from its proximity and radio-quiet nature (both helping in not hindering the faint diffuse radio emission), other relatively near and energetic radio-quiet pulsars could show similar structures in dedicated interferometric observations.
Predictors of Poststroke Mobility: Systematic Review
Authors: Craig Louise E. , Wu Olivia , Bernhardt Julie , Langhorne Peter
Published: July 2011

Regaining poststroke mobility is considered a primary goal of the stroke patient in early rehabilitation. Predictive recovery of poststroke mobility is clinically important, and provides important information to healthcare professionals, patients and their families. We conducted a systematic review aimed at identifying the predictive or associated baseline factors, assessed within one-week of stroke onset, and the recovery of poststroke mobility within 30 days. A comprehensive search strategy was applied to all major electronic databases to identify potentially relevant studies. Included in the review are two studies that evaluate the predictive value of baseline factors by developing a prognostic model, and three studies that assess the baseline factors that were associated with the outcome by univariate analysis. Walking is the most commonly assessed mobility outcome; age, the severity of paresis, reduced leg power, presence of hemianopia, size of brain lesion and type of stroke were shown to be predictive or associated with walking within 30 days poststroke. This review has identified the potential predictors of the recovery of mobility poststroke. There is a need to explore and validate these predictors in other patient cohorts, and consider additional factors believed to be associated with mobility. The recovery of mobility other than walking also needs investigation. In order to move prognostic research in stroke forward, a collaborative approach to sharing and collecting data is recommended.
Risk Factor Profiles of South Asians with Cerebrovascular Disease
Authors: Itrat Ahmad , Ahmed Bilal , Khan Maria , Muhammad Murtaza , Thaver Danyal , Khowaja Zubair , Ali Shehzad , Bawa Zeeshan , Rahat Muhammad , Kamal Ayeesha Kamran
Published: July 2011

Background

There is a paucity of population based data about the coexistent proportions of risk factors for stroke in South Asians.

Methods

In this cross sectional survey performed in an urban slum, individuals 35 years of age or older were invited for participation through a simple random sample drawn from baseline census data. For each participant a systematic history and examination was performed to confirm the following risk factors: diabetes, hypertension, obesity, tobacco use, coronary artery disease, family history of coronary artery disease and/or stroke. Cerebrovascular events (stroke and TIA) were verified by a vascular neurologist. We report the association of risk factor groups and the presence of contemporaneous cerebrovascular event.

Results

Five hundred and forty-five individuals (49.4% females) participated in the study. One hundred and nineteen (21.8%) individuals had a cerebrovascular event (stroke and / or TIA). Obesity was found to be the predominant risk factor, occurring in 310 individuals (56.9%), followed by total hypertension (284; 52.1 %) and tobacco use respectively (213; 39 %). Cerebrovascular event increased in percentage with quantitative increase in risk factors. Cerebrovascular event prevalence was 14.3% with one risk factor, 22% with two, 27% with three, 33% with four, and 86% with five risk factors respectively. The combination of 4 risk factors (hypertension, diabetes, obesity and cigarette smoking) conferred the highest odds of having cerebrovascular event at 4.9 ( P 0.03).

Conclusion

South Asians in an urban slum often have multiple modifiable risk factors for cerebrovascular event, increasing numbers of risk factors increase the risk of stroke and TIA.
Creep Behavior of Pressurized Tank Composed of Functionally Graded Materials
Authors: Chen JianJun , Yoon KeeBong , Tu Shan-Tung
Published: July 2011

The creep behavior of a pressurized tank, which is assumed to be made of functionally graded materials, is studied in this paper. The elastic response under the internal and external pressures is first obtained when Young’s modulus obeys a power function along with the wall thickness. If the creep exponent remains constant and the creep coefficient varies with the radial coordinate, a closed-form solution can be derived for the time-dependent behavior of the spherical tank. The effects of material gradients on the creep stress and strain are investigated in detail. The results show that the stress level under the steady creep state is determined by the distribution of the creep properties. However, the magnitude of the creep strain is influenced by the elastic modulus distribution, as well as the creep property distribution inside the functionally graded materials. Compared with the finite element analysis results, the optimum time step value is also investigated. Some fundamental knowledge of the materials distribution is achieved to reduce the maximum creep stress/strain and to uniformize the stress level inside the functionally graded materials tank.
Decrease in the Autotrophic-to-Heterotrophic Biomass Ratio of Picoplankton in Oligotrophic Marine Waters Due to Bottle Enclosure
Authors: Calvo-Díaz Alejandra , Díaz-Pérez Laura , Suárez Luis Ángel , Morán Xosé Anxelu G. , Teira Eva , Marañón Emilio
Published: July 2011

We investigated the effects of bottle enclosure on autotrophic and heterotrophic picoplankton in North and South subtropical Atlantic oligotrophic waters, where the biomass and metabolism of the microbial community are dominated by the picoplankton size class. We measured changes in both autotrophic (
Prochlorococcus
,
Synechococcus
, and picoeukaryotes) and heterotrophic picoplankton biomass during three time series experiments and in 16 endpoint experiments over 24 h in light and dark treatments. Our results showed a divergent effect of bottle incubation on the autotrophic and heterotrophic components of the picoplankton community. The biomass of picophytoplankton showed, on average, a >50% decrease, mostly affecting the picoeukaryotes and, to a lesser extent,
Prochlorococcus
. In contrast, the biomass of heterotrophic bacteria remained constant or increased during the incubations. We also sampled 10 stations during a Lagrangian study in the North Atlantic subtropical gyre, which enabled us to compare the observed changes in the auto- to heterotrophic picoplankton biomass ratio (AB:HB ratio) inside the incubation bottles with those taking place
in situ
. While the AB:HB ratio
in situ
remained fairly constant during the Lagrangian study, it decreased significantly during the 24 h of incubation experiments. Thus, the rapid biomass changes observed in the incubations are artifacts resulting from bottle confinement and do not take place in natural conditions. Our results suggest that short (<1 day) bottle incubations in oligotrophic waters may lead to biased estimates of the microbial metabolic balance by underestimating primary production and/or overestimating bacterial respiration.