bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aphids and associated natural enemies on Ile Amsterdam and Ile Saint-Paul, Southern Indian Ocean
Authors: Hullé Maurice , Turpeau Evelyne , Hudaverdian Sylvie , Chaubet Bernard , Outreman Yannick , Lebouvier Marc 
Published: April 2010

AbstractIle Amsterdam (37°50′S, 77°30′E, 55 km2) and Ile Saint-Paul (38°43′S, 77°31′E, 7 km2) are very isolated volcanic islands which were originally colonized by a few invertebrate fauna and flora. Invasive species richness has then increased along with human activity. A three-year monitoring programme (1997, 2000, 2001) and a summer campaign (2007) allowed species diversity, host plants, abundance and phenology of introduced aphids and natural enemies to be described. Seven cosmopolitan aphid species have been found on Ile Amsterdam (Aulacorthum solani,A. circumflexum,Macrosiphum euphorbiae,Myzus ascalonicus,M. cymbalariae,M. ornatusandRhopalosiphum padi) and three on Ile Saint-Paul (A. solani,M. cymbalariaeandR. padi). On Ile Amsterdam, these aphids were found on 28 host plants (out of 57 sampled plants), mainly introduced species.Phylica arboreawas the only native plant much colonized by one aphid species,A. circumflexum. Aphids were mainly present on the base or in this vicinity. One Hymenopteran parasitoid,Aphidius matricariae, and two hyperparasites (Dendrocerus aphidumandPhaenoglyphis villosa), probably introduced along with their host, were collected. Aphid activity is very low during the autumn (March–May) and at a maximum in spring and summer. Their density and diversity decrease with distance from the research station. From these results, the possible impact of aphids on native plants is discussed.
Approaching the end of life and dying with dementia in care homes: the accounts of family carers
Authors: Hennings J , Froggatt K , Keady J 
Published: April 2010

SummaryResearch into end of life and dying with dementia in care homes from the family carer's perspective is limited. From the available evidence, it appears that family carers find themselves in an unfamiliar situation about which they lack knowledge and experience. Whilst dementia tends not to be acknowledged as a terminal illness by many family carers, they are expected to make end of life decisions on behalf of their relatives. Family carer decision-making is underpinned by values of quality of life, previously expressed wishes, comfort provision and dignity preservation. This is often approached when family carers are grieving for the anticipated loss of their relative and have their own personal needs that require to be addressed. Within a care home setting, a curative care–palliative care split is unhelpful in resolving these tensions and a model of comprehensive care appears a more appropriate approach. This requires ongoing communication between the person with dementia, family members and professionals from the early stages of the condition.
An estimate of phytate intake and molar ratio of phytate to zinc in the diet of the people in the United Kingdom
Authors: Amirabdollahian F , Ash R 
Published: April 2010

AbstractObjectiveTo estimate the phytate intake and molar ratio of phytate to zinc in the diet of the people in the United Kingdom.DesignTables of the phytate content of foods were developed from twenty-eight published and unpublished studies. They were then applied to the nutrient databank of the National Diet and Nutrition Survey (NDNS). The study is a retrospective analysis of data on daily consumption of foods and drinks from the NDNS of children, adolescents, adults and the elderly based on 4–7 d weighed intakes.SubjectsA total of 6786 British participants aged 1·5 years and above, who participated in the NDNS, 1992–2001.SettingEngland, Scotland and Wales.ResultsThe median daily intakes of phytate for children, adolescents, adults and the elderly population were 496, 615, 809 and 629 mg/d, respectively. Although there were differences in phytate intakes between men and women, and for children, adolescents and elderly populations, after adjusting for differences in energy intake, there was no significant variation. The median phytate-to-zinc molar ratios for children, adolescents, adults and the elderly population were 11·8, 10·4, 9·7 and 8·7, respectively. Overall, the main sources of phytate were cereal and cereal products (e.g. breakfast cereals and breads), vegetables, potatoes and savoury snacks (e.g. chips and crisps), hot drinks and miscellaneous foods (e.g. commercial toddler foods and drinks, chocolate and soups), fruits and nuts.ConclusionsThe present study estimated the dietary intake of phytate and the phytate-to-zinc molar ratio of the diet of the UK population, which can be used for estimating the average requirement of zinc. Further research should focus on the completion and validation of the tables of phytate content of UK foods, to assess (and if necessary improve) the accuracy and precision of these findings.
Effects of a school-based intervention on adherence of 7–9-year-olds to food-based dietary guidelines and intake of nutrients
Authors: Kristjansdottir Asa G , Johannsson Erlingur , Thorsdottir Inga 
Published: April 2010

AbstractObjectiveTo assess the effects of a school-based intervention on the diets of 7–9-year-olds.DesignDietary intake of children in second and fourth grades was assessed with 3d weighed dietary records in autumn 2006 and autumn 2008, before and after a school-based intervention that started in the middle of second grade, and compared with control schools with no intervention. The diet was evaluated by comparison with food-based dietary guidelines (FBDG) and reference values for nutrient intake. The intervention aimed at several determinants of intake: knowledge, awareness, preferences/taste, self-efficacy and parental influence. Nutrition education material was developed for the intervention and implemented in collaboration with teachers. The main focus of the intervention was on fruit and vegetable intake as the children’s intake was far from meeting the FBDG on fruit and vegetables at baseline.SettingElementary schools in Reykjavik, Iceland.SubjectsComplete dietary records were available for 106 children both at baseline and follow-up.ResultsTotal fruit and vegetable intake increased by 47 % in the intervention schools (mean: 61·3 (sd126·4) g/d) and decreased by 27 % in the control schools (mean: 46·5 (sd105·3) g/d;P< 0·001). The majority of the children in the intervention schools did still not meet the FBDG on fruits and vegetables at follow-up. Fibre intake increased significantly in the intervention schools, as well as that of potassium, magnesium, β-carotene and vitamin C (borderline).ConclusionsThe school-based intervention in 7–9-year-olds was effective in increasing fruit and vegetable intake, by 47 % increase from baseline, which was mirrored in nutrient intake.
Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores
Authors: Liggenstoffer Audra S , Youssef Noha H , Couger M B , Elshahed Mostafa S 
Published: April 2010

Abstract
The phylogenetic diversity and community structure of members of the gut anaerobic fungi (AF) (phylum Neocallimastigomycota) were investigated in 30 different herbivore species that belong to 10 different mammalian and reptilian families using the internal transcribed spacer region-1 (ITS-1) ribosomal RNA (rRNA) region as a phylogenetic marker. A total of 267 287 sequences representing all known anaerobic fungal genera were obtained in this study. Sequences affiliated with the genus Piromyces were the most abundant, being encountered in 28 different samples, and representing 36% of the sequences obtained. On the other hand, sequences affiliated with the genera Cyllamyces and Orpinomyces were the least abundant, being encountered in 2, and 8 samples, and representing 0.7%, and 1.1% of the total sequences obtained, respectively. Further, 38.3% of the sequences obtained did not cluster with previously identified genera and formed eight phylogenetically distinct novel anaerobic fungal lineages. Some of these novel lineages were widely distributed (for example NG1 and NG3), whereas others were animal specific, being encountered in only one or two animals (for example NG4, NG6, NG7, and NG8). The impact of various physiological and environmental factors on the diversity and community structure of AF was examined. The results suggest that animal host phylogeny exerts the most significant role on shaping anaerobic fungal diversity and community composition. These results greatly expand the documented global phylogenetic diversity of members of this poorly studied group of fungi that has an important function in initiating plant fiber degradation during fermentative digestion in ruminant and non-ruminant herbivores.
Hdsp, a horizontally transferred gene required for social behavior and halotolerance in salt-tolerant Myxococcus fulvus HW-1
Authors: Pan Hong-wei , Tan Zai-gao , Liu Hong , Li Zhi-feng , Zhang Cui-ying , Li Cheng-yun , Li Jie , Li Yue-zhong 
Published: April 2010

Abstract
Myxococcus fulvus HW-1, a salt-tolerant bacterial strain, which was isolated from a coastal environment, changes its behavior with different salinities. To study the relationship between behavioral shifts and the adaption to oceanic conditions, the HW-1 strain was randomly mutagenized using transposon insertion, producing a dispersed-growing mutant, designated YLH0401. The mutant did not develop fruiting bodies and myxospores, was deficient in S-motility, produced less extracellular matrix and was less salt tolerant. The YLH0401 strain was determined to be mutated by a single insertion in a large gene of unknown function (7011 bp in size), which is located in a horizontally transferred DNA fragment. The gene is expressed during the vegetative growth stage, as well as highly and stably expressed during the development stage. This horizontally transferred gene may allow Myxococcus to adapt to oceanic conditions.
Distinct large-scale turbulent-laminar states in transitional pipe flow
Authors: Moxey David , Barkley Dwight 
Published: April 2010

When fluid flows through a channel, pipe, or duct, there are two basic forms of motion: smooth laminar motion and complex turbulent motion. The discontinuous transition between these states is a fundamental problem that has been studied for more than 100 yr. What has received far less attention is the large-scale nature of the turbulent flows near transition once they are established. We have carried out extensive numerical computations in pipes of variable lengths up to 125 diameters to investigate the nature of transitional turbulence in pipe flow. We show the existence of three fundamentally different turbulent states separated by two distinct Reynolds numbers. Below Re 1 ≃ 2,300, turbulence takes the form of familiar equilibrium (or longtime transient) puffs that are spatially localized and keep their size independent of pipe length. At Re 1the flow makes a striking transition to a spatio-temporally intermittent flow that fills the pipe. Irregular alternation of turbulent and laminar regions is inherent and does not result from random disturbances. The fraction of turbulence increases with Re until Re 2 ≃ 2,600 where there is a continuous transition to a state of uniform turbulence along the pipe. We relate these observations to directed percolation and argue that Re 1marks the onset of infinite-lifetime turbulence.
Anomalous expansion of the copper-apical-oxygen distance in superconducting cuprate bilayers
Authors: Zhou Hua , Yacoby Yizhak , Butko Vladimir Y. , Logvenov Gennady , Božović Ivan , Pindak Ron 
Published: April 2010

We have introduced an improved x-ray phase-retrieval method with unprecedented speed of convergence and precision, and used it to determine with sub-Ångstrom resolution the complete atomic structure of epitaxial La

2-
x

Sr

x

CuO
4
ultrathin films. We focus on superconducting heterostructures built from constituent materials that are not superconducting in bulk samples. Single-phase metallic or superconducting films are also studied for comparison. The results show that this phase-retrieval diffraction method enables accurate measurement of structural modifications in near-surface layers, which may be critically important for elucidation of surface-sensitive experiments. Specifically we find that, while the copper-apical-oxygen distance remains approximately constant in single-phase films, it shows a dramatic increase from the metallic-insulating interface of the bilayer towards the surface by as much as 0.45 Å. The apical-oxygen displacement is known to have a profound effect on the superconducting transition temperature.
Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets
Authors: Park Inho , Lee Kwang H. , Lee Doheon 
Published: April 2010

Abstract
Motivation: Gene set analysis has become an important tool for the functional interpretation of high-throughput gene expression datasets. Moreover, pattern analyses based on inferred gene set activities of individual samples have shown the ability to identify more robust disease signatures than individual gene-based pattern analyses. Although a number of approaches have been proposed for gene set-based pattern analysis, the combinatorial influence of deregulated gene sets on disease phenotype classification has not been studied sufficiently.
Results: We propose a new approach for inferring combinatorial Boolean rules of gene sets for a better understanding of cancer transcriptome and cancer classification. To reduce the search space of the possible Boolean rules, we identify small groups of gene sets that synergistically contribute to the classification of samples into their corresponding phenotypic groups (such as normal and cancer). We then measure the significance of the candidate Boolean rules derived from each group of gene sets; the level of significance is based on the class entropy of the samples selected in accordance with the rules. By applying the present approach to publicly available prostate cancer datasets, we identified 72 significant Boolean rules. Finally, we discuss several identified Boolean rules, such as the rule of glutathione metabolism (down) and prostaglandin synthesis regulation (down), which are consistent with known prostate cancer biology.
Availability: Scripts written in Python and R are available at http://biosoft.kaist.ac.kr/∼ihpark/. The refined gene sets and the full list of the identified Boolean rules are provided in the Supplementary Material.
Contact: khlee@biosoft.kaist.ac.kr; dhlee@biosoft.kaist.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
Low Reticulocyte Hemoglobin Content Is Associated with a Higher Blood Transfusion Rate in Critically Ill Patients
Authors: Fernandez Rafael , Tubau Isabel , Masip Jordi , Muñoz Luz , Roig Inmaculada , Artigas Antonio 
Published: April 2010

Background
Intensive care unit (ICU) patients often need blood transfusion, but no reliable predictors of transfusion requirements are available at ICU admission. The authors hypothesized that ICU patients with functional iron deficiency may be at higher risk for developing anemia, requiring blood transfusion. Their objective was to determine whether low reticulocyte hemoglobin content (CHr) was associated with transfusion requirements in ICU patients.

Methods
This is a prospective cohort study in a general ICU. The authors studied 62 patients, after excluding those transfused on or before ICU admission. The authors recorded age, diagnosis, severity score, presence of sepsis, ICU complications, ICU treatments, and transfusion-free interval. Threshold for low CHr was 29 pg. The authors also recorded ICU and hospital outcome. The statistical analysis included Cox proportional hazard function for transfusion.

Results
Twenty-three patients (37%) presented with low CHr on ICU admission and tended to be sicker and more likely to have sepsis than those with normal CHr. They were also more prone to complications, particularly acute renal failure (39 vs. 13% P = 0.02) and ICU-acquired infection (30 vs. 10% P = 0.04). The overall transfusion rate was 22.6%, being higher in low-CHr patients than in normal-CHr patients (39.1 vs. 12.8%, P = 0.02). After adjusting for severity of illness, age, trauma, and hemoglobin level, low CHr remained significantly associated with transfusion, with a hazard ratio of 3.6 (95% CI, 1.2-10.7; P = 0.02). Median ICU stay was also longer in patients with low CHr (8 vs. 5 days, P = 0.01). Differences in mortality did not reach statistical significance.

Conclusion
Low CHr is common at ICU admission and is associated with higher transfusion requirements.
Structures of the PKC-ι kinase domain in its ATP-bound and apo forms reveal defined structures of residues 533–551 in the C-terminal tail and their roles in ATP binding
Authors: Takimura Tetsuo , Kamata Kenji , Fukasawa Kazuhiro , Ohsawa Hirokazu , Komatani Hideya , Yoshizumi Takashi , Takahashi Ikuko , Kotani Hidehito , Iwasawa Yoshikazu 
Published: April 2010

Protein kinase C (PKC) plays an essential role in a wide range of cellular functions. Although crystal structures of the PKC-θ, PKC-ι and PKC-βII kinase domains have previously been determined in complexes with small-molecule inhibitors, no structure of a PKC–substrate complex has been determined. In the previously determined PKC-ι complex, residues 533–551 in the C-terminal tail were disordered. In the present study, crystal structures of the PKC-ι kinase domain in its ATP-bound and apo forms were determined at 2.1 and 2.0 Å resolution, respectively. In the ATP complex, the electron density of all of the C-terminal tail residues was well defined. In the structure, the side chain of Phe543 protrudes into the ATP-binding pocket to make van der Waals interactions with the adenine moiety of ATP; this is also observed in other AGC kinase structures such as binary and ternary substrate complexes of PKA and AKT. In addition to this interaction, the newly defined residues around the turn motif make multiple hydrogen bonds to glycine-rich-loop residues. These interactions reduce the flexibility of the glycine-rich loop, which is organized for ATP binding, and the resulting structure promotes an ATP conformation that is suitable for the subsequent phosphoryl transfer. In the case of the apo form, the structure and interaction mode of the C-terminal tail of PKC-ι are essentially identical to those of the ATP complex. These results indicate that the protein structure is pre-organized before substrate binding to PKC-ι, which is different from the case of the prototypical AGC-branch kinase PKA.
Structure ofD-tyrosyl-tRNATyrdeacylase using home-source Cu Kα and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme states
Authors: Yogavel Manickam , Khan Sameena , Bhatt Tarun Kumar , Sharma Amit 
Published: April 2010

D-Tyrosyl-tRNATyrdeacylase (DTD) is an editing enzyme that removes D-amino acids from mischarged tRNAs. The crystal structure ofPlasmodium falciparumDTD (PfDTD) was determined using the iodide-SAD phasing method. Iodide-derivatized PfDTD crystals were obtained using the quick cryo-soaking procedure in which native crystals were soaked for a short period of 10–30 s in cryoprotectant solution containing 0.2–1 MNaI. Iodide-SAD data sets were collected to 3.3 and 2.74 Å resolution from PfDTD crystals that belonged to two different space groups,P43andP1, using an in-house X-ray copper-anode source. This is the first report to detail structure solution using low iodide anomalous signal, modest resolution and redundancy and average solvent content for SAD phasing of 984 and 1312 amino acids in the triclinicP1 and tetragonalP43space groups, respectively. A total of 85% and 56% of the residues were automatically built into the iodide-phased electron-density maps usingPHENIX AutoBuild. The structure of HEPES-bound PfDTD was subsequently determined by molecular replacement and refined to 2.83 Å resolution. The crystals obtained from various batches of crystallization trials of PfDTD exhibited polymorphism in terms of belonging to different crystal forms and space groups. Even within a given crystal system the unit-cell parameters showed high non-isomorphism. These packing variations were exploited in order to conduct a systematic study of conformational changes in PfDTD. It is shown that the disposition of a ten-residue insertion loop affects packing within the PfDTD crystals and seems to determine the non-isomorphism in unit-cell parameters. By tracking the changes in PfDTD unit cells, it was possible to map conformational differences within PfDTD that may be of significance for enzyme activity.
Application of protein engineering to enhance crystallizability and improve crystal properties
Authors: Derewenda Zygmunt S. 
Published: April 2010

Until recently, protein crystallization has mostly been regarded as a stochastic event over which the investigator has little or no control. With the dramatic technological advances in synchrotron-radiation sources and detectors and the equally impressive progress in crystallographic software, including automated model building and validation, crystallization has increasingly become the rate-limiting step in X-ray diffraction studies of macromolecules. However, with the advent of recombinant methods it has also become possible to engineer target proteins and their complexes for higher propensity to form crystals with desirable X-ray diffraction qualities. As most proteins that are under investigation today are obtained by heterologous overexpression, these techniques hold the promise of becoming routine tools with the potential to transform classical crystallization screening into a more rational high-success-rate approach. This article presents an overview of protein-engineering methods designed to enhance crystallizability and discusses a number of examples of their successful application.
Characterization of four rice mutants with alterations in the defence response pathway
Authors: CAMPBELL M. A. , RONALD P. C. 
Published: April 2010

SUMMARYA fast‐neutron mutagenized population of rice seedlings was screened with Magnaporthe grisea, the causal agent of rice blast disease, to identify mutants with alterations in the defence response. Three mutant lines, ebr1, ebr2 and ebr3 (enhanced blast resistance) were identified that display enhanced resistance to M. grisea. ebr1 and ebr3 also confer enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo). ebr3 develops a lesion mimic (LM) phenotype upon inoculation with M. grisea, and the phenotype is also induced by a shift in environmental conditions. The fourth mutant line, ncr1 (necrosis in rice), has an LM phenotype under all conditions tested and lacks enhanced resistance to either M. grisea or Xoo. Complementation testing using the mutant lines ebr3 and ncr1 indicates that the ebr3 and ncr1 loci are nonallelic and recessive. ebr1 and ebr2 display no alterations in expression of the rice pathogenesis‐related (PR) genes PBZ1 and PR1, compared to wild‐type CO39. ebr3 has an elevated expression of PBZ1 and PR1 only in tissue displaying the LM phenotype. ncr1 strongly expresses PBZ1 in tissue displaying the LM phenotype, whereas PR1 expression in this tissue is similar to wild‐type CO39.