bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural domain–domain interactions: Assessment and comparison with protein–protein interaction data to improve the interactome
Authors: Prieto C. , De Las Rivas J. 
Published: August 2009

AbstractAssessment and improvement of the reliability of protein–protein interaction (ppi) data is critical for the progress of the currently active research on interactomes. Some interesting questions in this respect are: How three‐dimensional (3D) protein structural data is present in known ppi data?, and How this kind of information can be used to validate and improve the interactomes? To address this problem, analysis and unification of six structural domain–domain interaction (sddi) datasets is presented; followed by a comparative study of these sddi data in three ppi reference sets produced at different levels of confidence. The results show that protein structural and interactomic data are partially complementary and that a larger proportion of structural information is observed in more confident interactomes. We also present, focused on the human interactome, an analysis of the domains that are more frequently present in: (i) an interactome based on validation by at least two experimental methods versus (ii) another interactome based on validation by 3D structural interaction data. These results allow to distinguish between domain pairs associated to protein interactions supported by 3D structures and domain pairs that at present are not supported by structural information. The domain pairs exclusive of interactions without associated 3D data reveal interacting conserved modules that are probably flexible, disordered, and difficult to crystallize; and which are often found in proteins involved in signaling pathways and DNA processing. Proteins 2010. © 2009 Wiley‐Liss, Inc.
A laboratory evaluation to determine the compatibility of microbiological control agents with the pollinator Bombus terrestris
Authors: Mommaerts Veerle , Sterk Guido , Hoffmann Lucien , Smagghe Guy 
Published: August 2009

AbstractBACKGROUND: This study was undertaken to identify any potential adverse side effects of the use of seven microbiological control agents (MCAs) on the bumblebee, Bombus terrestris L., in the context of combined use in integrated pest management (IPM). AQ10® (Ampelomyces quisqualis), Binab‐T‐vector® (Hypocrea parapilulifera + T. atroviride; 1/1), Prestop‐Mix® (Gliocladium catenulatum J1446), Serenade® (Bacillus subtilis QST713), Trianum‐P® (Trichoderma harzianum T22), Botanigard® (Beauveria bassiana GHA) and Granupom® (Cydia pomonella granulovirus), comprising five biofungicides and two bioinsecticides, were investigated. Bumblebee workers were exposed under laboratory conditions to each MCA at its maximum field recommended concentration (MFRC) via three different routes of exposure: dermal contact and orally via either treated sugar water or pollen.RESULTS: The tested MCAs were found to be safe for workers of B. terrestris, with the exception of Botanigard® and Serenade®. Exposure to Botanigard® via contact at its MFRC caused 92% mortality after 11 weeks, while the 1/10 MFRC killed 46% of exposed workers. For Serenade®, topical contact and oral delivery via sugar water resulted in 88 and 100% worker mortality respectively. With lower concentrations (1/2, 1/5 and 1/10 MFRC) the toxicity decreased, but the effect depended on the route of exposure. In addition to lethal effects, nests were also evaluated for sublethal effects after treatment with the seven MCAs at their respective MFRCs over 11 weeks. In these bioassays, only Botanigard® and Serenade® gave rise to a significant (P < 0.05) decrease in drone production. Sublethal effects on foraging behaviour were also evaluated, and only Botanigard at its MFRC delivered via treated sugar water induced negative effects.CONCLUSION: The results demonstrated that most of the MCAs tested can be considered safe for use in combination with B. terrestris, based on the International Organisation for Biological Control of Noxious Animals and Plants (IOBC) classification. However, some can be harmful, such as the biofungicide Serenade® and the bioinsecticide Botanigard®. Therefore, it is recommended that all should be tested before use in combination with pollinators. In this context, it is also advisable that these MCAs should be evaluated in more realistic field situations for the assessment of potentially deleterious effects on foraging behaviour. Copyright © 2009 Society of Chemical Industry
Using a selectivity index to evaluate logarithmic spraying in grass seed crops
Authors: Tind Tina , Mathiesen Tenna J , Jensen Jens E , Ritz Christian , Streibig Jens C 
Published: August 2009

AbstractBACKGROUND: Grass seed crops are minor crops that cannot support the development of selective herbicides for grass weed control in grass seed crops. An option is to screen for selective herbicides with the use of logarithmic spraying technology. The aim of this paper is to assess selectivity of various herbicides in grass seed crops by using dose–response curves.RESULTS: Six grass species were subjected to logarithmic spraying with 11 herbicides and with Poa pratensis L. as a weed. The ratio between the doses that caused 10% of damage to the crop and 90% of damage to the weed was used as a selectivity index. Compounds with selectivity indices above 2 can be safely used in a crop. The two ACCase herbicides clodinafop‐propargyl and fenoxaprop‐P‐ethyl and a mixture of the two ALS herbicides mesosulfuron and iodosulfuron could be used selectively to control P. pratensis in Festuca rubra L., although the selectivity indices in no instances were greater than the desired 2.0.CONCLUSION: The logarithmic sprayer can be a rapid screening tool for identifying compounds with favourable selectivity indices. Good experimental design is needed to alleviate rates being systematically distributed and confounded with growth rate and soil fertility gradients. Copyright © 2009 Society of Chemical Industry
Epitaxial graphene: the material for graphene electronics
Authors: Sprinkle M. , Soukiassian P. , de Heer W. A. , Berger C. , Conrad E. H. 
Published: August 2009

AbstractThe search for an ideal graphene sheet has been a quest driving graphene research. While most research has focused on exfoliated graphene, intrinsic substrate interactions and mechanical disorder have precluded the observation of a number of graphene's expected physical properties in this material. The only graphene candidate that has demonstrated all the essential properties of an ideal sheet is multilayer graphene grown on the SiC(000$ \bar 1 $) surface. Its unique stacking allows nearly all the sheets in the stack to behave like isolated graphene, while the weak graphene‐graphene interaction prevents any significant doping or distortion in the band near the Fermi level. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Derivation of Functional Retinal Pigmented Epithelium from Induced Pluripotent Stem Cells
Authors: Buchholz David E. , Hikita Sherry T. , Rowland Teisha J. , Friedrich Amy M. , Hinman Cassidy R. , Johnson Lincoln V. , Clegg Dennis O. 
Published: August 2009

Abstract
Human induced pluripotent stem cells (iPSCs) have great promise for cellular therapy, but it is unclear if they have the same potential as human embryonic stem cells (hESCs) to differentiate into specialized cell types. Ocular cells such as the retinal pigmented epithelium (RPE) are of particular interest because they could be used to treat degenerative eye diseases, including age-related macular degeneration and retinitis pigmentosa. We show here that iPSCs generated using Oct4, Sox2, Nanog, and Lin28 can spontaneously differentiate into RPE cells, which can then be isolated and cultured to form highly differentiated RPE monolayers. RPE derived from iPSCs (iPS-RPE) were analyzed with respect to gene expression, protein expression, and rod outer segment phagocytosis, and compared with cultured fetal human RPE (fRPE) and RPE derived from hESCs (hESC-RPE). iPS-RPE expression of marker mRNAs was quantitatively similar to that of fRPE and hESC-RPE, and marker proteins were appropriately expressed and localized in polarized monolayers. Levels of rod outer segment phagocytosis by iPS-RPE, fRPE, and hESC-RPE were likewise similar and dependent on integrin αvβ5. This work shows that iPSCs can differentiate into functional RPE that are quantitatively similar to fRPE and hESC-RPE and further supports the finding that iPSCs are similar to hESCs in their differentiation potential.
Depot-Specific Differences in Adipogenic Progenitor Abundance and Proliferative Response to High-Fat Diet
Authors: Joe Aaron W.B. , Yi Lin , Even Yasmine , Vogl A. Wayne , Rossi Fabio M.V. 
Published: August 2009

Abstract
White adipose tissue (fat) is the primary organ for energy storage and its regulation has serious implications on human health. Excess fat tissue causes significant morbidity, and adipose tissue dysfunction caused by excessive adipocyte hypertrophy has been proposed to play a significant role in the pathogenesis of metabolic disease. Studies in both humans and animal models show that metabolic dysfunction is more closely associated with visceral than subcutaneous fat accumulation. Here, we show that in mice fed a high-fat diet, visceral fat (VAT) grows mostly by hypertrophy and subcutaneous fat (SAT) by hyperplasia, providing a rationale for the different effects of specific adipose depots on metabolic health. To address whether depot expansion is controlled at the level of stem/progenitor cells, we developed a strategy to prospectively identify adipogenic progenitors (APs) from both depots. Clonogenic assays and in vivo bromodeoxyuridine (BrdU) studies show that APs are eightfold more abundant in SAT than VAT, and that AP proliferation is significantly increased in SAT but not VAT in response to high-fat diet. Our results suggest that depot-specific differences in AP abundance and proliferation underlie whether a fat depot expands by hypertrophy or hyperplasia, and thus may have important implications on the development of metabolic disease. In addition, we provide the first evidence that dietary inputs can modulate the proliferation of adipogenic progenitors in adults.
Stem-Like Ovarian Cancer Cells Can Serve as Tumor Vascular Progenitors
Authors: Alvero Ayesha B. , Fu Han-Hsuan , Holmberg Jennie , Visintin Irene , Mor Liora , Marquina Carlos Cano , Oidtman Jessica , Silasi Dan-Arin , Mor Gil 
Published: August 2009

Abstract
Neovascularization is required for solid tumor maintenance, progression, and metastasis. The most described contribution of cancer cells in tumor neovascularization is the secretion of factors, which attract various cell types to establish a microenvironment that promotes blood vessel formation. The cancer stem cell hypothesis suggests that tumors are composed of cells that may share the differentiation capacity of normal stem cells. Similar to normal stem cells, cancer stem cells (CSCs) have the capacity to acquire different phenotypes. Thus, it is possible that CSCs have a bigger role in the process of tumor neovascularization. In this study, we show the capacity of a specific population of ovarian cancer cells with stem-like properties to give rise to xenograft tumors containing blood vessels, which are lined by human CD34+ cells. In addition, when cultured in high-density Matrigel, these cells mimic the behavior of normal endothelial cells and can form vessel-like structures in 24 hours. Microscopic analysis showed extensive branching and maturation of vessel-like structures in 7 days. Western blot and flow cytometry analysis showed that this process is accompanied by the acquisition of classic endothelial markers, CD34 and VE-cadherin. More importantly, we show that this process is vascular endothelial growth factor–independent, but IKKβ-dependent. Our findings suggest that anti-angiogenic therapies should take into consideration the inherent capacity of these cells to serve as vascular progenitors.
Confronting assumptions, biases, and stereotypes in preservice teachers' conceptualizations of science teaching through the use of book club
Authors: Mensah Felicia Moore 
Published: August 2009

AbstractThis study focuses on the structure and theoretical foundations of the book club for promoting multicultural understandings in science teacher education. The book club was defined as an informal, peer‐directed group discussion that met regularly to discuss an ethnographic, multicultural text regarding issues pertinent to science teaching and learning in urban classrooms. Twenty‐three preservice teachers (PSTs) enrolled in a 16‐week elementary science methods course at a large urban university participated in the study. From the qualitative analyses of PSTs' written reflections and researcher journal notes, five themes which emphasizeIndividual,Collaborative, andCollective learningare presented. These findings highlight how the book club structure and theoretical foundation fostered critical, reflective inquiry and served as a method for effecting ideological change which is needed in order to embrace issues of diversity in urban science education. Implications for science teacher education concerning the relevancy of pedagogical strategies, the use of multiple theoretical perspectives, and the book club as a strategy in teacher education and urban education are discussed. © 2009 Wiley Periodicals, Inc. J Res Sci Teach 46: 1041–1066, 2009
Learning from and responding to students' questions: The authoritative and dialogic tension
Authors: Aguiar Orlando G. , Mortimer Eduardo F. , Scott Phil 
Published: August 2009

AbstractIn this study we present an analysis of classroom interactions initiated by students' wonderment questions. Our interest in such events arises from their potential to stimulate active intellectual engagement in classrooms, which can impact upon the subsequent development of the classroom discourse. In investigating this issue we shall address the following research question: How do student questions impact upon the teaching explanatory structure and modify the form of the ongoing classroom discourse, in selected science lessons? From data collected in a Brazilian secondary school we have selected three classroom episodes, with large differences in both the context in which the student's question emerges and in the communicative approach developed in response to it. The analysis, based on the framework proposed by Mortimer and Scott [Mortimer and Scott (2003). Meaning making in secondary science classrooms. Maidenhead: Open University Press], shows that questions made by students are important in providing feedback from students to the teacher, enabling adjustments to the teaching explanatory structure. These adjustments sometimes occur smoothly, at other times with major changes to the features of the classroom discourse, and elsewhere with misunderstanding and disagreement. The data also suggest the need to consider students' intentions and their active participation in the negotiation of both the content and structure of classroom discourse. © 2009 Wiley Periodicals, Inc. J Res Sci Teach 47:174–193, 2010
Developing a hypothetical multi‐dimensional learning progression for the nature of matter
Authors: Stevens Shawn Y. , Delgado César , Krajcik Joseph S. 
Published: August 2009

AbstractWe describe efforts toward the development of a hypothetical learning progression (HLP) for the growth of grade 7–14 students' models of the structure, behavior and properties of matter, as it relates to nanoscale science and engineering (NSE). This multi‐dimensional HLP, based on empirical research and standards documents, describes how students need to incorporate and connect ideas within and across their models of atomic structure, the electrical forces that govern interactions at the nano‐, molecular, and atomic scales, and information in the Periodic Table to explain a broad range of phenomena. We developed a progression from empirical data that characterizes how students currently develop their knowledge as part of the development and refinement of the HLP. We find that most students are currently at low levels in the progression, and do not perceive the connections across strands in the progression that are important for conceptual understanding. We suggest potential instructional strategies that may help students build organized and integrated knowledge structures to consolidate their understanding, ready them for new ideas in science, and help them construct understanding of emerging disciplines such as NSE, as well as traditional science disciplines. © 2009 Wiley Periodicals, Inc. J Res Sci Teach 47:687–715, 2010
Brief report: The KIDSCREEN follow‐up study on Health‐related Quality of Life (HRQoL) in Spanish children and adolescents. Pilot test and representativeness☆
Authors: Palacio‐Vieira J.A. , Villalonga‐Olives E. , Alonso J. , Valderas J.M. , Herdman M. , Espallargues M. , Berra S. , Rajmil L. 
Published: August 2009

ABSTRACTThe Spanish KIDSCREEN follow‐up study reassessed the Spanish baseline sample (n = 840) of the European KIDSCREEN study 3 years later (2006). The aims of this paper were to describe the KIDSCREEN follow‐up study and the pilot test, and to analyze participation rates and representativeness. Instruments included the KIDSCREEN‐52 HRQoL measure and a set of scales including the possible explanatory variables. Focus groups and individual interviews were carried out in a pilot test. Participants were compared with non‐participants at baseline, and also with Eurostat census data. Twenty‐two out of 24 subjects were interviewed in the pilot test. Fifteen items needed to be modified after the pilot test. Participation rate reached 54% (n = 454). Participants (mean age = 12.71 years old) were on average 6 months younger than non‐participants (p = 0.03), and from more educated families. KIDSCREEN follow‐up instrumentation seems adequate for collecting factors with potential influence on HRQoL. Follow‐up respondents' representativeness seems to be acceptable.
Efficacy of wheat-based biscuits fortified with microcapsules containing ferrous sulfate and potassium iodate or a new hydrogen-reduced elemental iron: a randomised, double-blind, controlled trial in Kuwaiti women
Authors: Biebinger Ralf , Zimmermann Michael B. , Al-Hooti Suad N. , Al-Hamed Nawal , Al-Salem Ebtehal , Zafar Tasleem , Kabir Yearul , Al-Obaid I'nam , Petry Nicolai , Hurrell Richard F. 
Published: August 2009

Adverse sensory changes prevent the addition of highly bioavailable ferrous sulfate (FeSO4) to most wheat flours. Poorly absorbable reduced Fe powders are commonly used. Encapsulation of FeSO4can overcome these sensory changes, but the particle size of commercial compounds is too large to be used by flour mills. The first objective of the study was to measure the efficacy in wheat flour of two newly developed Fe compounds, an H-reduced Fe powder (NutraFine™ RS; North America Höganäs High Alloys LLC, Johnstown, PA, USA) and small particle-sized (40 μm) encapsulated FeSO4. As a second objective, the microcapsules were evaluated as a vehicle for iodine fortification. A randomised, double-blind controlled intervention trial was conducted in Kuwaiti women (n279; aged 18–35 years) with low body Fe stores (serum ferritin (SF) < 25 μg/l) randomly assigned to one of three groups (20 mg Fe as NutraFine™ RS, 10 mg Fe as encapsulated FeSO4and 150 μg iodine, or no fortification Fe) who consumed wheat-based biscuits 5 d per week. At baseline and 22 weeks, Hb, SF, transferrin receptor, urinary iodine and body Fe stores were measured. Relative to control, mean SF in the encapsulated FeSO4group increased by 88 % (P < 0·001) and body Fe stores increased from − 0·96 to 2·24 mg/kg body weight (P < 0·001), while NutraFine™ RS did not significantly increase SF or body Fe stores. The median urinary iodine concentration increased from 140 to 213 μg/l (P < 0·01). NutraFine™ RS added at double the amount of Fe as FeSO4was not efficacious in improving Fe status. The newly developed microcapsules were highly efficacious in improving both Fe stores and iodine status.
Length–depth relations of Enchelyopus cimbrius fourbeard rockling (Gadiformes: Phycidae) from the southern Gulf of St Lawrence and Cabot Strait in relation to abiotic factors
Authors: Aubry Eliane , Methven D.A. , Hurlbut Tom 
Published: August 2009

Research vessel survey data collected by Fisheries and Oceans Canada in the southern Gulf of St Lawrence (1971–2002) and Cabot Strait (1994–1997) were analysed to determine if Enchelyopus cimbrius the fourbeard rockling, distributed itself with larger individuals occurring in deeper water. A positive size–depth relationship was first observed for the European plaice, Pleuronectes platessa in the North Sea and has been reported for other fish. Positive relationships were found between the total length of E. cimbrius and depths where it occurred in this study. However, the biological relationship was not significant since the linear regression slopes were very weak, explaining less than approximately five per cent of the variance observed. Data were analysed further to determine the water depth, temperature and salinity ranges where the fourbeard rockling was most abundant. Enchelyopus cimbrius occurred throughout the depth-ranges sampled with highest catches occurring at 25–50 m (southern Gulf of St Lawrence) and deeper than 200 m (southern Gulf of St Lawrence and Cabot Strait). Low catches at intermediate depths (~50–100 m) in the southern Gulf of St Lawrence may have been due to the lack of suitable mud substrate and colder bottom temperatures in the Magdalen Shallows, a large central region of the southern Gulf. Enchelyopus cimbrius was mostly caught at relatively narrow temperature and salinity ranges of 4–6°C and 34–34.9 ppt in both regions, and only occurred in areas with a mud substratum, predominantly in the eastern Northumberland Strait, Baie des Chaleurs and in the deeper water of the Cape Breton Trough, Laurentian Channel and Cabot Strait. Enchelyopus cimbrius was caught throughout the day and night, contradicting a previous study that characterized it as being nocturnal in shallow coastal waters off Newfoundland.
Reproductive biology of the banded guitarfish, Zapteryx exasperata, from the Gulf of California, México
Authors: Blanco-Parra María-Del-Pilar , Márquez-Farías J. Fernando , Galván-Magaña Felipe 
Published: August 2009

The banded guitarfish, Zapteryx exasperata, is a common species in the artisanal elasmobranch fisheries in the Gulf of California. Fishery-derived specimens were examined to determine critical aspects of the reproductive biology of this poorly known group of rays. Two functional testes and ovaries were found in males and females respectively. Median size at maturity (L50%) for males was 64 cm total length (TL) and for females 69 cm TL. Average length of gravid females was 78.8±3.8 cm TL. Histological analysis showed no evidence of sperm storage in the oviducal gland. Gestation was estimated to occur over a five to six month period (February–July) and was concurrent with vitellogenesis. Mean uterine fecundity was estimated as 7 (range 2–13, SD. = 3). The sex-ratio of embryos was 1:1. The reproductive cycle for Z. exasperata from the Gulf of California was estimated to last one year with parturition, ovulation and copulation occurring during the summer months. Differences found in the reproductive cycle of Z. exasperata between the Gulf of California and the west coast of Baja California could have implications in the future management plans for this fishery in the Gulf of California.