bluuebunny/crossref_metadata_2025_split huggingface dataset:
The relic Criollo cacao in Belize – genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank, Trinidad
Authors: Motilal Lambert A. , Zhang Dapeng , Umaharan Pathmanathan , Mischke Sue , Mooleedhar Vishnarayan , Meinhardt Lyndel W. 
Published: January 2010

Cacao (Theobroma cacaoL.) was domesticated in Mesoamerica and is native to the South American rainforest. Belizean Criollo is a group of relic landraces that are thought to be similar to those used by the Olmecs and Mayans during early domestication. Knowledge of genetic diversity is essential for efficient conservation and use of these relic landraces. Using 30 microsatellite markers, we characterized genetic diversity in 77 Belize Criollo accessions collected from the Maya Mountains in Belize, and assessed their relationship with 62 cacao accessions including 25 Trinitario accessions. Genetic diversity and heterozygosity were low in Belizean Criollo germplasm. Eleven distinctive genotypes were identified among the Belizean germplasm. Results of ordination and cluster analysis supported their putative ancestral contribution to the Trinitario cacao. However, results of Bayesian assignment and parentage analysis both suggested that the contribution of Criollo cacao to the Imperial College Selections Trinitario is small. Our preferred hypothesis for the genesis of Trinitario cacao is that a limited population of Criollo × Forastero hybrids emanated from the introduced Forastero population of Trinidad. The present study provides new insights into the origin of the Trinitario cacao, which will be useful in theex situandin situconservation of cacao landraces from Mesoamerica.
Cultural Diplomacy as Cultural Globalization: The University of Michigan Jazz Band in Latin America
Authors: FOSLER-LUSSIER DANIELLE 
Published: January 2010

AbstractFrom January to May 1965 the University of Michigan Jazz Band traveled extensively in Latin America for the State Department's Cultural Presentations Program. This tour serves as a case study through which we can see the far-reaching effects of cultural diplomacy. The State Department initially envisioned its cultural and informational programs as one-way communication that brought ideas from the United States to new places; yet the tours changed not only audiences, but also the musicians themselves and even the communities to which the musicians returned. Both archival and oral history evidence indicate that the Michigan jazz band's tour succeeded in building vital imagined connections across international borders. The nature of these connections demonstrates that the cold war practice of pushing culture across borders for political purposes furthered cultural globalization—even though the latter process is often regarded by scholars as a phenomenon that began only after the end of the cold war. The jazz band's tour highlights the essential role of music and musicians in fostering new transnational sensibilities in the politicized context of the cold war.
Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico
Authors: Spirov Alexander , Holloway David 
Published: January 2010

AbstractA new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The effectiveness of the approach is demonstrated on a series of benchmark tests.
Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability
Authors: Guzmán Dora L. , Randall Arlo , Baldi Pierre , Guan Zhibin 
Published: January 2010

Resolving molecular determinants of mechanical stability of proteins is crucial in the rational design of advanced biomaterials for use in biomedical and nanotechnological applications. Here we present an interdisciplinary study combining bioinformatics screening, steered molecular dynamics simulations, protein engineering, and single-molecule force spectroscopy that explores the mechanical properties of a macro domain protein with mixed
α
+
β
topology. The unique architecture is defined by a single seven-stranded
β
-sheet in the core of the protein flanked by five
α
-helices. Unlike mechanically stable proteins studied thus far, the macro domain provides the distinct advantage of having the key load-bearing hydrogen bonds (H bonds) buried in the hydrophobic core protected from water attacks. This feature allows direct measurement of the force required to break apart the load-bearing H bonds under locally hydrophobic conditions. Steered molecular dynamics simulations predicted extremely high mechanical stability of the macro domain by using constant velocity and constant force methods. Single-molecule force spectroscopy experiments confirm the exceptional mechanical strength of the macro domain, measuring a rupture force as high as 570 pN. Furthermore, through selective deletion of shielding peptide segments, we examined the same key H bonds under hydrophilic environments in which the
β
-strands are exposed to solvent and verify that the high mechanical stability of the macro domain results from excellent shielding of the load-bearing H bonds from competing water. Our study reveals that shielding water accessibility to the load-bearing strands is a critical molecular determinant for enhancing the mechanical stability of proteins.
BamView: viewing mapped read alignment data in the context of the reference sequence
Authors: Carver Tim , Böhme Ulrike , Otto Thomas D. , Parkhill Julian , Berriman Matthew 
Published: January 2010

Abstract
Summary: BamView is an interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence. It supports the BAM (Binary Alignment/Map) format. It can be used in a number of contexts including SNP calling and structural annotation. BamView has also been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features.
Availability: BamView and Artemis are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at: http://bamview.sourceforge.net/
Contact: artemis@sanger.ac.uk
Ions first: Na+uptake shifts from the skin to the gills before O2uptake in developing rainbow trout,Oncorhynchus mykiss
Authors: Fu Clarice , Wilson Jonathan M. , Rombough Peter J. , Brauner Colin J. 
Published: January 2010

This is the first direct physiological evidence in support of the ionoregulatory hypothesis, challenging the long-held assumption that teleost gills develop initially for gas exchange. Resting unidirectional sodium (Na+) uptake and oxygen (O2) uptake across the skin and gills were measured simultaneously in larval rainbow trout,Oncorhynchus mykiss, during development. In soft and hard water, Na+uptake shifted to the gills by 15 and 16 days post-hatch (dph) while O2uptake took 50–80% longer and shifted by 23 and 28 dph, respectively. This suggests that gills are required for ionoregulation prior to gas exchange in developing rainbow trout. The age of transition for Na+uptake, gill Na+, K+-ATPase (NKA) α-subunit protein expression and gill NKA enzyme activity were not significantly different between soft and hard water-reared groups, which suggests a lack of plasticity in gill ionoregulatory development.In rainbow trout, the gills assume a dominant role in ionoregulation before gas exchange, suggesting that ionoregulation may be the initial driving force for gill development. Further investigation is required to determine whether this pattern is consistent with other teleosts and more basal fishes during early development to gain insight into the role of ionoregulation in vertebrate gill evolution.
Maturation Stress Generation in Poplar Tension Wood Studied by Synchrotron Radiation Microdiffraction
Authors: Clair Bruno , Alméras Tancrède , Pilate Gilles , Jullien Delphine , Sugiyama Junji , Riekel Christian 
Published: January 2010

Abstract
Tension wood is widespread in the organs of woody plants. During its formation, it generates a large tensile mechanical stress, called maturation stress. Maturation stress performs essential biomechanical functions such as optimizing the mechanical resistance of the stem, performing adaptive movements, and ensuring long-term stability of growing plants. Although various hypotheses have recently been proposed, the mechanism generating maturation stress is not yet fully understood. In order to discriminate between these hypotheses, we investigated structural changes in cellulose microfibrils along sequences of xylem cell differentiation in tension and normal wood of poplar (Populusdeltoides × Populustrichocarpa ‘I45-51’). Synchrotron radiation microdiffraction was used to measure the evolution of the angle and lattice spacing of crystalline cellulose associated with the deposition of successive cell wall layers. Profiles of normal and tension wood were very similar in early development stages corresponding to the formation of the S1 and the outer part of the S2 layer. The microfibril angle in the S2 layer was found to be lower in its inner part than in its outer part, especially in tension wood. In tension wood only, this decrease occurred together with an increase in cellulose lattice spacing, and this happened before the G-layer was visible. The relative increase in lattice spacing was found close to the usual value of maturation strains, strongly suggesting that microfibrils of this layer are put into tension and contribute to the generation of maturation stress.
The Arabidopsis PHYTOCHROME KINASE SUBSTRATE2 Protein Is a Phototropin Signaling Element That Regulates Leaf Flattening and Leaf Positioning
Authors: de Carbonnel Matthieu , Davis Phillip , Roelfsema M. Rob G. , Inoue Shin-ichiro , Schepens Isabelle , Lariguet Patricia , Geisler Markus , Shimazaki Ken-ichiro , Hangarter Roger , Fankhauser Christian 
Published: January 2010

AbstractIn Arabidopsis (Arabidopsis thaliana), the blue light photoreceptor phototropins (phot1 and phot2) fine-tune the photosynthetic status of the plant by controlling several important adaptive processes in response to environmental light variations. These processes include stem and petiole phototropism (leaf positioning), leaf flattening, stomatal opening, and chloroplast movements. The PHYTOCHROME KINASE SUBSTRATE (PKS) protein family comprises four members in Arabidopsis (PKS1–PKS4). PKS1 is a novel phot1 signaling element during phototropism, as it interacts with phot1 and the important signaling element NONPHOTOTROPIC HYPOCOTYL3 (NPH3) and is required for normal phot1-mediated phototropism. In this study, we have analyzed more globally the role of three PKS members (PKS1, PKS2, and PKS4). Systematic analysis of mutants reveals that PKS2 (and to a lesser extent PKS1) act in the same subset of phototropin-controlled responses as NPH3, namely leaf flattening and positioning. PKS1, PKS2, and NPH3 coimmunoprecipitate with both phot1-green fluorescent protein and phot2-green fluorescent protein in leaf extracts. Genetic experiments position PKS2 within phot1 and phot2 pathways controlling leaf positioning and leaf flattening, respectively. NPH3 can act in both phot1 and phot2 pathways, and synergistic interactions observed between pks2 and nph3 mutants suggest complementary roles of PKS2 and NPH3 during phototropin signaling. Finally, several observations further suggest that PKS2 may regulate leaf flattening and positioning by controlling auxin homeostasis. Together with previous findings, our results indicate that the PKS proteins represent an important family of phototropin signaling proteins.
Combined Bimolecular Fluorescence Complementation and Förster Resonance Energy Transfer Reveals Ternary SNARE Complex Formation in Living Plant Cells
Authors: Kwaaitaal Mark , Keinath Nana F. , Pajonk Simone , Biskup Christoph , Panstruga Ralph 
Published: January 2010

Abstract
Various fluorophore-based microscopic methods, comprising Förster resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC), are suitable to study pairwise interactions of proteins in living cells. The analysis of interactions between more than two protein partners using these methods, however, remains difficult. In this study, we report the successful application of combined BiFC-FRET-fluorescence lifetime imaging microscopy and BiFC-FRET-acceptor photobleaching measurements to visualize the formation of ternary soluble N-ethylmaleimide-sensitive factor attachment receptor complexes in leaf epidermal cells. This method expands the repertoire of techniques to study protein-protein interactions in living plant cells by a procedure capable of visualizing simultaneously interactions between three fluorophore-tagged polypeptide partners.
The Arabidopsis Prohibitin Gene PHB3 Functions in Nitric Oxide–Mediated Responses and in Hydrogen Peroxide–Induced Nitric Oxide Accumulation
Authors: Wang Yong , Ries Amber , Wu Kati , Yang Albert , Crawford Nigel M. 
Published: January 2010

Abstract
To discover genes involved in nitric oxide (NO) metabolism, a genetic screen was employed to identify mutants defective in NO accumulation after treatment with the physiological inducer hydrogen peroxide. In wild-type Arabidopsis thaliana plants, NO levels increase eightfold in roots after H2O2 treatment for 30 min. A mutant defective in H2O2-induced NO accumulation was identified, and the corresponding mutation was mapped to the prohibitin gene PHB3, converting the highly conserved Gly-37 to an Asp in the protein's SPFH domain. This point mutant and a T-DNA insertion mutant were examined for other NO-related phenotypes. Both mutants were defective in abscisic acid–induced NO accumulation and stomatal closure and in auxin-induced lateral root formation. Both mutants were less sensitive to salt stress, showing no increase in NO accumulation and less inhibition of primary root growth in response to NaCl treatment. In addition, light-induced NO accumulation was dramatically reduced in cotyledons. We found no evidence for impaired H2O2 metabolism or signaling in the mutants as H2O2 levels and H2O2-induced gene expression were unaffected by the mutations. These findings identify a component of the NO homeostasis system in plants and expand the function of prohibitin genes to include regulation of NO accumulation and NO-mediated responses.
Role of the bedrock topography in the Quaternary filling of a giant estuarine basin: the Lower St. Lawrence Estuary, Eastern Canada
Authors: Duchesne Mathieu J. , Pinet Nicolas , Bédard Karine , St‐Onge Guillaume , Lajeunesse Patrick , Campbell D. Calvin , Bolduc Andrée 
Published: January 2010

ABSTRACTThe geometry of estuarine and/or incised‐valley basins and their protected character compared with open sea basins are favourable for the preservation of sedimentary successions. The Lower St. Lawrence Estuary Basin (LSLEB, eastern Canada) is characterized by a thick (>400 m in certain areas) Quaternary succession. High‐ and very high‐resolution seismic reflection data, multibeam bathymetry coverage completed by core and chronostratigraphic data as well as a 3‐D seismic stratigraphic model are used to document the geometrical relationships between the bedrock and the Quaternary units of the LSLEB. The bedrock geometry of LSLEB is characterized by two large troughs that are interpreted as resulting mainly from repeated (?) periods of glacial overdeepening of a pre‐Quaternary drainage system. However, other mechanisms with complex feedback effects such as differential glacio‐isostatic uplift, erosion, sedimentary supply, and subsidence may have contributed to the formation of bedrock troughs. The two large bedrock troughs are mostly filled by ∼200 m thick Wisconsinan (Marine Isotopic Stages 2–4) and possibly older sediments. Overlying units recorded the retreat of the Laurentian Ice Sheet during the Late Wisconsinan (Marine Isotopic Stage 2) and estuarine conditions during the Holocene. The strong correlation existing between the bedrock topography and the thickness of the Quaternary succession is indicative of the effectiveness of the LSLEB as a sediment trap.
Health status of caregivers of children with cerebral palsy
Authors: Byrne M. B. , Hurley D. A. , Daly L. , Cunningham C. G. 
Published: January 2010

AbstractBackground and Aims  While a ‘Family‐Centered’ approach to care is accepted as best practice in the context of childhood disability, it may lead to increased demands on family members by requiring them to be active participants in their child's care. This may impact upon the physical and mental health of the caregiver and therefore needs to be investigated. This study aimed to assess the health status of caregivers of children with cerebral palsy (CP) in Ireland and to identify vulnerable subgroups.Methods  A cross‐sectional postal survey was conducted using a questionnaire incorporating the SF‐36v2.0. The sample consisted of male and female caregivers of children with CP, representing all levels of ability. Two questionnaires were sent to each child's home; a total of 312 questionnaires were sent to the homes of 156 children.Results  Completed questionnaires were returned by 161 caregivers (100 women, 61 men) of 101 children, giving a response rate of 65%. Caregivers of children with CP were found to have poorer health than the Irish general population, for whom normative data exist. Female caregivers had poorer health than male caregivers in both the physical (P < 0.05) and mental health (P < 0.001) domains of the SF‐36. Caregivers spending more time caring had significantly poorer mental health than those spending less time caring (P < 0.05). There was no difference in the health of caregivers of ‘more independent’ versus ‘more dependent’ children, apart from the latter group reporting higher levels of bodily pain (P < 0.05).Conclusion  This study provides evidence of the inferior health status of caregivers of children with CP in Ireland, particularly that of women.
Forty‐four juvenile thieves revisited: from bowlby to reactive attachment disorder
Authors: Follan M. , Minnis H. 
Published: January 2010

AbstractBackground  John Bowlby's work on attachment has had a major influence on practice in child and adolescent psychiatry and developed from observations Bowlby made in his clinical work. In a published case series of work with juvenile offenders, he provided a case description of the differing sets of problems that drove his interest. Clinical features described in a subgroup of these offenders, the ‘affectionless psychopaths’, might be recognized now as reactive attachment disorder (RAD).Methods  We scrutinized Bowlby's case series ‘44 Juvenile Thieves’ and compared the aetiology and clinical features of a subgroup of these children with the other 74 cases described by Bowlby. We selected one typical case as an exemplar and provide an edited version here. We then present one composite case from a recent study of RAD and provide a comparison with typically developing children.Results  Of the Bowlby cases, 86% had experienced early prolonged separation from their primary caregivers and had experienced multiple care placements. In total, 10% of clinical comparisons had been similarly separated. In our recent sample, 66% of children experienced separation from primary caregivers compared with none of the comparison group. A similar proportion of our sample of children with RAD had been removed from home as a result of neglect or had experienced other forms of maltreatment.Conclusions  Bowlby beleived that a main aetiological factor in the development of difficulties was the experience of separation. We suspect that a main aetiological factor in both his and our cases is the experience of maltreatment. We suggest that RAD arises from a complex interplay of genetic and environmental triggers.
Gene expression microarray analysis of heat stress in the soil invertebrate Folsomia candida
Authors: Nota B. , Van Straalen N. M. , Ylstra B. , Roelofs D. 
Published: January 2010

AbstractSudden temperature changes in soil can induce stress in soil‐dwelling invertebrates. Hyperthermic conditions have an impact on gene expression as one of the first steps. We use a transcriptomics approach using microarrays to identify expression changes in response to heat in the springtail Folsomia candida. An elevation of temperature (Δ 10 °C) altered the expression of 142 genes (116 up‐, 26 down‐regulated). Many up‐regulated genes encoded heat shock proteins, enzymes involved in ATP synthesis, oxidative stress responsive enzymes and anion‐transporting ATPases. Down‐regulated were glycoside hydrolases, involved in catalysis of disaccharides. The small number of altered transcripts suggest a mild response to heat in this soil invertebrate, but further research is needed to confirm this. This study presents candidate genes for future functional studies concerning thermal stress in soil‐dwelling invertebrates.
Caveat reporting in ultrasound interpretation of surgical pathology: a comparison of sonographer versus radiologist
Authors: Garcea Giuseppe , Mahmoud Asif , Ong Seok Ling , Rees Yvonee , Berry David P. , Dennison Ashely R. 
Published: January 2010

AbstractBackground  Radiology reports provide specialist interpretation of images and relate these findings to the patient's symptoms and signs. This study compared ultrasound (USS) reports generated by radiologists and sonographers to determine if any significant or clinically relevant differences existed.Methods  A retrospective analysis of 624 consecutive USS reports was carried out. The reports were assessed for the presence of a ‘disclaimer’ or ‘caveat’ pertaining to the quality of the images and were analysed with respect to the clarity of their wording and ability to answer the clinical request.Results  The majority of sonographer USS reports contained a disclaimer regarding the quality of the USS images (57.1%) compared with a smaller proportion of radiologist scans (9.9%) (P < 0.001). Overall, radiologists performed significantly better in providing a clear negative or positive diagnosis to the clinical question on the request form, when compared with sonographers (88.5% vs. 65.4%, P < 0.001).Conclusion  ‘Disclaimer’ comments and ‘hedging’ must be avoided in radiology reporting. While feedback as to the accuracy of the radiology images is important, overuse of such terms undermines the validity of the radiology report.
Microstructure evolution in hot worked steel after heating to semi‐solid state
Authors: SOŁEK K. , MITURA Z. , KARBOWNICZEK M. , DUTKIEWICZ J. , FARYNA M. , ROGAL Ł. 
Published: January 2010

SummaryMetal alloys can be formed successfully in a partially liquid state if they display a particular globular microstructure. The article presents an analysis of a study carried out of the development, by means of the strain‐induced melt‐activated method, of such a microstructure for an X210CrW12 steel. Hot rolled samples, with subsequent cooling, were heated to the temperature range at which the liquid and solid phases coexist in the material. The spheroidal shapes for solid particles, required for semi‐solid processing, were found. The investigations were carried out using scanning electron microscopy in combination with energy dispersive spectroscopy.