bluuebunny/crossref_metadata_2025_split huggingface dataset:
A community-based health promotion intervention using brief negotiation techniques and a pledge on dietary intake, physical activity levels and weight outcomes: lessons learnt from an exploratory trial
Authors: Hillier Frances C , Batterham Alan M , Nixon Catherine A , Crayton Alisha M , Pedley Claire L , Summerbell Carolyn D 
Published: November 2011

AbstractObjectiveTo assess the effectiveness of a brief face-to-face health promotion intervention which included a ‘pledge’ using brief negotiation techniques, compared with standard advice-giving techniques, delivered in a community setting.DesignA parallel group pre–post design using randomised matched groups. Lifestyle helpers delivered the intervention (one consultation per participant). Diet, physical activity and anthropometric measurements were collected at baseline, 6 months and 12 months. Qualitative data were also collected.SettingMiddlesbrough (UK).SubjectsAdults living in low socio-economic areas.ResultsRecruitment and engagement of lifestyle helpers was difficult, and initial expectations that local health authority staff working in the community and community champions would act as lifestyle helpers were not realised. As a consequence, recruitment of participants was lower than anticipated. One hundred and twenty-eight adults were recruited and the retention rate was 48 % at 12 months. Barriers to participation included poor health and competing commitments. No significant differences in change in diet or physical activity behaviours, or BMI, between the intervention and control groups were observed. The control group had a significantly greater decrease in waist circumference at 12 months compared with the intervention group.ConclusionsThis exploratory trial provides important insights in terms of recruiting lifestyle helpers for community-based health promotion interventions, specifically (i) the priorities and limitations in terms of time (regardless of their general enthusiasm) for staff employed by the local health authority, and (ii) the willingness of potential community champions to serve their local community in areas where community identity and ‘spirit’ are seen as lacking.
Energy balance-related behavioural patterns in 5-year-old children and the longitudinal association with weight status development in early childhood
Authors: Gubbels Jessica S , Kremers Stef PJ , Goldbohm R Alexandra , Stafleu Annette , Thijs Carel 
Published: November 2011

AbstractObjectiveThe current study examined clustering of dietary intake and activity behaviours (i.e. physical activity (PA) and sedentary behaviour) in 5-year-old children, as well as the longitudinal association with BMI and overweight development.DesignPrincipal component analysis (PCA) was used to identify behavioural patterns. Backward regression analyses were used to examine the association of behavioural patterns with parent and child background characteristics, as well as the association of the patterns with BMI Z-score and overweight development up to ages 7 and 8 years.SettingThe Netherlands.SubjectsData originated from the KOALA Birth Cohort Study (n 2074 at age 5 years).ResultsFour patterns emerged: a ‘sedentary-snacking’ pattern (including television viewing and snack consumption), a ‘healthy intake’ pattern (including healthy items such as fruit, vegetables and fish), a ‘sandwich’ pattern (including bread and sandwich fillings) and a ‘sporty-traditional meal’ pattern (including sports, meat and potatoes). The patterns were related to child gender, general appetite and various parental characteristics. The sedentary-snacking pattern was positively associated with longitudinal BMI development.ConclusionsCross-behavioural energy balance-related behavioural patterns exist at age 5 years. Different activity types (e.g. sports, television viewing) clustered differently with the behavioural patterns, indicating the need to incorporate these different types instead of one general PA measure in energy balance-related pattern analyses. The clustering and potential synergy between activity behaviours and dietary intake, as well as the associations with weight status development, stress the importance of an integrated approach to PA and healthy nutrition promotion in preventing childhood overweight.
Real Feelings: Music as Path to Philosophy in2001: A Space Odyssey
Authors: CODE DAVID J. 
Published: November 2011

AbstractA recurring trope in the literature on Kubrick's2001: A Space Odysseyholds that the HAL 9000 computer has more feelings than any of the human characters. But the film itself presents the question of HAL's ‘real feelings’ as something no one can truthfully answer. One way to begin negotiating this contradiction is by attending anew to the way the Jupiter Mission episode, in which HAL appears, is cut to the Adagio from Khachaturian's balletGayane, the excerpt that remains the least discussed in this renowned compilation score. Suggesting that the elusive affect of this music, as it is deployed through several interrelated scenes, brings focus to questions of emotion and embodiment that fundamentally inform the conflict between human and machine, I go on to offer a new hearing of HAL's unforgettable death song ‘Daisy Bell’ in this light, and to re-evaluate some of the director's own words about his film. Ultimately, I carry the same questions forward to inform a contribution to the ongoing debate about the Nietzschean philosophical inflections occasionally thought to enter the film with its much more famous cue from Richard Strauss'sAlso sprach Zarathustra.
SiGe heterojunction bipolar phototransistor for optics–microwaves interfacing
Authors: Lecoy Pierre , Delacressonniere Bruno , Pasquet Daniel 
Published: December 2011

A new SiGe heterojunction bipolar phototransistor (HPT) based on a commercially available process was designed, realized, and experimentally characterized. Its internal characteristics, mainly the collector-to-base capacitance, vary significantly with the received light power, making it suitable as an active element of a light-controlled photo-oscillator. It can also be a key component of optical network-on-chip (ONoC). Its responsivity was improved and its transition frequency remains in the range of 30 GHz.
Seismic velocities and anisotropy of core samples from the Chinese Continental Scientific Drilling borehole in the Sulu UHP terrane, eastern China
Authors: Sun Shengsi , Ji Shaocheng , Wang Qian , Xu Zhiqin , Salisbury Matthew , Long Changxing 
Published: December 2011

A detailed study of seismic properties (P and S wave velocities, hysteresis, anisotropy and shear wave splitting) has been carried out on a unique suite of deep borehole core samples from the Chinese Continental Scientific Drilling (CCSD) project, which penetrated 5158 m into the Sulu ultrahigh‐pressure (UHP) metamorphic terrane (China). Seismic velocities of the deep core samples are more and less sensitive to pressure in the low pressure (<200–300 MPa) nonlinear and high pressure (>200–300 MPa) linear regimes, respectively, than samples from the surface. The comparison suggests that the high pressure data from the core samples are much more reliable for extrapolation to deeper crust than the data from surface analogs that have been subjected to long histories of weathering and alteration along intergranular and transgranular cracks. The significant increases in the pressure sensitivity of seismic velocities for the core samples in the nonlinear regime indicate that drilling‐induced and stress‐relief microcracks with small aspect ratios are fresh and clean without secondary mineral in‐fillings, and are thus easy to close completely under the applied hydrostatic pressure conditions of the laboratory. The data also elucidate that the velocity‐pressure data can successfully provide important hints about the preferred orientation of microcracks that causes P wave velocity anisotropy and shear wave splitting in cracked rocks, and that the effect of compression on the Vp/Vsratios is negligible for crack‐free compacted rocks. The seismic velocities of equivalent isotropic (fabric‐free) and crack‐free crystalline aggregates calculated from room pressure single crystal elastic constants using the Voigt average are in good agreement with the laboratory data at ∼200 MPa. Comparison of the seismic reflection image from the vicinity of the borehole with the normal‐incidence reflection coefficient profile computed from the laboratory‐measured velocities and densities infers that the seismic reflections originate from mafic (eclogite and retrograde eclogite) or ultramafic units within dominantly felsic rocks.
Photoelectron spectroscopy of HC4N−
Authors: Vogelhuber Kristen M. , Wren Scott W. , Shaffer Christopher J. , McMahon Robert J. , McCoy Anne B. , Lineberger W. Carl 
Published: December 2011

We report the 364-nm photoelectron spectrum of HC4N−. We observe electron photodetachment from the bent $\tilde X$X̃2A″ state of HC4N− to both the near-linear $\tilde X$X̃3A″ and the bent ã 1A′ states of neutral HC4N. We observe an extended, unresolved vibrational progression corresponding to $\tilde X$X̃3A″ ← $\tilde X$X̃2A″ photodetachment, and we measure the electron affinity (EA) of the $\tilde X$X̃3A″ state of HC4N to be 2.05(8) eV. Photodetachment to the bent ã 1A′ state results in a single intense origin peak at a binding energy of 2.809(4) eV, from which we determine the singlet-triplet splitting (ΔEST) of HC4N: 0.76(8) eV. For comparison and to aid in the interpretation of the HC4N− spectrum, we also report the 364-nm photoelectron spectra of HCCN− and DCCN−. Improved signal-to-noise over the previous HCCN− and DCCN− photoelectron spectra allows for a more precise determination of the EAs and ΔESTs of HCCN and DCCN. The EAs of HCCN and DCCN are measured to be 2.001(15) eV and 1.998(15) eV, respectively; ΔEST(HCCN) is 0.510(15) eV and ΔEST(DCCN) is 0.508(15) eV. These results are discussed in the context of other organic carbene chains.
Hand attractiveness—its determinants and associations with facial attractiveness
Authors: Kościński Krzysztof 
Published: November 2011

Abstract
Although attractiveness of the human hand seems to be of some importance in the social and mating context, it has attracted little scientific interest thus far. Here, we investigated physical determinants of hand attractiveness and its associations with facial appeal. Photographs of faces and the dorsal and ventral side of hands of young women and men were measured and assessed for attractiveness and several other features. Typicality and femininity of shape, perceived fattiness and skin healthiness, the appearance of nail vicinity, and grooming influenced hand attractiveness in men and women. Hand and facial attractiveness were correlated with each other for each sex. This relationship was mediated by shape typicality and fattiness in men and by grooming and, possibly, fattiness in women. Results are discussed from an evolutionary psychology perspective with special reference to biological signaling and mate selection.
Inferring sequence regions under functional divergence in duplicate genes
Authors: Huang Yi-Fei , Golding G. Brian 
Published: November 2011

Abstract
Motivation: A number of statistical phylogenetic methods have been proposed to identify type-I functional divergence in duplicate genes by detecting heterogeneous substitution rates in phylogenetic trees. A common disadvantage of the existing methods is that autocorrelation of substitution rates along sequences is not modeled. This reduces the power of existing methods to identify regions under functional divergence.
Results: We design a phylogenetic hidden Markov model to identify protein regions relevant to type-I functional divergence. A C++ program, HMMDiverge, has been developed to estimate model parameters and to identify regions under type-I functional divergence. Simulations demonstrate that HMMDiverge can successfully identify protein regions under type-I functional divergence unless the discrepancy of substitution rates between subfamilies is very limited or the regions under functional divergence are very short. Applying HMMDiverge to G protein α subunits in animals, we identify a candidate region longer than 20 amino acids, which overlaps with the α-4 helix and the α4-β6 loop in the GTPase domain with divergent rates of substitutions. These sites are different from those reported by an existing program, DIVERGE2. Interestingly, previous biochemical studies suggest the α-4 helix and the α4-β6 loop are important to the specificity of the receptor–G protein interaction. Therefore, the candidate region reported by HMMDiverge highlights that the type-I functional divergence in G protein α subunits may be relevant to the change of receptor–G protein specificity after gene duplication. From these results, we conclude that HMMDiverge is a useful tool to identify regions under type-I functional divergence after gene duplication.
Availability: C++ source codes of HMMDiverge and simulation programs used in this study, as well as example datasets, are available at http://info.mcmaster.ca/yifei/software/HMMDiverge.html
Contact: golding@mcmaster.ca
Supplementary Information: Supplementary data are available at Bioinformatics online.
A novel specific edge effect correction method for RNA interference screenings
Authors: Carralot Jean-Philippe , Ogier Arnaud , Boese Annette , Genovesio Auguste , Brodin Priscille , Sommer Peter , Dorval Thierry 
Published: November 2011

Abstract
Motivation: High-throughput screening (HTS) is an important method in drug discovery in which the activities of a large number of candidate chemicals or genetic materials are rapidly evaluated. Data are usually obtained by measurements on samples in microwell plates and are often subjected to artefacts that can bias the result selection. We report here a novel edge effect correction algorithm suitable for RNA interference (RNAi) screening, because its normalization does not rely on the entire dataset and takes into account the specificities of such a screening process. The proposed method is able to estimate the edge effects for each assay plate individually using the data from a single control column based on diffusion model, and thus targeting a specific but recurrent well-known HTS artefact. This method was first developed and validated using control plates and was then applied to the correction of experimental data generated during a genome-wide siRNA screen aimed at studying HIV–host interactions. The proposed algorithm was able to correct the edge effect biasing the control data and thus improve assay quality and, consequently, the hit-selection step.
Contact: dorvalt@ip-korea.org; jean-philippe.carralot@roche.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Modelling time course gene expression data with finite mixtures of linear additive models
Authors: Grün Bettina , Scharl Theresa , Leisch Friedrich 
Published: November 2011

Abstract
Summary: A model class of finite mixtures of linear additive models is presented. The component-specific parameters in the regression models are estimated using regularized likelihood methods. The advantages of the regularization are that (i) the pre-specified maximum degrees of freedom for the splines is less crucial than for unregularized estimation and that (ii) for each component individually a suitable degree of freedom is selected in an automatic way. The performance is evaluated in a simulation study with artificial data as well as on a yeast cell cycle dataset of gene expression levels over time.
Availability: The latest release version of the R package flexmix is available from CRAN (http://cran.r-project.org/).
Contact: Bettina.Gruen@jku.at
An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
Authors: Wimalaratne Sarala M. , Grenon Pierre , Hoehndorf Robert , Gkoutos Georgios V. , de Bono Bernard 
Published: December 2011

Abstract
Summary: The article presents an infrastructure for supporting the semantic interoperability of biomedical resources based on the management (storing and inference-based querying) of their ontology-based annotations. This infrastructure consists of: (i) a repository to store and query ontology-based annotations; (ii) a knowledge base server with an inference engine to support the storage of and reasoning over ontologies used in the annotation of resources; (iii) a set of applications and services allowing interaction with the integrated repository and knowledge base. The infrastructure is being prototyped and developed and evaluated by the RICORDO project in support of the knowledge management of biomedical resources, including physiology and pharmacology models and associated clinical data.
Availability and implementation: The RICORDO toolkit and its source code are freely available from http://ricordo.eu/relevant-resources.
Contact: sarala@ebi.ac.uk
GbPDF1 Is Involved in Cotton Fiber Initiation via the Core cis-Element HDZIP2ATATHB2
Authors: Deng Fenglin , Tu Lili , Tan Jiafu , Li Yang , Nie Yichun , Zhang Xianlong 
Published: November 2011

AbstractCotton (Gossypium spp.) fiber cells are seed trichomes derived from the epidermal layer of the cotton seed coat. The molecular components responsible for regulating fiber cell differentiation have not been fully elucidated. A cotton PROTODERMAL FACTOR1 gene (GbPDF1) was found to be expressed preferentially during fiber initiation and early elongation, with highest accumulation in fiber cells 5 d post anthesis. PDF1 silencing caused retardation of fiber initiation and produced shorter fibers and lower lint percentage compared with the wild type, indicating that the gene is required for cotton fiber development. Further analysis showed that a higher accumulation of hydrogen peroxide occurred in the RNA interference transgenic cotton lines. Meanwhile, the expression of several genes related to ethylene and pectin synthesis or sugar transport during cotton fiber growth was found to be significantly reduced in the PDF1-suppressed cotton. Three proteins interacting with GbPDF1 in yeast and in planta might involve cellular signaling or metabolism. GbPDF1 promoter::GUS constructs in transgenic cotton were predominantly expressed in the epidermis of ovules and developing fibers. Progressive deletions of the GbPDF1 promoter showed that a 236-bp promoter fragment was sufficient for basal GbPDF1 transcription in cotton. Mutation of putative regulatory sequences showed that HDZIP2ATATHB2, an element within the fragment, was essential for PGbPDF1-1 expression. The binding activity between this cis-element and nuclear extracts from fiber-bearing cotton ovules at 5 d post anthesis was specific. We conclude that GbPDF1 plays a critical role together with interaction partners in hydrogen peroxide homeostasis and steady biosynthesis of ethylene and pectin during fiber development via the core cis-element HDZIP2ATATHB2.
Evidence for a SAL1-PAP Chloroplast Retrograde Pathway That Functions in Drought and High Light Signaling in Arabidopsis
Authors: Estavillo Gonzalo M. , Crisp Peter A. , Pornsiriwong Wannarat , Wirtz Markus , Collinge Derek , Carrie Chris , Giraud Estelle , Whelan James , David Pascale , Javot Hélène , Brearley Charles , Hell Rüdiger , Marin Elena , Pogson Barry J. 
Published: December 2011

Abstract
Compartmentation of the eukaryotic cell requires a complex set of subcellular messages, including multiple retrograde signals from the chloroplast and mitochondria to the nucleus, to regulate gene expression. Here, we propose that one such signal is a phosphonucleotide (3′-phosphoadenosine 5′-phosphate [PAP]), which accumulates in Arabidopsis thaliana in response to drought and high light (HL) stress and that the enzyme SAL1 regulates its levels by dephosphorylating PAP to AMP. SAL1 accumulates in chloroplasts and mitochondria but not in the cytosol. sal1 mutants accumulate 20-fold more PAP without a marked change in inositol phosphate levels, demonstrating that PAP is a primary in vivo substrate. Significantly, transgenic targeting of SAL1 to either the nucleus or chloroplast of sal1 mutants lowers the total PAP levels and expression of the HL-inducible ASCORBATE PEROXIDASE2 gene. This indicates that PAP must be able to move between cellular compartments. The mode of action for PAP could be inhibition of 5′ to 3′ exoribonucleases (XRNs), as SAL1 and the nuclear XRNs modulate the expression of a similar subset of HL and drought-inducible genes, sal1 mutants accumulate XRN substrates, and PAP can inhibit yeast (Saccharomyces cerevisiae) XRNs. We propose a SAL1-PAP retrograde pathway that can alter nuclear gene expression during HL and drought stress.
Cloning, purification and crystallographic analysis of a hypothetical protein, BPSL1549, from Burkholderia pseudomallei
Authors: Cruz-Migoni Abimael , Ruzheinikov Sergey N. , Sedelnikova Svetlana E. , Obeng Barbara , Chieng Sylvia , Mohamed Rahmah , Nathan Sheila , Baker Patrick J. , Rice David W. 
Published: December 2011

Burkholderia pseudomallei BPSL1549, a putative protein of unknown function, has been overexpressed in Escherichia coli, purified and subsequently crystallized by the hanging-drop vapour-diffusion method using PEG as a precipitant to give crystals with overall dimensions of 0.15 × 0.15 × 0.1 mm. Native data were collected to 1.47 Å resolution at the European Synchrotron Radiation Facility (ESRF). The crystals belonged to space group P212121, with unit-cell parameters a = 37.1, b = 45.4, c = 111.9 Å and with a single polypeptide chain in the asymmetric unit.
Crystallization and preliminary X-ray diffraction analysis of mouse prostaglandin F2αsynthase, AKR1B3
Authors: Takashima Yasuhide , Hatanaka Seika , Mizohata Eiichi , Nagata Nanae , Fukunishi Yoshifumi , Matsumura Hiroyoshi , Urade Yoshihiro , Inoue Tsuyoshi 
Published: December 2011

Aldo-keto reductase 1B3 (AKR1B3) catalyzes the NADPH-dependent reduction of prostaglandin H2(PGH2), which is a common intermediate of various prostanoids, to form PGF2α. AKR1B3 also reduces PGH2to PGD2in the absence of NADPH. AKR1B3 produced inEscherichia coliwas crystallized in complex with NADPH by the sitting-drop vapour-diffusion method. The crystal was tetragonal, belonging to space groupP41212 orP43212, with unit-cell parametersa = b = 107.62,c= 120.76 Å. X-ray diffraction data were collected to 2.4 Å resolution at 100 K using a synchrotron-radiation source.