bluuebunny/crossref_metadata_2025_split huggingface dataset:
The dynamic modeling, redundant-force optimization, and dynamic performance analyses of a parallel kinematic machine with actuation redundancy
Authors: Jiang Yao , Li Tiemin , Wang Liping 
Published: February 2014

SUMMARYThis paper discusses a planar 2-DOF (degrees of freedom) parallel kinematic machine with actuation redundancy. Its inverse dynamic model is constructed by utilizing the Newton–Euler method based on the kinematic analysis. However, the dynamic model cannot be solved directly because the number of equations is less than the number of unknowns, which is due to the redundant force. In order to solve this problem, the relationship between the deformations of the links and the position errors of the moving platform are further explored. Then a novel method, which aims at minimizing the position errors of the machine, is proposed to optimize the redundant force. It also enables to solve the dynamic model. Finally, the dynamic performance analyses of this machine and its non-redundant counterpart are provided by numerical examples. Besides, another optimization method proposed for minimizing the constraint forces is also applied for comparison. The results show the effectiveness of the novel methods in improving the position precision of the machine.
Collective levels of stigma and national suicide rates in 25 European countries
Authors: Schomerus G. , Evans-Lacko S. , Rüsch N. , Mojtabai R. , Angermeyer M. C. , Thornicroft G. 
Published: February 2014

Aims.There is substantial diversity in national suicide rates, which has mainly been related to socio-economic factors, as well as cultural factors. Stigma is a cultural phenomenon, determining the level of social acceptance or rejection of persons with mental illness in a society. In this study, we explore whether national suicide rates are related to the degree of mental illness stigma in that country.Methods.We combine the data on country-level social acceptance (Eurobarometer) with the data on suicide rates and socio-economic indicators (Eurostat) for 25 European countries.Results.In a linear regression model controlling for socio-economic indicators, the social acceptance of someone with a significant mental health problem in 2010 was negatively correlated with age standardised national suicide rates in the same year (β −0.46, p = 0.014). This association also held true when combining national suicide rates with death rates due to events of undetermined intent.Conclusions.Stigma towards persons with mental health problems may contribute to differences in suicide rates in a country. We hypothesise possible mechanisms explaining this link, including stigma as a stressor and social isolation as a consequence of stigma.
The effect of ecological and temporal factors on the composition of Bartonella infection in rodents and their fleas
Authors: Gutiérrez Ricardo , Morick Danny , Cohen Carmit , Hawlena Hadas , Harrus Shimon 
Published: February 2014

Abstract
The composition of Bartonella infection was explored in wild Gerbillus andersoni rodents and their Synosternus cleopatrae fleas. Rodent blood samples and fleas were collected in two periods (two different seasons; 4 months apart) from juveniles and adult hosts, and their bartonellae lineages were identified by a 454-pyrosequencing analysis targeting a specific Bartonella citrate synthase gene (gltA) fragment. The rate of Bartonella spp. co-infection was estimated and the assemblage and distribution of bartonellae lineages across the samples with respect to ecological and phylogenetic distance similarities were analyzed. Moreover, environmental factors that could explain potential differences between samples were investigated. Out of the 91 bartonellae-positive samples, 89% were found to be co-infected with more than two phylogenetically distant Bartonella genotypes and additional closely related (but distinguishable) variants. These bartonellae lineages were distributed in a non-random manner, and a negative interaction between lineages was discovered. Interestingly, the overall composition of those infections greatly varied among samples. This variability was partially explained by factors, such as type of sample (blood versus fleas), flea sex and period of collection. This investigation sheds light on the patterns of Bartonella infection and the organization of Bartonella lineages in fleas and rodents in nature.
An antagonistic interaction between PlexinB2 and Rnd3 controls RhoA activity and cortical neuron migration
Authors: Azzarelli Roberta , Pacary Emilie , Garg Ritu , Garcez Patricia , van den Berg Debbie , Riou Philippe , Ridley Anne J. , Friedel Roland H. , Parsons Maddy , Guillemot François 
Published: February 2014

AbstractA transcriptional programme initiated by the proneural factors Neurog2 and Ascl1 controls successive steps of neurogenesis in the embryonic cerebral cortex. Previous work has shown that proneural factors also confer a migratory behaviour to cortical neurons by inducing the expression of the small GTP-binding proteins such as Rnd2 and Rnd3. However, the directionality of radial migration suggests that migrating neurons also respond to extracellular signal-regulated pathways. Here we show that the Plexin B2 receptor interacts physically and functionally with Rnd3 and stimulates RhoA activity in migrating cortical neurons. Plexin B2 competes with p190RhoGAP for binding to Rnd3, thus blocking the Rnd3-mediated inhibition of RhoA and also recruits RhoGEFs to directly stimulate RhoA activity. Thus, an interaction between the cell-extrinsic Plexin signalling pathway and the cell-intrinsic Ascl1-Rnd3 pathway determines the level of RhoA activity appropriate for cortical neuron migration.
Interferon β protects against lethal endotoxic and septic shock through SIRT1 upregulation
Authors: Yoo Chae-Hwa , Yeom Ji-Hyun , Heo Jin-Ju , Song Eun-Kyung , Lee Sang-Il , Han Myung-Kwan 
Published: February 2014

AbstractLipopolysaccharide (LPS), an endotoxin derived from gram-negative bacteria, promotes the secretion of proinflammatory cytokines and mediates endotoxemia through activation of mitogen activated protein kinases, NF-κB and interferon regulatory factor-3. Silent information regulator transcript-1 (SIRT1), an NAD-dependent deacetylase, mediates NF-κB deacetylation and inhibits its function. SIRT1 may affect LPS-mediated signaling pathways and endotoxemia. Here we demonstrate that SIRT1 blocks LPS-induced secretion of interleukin 6 and tumor necrosis factor α in murine macrophages and protects against lethal endotoxic and septic shock in mice. We also demonstrate that interferon β increases SIRT1 expression by activating the Janus kinase – signal transducer and activator of transcription (JAK-STAT) pathway in mouse bone marrow derived macrophages.In vivotreatment of interferon β protects against lethal endotoxic and septic shock, which is abrogated by infection with dominant negative SIRT1-expressing adenovirus. Our work suggests that both SIRT1 and SIRT1-inducing cytokines are useful targets for treating patients with sepsis.
Crystallized and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates
Authors: Liu Chao-Fei , Fan Heng , Gou Shih-Chuan , Liu Wu-Ming 
Published: February 2014

AbstractVortex is a topological defect with a quantized winding number of the phase in superfluids and superconductors. Here, we investigate the crystallized (triangular, square, honeycomb) and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates (BECs) by using the damped projected Gross-Pitaevskii equation. The amorphous vortices are the result of the considerable deviation induced by the interaction of atomic-molecular vortices. By changing the atom-molecule interaction from attractive to repulsive, the configuration of vortices can change from an overlapped atomic-molecular vortices to carbon-dioxide-type ones, then to atomic vortices with interstitial molecular vortices and finally into independent separated ones. The Raman detuning can tune the ratio of the atomic vortex to the molecular vortex. We provide a phase diagram of vortices in rotating atomic-molecular BECs as a function of Raman detuning and the strength of atom-molecule interaction.
Selective treatment and monitoring of disseminated cancer micrometastases in vivo using dual-function, activatable immunoconjugates
Authors: Spring Bryan Q. , Abu-Yousif Adnan O. , Palanisami Akilan , Rizvi Imran , Zheng Xiang , Mai Zhiming , Anbil Sriram , Sears R. Bryan , Mensah Lawrence B. , Goldschmidt Ruth , Erdem S. Sibel , Oliva Esther , Hasan Tayyaba 
Published: February 2014

SignificanceResidual micrometastases following standard therapies limit our ability to cure many cancers. This article demonstrates a new therapy and visualization platform that targets residual cancer micrometastases with enhanced sensitivity and selectivity based on “tumor-targeted activation.” This targeted activation feature not only provides a potent therapeutic arm that is effective against chemoresistant disease while minimizing side effects due to nonspecific toxicities but also enables micrometastasis imaging in common sites of disease recurrence to screen patients harboring residual tumor deposits. This approach offers promise for treating and monitoring drug-resistant micrometastases presently “invisible” to clinicians.
La paix ailée de l’évangéliaire de Saint Francois d’Assise (les oiseaux du franciscanisme)
Authors: Lacroix Jean 
Published: February 2014

I. Le bestiaire de Saint François est marqué au sceau de la non-agressivité d’une part et caractérisé, d’autre part, par des animaux qui appartiennent en général à l’univers familier et domestique des humains.
II. Parmi ces créatures priment les oiseaux, trait d’union “naturel” entre ciel et terre, entre Dieu et les hommes, faits aussi bien les premiers que les seconds “à l’image de la Divinité”.
III. Dans les écrits de Saint François d’Assise comme dans ceux de ses successeurs, héritiers ou épigones, l’oiseau “accompagne” la geste des frères mineurs, comme encore les peintres du XIIIè siècles et des XIVesiècles l’ont représenté sur leurs tableaux ou sur leurs fresques. L’oiseau de Saint François et des ses disciples est un emblème supplémentaire à un idéal de paix, de charitée et de pauvretée.
Effects of 12 weeks of dynamic strength training with local vibration
Authors: Drummond Marcos D. M. , Couto Bruno P. , Augusto Izabela G. , Rodrigues Sara A. , Szmuchrowski Leszek A. 
Published: February 2014

AbstractThe purpose of this study was to investigate the chronic effects of dynamic strength training (ST) with local vibration on the maximum strength of elbow flexor muscles. Twenty healthy male untrained volunteers were divided randomly into the following two groups: the conventional training group (CTG) or the vibration training group (VTG). Both groups performed ST for 12 weeks, three times a week. The ST protocol included four sets of 8–10 repetition maximums (RMs) of unilateral elbow flexion exercise. The VTG performed this training protocol with local vibration at a frequency of 30 Hz and amplitude of 6 mm. The mean values of the one repetition maximum (1RM) tests for both groups increased significantly from the pretest week to the fourth week and from the fourth week to the eighth week (CTG: mean 19.02, s = 7.88%, p = 0.01; mean 10.50, s = 6.86%, p = 0.019, respectively; VTG: mean 16.02, s = 8.30%, p = 0.017; mean 12.55, s = 8.76%, p = 0.019, respectively). The increases in the maximal voluntary contraction (MVC) tests were also statistically significant from the pretest week to the fourth week and from the fourth week to the eighth week (CTG: mean 12.32, s = 8.33%, p = 0.004; mean 9.95, s = 5.32%, p = 0.006, respectively; VTG: mean 10.16, s = 11.71%, p = 0.003; mean 10.36, s = 2.96%, p = 0.01, respectively). There was no significant difference between the 1RM and MVC test results in the eighth and twelfth weeks in either group. No significant differences were observed between the groups (p < 0.05). In conclusion, the application of local vibration does not change the chronic effects of dynamic ST in untrained individuals.
Mehler–Heine formulas for orthogonal polynomials with respect to the modified Jacobi weight
Authors: Fejzullahu Bujar 
Published: February 2014

In this paper the ladder operator approach has been applied to deduce the Mehler–Heine type formulas for orthogonal polynomials with respect to the modified Jacobi weight
\[

ω

α
,
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,
h

(
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)
=
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(
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)
(
1
−
x

)
α

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x

)
β

,

x
∈
[
−
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]
,

\omega _{\alpha ,\beta ,h}(x)=h(x) (1-x)^\alpha (1+x)^\beta , \hspace {0.5cm} x\in [-1,1],

\]
where

α
,
β
>
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,

\alpha ,\beta >0,

and with

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real analytic and strictly positive on

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.

[-1, 1].
Canto: an online tool for community literature curation
Authors: Rutherford Kim M. , Harris Midori A. , Lock Antonia , Oliver Stephen G. , Wood Valerie 
Published: February 2014

Abstract
Motivation: Detailed curation of published molecular data is essential for any model organism database. Community curation enables researchers to contribute data from their papers directly to databases, supplementing the activity of professional curators and improving coverage of a growing body of literature. We have developed Canto, a web-based tool that provides an intuitive curation interface for both curators and researchers, to support community curation in the fission yeast database, PomBase. Canto supports curation using OBO ontologies, and can be easily configured for use with any species.
Availability: Canto code and documentation are available under an Open Source license from http://curation.pombase.org/. Canto is a component of the Generic Model Organism Database (GMOD) project (http://www.gmod.org/).
Contact: helpdesk@pombase.org
BioPlat: a software for human cancer biomarker discovery
Authors: Butti Matias D. , Chanfreau Hernan , Martinez Diego , García Diego , Lacunza Ezequiel , Abba Martin C. 
Published: February 2014

Abstract
Summary: Development of effective tools such as oligo-microarrays and next-generation sequencing methods for monitoring gene expression on a large scale has resulted in the discovery of gene signatures with prognostic/predictive value in various malignant neoplastic diseases. However, with the exponential growth of gene expression databases, biologists are faced with the challenge of extracting useful information from these repositories. Here, we present a software package, BioPlat (Biomarkers Platform), which allows biologists to identify novel prognostic and predictive cancer biomarkers based on the data mining of gene expression signatures and gene expression profiling databases. BioPlat has been designed as an easy-to-use and flexible desktop software application, which provides a set of analytical tools related to data extraction, preprocessing, filtering, gene expression signature calculation, in silico validation, feature selection and annotation that leverage the integration and reuse of gene expression signatures in the context of follow-up data.
Availability and implementation: BioPlat is a platform-independent software implemented in Java and supported on GNU/Linux and MS Windows, which is freely available for download at http://www.cancergenomics.net.
Contact: mcabba@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
CanSNPer: a hierarchical genotype classifier of clonal pathogens
Authors: Lärkeryd Adrian , Myrtennäs Kerstin , Karlsson Edvin , Dwibedi Chinmay Kumar , Forsman Mats , Larsson Pär , Johansson Anders , Sjödin Andreas 
Published: February 2014

Summary: Advances in typing methodologies have recently reformed the field of molecular epidemiology of pathogens. The falling cost of sequencing technologies is creating a deluge of whole genome sequencing data that burdens bioinformatics resources and tool development. In particular, single nucleotide polymorphisms in core genomes of pathogens are recognized as the most important markers for inferring genetic relationships because they are evolutionarily stable and amenable to high-throughput detection methods. Sequence data will provide an excellent opportunity to extend our understanding of infectious disease when the challenge of extracting knowledge from available sequence resources is met. Here, we present an efficient and user-friendly genotype classification pipeline, CanSNPer, based on an easily expandable database of predefined canonical single nucleotide polymorphisms.
Availability and implementation: All documentation and Python-based source code for the CanSNPer are freely available at http://github.com/adrlar/CanSNPer.
Contact: adrian.larkeryd@foi.se
Estimating concentrations of essential omega-3 fatty acids in the ocean: supply and demand
Authors: Budge Suzanne M. , Devred Emmanuel , Forget Marie-Hélène , Stuart Venetia , Trzcinski M. Kurtis , Sathyendranath Shubha , Platt Trevor 
Published: February 2014

Abstract
Vertebrates have a universal requirement for essential fatty acids (FAs), but in the ocean these FAs are synthesized only by phytoplankton. All other marine organisms must source their essential FA directly from phytoplankton or indirectly through the food web. Thus, the growth and abundance of all organisms in the marine ecosystem is constrained not just by the rate of carbon fixation in photosynthesis but also by the rate of synthesis of essential FAs. Despite the significance of this controlling step, we have had until now only very limited knowledge of the amount, distribution and rate of synthesis of essential FAs in the sea. Here, we report results on the quantity of a specific essential omega-3 FA, eicosapentaenoic acid (EPA) in the ocean, obtained with a novel application of ocean-colour data collected by remote sensing. Using in situ samples collected in the Northwest Atlantic, we developed a simple model to describe the relationship between total FAs and total chlorophyll-a. We refined these by examining the relationships of FAs produced predominantly by diatoms with the fraction of total chlorophyll-a derived from diatoms. These models were then applied to satellite data to map the distribution of EPA relative to diatom carbon in the Northwest Atlantic. With extrapolation to the global oceans, we were able to provide a first estimate of annual production of EPA, which demonstrated that the supply was barely sufficient to meet the nutritional demand of the world population in the present day; as the world population increases, this resource may become inadequate to meet those demands. This approach will allow us to begin to address issues such as the budget of essential FAs in the ocean and the maximum sustainable rate at which these FAs could be harvested from the ocean without compromising the integrity of the marine ecosystem.
Variability of fishing effort for the German brown shrimp (Crangon crangon) fishing fleet: influencing factors, and seasonal and spatial patterns
Authors: Respondek G. , Gröger J. , Floeter J. , Temming A. 
Published: February 2014

Abstract
We examined factors affecting the fishing effort in the German brown shrimp (Crangon crangon) fishery, including shrimp and fuel price, catch per unit effort (cpue), number of days with strong wind, fishing port, and season. Time-series analysis (TS) using rational transfer functions (ARIMAX, an extension of autoregressive integrated moving average (ARIMA) modelling) were applied to model mean monthly boat effort (MBE, in hours), aggregated from the logbook data of five German ports for the years 2000–2008. We addressed two major areas: (i) whether cyclic effort patterns and the effect of external factors such as wind differ regionally, and (ii) whether external factors such as cpue, shrimp and fuel prices have a significant influence on the effort pattern. The estimated ARIMAX models accounted for 52–77% of the variance in MBE if analysed separately for each port, indicating a stable seasonal pattern of fishing effort without major interannual variations or significant trends. In spite of considerable variability in the external factors, none of cpue, shrimp or fuel price had a significant effect on the fishing effort. We interpreted this stability as a lack of alternative target species and discuss the theory that a response of a fishery to these external factors might only occur once certain critical threshold values have been exceeded, which was not the case during the investigated period. The models indicated differences in the seasonal patterns of the different harbours, with shorter trips and an earlier start for the main fishing season in the southwest (SW) regions, whereas in the northeast (NE) harbours, trips were longer, peak effort was shifted by 1–2 months and the spring season was of greater importance. The relationships of these regional patterns to the shrimp life cycle and coast topography, as well as implications for future management, are discussed.
Trait diversity enhances yield in algal biofuel assemblages
Authors: Shurin Jonathan B. , Mandal Shovon , Abbott Rachel L. 
Published: February 2014

Summary

Phytoplankton offer great potential as a bioenergy crop; however, technological advances are needed to intensify their yield and reduce their footprints for water, nutrients and land. One approach to enhance productivity is to grow polycultures of mixed species, which convert abiotic resources into biomass more efficiently than any single taxon.

We measured traits related to nutrient and light use, growth rate, biomass production, stoichiometry and neutral lipid concentration in 16 diverse microalgal taxa. Species with large cells (primarily Chlorophyta) showed rapid growth, high asymptotic biomass, low minimum nutrient demands, and high cellular C : N and C : P ratios. These same species also exhibited high minimum demands for light and low lipid concentrations. We grew all 119 possible species pairs and found that biomass yield exceeded the component monocultures in polycultures consisting of species with highly divergent traits. However, underyielding occurred frequently as many pairs produced less biomass than either the mean or the maximum of the two component monocultures.

In terms of ecological trade‐offs, competitive ability for N and P were positively correlated, but negatively related to ability to grow at low light. In terms of bioenergy production, the species with high cellular lipid concentrations showed both slow growth and high demands for nutrients.

Synthesis and applications. Our results identify trade‐offs among functional traits that determine the suitability of different algal species as biofuel feedstocks and narrow the search for productive and robust species combinations to maximize bioenergy productivity. An approach based on the ecology of species traits will be more effective in optimizing yield in bioenergy communities than promoting high species diversity per se.