5,002 research outputs found
Nanoinformatics: developing new computing applications for nanomedicine
Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others
Long-finned pilot whale population diversity and structure in Atlantic waters assessed through biogeochemical and genetic markers
Acknowledgements. Cetacean samples were collected under the auspices of stranding monitoring programs run by the Sociedade Portuguesa de Vida Selvagem, the Coordinadora para o Estudio dos MamĂferos Mariños (supported by the regional government Xunta de Galicia), the UK Cetacean Strandings Investigation Programme and the Scottish Agriculture College Veterinary Science Division (jointly funded by Defra and the Devolved Governments of Scotland and Wales), the Marine Mammals Research Group of the Institute of Marine Research (Norway), the Museum of Natural History of the Faroe Islands and the International Fund for Animal Welfare Marine Mammal Rescue and Research Program (USA). The authors thank all the members of these institutions and organizations for their assistance with data and sample collection. S.S.M., P.M.F. and M.F. were supported by PhD grants from the Fundação para a CiĂȘncia e Tecnologia (POPH/FSE ref SFRH/BD/ 38735/ 2007, SFRH/BD/36766/2007 and SFRH/BD/30240/ 2006, respectively). A.L. was supported by a postdoctoral grant from the Fundação para a CiĂȘncia e Tecnologia (ref SFRH/BPD/82407/2011). The work related to strandings and tissue collection in Portugal was partially supported by the SafeSea project EEAGrants PT 0039 (supported by Iceland, Liechtenstein and Norway through the EEA Financial Mechanism), the MarPro project Life09 NAT/PT/000038 (funded by the European Union program LIFE+) and the project CetSenti FCT RECI/AAG-GLO/0470/2012 (FCOMP- 01-0124-FEDER-027472) (funded by the program COMPETE and the Fundação para a CiĂȘncia e Tecnologia). G.J.P. thanks the University of Aveiro and Caixa Geral de DepĂłsitos (Portugal) for financial support. The authors acknowledge the assistance of the chemical analysts at Marine Scotland Science with the fatty acid analysis.Peer reviewedPostprintPublisher PD
Proteomic analysis of Chromobacterium violaceum and its adaptability to stress
Chromobacterium violaceum (C. violaceum) occurs abundantly in a variety of ecosystems, including ecosystems that place the bacterium under stress. This study assessed the adaptability of C. violaceum by submitting it to nutritional and pH stresses and then analyzing protein expression using bi-dimensional electrophoresis (2-DE) and Maldi mass spectrometry. Chromobacterium violaceum grew best in pH neutral, nutrient-rich medium (reference conditions); however, the total protein mass recovered from stressed bacteria cultures was always higher than the total protein mass recovered from our reference culture. The diversity of proteins expressed (repressed by the number of identifiable 2-DE spots) was seen to be highest in the reference cultures, suggesting that stress reduces the overall range of proteins expressed by C. violaceum. Database comparisons allowed 43 of the 55 spots subjected to Maldi mass spectrometry to be characterized as containing a single identifiable protein. Stress-related expression changes were noted for C. violaceum proteins related to the previously characterized bacterial proteins: DnaK, GroEL-2, Rhs, EF-Tu, EF-P; MCP, homogentisate 1,2-dioxygenase, Arginine deiminase and the ATP synthase ÎČ-subunit protein as well as for the ribosomal protein subunits L1, L3, L5 and L6. The ability of C. violaceum to adapt its cellular mechanics to sub-optimal growth and protein production conditions was well illustrated by its regulation of ribosomal protein subunits. With the exception of the ribosomal subunit L3, which plays a role in protein folding and maybe therefore be more useful in stressful conditions, all the other ribosomal subunit proteins were seen to have reduced expression in stressed cultures. Curiously, C. violeaceum cultures were also observed to lose their violet color under stress, which suggests that the violacein pigment biosynthetic pathway is affected by stress. Analysis of the proteomic signatures of stressed C. violaceum indicates that nutrient-starvation and pH stress can cause changes in the expression of the C. violaceum receptors, transporters, and proteins involved with biosynthetic pathways, molecule recycling, energy production. Our findings complement the recent publication of the C. violeaceum genome sequence and could help with the future commercial exploitation of C. violeaceum
Inter-species differences in polychlorinated biphenyls patterns from five sympatric species of odontocetes : Can PCBs be used as tracers of feeding ecology?
The authors gratefully acknowledge the assistance of volunteers from the Galician (CEMMA) and Portuguese (SPVS) stranding networks. The authors would like to thank R. Gallois and C. Trichet for their participation on total lipid content analysis. P. MĂ©ndez-Fernandez was supported during the research period through a PhD grant from the Fundação do MinistĂ©rio de CiĂȘncia e Tecnologia de Portugal and ANIMATE project (SFRH/BD/36766/2007) and through a Science Without Borders (CSF) young talent postdoctoral grant of the Brazilian government. G. J. Pierce acknowledges support from the EU ANIMATE project (MEXC-CT-2006-042337), University of Aveiro and Caixa Geral de DepĂłsitos (Portugal).Peer reviewedPostprin
Charged-Higgs phenomenology in the Aligned two-Higgs-doublet model
The alignment in flavour space of the Yukawa matrices of a general
two-Higgs-doublet model results in the absence of tree-level flavour-changing
neutral currents. In addition to the usual fermion masses and mixings, the
aligned Yukawa structure only contains three complex parameters, which are
potential new sources of CP violation. For particular values of these three
parameters all known specific implementations of the model based on discrete
Z_2 symmetries are recovered. One of the most distinctive features of the
two-Higgs-doublet model is the presence of a charged scalar. In this work, we
discuss its main phenomenological consequences in flavour-changing processes at
low energies and derive the corresponding constraints on the parameters of the
aligned two-Higgs-doublet model.Comment: 46 pages, 19 figures. Version accepted for publication in JHEP.
References added. Discussion slightly extended. Conclusions unchange
Differential branching fraction and angular analysis of the decay B0âKâ0ÎŒ+ÎŒâ
The angular distribution and differential branching fraction of the decay B 0â K â0 ÎŒ + ÎŒ â are studied using a data sample, collected by the LHCb experiment in pp collisions at sâ=7 TeV, corresponding to an integrated luminosity of 1.0 fbâ1. Several angular observables are measured in bins of the dimuon invariant mass squared, q 2. A first measurement of the zero-crossing point of the forward-backward asymmetry of the dimuon system is also presented. The zero-crossing point is measured to be q20=4.9±0.9GeV2/c4 , where the uncertainty is the sum of statistical and systematic uncertainties. The results are consistent with the Standard Model predictions
Determination of the b quark mass at the M_Z scale with the DELPHI detector at LEP
An experimental study of the normalized three-jet rate of b quark events with
respect to light quarks events (light= \ell \equiv u,d,s) has been performed
using the CAMBRIDGE and DURHAM jet algorithms. The data used were collected by
the DELPHI experiment at LEP on the Z peak from 1994 to 2000. The results are
found to agree with theoretical predictions treating mass corrections at
next-to-leading order. Measurements of the b quark mass have also been
performed for both the b pole mass: M_b and the b running mass: m_b(M_Z). Data
are found to be better described when using the running mass. The measurement
yields: m_b(M_Z) = 2.85 +/- 0.18 (stat) +/- 0.13 (exp) +/- 0.19 (had) +/- 0.12
(theo) GeV/c^2 for the CAMBRIDGE algorithm. This result is the most precise
measurement of the b mass derived from a high energy process. When compared to
other b mass determinations by experiments at lower energy scales, this value
agrees with the prediction of Quantum Chromodynamics for the energy evolution
of the running mass. The mass measurement is equivalent to a test of the
flavour independence of the strong coupling constant with an accuracy of 7
permil.Comment: 24 pages, 10 figures, Accepted by Eur. Phys. J.
Measurement of the CKM angle Îł from a combination of B±âDh± analyses
A combination of three LHCb measurements of the CKM angle Îł is presented. The decays B±âD K± and
B±âDϱ are used, where D denotes an admixture of D0 and D0 mesons, decaying into K+Kâ, Ï+Ïâ, K±Ïâ, K±ÏâϱÏâ, K0SÏ+Ïâ, or K0S K+Kâ ïŹnal states. All measurements use a dataset corresponding to 1.0 fbâ1 of integrated luminosity. Combining results from B±âD K± decays alone a best-ïŹt value of
Îł =72.0⊠is found, and conïŹdence intervals are set
Îł â [56.4,86.7]⊠at 68% CL,
Îł â [42.6,99.6]⊠at 95% CL.
The best-ïŹt value of Îł found from a combination of results from B±âDϱ decays alone, is Îł =18.9âŠ,
and the conïŹdence intervals
Îł â [7.4,99.2]⊠âȘ [167.9,176.4]⊠at 68% CL
are set, without constraint at 95% CL. The combination of results from B± â D K± and B± â Dϱ
decays gives a best-ïŹt value of Îł =72.6⊠and the conïŹdence intervals
Îł â [55.4,82.3]⊠at 68% CL,
Îł â [40.2,92.7]⊠at 95% CL
are set. All values are expressed modulo 180âŠ, and are obtained taking into account the effect of D0âD0
mixing
Measurement of the ratio of branching fractions BR(B0 -> K*0 gamma)/BR(Bs0 -> phi gamma)
The ratio of branching fractions of the radiative B decays B0 -> K*0 gamma
and Bs0 -> phi gamma has been measured using 0.37 fb-1 of pp collisions at a
centre of mass energy of sqrt(s) = 7 TeV, collected by the LHCb experiment. The
value obtained is BR(B0 -> K*0 gamma)/BR(Bs0 -> phi gamma) = 1.12 +/- 0.08
^{+0.06}_{-0.04} ^{+0.09}_{-0.08}, where the first uncertainty is statistical,
the second systematic and the third is associated to the ratio of fragmentation
fractions fs/fd. Using the world average for BR(B0 -> K*0 gamma) = (4.33 +/-
0.15) x 10^{-5}, the branching fraction BR(Bs0 -> phi gamma) is measured to be
(3.9 +/- 0.5) x 10^{-5}, which is the most precise measurement to date.Comment: 15 pages, 1 figure, 2 table
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