RBF-TSS: Identification of Transcription Start Site in Human Using Radial Basis Functions Network and Oligonucleotide Positional Frequencies

Accurate identification of promoter regions and transcription start sites (TSS) in genomic DNA allows for a more complete understanding of the structure of genes and gene regulation within a given genome. Many recently published methods have achieved high identification accuracy of TSS. However, models providing more accurate modeling of promoters and TSS are needed. A novel identification method for identifying transcription start sites that improves the accuracy of TSS recognition for recently published methods is proposed. This method incorporates a metric feature based on oligonucleotide positional frequencies, taking into account the nature of promoters. A radial basis function neural network for identifying transcription start sites (RBF-TSS) is proposed and employed as a classification algorithm. Using non-overlapping chunks (windows) of size 50 and 500 on the human genome, the proposed method achieves an area under the Receiver Operator Characteristic curve (auROC) of 94.75% and 95.08% respectively, providing increased performance over existing TSS prediction methods

Atypical blood glucose response to continuous and interval exercise in a person with type 1 diabetes: a case report

BackgroundTherapy must be adapted for people with type 1 diabetes to avoid exercise-induced hypoglycemia caused by increased exercise-related glucose uptake into muscles. Therefore, to avoid hypoglycemia, the preexercise short-acting insulin dose must be reduced for safety reasons. We report a case of a man with long-lasting type 1 diabetes in whom no blood glucose decrease during different types of exercise with varying exercise intensities and modes was found, despite physiological hormone responses.Case presentationA Caucasian man diagnosed with type 1 diabetes for 24 years performed three different continuous high-intensity interval cycle ergometer exercises as part of a clinical trial (ClinicalTrials.gov identifier NCT02075567). Intensities for both modes of exercises were set at 5% below and 5% above the first lactate turn point and 5% below the second lactate turn point. Short-acting insulin doses were reduced by 25%, 50%, and 75%, respectively. Measurements taken included blood glucose, blood lactate, gas exchange, heart rate, adrenaline, noradrenaline, cortisol, glucagon, and insulin-like growth factor-1. Unexpectedly, no significant blood glucose decreases were observed during all exercise sessions (start versus end, 12.97 ± 2.12 versus 12.61 ± 2.66 mmol L−1, p = 0.259). All hormones showed the expected response, dependent on the different intensities and modes of exercises.ConclusionsPeople with type 1 diabetes typically experience a decrease in blood glucose levels, particularly during low- and moderate-intensity exercises. In our patient, we clearly found no decline in blood glucose, despite a normal hormone response and no history of any insulin insensitivity. This report indicates that there might be patients for whom the recommended preexercise therapy adaptation to avoid exercise-induced hypoglycemia needs to be questioned because this could increase the risk of severe hyperglycemia and ketosis

On the continuous Cesàro operator in certain function spaces

“The final publication is available at Springer via http://dx.doi.org/10.1007/s11117-014-0321-5"Various properties of the (continuous) Cesàro operator C, acting on Banach and Fréchet spaces of continuous functions and L p-spaces, are investigated. For instance, the spectrum and point spectrum of C are completely determined and a study of certain dynamics of C is undertaken (eg. hyper- and supercyclicity, chaotic behaviour). In addition, the mean (and uniform mean) ergodic nature of C acting in the various spaces is identified.The research of the first two authors was partially supported by the projects MTM2010-15200 and GVA Prometeo II/2013/013 (Spain). The second author gratefully acknowledges the support of the Alexander von Humboldt Foundation.Albanese, AA.; Bonet Solves, JA.; Ricker, WJ. (2015). On the continuous Cesàro operator in certain function spaces. Positivity. 19:659-679. https://doi.org/10.1007/s11117-014-0321-5S65967919Albanese, A.A.: Primary products of Banach spaces. Arch. Math. 66, 397–405 (1996)Albanese, A.A.: On subspaces of the spaces $$L^p_{\rm loc}$$ L loc p and of their strong duals. Math. Nachr. 197, 5–18 (1999)Albanese, A.A., Moscatelli, V.B.: Complemented subspaces of sums and products of copies of $$L^1 [0,1]$$ L 1 [ 0 , 1 ] . Rev. Mat. Univ. Complut. Madr. 9, 275–287 (1996)Albanese, A.A., Bonet, J., Ricker, W.J.: Mean ergodic operators in Fréchet spaces. Ann. Acad. Sci. Fenn. Math. 34, 401–436 (2009)Albanese, A.A., Bonet, J., Ricker, W.J.: On mean ergodic operators. In: Curbera, G.P. (eds.) Vector Measures, Integration and Related Topics. Operator Theory: Advances and Applications, vol. 201, pp. 1–20. Birkhäuser, Basel (2010)Albanese, A.A., Bonet, J., Ricker, W.J.: $$C_0$$ C 0 -semigroups and mean ergodic operators in a class of Fréchet spaces. J. Math. Anal. Appl. 365, 142–157 (2010)Albanese, A.A., Bonet, J., Ricker, W.J.: Convergence of arithmetic means of operators in Fréchet spaces. J. Math. Anal. Appl. 401, 160–173 (2013)Bayart, F., Matheron, E.: Dynamics of linear operators. Cambridge Tracts in Mathematics, vol. 179. Cambridge University Press, Cambridge (2009)Bellenot, S.F., Dubinsky, E.: Fréchet spaces with nuclear Köthe quotients. Trans. Am. Math. Soc. 273, 579–594 (1982)Bonet, J., Frerick, L., Peris, A., Wengenroth, J.: Transitive and hypercyclic operators on locally convex spaces. Bull. Lond. Math. Soc. 37, 254–264 (2005)Boyd, D.W.: The spectrum of the Cesàro operator. Acta Sci. Math. (Szeged) 29, 31–34 (1968)Brown, A., Halmos, P.R., Shields, A.L.: Cesàro operators. Acta Sci. Math. (Szeged) 26, 125–137 (1965)Dierolf, S., Zarnadze, D.N.: A note on strictly regular Fréchet spaces. Arch. Math. 42, 549–556 (1984)Dunford, N., Schwartz, J.T.: Linear Operators I: General Theory (2nd Printing). Wiley-Interscience, New York (1964)Galaz Fontes, F., Solís, F.J.: Iterating the Cesàro operators. Proc. Am. Math. Soc. 136, 2147–2153 (2008)Galaz Fontes, F., Ruiz-Aguilar, R.W.: Grados de ciclicidad de los operadores de Cesàro–Hardy. Misc. Mat. 57, 103–117 (2013)González, M., León-Saavedra, F.: Cyclic behaviour of the Cesàro operator on $$L_2(0,+\infty )$$ L 2 ( 0 , + ∞ ) . Proc. Am. Math. Soc. 137, 2049–2055 (2009)Grosse-Erdmann, K.G., Peris Manguillot, A.: Linear chaos. In: Universitext. Springer, London (2011)Hardy, G.H., Littlewood, J.E., Pólya, G.: Inequalities. In: Reprint of the 1952 Edition. Cambridge Mathematical Library. Cambridge University Press, Cambridge (1988)Krengel, U.: Ergodic theorems. In: De Gruyter Studies in Mathematics, vol. 6. Walter de Gruyter Co., Berlin (1985)Leibowitz, G.M.: Spectra of finite range Cesàro operators. Acta Sci. Math. (Szeged) 35, 27–28 (1973)Leibowitz, G.M.: The Cesàro operators and their generalizations: examples in infinite-dimensional linear analysis. Am. Math. Mon. 80, 654–661 (1973)León-Saavedra, F., Piqueras-Lerena, A., Seoane-Sepúlveda, J.B.: Orbits of Cesàro type operators. Math. Nachr. 282, 764–773 (2009)Lin, M.: On the uniform ergodic theorem. Proc. Am. Math. Soc. 43, 337–340 (1974)Meise, R., Vogt, D.: Introduction to functional analysis. In: Oxford Graduate Texts in Mathematics, vol. 2. The Clarendon Press; Oxford University Press, New York (1997)Metafune, G., Moscatelli, V.B.: Quojections and prequojections. In: Terzioğlu, T. (ed.) Advances in the Theory of Fréchet spaces. NATO ASI Series, vol. 287, pp. 235–254. Kluwer Academic Publishers, Dordrecht (1989)Moscatelli, V.B.: Fréchet spaces without norms and without bases. Bull. Lond. Math. Soc. 12, 63–66 (1980)Piszczek, K.: Quasi-reflexive Fréchet spaces and mean ergodicity. J. Math. Anal. Appl. 361, 224–233 (2010)Piszczek, K.: Barrelled spaces and mean ergodicity. Rev R. Acad. Cienc. Exactas Fis. Nat. Ser. A Math. RACSAM 104, 5–11 (2010)Yosida, K.: Functional Analysis, 6th edn. Springer, Berlin (1980

In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans

The question whether fatty acids can be converted into glucose in humans has a long standing tradition in biochemistry, and the expected answer is “No”. Using recent advances in Systems Biology in the form of large-scale metabolic reconstructions, we reassessed this question by performing a global investigation of a genome-scale human metabolic network, which had been reconstructed on the basis of experimental results. By elementary flux pattern analysis, we found numerous pathways on which gluconeogenesis from fatty acids is feasible in humans. On these pathways, four moles of acetyl-CoA are converted into one mole of glucose and two moles of CO2. Analyzing the detected pathways in detail we found that their energetic requirements potentially limit their capacity. This study has many other biochemical implications: effect of starvation, sports physiology, practically carbohydrate-free diets of inuit, as well as survival of hibernating animals and embryos of egg-laying animals. Moreover, the energetic loss associated to the usage of gluconeogenesis from fatty acids can help explain the efficiency of carbohydrate reduced and ketogenic diets such as the Atkins diet

Noninertial effects on a Dirac neutral particle inducing an analogue of the Landau quantization in the cosmic string spacetime

We discuss the behaviour of external fields that interact with a Dirac neutral particle with a permanent electric dipole moment in order to achieve relativistic bound states solutions in a noninertial frame and in the presence of a topological defect spacetime. We show that the noninertial effects of the Fermi-Walker reference frame induce a radial magnetic field even in the absence of magnetic charges, which is influenced by the topology of the cosmic string spacetime. We then discuss the conditions that the induced fields must satisfy to yield the relativistic bound states corresponding to the Landau-He-McKellar-Wilkens quantization in the cosmic string spacetime. Finally we obtain the Dirac spinors for positive-energy solutions and the Gordon decomposition of the Dirac probability current.Comment: 15 pages, no figure, this paper will be published in volume 42 of the Brazilian Journal of Physic

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT

Search for R-parity-violating supersymmetry in events with four or more leptons in sqrt(s) =7 TeV pp collisions with the ATLAS detector

A search for new phenomena in final states with four or more leptons (electrons or muons) is presented. The analysis is based on 4.7 fb−1 of $\sqrt{s}=7\;\mathrm{TeV}$ proton-proton collisions delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in two signal regions: one that requires moderate values of missing transverse momentum and another that requires large effective mass. The results are interpreted in a simplified model of R-parity-violating supersymmetry in which a 95% CL exclusion region is set for charged wino masses up to 540 GeV. In an R-parity-violating MSUGRA/CMSSM model, values of m 1/2 up to 820 GeV are excluded for 10 < tan β < 40

Search for high-mass resonances decaying to dilepton final states in pp collisions at s√=7 TeV with the ATLAS detector

The ATLAS detector at the Large Hadron Collider is used to search for high-mass resonances decaying to an electron-positron pair or a muon-antimuon pair. The search is sensitive to heavy neutral Z′ gauge bosons, Randall-Sundrum gravitons, Z * bosons, techni-mesons, Kaluza-Klein Z/γ bosons, and bosons predicted by Torsion models. Results are presented based on an analysis of pp collisions at a center-of-mass energy of 7 TeV corresponding to an integrated luminosity of 4.9 fb−1 in the e + e − channel and 5.0 fb−1 in the μ + μ −channel. A Z ′ boson with Standard Model-like couplings is excluded at 95 % confidence level for masses below 2.22 TeV. A Randall-Sundrum graviton with coupling k/MPl=0.1 is excluded at 95 % confidence level for masses below 2.16 TeV. Limits on the other models are also presented, including Technicolor and Minimal Z′ Models