Academy of Sciences of the Czech Republic

About: Academy of Sciences of the Czech Republic is a government organization based out in Prague, Czechia. It is known for research contribution in the topics: Population & Catalysis. The organization has 27866 authors who have published 71021 publications receiving 1821686 citations.

Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation

Abstract: Hydrogen bonding of DNA bases was investigated by reliable nonempirical ab initio calculations. Gradient optimization was carried out on 30 DNA base pairs using the Hartree−Fock (HF) approximation and the 6-31G** basis set of atomic orbitals. The optimizations were performed within Cs symmetry. However, the harmonic vibrational analysis indicates that 13 of the studied base pairs are intrinsically nonplanar. Interaction energies of base pairs were then evaluated at the planar optimized geometries with inclusion of the electron correlation energy using the second-order Moller−Plesset (MP2) method. The stabilization energies of the studied base pairs range from −24 to −9 kcal/mol, and the calculated gas phase interaction enthalpies agree well (within 2 kcal/mol) with the available experimental values. The binding energies and molecular structures of the base pairs are not determined solely by the hydrogen bonds, but they are also strongly influenced by the polarity of the monomers and by a wide variety of s...

Performance of $b$-Jet Identification in the ATLAS Experiment

Abstract: The identification of jets containing b hadrons is important for the physics programme of the ATLAS experiment at the Large Hadron Collider. Several algorithms to identify jets containing b hadrons are described, ranging from those based on the reconstruction of an inclusive secondary vertex or the presence of tracks with large impact parameters to combined tagging algorithms making use of multi-variate discriminants. An independent b-tagging algorithm based on the reconstruction of muons inside jets as well as the b-tagging algorithm used in the online trigger are also presented. The b-jet tagging efficiency, the c-jet tagging efficiency and the mistag rate for light flavour jets in data have been measured with a number of complementary methods. The calibration results are presented as scale factors defined as the ratio of the efficiency (or mistag rate) in data to that in simulation. In the case of b jets, where more than one calibration method exists, the results from the various analyses have been combined taking into account the statistical correlation as well as the correlation of the sources of systematic uncertainty.

Bias and error in understanding plant invasion impacts

Abstract: Quantitative assessments of alien plant impacts are essential to inform management to ensure that resources are prioritized against the most problematic species and that restoration targets the worst-affected ecosystem processes. Here, we present the first detailed critique of quantitative field studies of alien plant impacts and highlight biases in the biogeography and life form of the target species, the responses assessed, and the extent to which spatial variability is addressed. Observed impacts often fail to translate to ecosystem services or evidence of environmental degradation. The absence of overarching hypotheses regarding impacts has reduced the consistency of approaches worldwide and prevented the development of predictive tools. Future studies must ensure that the links between species traits, ecosystem stocks, and ecosystem flows, as well as ecosystem services, are explicitly defined.

Genomic Characterization of Severe Acute Respiratory Syndrome-Related Coronavirus in European Bats and Classification of Coronaviruses Based on Partial RNA-Dependent RNA Polymerase Gene Sequences

Abstract: Bats may host emerging viruses, including coronaviruses (CoV). We conducted an evaluation of CoV in rhinolophid and vespertilionid bat species common in Europe. Rhinolophids carried severe acute respiratory syndrome (SARS)-related CoV at high frequencies and concentrations (26% of animals are positive; up to 2.4×10(8) copies per gram of feces), as well as two Alphacoronavirus clades, one novel and one related to the HKU2 clade. All three clades present in Miniopterus bats in China (HKU7, HKU8, and 1A related) were also present in European Miniopterus bats. An additional novel Alphacoronavirus clade (bat CoV [BtCoV]/BNM98-30) was detected in Nyctalus leisleri. A CoV grouping criterion was developed by comparing amino acid identities across an 816-bp fragment of the RNA-dependent RNA polymerases (RdRp) of all accepted mammalian CoV species (RdRp-based grouping units [RGU]). Criteria for defining separate RGU in mammalian CoV were a >4.8% amino acid distance for alphacoronaviruses and a >6.3% distance for betacoronaviruses. All the above-mentioned novel clades represented independent RGU. Strict associations between CoV RGU and host bat genera were confirmed for six independent RGU represented simultaneously in China and Europe. A SARS-related virus (BtCoV/BM48-31/Bulgaria/2008) from a Rhinolophus blasii (Rhi bla) bat was fully sequenced. It is predicted that proteins 3b and 6 were highly divergent from those proteins in all known SARS-related CoV. Open reading frame 8 (ORF8) was surprisingly absent. Surface expression of spike and staining with sera of SARS survivors suggested low antigenic overlap with SARS CoV. However, the receptor binding domain of SARS CoV showed higher similarity with that of BtCoV/BM48-31/Bulgaria/2008 than with that of any Chinese bat-borne CoV. Critical spike domains 472 and 487 were identical and similar, respectively. This study underlines the importance of assessments of the zoonotic potential of widely distributed bat-borne CoV.

Electron and photon energy calibration with the ATLAS detector using LHC Run 1 data

Abstract: This paper presents the electron and photon energy calibration achieved with the ATLAS detector using about 25 fb(-1) of LHC proton-proton collision data taken at centre-of-mass energies of root s = 7 and 8 TeV. The reconstruction of electron and photon energies is optimised using multivariate algorithms. The response of the calorimeter layers is equalised in data and simulation, and the longitudinal profile of the electromagnetic showers is exploited to estimate the passive material in front of the calorimeter and reoptimise the detector simulation. After all corrections, the Z resonance is used to set the absolute energy scale. For electrons from Z decays, the achieved calibration is typically accurate to 0.05% in most of the detector acceptance, rising to 0.2% in regions with large amounts of passive material. The remaining inaccuracy is less than 0.2-1% for electrons with a transverse energy of 10 GeV, and is on average 0.3% for photons. The detector resolution is determined with a relative inaccuracy of less than 10% for electrons and photons up to 60 GeV transverse energy, rising to 40% for transverse energies above 500 GeV.