28,739 research outputs found
Computational identification and analysis of protein short linear motifs
No full textShort linear motifs (SLiMs) in proteins can act as targets for proteolytic cleavage, sites of post-translational modification, determinants of sub-cellular localization, and mediators of protein-protein interactions. Computational discovery of SLiMs involves assembling a group of proteins postulated to share a potential motif, masking out residues less likely to contain such a motif, down-weighting shared motifs arising through common evolutionary descent, and calculation of statistical probabilities allowing for the multiple testing of all possible motifs. Much of the challenge for motif discovery lies in the assembly and masking of datasets of proteins likely to share motifs, since the motifs are typically short (between 3 and 10 amino acids in length), so that potential signals can be easily swamped by the noise of stochastically recurring motifs. Focusing on disordered regions of proteins, where SLiMs are predominantly found, and masking out non-conserved residues can reduce the level of noise but more work is required to improve the quality of high-throughput experimental datasets (e.g. of physical protein interactions) as input for computational discovery
B -> eta K-c(eta ' K-c) decays in QCD factorization
No full textWe study the exclusive decays of the B meson into pseudoscalar charmonium states eta(c) and eta(c)' within the QCD factorization approach and find that the non-factorizable corrections to naive factorization are infrared safe at leading-twist order. The spectator interactions arising from the kaon twist-3 effects are formally power suppressed but chirally and logarithmically enhanced. An important improvement by including the O(alpha(s)) corrections is the cancellation of the renormalization scale mu dependence of the decay amplitude. However, the calculated decay rates are too small to accommodate the experimental data. On the other hand, we compare the theoretical calculations for B meson decays to J/psi, psi', eta(c) and eta'(c), and find that the predicted relative decay rates of these four states are approximately compatible with the experimental data.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000223097800007&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Physics, Particles & FieldsSCI(E)17ARTICLE3365-3703
The study on the initial thorium correction of the 230Th-234U-238U dating of the speleothem by using isochron method.
No full textComplex Diversity in Stygobromus Amphipods of the Texas Edwards Plateau
No full textTroglomorphic, spring-associated cave amphipods (genus Stygobromus) occupy discontinuous localities m the Edwards plateau region of the south-central United States. Given the prevalence of subterranean cryptic species diversity among widely disparate animal taxa and general patterns of subterranean dispersal and vicariance, Stygobromus may contain undetected biodiversity at the species and population levels, with conservation implications for S. peckz, a federal and state of Texas endangered short-range endemic. To explore Stygobromus evolutionary history, mitochondrial sequence (COI), nuclear sequence (ITS1), and AFLP data were collected for S. peckz and Edwards plateau congeners. The morphology-based taxonomy and proposed phylogeny of Stygobromus species and species groups were treated as hypotheses and tested with molecular data. Stygobromus peckz, which emerges from multiple spring flows at Landa Lake, was examined with population genetics tools to characterize population structure and diversity, with diversity measures compared to congeners and previous findings for another spring endemic, the federally endangered Comal Springs riffle beetle, Heterelms comalensus, which shares habitat with S. peckt. The taxonomy of Stygobromus species and species groups conflicted with molecular phylogenetic data and there is strong evidence of significant cryptic diversity. Within S. peckz, COI data contained two significantly diverged clades that may reflect a history of isolation succeeded by current sympatry and admixture. S. pecki genetic diversity was similar to that for congeners and significantly greater than for H. comalensis. This study demonstrates that Edwards plateau Stygobromus are a complex and genetically diverse group with substantially more diversity than currently recognized.Biolog
Observation of a Charged Charmoniumlike Structure Z(c) (4020) and Search for the Z(c) (3900) in e(+)e(-) -> pi(+) pi(-)h(c)
No full text<p>We study e(+)e(-) -> pi(+) pi(-)h(c) at center-of-mass energies from 3.90 to 4.42 GeV by using data samples collected with the BESIII detector operating at the Beijing Electron Positron Collider. The Born cross sections are measured at 13 energies and are found to be of the same order of magnitude as those of e(+)e(-) -> pi(+) pi(-) J/Psi but with a different line shape. In the pi(+/-)h(c) mass spectrum, a distinct structure, referred to as Z(c)(4020) is observed at 4. 02 GeV/c(2). The Z(c)(4020) carries an electric charge and couples to charmonium. A fit to the pi(+/-)h(c) invariant mass spectrum, neglecting possible interferences, results in a mass of (4022.9 +/- 0.8 +/- 2.7) MeV/c(2) and a width of (7.9 +/- 2.7 +/- 2.6) MeV for the Z(c)(4020), where the first errors are statistical and the second systematic. The difference between the parameters of this structure and the Z(c) (4025) observed in the D*(D) over bar* final state is within 1.5 sigma, but whether they are the same state needs further investigation. No significant Z(c)(3900) signal is observed, and upper limits on the Z(c)(3900) production cross sections in pi +/- h(c) at center-of-mass energies of 4.23 and 4.26 GeVare set.</p>
Z(c)(4025) as the hadronic molecule with hidden charm
No full textWe have studied the loosely bound D*(D) over bar* system. Our results indicate that the recently observed charged charmonium-like structure Z(c)(4025) can be an ideal D*(D) over bar* molecular state. We have also investigated its pionic, dipionic, and radiative decays. We stress that both the scalar isovector molecular partner Z(c0) and three isoscalar partners (Z) over tilde (c0,c1,c2) should also exist if Z(c)(4025) is a D*(D) over bar* molecular state in the framework of the one-pion-exchange model. Z(c0) can be searched for in the channel e(+)e(-) -> Y -> Z(c0)(4025)(pi pi)(P-wave) where Y can be Y(4260) or any other excited 1(--) charmonium or charmonium-like states such as Y(4360), Y(4660), etc. The isoscalar D*(D) over bar* molecular states (Z) over tilde (c0,c2) with 0(+)(0(++)) and 0(+)(2(++)) can be searched for in the three pion decay channel e(+)e(-) -> Y -> (Z) over tilde (c0,c2)(3 pi)(P-wave)(I=0). The isoscalar molecular state (Z) over tilde (c1) with 0(-)(1(+-)) can be searched for in the channel (Z) over tilde (c1)eta. Experimental discovery of these partner states will firmly establish the molecular picture.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000327092600003&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Physics, Particles & FieldsSCI(E)19ARTICLE11null7
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins.
No full textBackground: large datasets of protein interactions provide a rich resource for the discovery of Short Linear Motifs (SLiMs) that recur in unrelated proteins. However, existing methods for estimating the probability of motif recurrence may be biased by the size and composition of the search dataset, such that p-value estimates from different datasets, or from motifs containing different numbers of non-wildcard positions, are not strictly comparable. Here, we develop more exact methods and explore the potential biases of computationally efficient approximations. Results: a widely used heuristic for the calculation of motif over-representation approximates motif probability by assuming that all proteins have the same length and composition. We introduce pv, which calculates the probability exactly. Secondly, the recently introduced SLiMFinder statistic Sig, accounts for multiple testing (across all possible motifs) in motif discovery. However, it approximates the probability of all other possible motifs, occurring with a score of p or less, as being equal to p. Here, we show that the exhaustive calculation of the probability of all possible motif occurrences that are as rare or rarer than the motif of interest, Sig', may be carried out efficiently by grouping motifs of a common probability (i.e. those which have permuted orders of the same residues). Sig'v, which corrects both approximations, is shown to be uniformly distributed in a random dataset when searching for non-ambiguous motifs, indicating that it is a robust significance measure. Conclusions: a method is presented to compute exactly the true probability of a non-ambiguous short protein sequence motif, and the utility of an approximate approach for novel motif discovery across a large number of datasets is demonstrated
D* (D)over-bar* molecule interpretation of Z(c)(4025)
No full textWe have used QCD sum rules to study the newly observed charged state Z(c)(4025) as a hidden-charm D*(D) over bar* molecular state with the quantum numbers I-G(J(P)) =1(+)(1(+)). Using a D*(D) over bar* molecular interpolating current, we have calculated the two-point correlation function and the spectral density up to dimension eight at leading order in alpha(s). The extracted mass is m(X) = (4.04 +/- 0.24) GeV. This result is compatible with the observed mass of Z(c)(4025) within the errors, which implies a possible molecule interpretation of this new resonance. We also predict the mass of the corresponding hidden-bottom B*(B) over bar* molecular state: m(Zb) = (9.98 +/- 0.21) GeV.Physics, Particles & FieldsSCI(E)[email protected]; [email protected]; [email protected]; [email protected]
GASP: gapped ancestral sequence prediction for proteins
No full textBackground: the prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments.Results: here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction), for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using descendant data only to assign probabilities, and then working back up from the root to the tips using descendant and outgroup data to make predictions. GASP was tested on a number of simulated datasets based on real phylogenies. Prediction accuracy for ungapped data was similar to three alternative algorithms tested, with GASP performing better in some cases and worse in others. Adding simple insertions and deletions to the simulated data did not have a detrimental effect on GASP accuracy.Conclusions: GASP (Gapped Ancestral Sequence Prediction) will predict ancestral sequences from multiple protein alignments of any size. Although not as accurate in all cases as some of the more sophisticated maximum likelihood approaches, it can process a wide range of input phylogenies and will predict ancestral sequences for gapped and ungapped residues alik
A ±25A Versatile Shunt-Based Current Sensor with 10kHz Bandwidth and ±0.25% Gain Error from -40°C to 85°C Using 2-Current Calibration
No full textAccurate current sensing is critical in many industrial applications, such as battery management and motor control. Precise shunt-based current sensors have been reported with gain errors of less than 1% over the industrial temperature range (-40°C to 85°C) [1]–[4]. However, since they are intended for coulomb counting, their bandwidth is limited to a few tens of Hz, making them unsuitable for battery impedance or motor-current sensing. This paper presents a current sensor with a wide (10kHz) bandwidth and a tunable temperature compensation scheme (TCS), which allows it to be flexibly used with different types of shunts while maintaining high accuracy. A low-cost room-temperature calibration scheme is proposed to optimize gain flatness over temperature by exploiting the shunt's self-heating at large currents. Over the industrial temperature range and a ±25A current range, it achieves state-of-the-art gain error (±0.25%) with both low-cost PCB and stable metal-alloy shunts.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Electronic InstrumentationMicroelectronic
- …
