An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data

High-throughput spectrometers are capable of producing data sets containing thousands of spectra for a single biological sample. These data sets contain a substantial amount of redundancy from peptides that may get selected multiple times in a LC-MS/MS experiment. In this paper, we present an efficient algorithm, CAMS (Clustering Algorithm for Mass Spectra) for clustering mass spectrometry data which increases both the sensitivity and confidence of spectral assignment. CAMS utilizes a novel metric, called F-set, that allows accurate identification of the spectra that are similar. A graph theoretic framework is defined that allows the use of F-set metric efficiently for accurate cluster identifications. The accuracy of the algorithm is tested on real HCD and CID data sets with varying amounts of peptides. Our experiments show that the proposed algorithm is able to cluster spectra with very high accuracy in a reasonable amount of time for large spectral data sets. Thus, the algorithm is able to decrease the computational time by compressing the data sets while increasing the throughput of the data by interpreting low S/N spectra.Comment: 4 pages, 4 figures, Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference o

Warabandi in Pakistan's canal irrigation systems: Widening gap between theory and practice

Irrigation scheduling / Irrigation systems / Irrigation canals / Privatization / Water rights / Social aspects / Economic aspects / Watercourses / Water supply / Equity / Water distribution / Water users' associations / Pakistan / Punjab

Generalized Parton Distributions from Hadronic Observables: Zero Skewness

We propose a physically motivated parametrization for the unpolarized generalized parton distributions. At zero value of the skewness variable, $\zeta$, the parametrization is constrained by simultaneously fitting the experimental data on both the nucleon elastic form factors and the deep inelastic structure functions. A rich phenomenology can be addressed based on this parametrization. In particular, we track the behavior of the average: {\it i)} interparton distances as a function of the momentum fraction, $X$, {\it ii)} $X$ as a function of the four-momentum transfer, $t$; and {\it iii)} the intrinsic transverse momentum $k_\perp$ as a function of $X$. We discuss the extension of our parametrization to $\zeta \neq 0$ where additional constraints are provided by higher moments of the generalized parton distributions obtained from {\it ab initio} lattice QCD calculations.Comment: 42 pages, 21 figure

Primary radiotherapy in progressive optic nerve sheath meningiomas: a long-term follow-up study

Background/aims: To report the outcome of primary radiotherapy in patients with progressive optic nerve sheath meningioma (ONSM). Methods: The clinical records of all patients were reviewed in a retrospective, observational, multicentre study. Results: Thirty-four consecutive patients were included. Twenty-six women and eight men received conventional or stereotactic fractionated radiotherapy, and were followed for a median 58 (range 51–156) months. Fourteen eyes (41%) showed improved visual acuity of at least two lines on the Snellen chart. In 17 (50%) eyes, the vision stabilised, while deterioration was noted in three eyes (9%). The visual outcome was not associated with age at the time of radiotherapy (p=0.83), sex (p=0.43), visual acuity at the time of presentation (p=0.22) or type of radiotherapy (p=0.35). Optic disc swelling was associated with improved visual acuity (p<0.01) and 4/11 patients with optic atrophy also showed improvement. Long-term complications were dry eyes in five patients, cataracts in three, and mild radiation retinopathy in four. Conclusion: Primary radiotherapy for patients with ONSM is associated with long-term improvement of visual acuity and few adverse effects.Peerooz Saeed, Leo Blank, Dinesh Selva, John G. Wolbers, Peter J.C.M. Nowak, Ronald B. Geskus, Ezekiel Weis, Maarten P. Mourits, Jack Rootma

Symmetric Operation of the Resonant Exchange Qubit

We operate a resonant exchange qubit in a highly symmetric triple-dot configuration using IQ-modulated RF pulses. At the resulting three-dimensional sweet spot the qubit splitting is an order of magnitude less sensitive to all relevant control voltages, compared to the conventional operating point, but we observe no significant improvement in the quality of Rabi oscillations. For weak driving this is consistent with Overhauser field fluctuations modulating the qubit splitting. For strong driving we infer that effective voltage noise modulates the coupling strength between RF drive and the qubit, thereby quickening Rabi decay. Application of CPMG dynamical decoupling sequences consisting of up to n = 32 {\pi} pulses significantly prolongs qubit coherence, leading to marginally longer dephasing times in the symmetric configuration. This is consistent with dynamical decoupling from low frequency noise, but quantitatively cannot be explained by effective gate voltage noise and Overhauser field fluctuations alone. Our results inform recent strategies for the utilization of partial sweet spots in the operation and long-distance coupling of triple-dot qubits.Comment: 6 pages, 5 figure