A rapid and accurate approach to identify single nucleotide polymorphisms of mitochondrial DNA using MALDI-TOF mass spectrometry

Background: Single nucleotide polymorphisms (SNPs) of mitochondrial DNA (mtDNA) are involved in physiological and pathological conditions. We developed a rapid, accurate, highly sensitive and high-throughput approach with low cost to identify mtDNA SNPs. Methods: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to detect 18 SNPs of mtDNA by uniplex and multiplex assays. The sensitivity and specificity of the MALDI-TOF MS were evaluated. The accuracy of the approach was validated by the comparison of using the robust sequencing analysis. Results: The detection limit achieved with the assays corresponded to the identification of five-genome equivalence of mtDNA per reaction after first round PCR amplification. The testing system enabled the discrimination of as little as 5% of mtDNA polymorphism in the predominating background of mtDNA not containing the SNP. No false positive and false negative results were obtained using the uniplex and multiplex MALDI-TOF MS assays for the analysis of the 18 SNPs compared with those obtained by sequencing analysis. Conclusions: Possible fields which could benefit from this powerful and sensitive tool include forensic medicine, tracing of matrilineage, transplantation immunology, transfusion medicine, the diagnosis of mtDNA mutation related disorders, and the research regarding aging, apoptosis and carcinogenesis based on physiologic and pathogenic alterations of mtDNA for the analysis of large-scale samples, multiple SNPs or rare mtDNA. Clin Chem Lab Med 2008;46:299-30

Sum Rules of Neutrino Masses and CP Violation in the Four-Neutrino Mixing Scheme

We show that the commutator of lepton mass matrices is invariant under terrestial matter effects in the four-neutrino mixing scheme. A set of model-independent sum rules for neutrino masses, which may be generalized to hold for an arbitrary number of neutrino families, are for the first time uncovered. Useful sum rules for the rephasing-invariant measures of leptonic CP violation have also been found. Finally we present a generic formula of T-violating asymmetries and expect it to be applicable to the future long-baseline neutrino oscillation experiments.Comment: RevTex 8 pages. 3 references added. Phys. Rev. D (in printing

Implications of the KamLAND Measurement on the Lepton Flavor Mixing Matrix and the Neutrino Mass Matrix

We explore some important implications of the KamLAND measurment on the lepton flavor mixing matrix $V$ and the neutrino mass matrix $M$. The model-independent constraints on nine matrix elements of $V$ are obtained to a reasonable degree of accuracy. We find that nine two-zero textures of $M$ are compatible with current experimental data, but two of them are only marginally allowed. Instructive predictions are given for the absolute neutrino masses, Majorana phases of CP violation, effective masses of the tritium beta decay and neutrinoless double beta decay.Comment: RevTex 15 pages (4 PS figures included

Rephasing Invariants of CP and T Violation in the Four-Neutrino Mixing Models

We calculate the rephasing invariants of CP and T violation in a favorable parametrization of the 4x4 lepton flavor mixing matrix. Their relations with the CP- and T-violating asymmetries in neutrino oscillations are derived, and the matter effects are briefly discussed.Comment: RevTex 9 pages. Slight changes. Phys. Rev. D (in press

Optimal scaling of average queue sizes in an input-queued switch: an open problem

We review some known results and state a few versions of an open problem related to the scaling of the total queue size (in steady state) in an n×n input-queued switch, as a function of the port number n and the load factor ρ. Loosely speaking, the question is whether the total number of packets in queue, under either the maximum weight policy or under an optimal policy, scales (ignoring any logarithmic factors) as O(n/(1 − ρ)).National Science Foundation (U.S.) (Grant CCF-0728554

Genomic profiling of post-transplant lymphoproliferative disorders using cell-free DNA

Diagnosing post-transplant lymphoproliferative disorder (PTLD) is challenging and often requires invasive procedures. Analyses of cell-free DNA (cfDNA) isolated from plasma is minimally invasive and highly effective for genomic profiling of tumors. We studied the feasibility of using cfDNA to profile PTLD and explore its potential to serve as a screening tool. We included seventeen patients with monomorphic PTLD after solid organ transplantation in this multi-center observational cohort study. We used low-coverage whole genome sequencing (lcWGS) to detect copy number variations (CNVs) and targeted next-generation sequencing (NGS) to identify Epstein-Barr virus (EBV) DNA load and somatic single nucleotide variants (SNVs) in cfDNA from plasma. Seven out of seventeen (41%) patients had EBV-positive tumors, and 13/17 (76%) had stage IV disease. Nine out of seventeen (56%) patients showed CNVs in cfDNA, with more CNVs in EBV-negative cases. Recurrent gains were detected for 3q, 11q, and 18q. Recurrent losses were observed at 6q. The fraction of EBV reads in cfDNA from EBV-positive patients was 3-log higher compared to controls and EBV-negative patients. 289 SNVs were identified, with a median of 19 per sample. SNV burden correlated significantly with lactate dehydrogenase levels. Similar SNV burdens were observed in EBV-negative and EBV-positive PTLD. The most commonly mutated genes were TP53 and KMT2D (41%), followed by SPEN, TET2 (35%), and ARID1A, IGLL5, and PIM1 (29%), indicating DNA damage response, epigenetic regulation, and B-cell signaling/NFkB pathways as drivers of PTLD. Overall, CNVs were more prevalent in EBV-negative lymphoma, while no difference was observed in the number of SNVs. Our data indicated the potential of analyzing cfDNA as a tool for PTLD screening and response monitoring.</p

Solvothermal synthesis of SnO2/graphene nanocomposites for supercapacitor application

A facile solvent-based synthesis route based on the oxidation–reduction reaction between graphene oxide (GO) and SnCl2·2H2O has been developed to synthesize SnO2/graphene (SnO2/G) nanocomposites. The reduction of GO and the in situ formation of SnO2 nanoparticles were achieved in one step. Characterization by X-ray diffraction (XRD), ultraviolet-visible (UV–vis) absorption spectroscopy, Raman spectroscopy, and field emission scanning electron microscopy (FESEM) confirmed the feasibility of using the solvothermally treated reaction system to simultaneously reduce GO and form SnO2 nanoparticles with an average particle size of 10 nm. The electrochemical performance of SnO2/graphene showed an excellent specific capacitance of 363.3 F/g, which was five-fold higher than that of the as-synthesized graphene (68.4 F/g). The contributing factors were the synergistic effects of the excellent conductivity of graphene and the nanosized SnO2 particles

Direct Measurements of the Branching Fractions for D0→K−e+νeD^0 \to K^-e^+\nu_e and D0→π−e+νeD^0 \to \pi^-e^+\nu_e and Determinations of the Form Factors f+K(0)f_{+}^{K}(0) and f+π(0)f^{\pi}_{+}(0)

The absolute branching fractions for the decays $D^0 \to K^-e ^+\nu_e$ and $D^0 \to \pi^-e^+\nu_e$ are determined using $7584\pm 198 \pm 341$ singly tagged $\bar D^0$ sample from the data collected around 3.773 GeV with the BES-II detector at the BEPC. In the system recoiling against the singly tagged $\bar D^0$ meson, $104.0\pm 10.9$ events for $D^0 \to K^-e ^+\nu_e$ and $9.0 \pm 3.6$ events for $D^0 \to \pi^-e^+\nu_e$ decays are observed. Those yield the absolute branching fractions to be $BF(D^0 \to K^-e^+\nu_e)=(3.82 \pm 0.40\pm 0.27)$ and $BF(D^0 \to \pi^-e^+\nu_e)=(0.33 \pm 0.13\pm 0.03)$. The vector form factors are determined to be $|f^K_+(0)| = 0.78 \pm 0.04 \pm 0.03$ and $|f^{\pi}_+(0)| = 0.73 \pm 0.14 \pm 0.06$. The ratio of the two form factors is measured to be $|f^{\pi}_+(0)/f^K_+(0)|= 0.93 \pm 0.19 \pm 0.07$.Comment: 6 pages, 5 figure

Measurements of J/psi Decays into 2(pi+pi-)eta and 3(pi+pi-)eta

Based on a sample of 5.8X 10^7 J/psi events taken with the BESII detector, the branching fractions of J/psi--> 2(pi+pi-)eta and J/psi-->3(pi+pi-)eta are measured for the first time to be (2.26+-0.08+-0.27)X10^{-3} and (7.24+-0.96+-1.11)X10^{-4}, respectively.Comment: 11 pages, 6 figure

BESII Detector Simulation

A Monte Carlo program based on Geant3 has been developed for BESII detector simulation. The organization of the program is outlined, and the digitization procedure for simulating the response of various sub-detectors is described. Comparisons with data show that the performance of the program is generally satisfactory.Comment: 17 pages, 14 figures, uses elsart.cls, to be submitted to NIM