A Computational Comparison of Optimization Methods for the Golomb Ruler Problem

The Golomb ruler problem is defined as follows: Given a positive integer n, locate n marks on a ruler such that the distance between any two distinct pair of marks are different from each other and the total length of the ruler is minimized. The Golomb ruler problem has applications in information theory, astronomy and communications, and it can be seen as a challenge for combinatorial optimization algorithms. Although constructing high quality rulers is well-studied, proving optimality is a far more challenging task. In this paper, we provide a computational comparison of different optimization paradigms, each using a different model (linear integer, constraint programming and quadratic integer) to certify that a given Golomb ruler is optimal. We propose several enhancements to improve the computational performance of each method by exploring bound tightening, valid inequalities, cutting planes and branching strategies. We conclude that a certain quadratic integer programming model solved through a Benders decomposition and strengthened by two types of valid inequalities performs the best in terms of solution time for small-sized Golomb ruler problem instances. On the other hand, a constraint programming model improved by range reduction and a particular branching strategy could have more potential to solve larger size instances due to its promising parallelization features

The impact of inter‐flood duration on non‐cohesive sediment bed stability

© 2019 John Wiley & Sons, Ltd. Limited field and flume data suggests that both uniform and graded beds appear to progressively stabilize when subjected to inter-flood flows as characterized by the absence of active bedload transport. Previous work has shown that the degree of bed stabilization scales with duration of inter-flood flow, however, the sensitivity of this response to bed surface grain size distribution has not been explored. This article presents the first detailed comparison of the dependence of graded bed stability on inter-flood flow duration. Sixty discrete experiments, including repetitions, were undertaken using three grain size distributions of identical D50 (4.8 mm); near-uniform (σg = 1.13), unimodal (σg = 1.63) and bimodal (σg = 2.08). Each bed was conditioned for between 0 (benchmark) and 960 minutes by an antecedent shear stress below the entrainment threshold of the bed (τ*c50). The degree of bed stabilization was determined by measuring changes to critical entrainment thresholds and bedload flux characteristics. Results show that (i) increasing inter-flood duration from 0 to 960 minutes increases the average threshold shear stress of the D50 by up to 18%; (ii) bedload transport rates were reduced by up to 90% as inter-flood duration increased from 0 to 960 minutes; (iii) the rate of response to changes in inter-flood duration in both critical shear stress and bedload transport rate is non-linear and is inversely proportional to antecedent duration; (iv) there is a grade dependent response to changes in critical shear stress where the magnitude of response in uniform beds is up to twice that of the graded beds; and (v) there is a grade dependent response to changes in bedload transport rate where the bimodal bed is most responsive in terms of the magnitude of change. These advances underpin the development of more accurate predictions of both entrainment thresholds and bedload flux timing and magnitude, as well as having implications for the management of environmental flow design. © 2019 John Wiley & Sons, Ltd. © 2019 John Wiley & Sons, Ltd

Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases

Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases, are expected to regulate the formation of structures encompassing coding sequences. Results: The sequence/folding energy (FE) relationship was studied by statistical, bioinformatic methods in 90 CDS containing 26,370 codons. I found that the FE (dG) associated with coding sequences is significant and negative (407 kcal/1000 bases, mean +/- S.E.M.) indicating that these sequences are able to form structures. However, the FE has only a small free component, less than 10% of the total. The contribution of the 1st and 3rd codon bases to the FE is larger than the contribution of the 2nd (central) bases. It is possible to achieve a ~ 4-fold change in FE by altering the wobble bases in synonymous codons. The sequence/FE relationship can be described with a simple algorithm, and the total FE can be predicted solely from the sequence composition of the nucleic acid. The contributions of different synonymous codons to the FE are additive and one codon cannot replace another. The accumulated contributions of synonymous codons of an amino acid to the total folding energy of an mRNA is strongly correlated to the relative amount of that amino acid in the translated protein. Conclusion: Synonymous codons are not interchangable with regard to their role in determining the mRNA FE and the relative amounts of amino acids in the translated protein, even if they are indistinguishable in respect of amino acid coding.Comment: 14 pages including 6 figures and 1 tabl

Diet, body size and menarche in a multiethnic cohort

A multiethnic cohort of 1378 Southern California school girls aged 8–13 years was followed for 4 years to evaluate factors predicting age at menarche, a risk factor for breast cancer. Height and weight were measured and dietary intake was assessed using a semi-quantitative food frequency questionnaire. Of 939 girls providing data on menarcheal status, 767 were premenarcheal at the start of the study; 679 girls provided acceptable dietary data and were included in the analyses. Cox proportional hazards models were used to assess the relationship between diet, body size, ethnicity and age at menarche. Hispanic, Asian/Pacific Island and African-American girls were more likely to experience early menarche than non-Hispanic white girls. Tall (> 148.6 cm) versus short (< 135.9 cm) girls experienced earlier menarche (relative hazard (RH) = 2.9, 95% confidence interval (CI) 2.1–4.1) as did those with high Quetelet's index (QI, kg m−2) (> 20.7) versus low QI (< 16.1) (RH = 2.2, 95% CI 1.7–2.9). Of all the dietary variables analysed, only energy intake was related to age at menarche. High versus low energy intake (> 12013 kJ vs < 7004 kJ) was associated with a delay in menarche (RH = 0.7, 95% CI 0.5–0.9); this finding was limited to a subset of heavy Hispanic girls who appeared to underreport their dietary intake. © 1999 Cancer Research Campaig

Affinity Inequality among Serum Antibodies That Originate in Lymphoid Germinal Centers

Upon natural infection with pathogens or vaccination, antibodies are produced by a process called affinity maturation. As affinity maturation ensues, average affinity values between an antibody and ligand increase with time. Purified antibodies isolated from serum are invariably heterogeneous with respect to their affinity for the ligands they bind, whether macromolecular antigens or haptens (low molecular weight approximations of epitopes on antigens). However, less is known about how the extent of this heterogeneity evolves with time during affinity maturation. To shed light on this issue, we have taken advantage of previously published data from Eisen and Siskind (1964). Using the ratio of the strongest to the weakest binding subsets as a metric of heterogeneity (or affinity inequality), we analyzed antibodies isolated from individual serum samples. The ratios were initially as high as 50-fold, and decreased over a few weeks after a single injection of small antigen doses to around unity. This decrease in the effective heterogeneity of antibody affinities with time is consistent with Darwinian evolution in the strong selection limit. By contrast, neither the average affinity nor the heterogeneity evolves much with time for high doses of antigen, as competition between clones of the same affinity is minimal.Ragon Institute of MGH, MIT and HarvardSamsung Scholarship FoundationNational Science Foundation (U.S.). Graduate Research Fellowship (Grant 1122374

A Proposal for a Near Detector Experiment on the Booster Neutrino Beamline: FINeSSE: Fermilab Intense Neutrino Scattering Scintillator Experiment

219 pages219 pagesUnderstanding the quark and gluon substructure of the nucleon has been a prime goal of both nuclear and particle physics for more than thirty years and has led to much of the progress in strong interaction physics. Still the flavor dependence of the nucleon's spin is a significant fundamental question that is not understood. Experiments measuring the spin content of the nucleon have reported conflicting results on the amount of nucleon spin carried by strange quarks. Quasi-elastic neutrino scattering, observed using a novel detection technique, provides a theoretically clean measure of this quantity. The optimum neutrino beam energy needed to measure the strange spin of the nucleon is 1 GeV. This is also an ideal energy to search for neutrino oscillations at high $\Delta m^2$ in an astrophysically interesting region. Models of the r-process in supernovae which include high-mass sterile neutrinos may explain the abundance of neutron-rich heavy metals in the universe. These high-mass sterile neutrinos are outside the sensitivity region of any previous neutrino oscillation experiments. The Booster neutrino beamline at Fermilab provides the world's highest intensity neutrino beam in the 0.5-1.0 GeV energy range, a range ideal for both of these measurements. A small detector located upstream of the MiniBooNE detector, 100 m from the recently commissioned Booster neutrino source, could definitively measure the strange quark contribution to the nucleon spin. This detector, in conjunction with the MiniBooNE detector, could also investigate $\nu_{\mu}$ disappearance in a currently unexplored, cosmologically interesting region

A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE

We provide a novel method, DRISEE (duplicate read inferred sequencing error estimation), to assess sequencing quality (alternatively referred to as “noise” or “error”) within and/or between sequencing samples. DRISEE provides positional error estimates that can be used to inform read trimming within a sample. It also provides global (whole sample) error estimates that can be used to identify samples with high or varying levels of sequencing error that may confound downstream analyses, particularly in the case of studies that utilize data from multiple sequencing samples. For shotgun metagenomic data, we believe that DRISEE provides estimates of sequencing error that are more accurate and less constrained by technical limitations than existing methods that rely on reference genomes or the use of scores (e.g. Phred). Here, DRISEE is applied to (non amplicon) data sets from both the 454 and Illumina platforms. The DRISEE error estimate is obtained by analyzing sets of artifactual duplicate reads (ADRs), a known by-product of both sequencing platforms. We present DRISEE as an open-source, platform-independent method to assess sequencing error in shotgun metagenomic data, and utilize it to discover previously uncharacterized error in de novo sequence data from the 454 and Illumina sequencing platforms

Protein kinase Cepsilon is important for migration of neuroblastoma cells

<p>Abstract</p> <p>Background</p> <p>Migration is important for the metastatic capacity and thus for the malignancy of cancer cells. There is limited knowledge on regulatory factors that promote the migration of neuroblastoma cells. This study investigates the hypothesis that protein kinase C (PKC) isoforms regulate neuroblastoma cell motility.</p> <p>Methods</p> <p>PKC isoforms were downregulated with siRNA or modulated with activators and inhibitors. Migration was analyzed with scratch and transwell assays. Protein phosphorylation and expression levels were measured with Western blot.</p> <p>Results</p> <p>Stimulation with 12-<it>O</it>-tetradecanoylphorbol-13-acetate (TPA) induced migration of SK-N-BE(2)C neuroblastoma cells. Treatment with the general protein kinase C (PKC) inhibitor GF109203X and the inhibitor of classical isoforms Gö6976 inhibited migration while an inhibitor of PKCβ isoforms did not have an effect. Downregulation of PKCε, but not of PKCα or PKCδ, with siRNA led to a suppression of both basal and TPA-stimulated migration. Experiments using PD98059 and LY294002, inhibitors of the Erk and phosphatidylinositol 3-kinase (PI3K) pathways, respectively, showed that PI3K is not necessary for TPA-induced migration. The Erk pathway might be involved in TPA-induced migration but not in migration driven by PKCε. TPA induced phosphorylation of the PKC substrate myristoylated alanine-rich C kinase substrate (MARCKS) which was suppressed by the PKC inhibitors. Treatment with siRNA oligonucleotides against different PKC isoforms before stimulation with TPA did not influence the phosphorylation of MARCKS.</p> <p>Conclusion</p> <p>PKCε is important for migration of SK-N-BE(2)C neuroblastoma cells. Neither the Erk pathway nor MARCKS are critical downstream targets of PKCε but they may be involved in TPA-mediated migration.</p

Measurement of the branching fraction and CP content for the decay B(0) -> D(*+)D(*-)

This is the pre-print version of the Article. The official published version can be accessed from the links below. Copyright @ 2002 APS.We report a measurement of the branching fraction of the decay B0→D*+D*- and of the CP-odd component of its final state using the BABAR detector. With data corresponding to an integrated luminosity of 20.4  fb-1 collected at the Υ(4S) resonance during 1999–2000, we have reconstructed 38 candidate signal events in the mode B0→D*+D*- with an estimated background of 6.2±0.5 events. From these events, we determine the branching fraction to be B(B0→D*+D*-)=[8.3±1.6(stat)±1.2(syst)]×10-4. The measured CP-odd fraction of the final state is 0.22±0.18(stat)±0.03(syst).This work is supported by DOE and NSF (USA), NSERC (Canada), IHEP (China), CEA and CNRS-IN2P3 (France), BMBF (Germany), INFN (Italy), NFR (Norway), MIST (Russia), and PPARC (United Kingdom). Individuals have received support from the A.P. Sloan Foundation, Research Corporation, and Alexander von Humboldt Foundation

Anti-Angiogenic Activity of a Small Molecule STAT3 Inhibitor LLL12

Background: Recent data indicate the Signal Transducer and Activator of Transcription 3 (STAT3) pathway is required for VEGF production and angiogenesis in various types of cancers. STAT3 inhibitors have been shown to reduce tumor microvessel density in tumors but a direct anti-angiogenic activity has not been described. Methodology/Principal Findings: We investigated the direct action of a small molecule inhibitor of STAT3 (LLL12) in human umbilical cord vascular endothelial cells (HUVECs) in vitro, in a Matrigel model for angiogenesis in vivo, and its antitumor activity in a xenograft model of osteosarcoma. LLL12 (100 nM) significantly inhibited VEGF-stimulated STAT3 phosphorylation in HUVECs, reduced their proliferation/migration and inhibited VEGF-induced tube formation. Morphologic analysis of LLL12 treated HUVECs demonstrated marked changes in actin/tubulin distribution and bundling. In scid mice, LLL12 reduced microvessel invasion into VEGF-infused Matrigel plugs by,90 % at a dose of 5 mg/kg daily. Following a period of tumor progression (2 weeks), LLL12 completely suppressed further growth of established OS-1 osteosarcoma xenografts. Pharmacodynamic studies showed robust phosphorylated STAT3 in control tumors, whereas phospho-STAT3 was not detected in LLL12-treated OS-1 tumors. Treated tumors demonstrated decreased proliferation (Ki67 staining), and decreased microvessel density (CD34 staining), but no significant increase in apoptosis (TUNEL staining), relative to controls. Assay of angiogenic factors, using an antibody array, showed VEGF, MMP-9, Angiopoietin1/2, Tissue Factor and FGF-