A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions

Abstract Motivation: The systematic integration of expression profiles and other types of gene information, such as chromosomal localization, ontological annotations and sequence characteristics, still represents a challenge in the gene expression arena. In particular, the analysis of transcriptional data in context of the physical location of genes in a genome appears promising in detecting chromosomal regions with transcriptional imbalances often characterizing cancer. Results: A computational tool named locally adaptive statistical procedure (LAP), which incorporates transcriptional data and structural information for the identification of differentially expressed chromosomal regions, is described. LAP accounts for variations in the distance between genes and in gene density by smoothing standard statistics on gene position before testing the significance of their differential levels of gene expression. The procedure smoothes parameters and computes p-values locally to account for the complex structure of the genome and to more precisely estimate the differential expression of chromosomal regions. The application of LAP to three independent sets of raw expression data allowed identifying differentially expressed regions that are directly involved in known chromosomal aberrations characteristic of tumors. Availability: Functions in R for implementing the LAP method are available at Contact: [email protected] Supplementary Information

Where Am I? A Meta-Analysis of Experiments on the Effects of Progress Indicators for Web Surveys

The use of progress indicators seems to be standard in many online surveys. Researchers include them in surveys in the hope they will help reduce drop-off rates. However, there is no consensus in the literature regarding their effects. In this meta-analysis, we analyzed 32 randomized experiments comparing drop-off rates of an experimental group who completed an online survey in which a progress indicator was shown to drop-off rates of a control group to whom the progress indicator was not shown. In all the studies, a drop-off was defined as a discontinuance of the survey (at any point) after it has begun, resulting in failure to complete the survey. Three types of progress indicators were analyzed: constant, fast-to-slow, and slow-to-fast. Our results show that, overall, using a constant progress indicator does not significantly help reduce drop-offs and that effectiveness of the progress indicator varies depending on the speed of indicator: Fast-to-slow indicators reduced drop-offs, whereas slow-to-fast indicators increased drop-offs. We also found that among the studies in which a small incentive was promised, showing a constant progress indicator increased the drop-off rate. These findings question the common belief that progress indicators help reduce drop-off rates

Using survival data in gene mapping : using survival data in genetic linkage and family-based association analysis

The largest part of this thesis is devoted to newly developed statistical methods for age at onset linkage analysis. We used frailty models in which random effects were introduced to model the dependence between outcomes of relatives due to sharing of marker alleles Identical By Descent. From the retrospective likelihood of the marker data conditional on the phenotypes, we derived score tests for genetic linkage analysis. The score statistics appear to be classical Non-Parametric Linkage statistics weighted by functions of the age at onset (or age at censoring) of the family members. These tests are based on allele-sharing, they can be applied to families ascertained through their phenotypes, and they do not require specification of genetic models or penetrance functions. Further, they can incorporate both affected and unaffected family members. In fact, the age at disease onset of the affecteds and the age at censoring of the unaffecteds are considered by this approach. Finally, with respect to the likelihood-ratio tests proposed in the literature the derived score tests are computationally faster, locally most powerful, and robust. For all these reasons, the proposed weighted NPL statistics provide a practical solution for mapping genes for complex diseases with variable age at onset.UBL - phd migration 201

Role of plasma-induced defects in the generation of 1/f noise in graphene

It has already been reported that 1/f noise in graphene can be dominated by fluctuations of charge carrier mobility. We show here that the increasing damage induced by oxygen plasma on graphene samples result in two trends: at low doses, the magnitude of the 1/f noise increases with the dose; and at high doses, it decreases with the dose. This behaviour is interpreted in the framework of 1/f noise generated by carrier mobility fluctuations where the concentration of mobility fluctuation centers and the mean free path of the carriers are competing factors. Published by AIP Publishing

Realization of the farad from the dc quantum Hall effect with digitally-assisted impedance bridges

A new traceability chain for the derivation of the farad from dc quantum Hall effect has been implemented at INRIM. Main components of the chain are two new coaxial transformer bridges: a resistance ratio bridge, and a quadrature bridge, both operating at 1541 Hz. The bridges are energized and controlled with a polyphase direct-digital-synthesizer, which permits to achieve both main and auxiliary equilibria in an automated way; the bridges and do not include any variable inductive divider or variable impedance box. The relative uncertainty in the realization of the farad, at the level of 1000 pF, is estimated to be 64E-9. A first verification of the realization is given by a comparison with the maintained national capacitance standard, where an agreement between measurements within their relative combined uncertainty of 420E-9 is obtained.Comment: 15 pages, 11 figures, 3 table

Fire, vegetation, and Holocene climate in a southeastern Tibetan lake: A multi-biomarker reconstruction from Paru Co

The fire history of the Tibetan Plateau over centennial to millennial timescales is not well known. Recent ice core studies reconstruct fire history over the past few decades but do not extend through the Holocene. Lacustrine sedimentary cores, however, can provide continuous records of local environmental change on millennial scales during the Holocene through the accumulation and preservation of specific organic molecular biomarkers. To reconstruct Holocene fire events and vegetation changes occurring on the southeastern Tibetan Plateau and the surrounding areas, we used a multi-proxy approach, investigating multiple biomarkers preserved in core sediment samples retrieved from Paru Co, a small lake located in the Nyainqentanglha Mountains (29°47045.600N, 92°21007.200 E; 4845ma.s.l.). Biomarkers include n-alkanes as indicators of vegetation, polycyclic aromatic hydrocarbons (PAHs) as combustion proxies, fecal sterols and stanols (FeSts) as indicators of the presence of humans or grazing animals, and finally monosaccharide anhydrides (MAs) as specific markers of vegetation burning processes. Insolation changes and the associated influence on the Indian summer monsoon (ISM) affect the vegetation distribution and fire types recorded in Paru Co throughout the Holocene. The early Holocene (10.7- 7.5 cal kyr BP) n-alkane ratios demonstrate oscillations between grass and conifer communities, resulting in respective smouldering fires represented by levoglucosan peaks, and high-temperature fires represented by high-molecular-weight PAHs. Forest cover increases with a strengthened ISM, where coincident high levoglucosan to mannosan (L = M) ratios are consistent with conifer burning. The decrease in the ISM at 4.2 cal kyr BP corresponds with the expansion of regional civilizations, although the lack of human FeSts above the method detection limits excludes local anthropogenic influence on fire and vegetation changes. The late Holocene is characterized by a relatively shallow lake surrounded by grassland, where all biomarkers other than PAHs display only minor variations. The sum of PAHs steadily increases throughout the late Holocene, suggesting a net increase in local to regional combustion that is separate from vegetation and climate change

Bringing Salary Transparency to the World: Computing Robust Compensation Insights via LinkedIn Salary

The recently launched LinkedIn Salary product has been designed with the goal of providing compensation insights to the world's professionals and thereby helping them optimize their earning potential. We describe the overall design and architecture of the statistical modeling system underlying this product. We focus on the unique data mining challenges while designing and implementing the system, and describe the modeling components such as Bayesian hierarchical smoothing that help to compute and present robust compensation insights to users. We report on extensive evaluation with nearly one year of de-identified compensation data collected from over one million LinkedIn users, thereby demonstrating the efficacy of the statistical models. We also highlight the lessons learned through the deployment of our system at LinkedIn.Comment: Conference information: ACM International Conference on Information and Knowledge Management (CIKM 2017

Recommended implementation of electrical resistance tomography for conductivity mapping of metallic nanowire networks using voltage excitation

The knowledge of the spatial distribution of the electrical conductivity of metallic nanowire networks (NWN) is important for tailoring the performance in applications. This work focuses on Electrical Resistance Tomography (ERT), a technique that maps the electrical conductivity of a sample from several resistance measurements performed on its border. We show that ERT can be successfully employed for NWN characterisation if a dedicated measurement protocol is employed. When applied to other materials, ERT measurements are typically performed with a constant current excitation; we show that, because of the peculiar microscopic structure and behaviour of metallic NWN, a constant voltage excitation protocols is preferable. This protocol maximises the signal to noise ratio in the resistance measurements—and thus the accuracy of ERT maps—while preventing the onset of sample alterations