Approximation algorithms for stochastic and risk-averse optimization

We present improved approximation algorithms in stochastic optimization. We prove that the multi-stage stochastic versions of covering integer programs (such as set cover and vertex cover) admit essentially the same approximation algorithms as their standard (non-stochastic) counterparts; this improves upon work of Swamy \& Shmoys which shows an approximability that depends multiplicatively on the number of stages. We also present approximation algorithms for facility location and some of its variants in the $2$-stage recourse model, improving on previous approximation guarantees. We give a $2.2975$-approximation algorithm in the standard polynomial-scenario model and an algorithm with an expected per-scenario $2.4957$-approximation guarantee, which is applicable to the more general black-box distribution model.Comment: Extension of a SODA'07 paper. To appear in SIAM J. Discrete Mat

What is Hacking’s argument for entity realism?

According to Ian Hacking’s Entity Realism, unobservable entities that scientists carefully manipulate to study other phenomena are real. Although Hacking presents his case in an intuitive, attractive, and persuasive way, his argument remains elusive. I present five possible readings of Hacking’s argument: a no-miracle argument, an indispensability argument, a transcendental argument, a Vichian argument, and a non-argument. I elucidate Hacking’s argument according to each reading, and review their strengths, their weaknesses, and their compatibility with each othe

Additional file 2: of Population cigarette consumption in Great Britain: novel insights using retail sales data

Trends in mean monthly cigarette sales per adult smoker, by pack size, Scotland and England/Wales, 2008–2015 (DOCX 71 kb

Additional file 2 of Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

Supplementary figures. This file contains the mentioned supplementary figures. (PDF 712 kb

Quantifying Protein Synthesis and Degradation in Arabidopsis

<p>Poster presented at Proteomics Forum 2015, Berlin.</p> <p>Hosted by the German Foundation for Proteomics Resarch (DGPF)</p

Additional file 1 of Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage

Supplementary figures, tables, and methods. Additional file 1 contains supplementary figures and tables referred to in the text. It also contains a description of the counting methods and a comparison of the isoform-guided filtering with bin-level filtering. (PDF 9520 KB

Additional file 2 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

Figure S2. Schema of the Galaxy pipeline: 1) to collapse FastQ file into the sequence and number of appearance ranked by the counts. 2) converts FASTA files into the Galaxy data file type “tabular” (tab-separated text files). 3) converts dashes in to tabs and 4) extracts selected columns of a given tabular file. 5) joins files by a selected identifier column. (PNG 4714 kb

Association between anti-HLA reactivity following vaccination with uninfected C8166 cells using different adjuvants and outcome of challenge.

<p>Virus infection status was determined by PCR for SIV<i>gag</i> proviral DNA and virus isolation (VI) from PBMC of macaques challenged with SIVmac₂₅₁32H (a) following vaccination with 4 doses of uninfected C8166 cells with Quil A adjuvant (group E) or with GMDP adjuvant (group F) (a) following vaccination with 2 doses of SIV infected C8166 cells (group C) or with uninfected C8166 cells (group D). Bar charts show the associated median fluorescence intensity (y axis) of serum samples for each macaque tested against HLA class I (red bars) and class II (green bars) bead sets (x axis). Background binding of pre-vaccination sera is shown as light red and light green for HLA class I and class II respectively. * indicates not tested, probe number refers HLA allele-specific bead sets.</p

Additional file 3 of Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

Table S1. Filtering details for potential miRNAs. (XLSX 73 kb

Infectivity neutralising activity against virus unrelated to vaccine.

<p>Neutralising antibody activity against SIVsmE660 propagated on human C8166 cells in sera from macaques immunised with uninfected C8166 cell vaccines (group E) in the absence (left panel) or presence (right panel) of complement. Pre-immune sera (black line) shows means of all animals with standard deviations. Dashed lines indicate unprotected animal.</p