'Not just bones': a cultural and political history of mass grave exhumations in Spain

In this paper I analyze the exhumations of mass graves of the Spanish Civil War (1936–39) and dictatorship (1939–75) as spaces where processes of attribution of meaning take place, and I’ll propose a provisional thesis on how cultural and political meaning is formed through the performance of forensic exhumations of mass graves. Hereby the focus is on the attribution of meaning to the exhumations in the public sphere, or, to say it with the words of Johannes Fabian, I consider death ‘a prime datum of communication’ (Fabian 2004). I argue that not only forensic truth is the object of the exhumations, but also the ‘making of’ truth, as a process of public acknowledgement and identification with the dead

RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification

Mass spectrometry-driven proteomics is increasingly relying on quantitative analyses for biological discoveries. As a result, different methods and algorithms have been developed to perform relative or absolute quantification based on mass spectrometry data. One of the most popular quantification methods are the so-called label-free approaches, which require no special sample processing, and can even be applied retroactively to existing data sets. Of these label-free methods, the MS/MS-based approaches are most often applied, mainly because of their inherent simplicity as compared to MS-based methods. The main application of these approaches is the determination of relative protein amounts between different samples, expressed as protein ratios. However, as we demonstrate here, there are some issues with the reproducibility across replicates of these protein ratio sets obtained from the various, MS/MS-based label-free methods, indicating that the existing methods are not optimally robust. We therefore present two new Methods (called RIBAR and xRIBAR) that use the available MS/MS data more effectively, achieving increased robustness. Both the accuracy and the precision of our novel methods are analyzed and compared to the existing methods to illustrate the increased robustness of our new methods over existing ones

History from the Grave? Politics of time in Spanish mass grave exhumations

During the last decade, Spanish memory movements have exhumed a great number of mass graves from the Civil War and Francoist repression. This exhumation campaign is often interpreted in psychopathological terms as a natural reaction to a traumatic past and as proving that this past should be healed by a therapeutic memory that fosters closure -- a vision that we call 'trauma-therapy-closure (TTC) time'. Although this vision is in line with widespread 'transitional justice' discourse it should be critically analyzed. We argue that the Spanish situation does not prove the naturalness and universal applicability of TTC time. Although we do identify an influential exhumation group that shares aspects of this TTC vision, its approach is contested by local actors and competing exhumation organizations that engage in alternative politics of time. Therefore we demonstrate how the case of Spain rather reveals how TTC time is actively disseminated and promoted on a local level

PiTRAQ, a strategy to simultaneously correlate protein expression and phosphorylation stoichiometry between different samples: evaluation on different mass spectrometers

C

The iceLogo web server and SOAP service for determining protein consensus sequences

he iceLogo web server and SOAP service implement the previously published iceLogo algorithm. iceLogo builds on probability theory to visualize protein consensus sequences in a format resembling sequence logos. Peptide sequences are compared against a reference sequence set that can be tailored to the studied system and the used protocol. As such, not only over-but also underrepresented residues can be visualized in a statistically sound manner, which further allows the user to easily analyse and interpret conserved sequence patterns in proteins. The web application and SOAP service can be found free and open to all users without the need for a login on http://iomics.ugent.be/icelogoserver/main.html

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. Accurate generation of sequence logos is often compromised by sequence redundancy and low number of observations. Moreover, most methods available for sequence logo generation focus on displaying the position-specific enrichment of amino acids, discarding the equally valuable information related to amino acid depletion. Seq2logo aims at resolving these issues allowing the user to include sequence weighting to correct for data redundancy, pseudo counts to correct for low number of observations and different logotype representations each capturing different aspects related to amino acid enrichment and depletion. Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein of interest. The output from the server is a sequence logo and a PSSM. Seq2Logo is available at http://www.cbs.dtu.dk/biotools/Seq2Logo (14 May 2012, date last accessed)