MoviCompile : An LLVM based compiler for heterogeneous SIMD code generation

Numerous applications in communication and multimedia domains show significant data-level parallelism (DLP). The amount of DLP varies between applications in the same domain or even within a single application. Most architectures support a single vector-, SIMD-width which may not be optimal. This may cause performance and energy inefficiency. We propose the use of multiple (heterogeneous) vector-widths to better serve applications with varying DLP. The SHAVE (Streaming Hybrid Architecture Vector Engine) VLIW vector processor shown in Figure 1 is an example of such an architecture. SHAVE is a unique VLIW processor that provides hardware support for native 32-bit (short) and 128-bit (long) vector operations. Vector arithmetic unit (VAU) supports 128-bit vector arithmetic of 8/16/32-bit integer and 16/32-bit floating point types. Scalar arithmetic unit (SAU) supports 32-bit vector arithmetic of 8/16-bit integer and 16-bit floating point types. The moviCompile compiler is an LLVM based commercial compiler targeting code generation for SHAVE processor family. The moviCompile compiler is capable of SIMD code generation for 128-bit (long) and 64-bit vector operations. This work focuses on compiler backend support for 32-bit (short) vector operations. More specifically, this work aims to generate SIMD code for short vector types (e.g. 4 x i8, 2 x i16, 2 x f16) that can be executed on 32-bit SAU next to the 128/64-bit SIMD code. As a result, moviCompile is able to generate heterogeneous assembly code consisting of both short and long vector SIMD operations. Currently, we are testing the compiler using TSVC (Test Suite for Vectorizing Compilers) and intend to measure the performance improvements

Determination of the inhibitory effects of microdiets used in routine commercial feeding protocols on protease activities of Argyrosomus regius (Asso, 1801) larva

The aim of this study was to determine the inhibitory effects of feed ingredients on protease activities of Argyrosomus regius larvae using in vitro techniques. A. regius larvae fed on a commercial feeding procedure were sampled thirteen times, during the sampling period (from 3 to 32 days after hatching (DAH)). The differences observed in protease activities of meagre larvae during the sampling period were statistically significant (p<0.05). The lowest and highest protease activities of meagre larvae were 5.95±0.6 U/mg protein (15 DAH) and 211.21±12.56 U/mg protein (7 DAH), respectively. The fluctuations observed in protease activities of A. regius larvae were between 10 DAH and 32 DAH. Commercial diets such as Orange Start-S (100-200µ), Orange Start-L (200-300µ), Orange Nurse-XS (300-500µ), Orange Grow-S (300-500µ) and Orange Grow-L (500-800µ) caused the inhibitions on protease activities in meagre larvae to range from 16 to 32 DAH. The results point to the inadequacy of commercial diets such as Orange Grow-S, Orange Grow-L and suitability of Orange Start-S, Orange Start-L, Orange Nurse-XS for feeding meagre larvae during the weaning stage. For the mass production of quality juveniles, future studies should take into account the inhibitory effects of commercial diets and feed ingredients before the manufacturing process. A similar approach may be used to determine the most suitable commercial diets for use during the weaning stages of marine fish larvae to obtain the best growth performance and survival

Mixed-length SIMD code generation for VLIW architectures with multiple native vector-widths

The degree of DLP parallelism in applications is not fixed and varies due to different computational characteristics of applications. On the contrary, most of the processors today include single-width SIMD (vector) hardware to exploit DLP. However, single-width SIMD architectures may not be optimal to serve applications with varying DLP and they may cause performance and energy inefficiency. We propose the usage of VLIW processors with multiple native vector-widths to better serve applications with changing DLP. SHAVE is an example of such VLIW processor and provides hardware support for the native 32-bit and 128-bit wide vector operations. This paper researches and implements the mixed-length SIMD code generation support for SHAVE processor. More specifically, we target generating 32-bit and 128/64-bit SIMD code for the native 32-bit and 128-bit wide vector units of SHAVE processor. In this way, we improved the performance of compiler generated SIMD code by reducing the number of overhead operations and by increasing the SIMD hardware utilization. Experimental results demonstrated that our methodology implemented in the compiler improves the performance of synthetic benchmarks up to 47%

Impossible protest: noborders in Calais

Since the closure of the Red Cross refugee reception centre in Sangatte, undocumented migrants in Calais hoping to cross the border to Britain have been forced to take refuge in a number of squatted migrant camps, locally known by all as ‘the jungles.’ Unauthorised shanty-like residences built by the migrants themselves, living conditions in the camps are very poor. In June 2009, European ‘noborder’ activists set up a week-long protest camp in the area with the intention of confronting the authorities over their treatment of undocumented migrants. In this article, we analyse the June 2009 noborder camp as an instance of ‘immigrant protest.’ Drawing on ethnographic materials and Jacques Rancière's work on politics and aesthetics, we construct a typology of forms of border control through which to analyse the different ways in which the politics of the noborder camp were staged, performed and policed. Developing a critique of policing practices which threatened to make immigrant protest ‘impossible’, we highlight moments of protest which, through the affirmation of an ‘axiomatic’ equality, disrupted and disarticulated the borders between citizens and non-citizens, the political and non-political

RNA with chemotherapeutic base analogues as a dual-functional anti-cancer drug

Nanoparticles of different sizes formulated with unmodified RNA and Protamine differentially engage Toll-like Receptors (TLRs) and activate innate immune responses in vitro. Here, we report that similar differential immunostimulation that depends on the nanoparticle sizes is induced in vivo in wild type as well as in humanized mice. In addition, we found that the schedule of injections strongly affects the magnitude of the immune response. Immunostimulating 130 nm nanoparticles composed of RNA and Protamine can promote lung metastasis clearance but provides no control of subcutaneous tumors in a CT26 tumor model. We further enhanced the therapeutic capacity of Protamine-RNA nanoparticles by incorporating chemotherapeutic base analogues in the RNA; we coined these immunochemotherapeutic RNAs (icRNAs). Protamine-icRNA nanoparticles were successful at controlling established subcutaneous CT26 and B16 tumors as well as orthotopic glioblastoma. These data indicate that icRNAs are promising cancer therapies, which warrants their further validation for use in the clinic. Keywords: 5FU; Chemotherapy; RNA; immunotherapy; toll like receptor; type I interferon

Highly-sensitive, label-free detection of microorganisms and viruses via interferometric reflectance imaging sensor

Pathogenic microorganisms and viruses can easily transfer from one host to another and cause disease in humans. The determination of these pathogens in a time- and cost-effective way is an extreme challenge for researchers. Rapid and label-free detection of pathogenic microorganisms and viruses is critical in ensuring rapid and appropriate treatment. Sensor technologies have shown considerable advancements in viral diagnostics, demonstrating their great potential for being fast and sensitive detection platforms. In this review, we present a summary of the use of an interferometric reflectance imaging sensor (IRIS) for the detection of microorganisms. We highlight low magnification modality of IRIS as an ensemble biomolecular mass measurement technique and high magnification modality for the digital detection of individual nanoparticles and viruses. We discuss the two different modalities of IRIS and their applications in the sensitive detection of microorganisms and viruses.Published versio

Governing Uncertainty in a Secular Age: Rationalities of Violence, Theodicy and Torture

This article explores the problem of governing uncertainty in a secular age by focusing on the theological notion of ‘theodicy’ as the underlying rationale for the use of torture in the so-called ‘war on terror’. With God’s departure from the world, the problem of uncertainty acquires new salience as human beings can no longer explain tragic events as part of a transcendent order and must find immanent causes for the ‘evils’ that surround them. Taking a cue from Max Weber, I discuss how the problem of theodicy – how to reconcile the existence of God with the presence of evil in the world – does not disappear in the secular age but is mobilized through a Foucauldian biopolitical logic. Secular theodicy governs uncertainty through the production of economies of knowledge that rationalize processes of criminalization and securitization of entire groups and justify the use of violence. This process is particularly striking when analysing the use of torture in the so-called ‘war on terror’. Through a comparison with medieval practices and focusing on the cases of Guantanamo and Abu Ghraib, the article shows how secular torture is the product of a biopolitical theodicy aimed at governing uncertainty through the construction of the tortured as immanent evils who threaten our ‘good life’ and ‘deserve’ their treatment. Secular theodicy turns torture into an extreme form of governmentality of uncertainty in which the disciplining of conduct becomes the construction of subjectivities based on essentialist, stereotypical and racist – and for these very reasons, reassuring – economies of knowledge

MC38 colorectal tumor cell lines from two different sources display substantial differences in transcriptome, mutanome and neoantigen expression

IntroductionThe cell line MC38 is a commonly used murine model for colorectal carcinoma. It has a high mutational burden, is sensitive to immune checkpoint immunotherapy and endogenous CD8+ T cell responses against neoantigens have been reported. MethodsHere, we re-sequenced exomes and transcriptomes of MC38 cells from two different sources, namely Kerafast (originating from NCI/NIH, MC38-K) and the Leiden University Medical Center cell line collection (MC38-L), comparing the cell lines on the genomic and transcriptomic level and analyzing their recognition by CD8+ T cells with known neo-epitope specificity. ResultsThe data reveals a distinct structural composition of MC38-K and MC38-L cell line genomes and different ploidies. Further, the MC38-L cell line harbored about 1.3-fold more single nucleotide variations and small insertions and deletions than the MC38-K cell line. In addition, the observed mutational signatures differed; only 35.3% of the non-synonymous variants and 5.4% of the fusion gene events were shared. Transcript expression values of both cell lines correlated strongly (p = 0.919), but we found different pathways enriched in the genes that were differentially upregulated in the MC38-L or MC38-K cells, respectively. Our data show that previously described neoantigens in the MC38 model such as Rpl18(mut) and Adpgk(mut) were absent in the MC38-K cell line resulting that such neoantigen-specific CD8+ T cells recognizing and killing MC38-L cells did not recognize or kill MC38-K cells. ConclusionThis strongly indicates that at least two sub-cell lines of MC38 exist in the field and underlines the importance of meticulous tracking of investigated cell lines to obtain reproducible results, and for correct interpretation of the immunological data without artifacts. We present our analyses as a reference for researchers to select the appropriate sub-cell line for their own studies