Towards Composable GPU Programming: Programming GPUs with Eager Actions and Lazy Views

In this paper, we advocate a composable approach to programming systems with Graphics Processing Units (GPU): programs are developed as compositions of generic, reusable patterns. Current GPU programming approaches either rely on low-level, monolithic code without patterns (CUDA and OpenCL), which achieves high performance at the cost of cumbersome and error-prone programming, or they improve the programmability by using pattern-based abstractions (e.g., Thrust) but pay a performance penalty due to inefficient implementations of pattern composition. We develop an API for GPUs based programming on C++ with STL-style patterns and its compiler-based implementation. Our API gives the application developers the native C++ means (views and actions) to specify precisely which pattern compositions should be automatically fused during code generation into a single efficient GPU kernel, thereby ensuring a high target performance. We implement our approach by extending the range-v3 library which is currently being developed for the forthcoming C++ standards. The composable programming in our approach is done exclusively in the standard C++14, with STL algorithms used as patterns which we re-implemented in parallel for GPU. Our compiler implementation is based on the LLVM and Clang frameworks, and we use advanced multi-stage programming techniques for aggressive runtime optimizations. We experimentally evaluate our approach using a set of benchmark applications and a real-world case study from the area of image processing. Our codes achieve performance competitive with CUDA monolithic implementations, and we outperform pattern-based codes written using Nvidia’s Thrust

Visual consumption, collective memory and the representation of war

Conceiving of the visual as a significant force in the production and dissemination of collective memory, we argue that a new genre of World War Two films has recently emerged that form part of a new discursive “regime of memory” about the war and those that fought and lived through it, constituting a commemoration as much about reflecting on the present as it is about remembering the past. First, we argue that these films seek to reaffirm a (particular conception of a) US national identity and military patriotism in the post–Cold War era by importing World War Two as the key meta‐narrative of America’s relationship to war in order to “correct” and help “erase” Vietnam’s more negative discursive rendering. Second, we argue that these films attempt to rewrite the history of World War Two by elevating and illuminating the role of the US at the expense of the Allies, further serving to reaffirm America’s position of political and military dominance in the current age, and third, that these films form part of a celebration of the generation that fought World War Two, which may accord them a position of nostalgic and sentimental greatness, as their collective spirit and notions of duty and service shine against the foil of what might frequently be seen as our own present moral ambivalence

The German National Registry of Primary Immunodeficiencies (2012-2017)

Introduction: The German PID-NET registry was founded in 2009, serving as the first national registry of patients with primary immunodeficiencies (PID) in Germany. It is part of the European Society for Immunodeficiencies (ESID) registry. The primary purpose of the registry is to gather data on the epidemiology, diagnostic delay, diagnosis, and treatment of PIDs. Methods: Clinical and laboratory data was collected from 2,453 patients from 36 German PID centres in an online registry. Data was analysed with the software Stata® and Excel. Results: The minimum prevalence of PID in Germany is 2.72 per 100,000 inhabitants. Among patients aged 1–25, there was a clear predominance of males. The median age of living patients ranged between 7 and 40 years, depending on the respective PID. Predominantly antibody disorders were the most prevalent group with 57% of all 2,453 PID patients (including 728 CVID patients). A gene defect was identified in 36% of patients. Familial cases were observed in 21% of patients. The age of onset for presenting symptoms ranged from birth to late adulthood (range 0–88 years). Presenting symptoms comprised infections (74%) and immune dysregulation (22%). Ninety-three patients were diagnosed without prior clinical symptoms. Regarding the general and clinical diagnostic delay, no PID had undergone a slight decrease within the last decade. However, both, SCID and hyper IgE- syndrome showed a substantial improvement in shortening the time between onset of symptoms and genetic diagnosis. Regarding treatment, 49% of all patients received immunoglobulin G (IgG) substitution (70%—subcutaneous; 29%—intravenous; 1%—unknown). Three-hundred patients underwent at least one hematopoietic stem cell transplantation (HSCT). Five patients had gene therapy. Conclusion: The German PID-NET registry is a precious tool for physicians, researchers, the pharmaceutical industry, politicians, and ultimately the patients, for whom the outcomes will eventually lead to a more timely diagnosis and better treatment

The Lighthouse, Bellevue Washington. NAIOP Workshop Project

Sustainable Venture Partners (SVP) is seeking Investment Committee approval for The Lighthouse, a mixed-use multifamily and retail building to be located in downtown Bellevue. The Lighthouse sits at the northeast corner of the intersection of NE 8th Street and 102nd Avenue NE. The parcel is currently owned by McAusland Real Properties LLC. The Lighthouse is proud to be the first cross laminated timber building (CLT) in downtown Bellevue. The Lighthouse has one core theme: to be the beacon in Bellevue of innovative, sustainable and memorable design. The Lighthouse is a 221,942 GSF nine-story mixed use residential project with 121 residential units, 8,142 GSF of Class-A active use retail, and two levels of underground parking for 178 vehicles, and 60 bicycles. Ground level retail tenants will be located on the 8th Street frontage, while the residential lobby will front 102nd. An outdoor community open space is housed in the courtyard to the northeast of the structure. Apartments are situated on floors two through nine. The nine story mass timber building will have magnificent protected views to the southwest and west with views of Meydenbauer Bay, Lake Washington, and Downtown Seattle. The Lighthouse will pay homage to the history of the Pacific Northwest’s timber industry and serve tomorrow’s tech and environmental innovation for which Washington and Bellevue are renowned for. The look and feel will honor the Northwest with minimal, modern, and natural designs. This property has been family owned for many years and its tenants have offered a gathering place for the community of Bellevue, we look to continue this tradition. The Lighthouse will serve as a beacon for individuals and families looking to put their roots down in a natural, healthy and beautiful home in the heart of Bellevue

Characterization of three novel DyP-type peroxidases from Streptomyces chartreusis NRRL 3882

Abstract Aims Actinobacteria are known to produce extracellular enzymes including DyPs. We set out to identify and characterize novel peroxidases from Streptomyces chartreusis NRRL 3882, because S. chartreusis belongs to the small group of actinobacteria with three different DyPs. Methods and Results The genome of the actinomycete S. chartreusis NRRL 3882 was mined for novel DyP-type peroxidases. Three genes encoding for DyP-type peroxidases were cloned and overexpressed in Escherichia coli. Subsequent characterization of the recombinant proteins included examination of operating conditions such as pH, temperature and H2O2 concentrations, as well as substrate spectrum. Despite their high sequence similarity, the enzymes named SCDYP1-SCDYP3 presented distinct preferences regarding their operating conditions. They showed great divergence in H2O2 tolerance and stability, with SCDYP2 being most active at concentrations above 50 mmol l−1. Moreover, SCDYP1 and SCDYP3 preferred acidic pH (typical for DyP-type peroxidases), whereas SCDYP2 was most active at pH 8. Conclusions Regarding the function of DyPs in nature, these results suggest that availability of different DyP variants with complementary activity profiles in one organism might convey evolutionary benefits. Significance and Impact of the Study DyP-type peroxidases are able to degrade xenobiotic compounds and thus can be applied in biocatalysis and bioremediation. However, the native function of DyPs and the benefits for their producers largely remain to be elucidated. </jats:sec

Supplementary Figures S1-S3 from The cold atmospheric pressure plasma-generated species superoxide, singlet oxygen and atomic oxygen activate the molecular chaperone Hsp33

Cold atmospheric pressure plasmas are used for surface decontamination or disinfection, e.g. in clinical settings. Protein aggregation has been shown to significantly contribute to the antibacterial mechanisms of plasma. To investigate the potential role of the redox-activated zinc-binding chaperone Hsp33 in preventing protein aggregation and thus mediating plasma resistance, we compared the plasma sensitivity of wild-type E. coli to that of an hslO deletion mutant lacking Hsp33 as well as an over-producing strain. Over-production of Hsp33 increased plasma survival rates above wild-type levels. Hsp33 was previously shown to be activated by plasma in vitro. For the PlasmaDerm source applied in dermatology, reversible activation of Hsp33 was confirmed. Thiol oxidation and Hsp33 unfolding, both crucial for Hsp33 activation, occurred during plasma treatment. After prolonged plasma exposure, however, unspecific protein oxidation was detected, the ability of Hsp33 to bind zinc ions was decreased without direct modifications of the zinc-binding motif, and the protein was inactivated. To identify chemical species of potential relevance for plasma-induced Hsp33 activation, reactive oxygen species were tested for their ability to activate Hsp33 in vitro. Superoxide, singlet oxygen and potentially atomic oxygen activate Hsp33, while no evidence was found for activation by ozone, peroxynitrite or hydroxyl radicals

Protection strategies for biocatalytic proteins under plasma treatment

In plasma-driven biocatalysis, enzymes are employed to carry out reactions using species generated by non-thermal plasmas as the precursors. We have previously demonstrated that this is feasible in principle, but that the approach suffers from the short lifetime of the biocatalyst under operating conditions. In this work, protection strategies were investigated to prevent the dielectric barrier discharge plasma-induced inactivation of biocatalysts, using recombinant unspecific peroxygenase from Agrocybe aegerita (rAaeUPO), one of the most promising enzymes for plasma-driven biocatalysis. Treatment in oxygen-free atmospheres did not provide any advantage over treatment in synthetic air, indicating that the detrimental reactive species did not originate from oxygen in the plasma phase. Chemical scavengers were employed to eliminate undesired reactive species, without any long-term effect on enzyme lifetime. Similarly, chaperones, including the known stress response proteins Hsp33, CnoX, and RidA did not increase the lifetime of rAaeUPO. Immobilization of the biocatalyst proved effective in preserving enzyme activity. The residual activity of rAaeUPO after plasma treatment strongly depended on the specific immobilization support. Essentially complete protection for at least 15 min of plasma exposure was achieved with an epoxy-butyl-functionalized carrier. This study presents new insights into plasma-protein interactions and plots a path forward for protecting biocatalytic proteins from plasma-mediated inactivation. </p