Using Instancing to Efficiently Render Carbon Nanotubes

In this paper, we present an effcient way to visualize Super Carbon Nanotubes (SCNTs). SCNTs are complex, hierarchical structures and their models easily consist of more than 1 million atoms. Our SCNTs are modeled as graphs of uniform nodes and egdes. We show that OpenGL instancing is a very suitable technique for rendering such large graphs, because they only consist of two different types of geometry. Our visualizer software exploits this property and we demonstrate that it allows to render the tubes in a fashion that is time- and space-effective. We implemented auto-tuning of the model to the underlying graphics card through adaptive mesh-resolution-choices. We also designed and implemented our own shading programs in the OpenGL Shading Language (GLSL) to realize a sufficient but performant and configurable lighting computation. This allows us to render big models even on laptop GPUs and to cope with models that consist of 150 million triangles, which is still a challenging amount for most of today's graphics cards

qTESLA: Practical Implementations of a Quantum Attack Resistant Signature Scheme

Due to the advent of quantum computers, the security of existing public-key cryptography is threatened since quantum computers are expected to be able to solve the underlying mathematical problems efficiently. Hence, quantum resistant alternatives are required. Consequently, about 70 post-quantum scheme candidates were submitted to the National Institute of Standards and Technology (NIST) standardization effort. One candidate is the qTESLA signature scheme. We present an efficient shared-memory parallelization of qTESLA’s core routines, analyze the speedup in-depth and show that it can compete with the two most commonly used signature schemes RSA and ECDSA which are quantum-vulnerable. The speed is further increased by semi-automatic tuning of qTESLA’s configuration parameters based on results of multi-parameter performance models. We show how to considerably increase qTESLA’s usability through the Java Native Interface (JNI) without performance penalty. The analysis on x86 and ARM architecture employing three operating systems demonstrates the achieved portability. The enhanced performance, its straight forward usability and the high portability of our implementation make it a quantum-safe replacement for the state-of-the-art schemes

A new Parallelization for p3Enum and Parallelized Generation of Optimized Pruning Functions

Since quantum computers will be able to break all public-key encryption schemes employed today efficiently, quantum-safe cryptographic alternatives are required. One group of candidates are lattice-based schemes since they are efficient and versatile. To make them practical, their security level must be assessed on classical HPC systems in order to determine efficient but secure parameterization. In this paper, we propose a novel parallelization strategy for the open source framework p3Enum which is designed to solve the important lattice problem of finding the shortest non-zero vector in a lattice (SVP). We also present the p3Enum extreme pruning function generator (p3Enum-epfg) which generates optimized extreme pruning functions for p3Enum’s pruned lattice enumeration by employing a parallelized simulated annealing approach. We demonstrate the quality of the pruning functions delivered. Combining the new parallelization with optimized pruning functions speeds up p3Enum by a factor up to 3 compared to the previous version. Additionally, we compare the required runtime to solve the SVPs with state-of-the art tools and, for the first time, also visualize the statistical effects in the runtime of the algorithms under consideration. This allows a considerably better understanding of the behavior of the implementations than previous average-value considerations and demonstrates the relative stability of p3Enum’s parallel runtimes which improve reproducibility and predictability. All these advancements make it the fastest SVP solver for lattice dimensions 66 to 92 and a suitable building block as SVP-oracle in lattice basis reduction

SimAnMo — A parallelized runtime model generator

In this article, we present the novel features of the recent version of SimAnMo, the Simulated Annealing Modeler. The tool creates models that correlate the size of one input parameter of an application to the corresponding runtime and thus SimAnMo allows predictions for larger input sizes. A focus lies on applications whose runtime grows exponentially in the input parameter size. Such programs are, for example, of high interest for cryptanalysis to analyze practical security of traditional and post‐quantum secure schemes. However, SimAnMo also generates reliable models for the widespread case of polynomial runtime behavior and also for the important case of factorial runtime increase. SimAnMo's model generation is based on a parallelized simulated annealing procedure and heuristically minimizes the costs of a model. Those may rely on different quality metrics. Insights into SimAnMo's software design and its usage are provided. We demonstrate the quality of SimAnMo's models for different algorithms from various application fields. We show that our approach also works well on ARM architectures

ErbB2/HER2-specific NK cells for adoptive cancer immunotherapy

Poster presentation: 28th Annual Scientific Meeting of the Society for Immunotherapy of Cancer (SITC) Significant progress has been made over the last decade towards realizing the potential of natural killer (NK) cells for cancer immunotherapy. NK cells can respond rapidly to transformed and stressed cells, and have the intrinsic potential to extravasate and reach their targets in almost all body tissues. In addition to donor-derived primary NK cells, also continuously expanding cytotoxic cell lines such as NK-92 are being considered for adoptive cancer immunotherapy. High cytotoxicity of NK-92 has previously been shown against malignant cells of hematologic origin in preclinical studies, and general safety of infusion of NK-92 cells has been established in phase I clinical trials. To enhance their therapeutic utility, we genetically modified NK-92 cells to express chimeric antigen receptors (CAR) specific for tumor-associated surface antigens. Such CAR were composed of a tumor-specific scFv antibody fragment fused via hinge and transmembrane domains to intracellular signaling moieties such as CD3 zeta chain, or composite fusion molecules also containing a costimulatory protein domain in addition to CD3 zeta. For development towards clinical applications, here a codon-optimized second generation CAR was constructed that consists of an ErbB2-specific scFv antibody domain fused via a linker to a composite CD28-CD3 zeta signaling domain. GMP-compliant protocols for vector production, lentiviral transduction and expansion of a genetically modified NK-92 single cell clone (NK-92/5.28.z) were established. Functional analysis of NK-92/5.28.z cells revealed high and stable CAR expression, selective cytotoxicity against ErbB2-expressing but otherwise NK-resistant tumor cells of different origins in vitro, as well as homing to ErbB2-expressing tumors in vivo. Furthermore, antigen specificity and selective cytotoxicity of these cells were retained in vivo, resulting in antitumoral activity against subcutaneous and intracranial glioblastoma xenografts in NSG mice. Ongoing work now focuses on the development of these cells for adoptive immunotherapy of ErbB2-positive glioblastoma

DNA barcodes reveal species-specific mercury levels in tuna sushi that pose a health risk to consumers

Excessive ingestion of mercury—a health hazard associated with consuming predatory fishes—damages neurological, sensory-motor and cardiovascular functioning. The mercury levels found in Bigeye Tuna (Thunnus obesus) and bluefin tuna species (Thunnus maccoyii, Thunnus orientalis, and Thunnus thynnus), exceed or approach levels permissible by Canada, the European Union, Japan, the US, and the World Health Organization. We used DNA barcodes to identify tuna sushi samples analysed for mercury and demonstrate that the ability to identify cryptic samples in the market place allows regulatory agencies to more accurately measure the risk faced by fish consumers and enact policies that better safeguard their health

Ischemic preconditioning protects against cardiac ischemia reperfusion injury without affecting succinate accumulation or oxidation.

Ischemia-reperfusion (IR) injury occurs when blood supply to an organ is disrupted and then restored, and underlies many disorders, notably myocardial infarction and stroke. While reperfusion of ischemic tissue is essential for survival, it also initiates cell death through generation of mitochondrial reactive oxygen species (ROS). Recent work has revealed a novel pathway underlying ROS production at reperfusion in vivo in which the accumulation of succinate during ischemia and its subsequent rapid oxidation at reperfusion drives ROS production at complex I by reverse electron transport (RET). Pharmacologically inhibiting ischemic succinate accumulation, or slowing succinate metabolism at reperfusion, have been shown to be cardioprotective against IR injury. Here, we determined whether ischemic preconditioning (IPC) contributes to cardioprotection by altering kinetics of succinate accumulation and oxidation during IR. Mice were subjected to a 30-minute occlusion of the left anterior descending coronary artery followed by reperfusion, with or without a protective IPC protocol prior to sustained ischemia. We found that IPC had no effect on ischemic succinate accumulation with both control and IPC mice having profound increases in succinate compared to normoxia. Furthermore, after only 1-minute reperfusion succinate was rapidly metabolised returning to near pre-ischemic levels in both groups. We conclude that IPC does not affect ischemic succinate accumulation, or its oxidation at reperfusion

A third of the radiotracer dose: two decades of progress in pediatric [18^{18}F]fluorodeoxyglucose PET/CT and PET/MR imaging

OBJECTIVES To assess the evolution of administered radiotracer activity for F-18-fluorodeoxyglucose (18F-FDG) PET/CT or PET/MR in pediatric patients (0-16 years) between years 2000 and 2021. METHODS Pediatric patients (≤ 16 years) referred for 18F-FDG PET/CT or PET/MR imaging of the body during 2000 and 2021 were retrospectively included. The amount of administered radiotracer activity in megabecquerel (MBq) was recorded, and signal-to-noise ratio (SNR) was measured in the right liver lobe with a 4 cm$^{3}$ volume of interest as an indicator for objective image quality. Descriptive statistics were computed. RESULTS Two hundred forty-three children and adolescents underwent a total of 466 examinations. The median injected 18F-FDG activity in MBq decreased significantly from 296 MBq in 2000-2005 to 100 MBq in 2016-2021 (p < 0.001), equaling approximately one-third of the initial amount. The median SNR ratio was stable during all years with 11.7 (interquartile range [IQR] 10.7-12.9, p = 0.133). CONCLUSIONS Children have benefited from a massive reduction in the administered 18F-FDG dose over the past 20 years without compromising objective image quality. CLINICAL RELEVANCE STATEMENT Radiotracer dose was reduced considerably over the past two decades of pediatric F-18-fluorodeoxyglucose PET/CT and PET/MR imaging highlighting the success of technical innovations in pediatric PET imaging. KEY POINTS • The evolution of administered radiotracer activity for F-18-fluorodeoxyglucose (18F-FDG) PET/CT or PET/MR in pediatric patients (0-16 years) between 2000 and 2021 was assessed. • The injected tracer activity decreased by 66% during the study period from 296 megabecquerel (MBq) to 100 MBq (p < 0.001). • The continuous implementation of technical innovations in pediatric hybrid 18F-FDG PET has led to a steady decrease in the amount of applied radiotracer, which is particularly beneficial for children who are more sensitive to radiation