Computational performance of a parallelized three-dimensional high-order spectral element toolbox

In this paper, a comprehensive performance review of an MPI-based high-order three-dimensional spectral element method C++ toolbox is presented. The focus is put on the performance evaluation of several aspects with a particular emphasis on the parallel efficiency. The performance evaluation is analyzed with the help of a time prediction model based on a parameterization of the application and the hardware resources. Two tailor-made benchmark cases in computational fluid dynamics (CFD) are introduced and used to carry out this review, stressing the particular interest for clusters with up to thousands of cores. Some problems in the parallel implementation have been detected and corrected. The theoretical complexities with respect to the number of elements, to the polynomial degree, and to communication needs are correctly reproduced. It is concluded that this type of code has a nearly perfect speedup on machines with thousands of cores, and is ready to make the step to next-generation petaFLOP machines.     

Robust interactive cutting based on an adaptive octree simulation mesh

We present an adaptive octree based approach for interactive cutting of deformable objects. Our technique relies on efficient refine- and node split-operations. These are sufficient to robustly represent cuts in the mechanical simulation mesh. A high-resolution surface embedded into the octree is employed to represent a cut visually. Model modification is performed in the rest state of the object, which is accomplished by back-transformation of the blade geometry. This results in an improved robustness of our approach. Further, an efficient update of the correspondences between simulation elements and surface vertices is proposed. The robustness and efficiency of our approach is underlined in test examples as well as by integrating it into a prototype surgical simulator.     

Yield and transient effects during the plastic deformation of solid polymers

Tensile tests were performed on seven commercial polymers at 22° C and at constant true strain rates of 10^–4 to 10^–1 sec^–1. The constant strain rates were imposed on the minimum section of each sample with the aid of a diametral transducer, an exponential function generator and a closed-loop hydraulic testing machine. The polymers investigated were: high and low density polyethylene, polytetrafluoroethylene, polypropylene. polyvinylchloride and polyamide 6 and 66. True yield drops were observed in the rigid glassy polymers, whereas yielding was more gradual in the semi-crystalline or plasticized polymers. Strain rate change tests were also performed, during which one order of magnitude increases and decreases were imposed on the specimens. Normal transients were observed at small strains in the samples containing a rubbery phase, while the transients were of an inverse nature in the samples containing a glassy phase. With an increase in the strain at which the change was initiated, the normal transients changed in character to inverse. Transient tests were also performed in which straining was interrupted to permit a period of stress relaxation or of holding in the unloaded condition prior to the resumption of straining. A quantitative model is proposed, based on the dynamics of plastic waves which accounts for the transition from normal to inverse transient behaviour with increasing strain, and also explains the opposite effects of stress relaxation and of specimen unloading on the restraining transients.     

Navigation Aided Image Processing in UAV Surveillance: Preliminary Results and Design of an Airborne Experimental System

This paper describes an airborne reconfigurable measurement system being developed at Swedish Defence Research Agency (FOI), Sensor Technology, Sweden. An image processing oriented sensor management architecture for UAV (unmanned aerial vehicles) IR/EO-surveillance is presented. Some preliminary results of navigation aided image processing in UAV applications are demonstrated, such as SLAM (simultaneous localization and mapping), structure from motion and geolocation, target tracking, and detection of moving objects. The design goal of the measurement system is to emulate a UAV-mounted sensor gimbal using a stand-alone system. The minimal configuration of the system consists of a gyro-stabilized gimbal with IR and CCD sensors and an integrated high-performance navigation system. The navigation system combines dGPS real-time kinematics (RTK) data with data from an inertial measurement unit (IMU) mounted with reference to the optical sensors. The gimbal is to be used as an experimental georeferenced sensor platform, using a choice of carriers, to produce military relevant image sequences for studies of image processing and sensor control on moving surveillance and reconnaissance platforms. Furthermore, a high resolution synthetic environment, developed for sensor simulations in the visual and infrared wavelengths, is presented. © 2004 Wiley Periodicals, Inc.     

Formalization of Shannon’s Theorems

The most fundamental results of information theory are Shannon’s theorems. These theorems express the bounds for (1) reliable data compression and (2) data transmission over a noisy channel. Their proofs are non-trivial but are rarely detailed, even in the introductory literature. This lack of formal foundations is all the more unfortunate that crucial results in computer security rely solely on information theory: this is the so-called “unconditional security”. In this article, we report on the formalization of a library for information theory in the SSReflect extension of the Coq proof-assistant. In particular, we produce the first formal proofs of the source coding theorem, that introduces the entropy as the bound for lossless compression, and of the channel coding theorem, that introduces the capacity as the bound for reliable communication over a noisy channel.     

Disease Recurrence during Adjuvant Immune Checkpoint Inhibitor Treatment in Metastatic Melanoma: Clinical,Laboratory, and Radiological Characteristics in Patients from a Single Tertiary Referral Center

Despite the dramatic improvements in recurrence-free survival in patients with metastatic melanoma treated with immune checkpoint inhibitors (ICI), a number of patients develop metastases during adjuvant therapy. It is not currently possible to predict which patients are most likely to develop disease recurrence due to a lack of reliable biomarkers. Thus, we retrospectively analyzed the case records of all patients who commenced adjuvant ICI therapy between January 2018 and December 2021 in a single university skin cancer center (n = 46) (i) to determine the rates of disease recurrence, (ii) to examine the utility of established markers, and (iii) to examine whether re-challenge with immunotherapy resulted in clinical response. Twelve out of forty-six (26%) patients developed a relapse on adjuvant immunotherapy in our cohort, and the median time to relapse was 139 days. Adjuvant immunotherapy was continued in three patients. Of the twelve patients who developed recurrence during adjuvant immunotherapy, seven had further disease recurrence within the observation period, with a median time of 112 days after the first progress. There was no significant difference comparing early recurrence (<180 days after initiation) on adjuvant immunotherapy to late recurrence (>180 days after initiation) on adjuvant immunotherapy. Classical tumor markers, including serum lactate dehydrogenase (LDH) and S-100, were unreliable for the detection of disease recurrence. Baseline lymphocyte and eosinophil counts and those during immunotherapy were not associated with disease recurrence. Interestingly, patients with NRAS mutations were disproportionately represented (60%) in the patients who developed disease recurrence, suggesting that these patients should be closely monitored during adjuvant therapy.     

Leukotriene A4 Hydrolase and Hepatocyte Growth Factor Are Risk Factors of Sudden Cardiac Death Due to First-Ever Myocardial Infarction

Patients at a high risk for sudden cardiac death (SCD) without previous history of cardiovascular disease remain a challenge to identify. Atherosclerosis and prothrombotic states involve inflammation and non-cardiac tissue damage that may play active roles in SCD development. Therefore, we hypothesized that circulating proteins implicated in inflammation and tissue damage are linked to the future risk of SCD. We conducted a prospective nested case–control study of SCD cases with verified myocardial infarction (N = 224) and matched controls without myocardial infarction (N = 224), aged 60 ± 10 years time and median time to event was 8 years. Protein concentrations (N = 122) were measured using a proximity extension immunoassay. The analyses revealed 14 proteins significantly associated with an increased risk of SCD, from which two remained significant after adjusting for smoking status, systolic blood pressure, BMI, cholesterol, and glucose levels. We identified leukotriene A4 hydrolase (LTA4H, odds ratio 1.80, corrected confidence interval (CI_corr) 1.02–3.17) and hepatocyte growth factor (HGF; odds ratio 1.81, CI_corr 1.06–3.11) as independent risk markers of SCD. Elevated LTA4H may reflect increased systemic and pulmonary neutrophilic inflammatory processes that can contribute to atherosclerotic plaque instability. Increased HGF levels are linked to obesity-related metabolic disturbances that are more prevalent in SCD cases than the controls.     

Silencing DTX3L Inhibits the Progression of Cervical Carcinoma by Regulating PI3K/AKT/mTOR Signaling Pathway

Cervical carcinoma (CC) is the second most prevalent gynecologic cancer in females across the world. To obtain a better understanding of the mechanisms underlying the development of CC, high-resolution label-free mass spectrometry was performed on CC and adjacent normal tissues from eight patients. A total of 2631 proteins were identified, and 46 significant differently expressed proteins (DEPs) were found between CC and normal tissues (p < 0.01, fold change >10 or <0.1). Ingenuity pathway analysis revealed that the majority of the proteins were involved in the regulation of eIF4 and p70S6K signaling and mTOR signaling. Among 46 DEPs, Integrinβ6 (ITGB6), PPP1CB, TMPO, PTGES3 (P23) and DTX3L were significantly upregulated, while Desmin (DES) was significantly downregulated in CC tissues compared with the adjacent normal tissues. In in vivo and in vitro experiments, DTX3L knockdown suppressed CC cell proliferation, migration, invasion and xenograft tumorigenesis, and enhanced cell apoptosis. Combination of silencing DTX3L and cisplatin treatment induced higher apoptosis percentage compared to cisplatin treatment alone. Moreover, DTX3L silencing inhibited the PI3K/AKT/mTOR signal pathway. Thus, our results suggested DTX3L could regulate CC progression through the PI3K/AKT/mTOR signal pathway and is potentially a novel biomarker and therapeutic target for CC.     

Sucrose hydrolysis by gelatin-immobilized inulinase from Kluyveromyces marxianus var. bulgaricus

The crude cell-free medium from a culture of Kluyveromyces marxianus var. bulgaricus was immobilized in a gelatin-water support, with an immobilization yield of 82.60% for inulinase activity. The optimum pH for both free and immobilized inulinase was the same (3.5) and the optimum temperatures were 55 °C for the free and 60 °C for the immobilized enzyme. The Arrhenius plots were linear and activation energies were 56.20 (free enzyme) and 20.27 kJ/mol K (immobilized enzyme). The kinetic parameters were calculated by Lineweaver–Burk plots and the V_max and K_m were 37.60 IU/mg protein and 61.83 mM for the free inulinase and 31.45 IU/mg protein and 149.28 mM for the immobilized enzyme, respectively. The operational stability of the immobilized inulinase was studied in a continuous fixed-bed column reactor for 33 days, at the end of which the sucrose conversion was 58.12%.     

Alpha-Synuclein Autoimmune Decline in Prodromal Multiple System Atrophy and Parkinson’s Disease

Multiple-system trophy (MSA) and Parkinson’s Disease (PD) are both progressive, neurodegenerative diseases characterized by neuropathological deposition of aggregated alpha-synuclein (αSyn). The causes behind this aggregation are still unknown. We have reported aberrancies in MSA and PD patients in naturally occurring autoantibodies (nAbs) against αSyn (anti-αSyn-nAbs), which are important partakers in anti-aggregatory processes, immune-mediated clearance, and anti-inflammatory functions. To elaborate further on the timeline of autoimmune aberrancies towards αSyn, we investigated here the Immunoglobulin (Ig) affinity profile and subclass composition (IgG-total, IgG1-4 and IgM) of anti-αSyn-nAbs in serum samples from prodromal (p) phases of MSA and PD. Using an electrochemiluminescence competition immunoassay, we confirmed that the repertoire of high-affinity anti-αSyn-nAbs is significantly reduced in pMSA and pPD. Further, we demonstrated that pPD had increased anti-αSyn IgG-total levels compared to pMSA and controls, concordant with increased anti-αSyn IgG1 levels in pPD. Anti-αSyn IgG2 and IgG4 levels were reduced in pMSA and pPD compared with controls, whereas anti-αSyn IgG3 levels were reduced in pMSA compared to pPD and controls. The results indicate that the impaired reactivity towards αSyn occurs prior to disease onset. The apparent lack of high-affinity anti-αSyn nAbs may result in reduced clearance of αSyn, leading to aggregation of the protein. Thus, this study provides novel insights into possible causes behind the pathogenesis in synucleinopathies such as MSA and PD.