Massively Parallel Stencil Strategies for Radiation Transport Moment Model Simulations

The radiation transport equation is a mesoscopic equation in high dimensional phase space. Moment methods approximate it via a system of partial differential equations in traditional space-time. One challenge is the high computational intensity due to large vector sizes (1600 components for P39) in each spatial grid point. In this work, we extend the calculable domain size in 3D simulations considerably, by implementing the StaRMAP methodology within the massively parallel HPC framework NAStJA, which is designed to use current supercomputers efficiently. We apply several optimization techniques, including a new memory layout and explicit SIMD vectorization. We showcase a simulation with 200 billion degrees of freedom, and argue how the implementations can be extended and used in many scientific domains.Comment: ICCS 2020 Proceeding

Grid technology in tissue-based diagnosis: fundamentals and potential developments

Tissue-based diagnosis still remains the most reliable and specific diagnostic medical procedure. It is involved in all technological developments in medicine and biology and incorporates tools of quite different applications. These range from molecular genetics to image acquisition and recognition algorithms (for image analysis), or from tissue culture to electronic communication services. Grid technology seems to possess all features to efficiently target specific constellations of an individual patient in order to obtain a detailed and accurate diagnosis in providing all relevant information and references. Grid technology can be briefly explained by so-called nodes that are linked together and share certain communication rules in using open standards. The number of nodes can vary as well as their functionality, depending on the needs of a specific user at a given point in time. In the beginning of grid technology, the nodes were used as supercomputers in combining and enhancing the computation power. At present, at least five different Grid functions can be distinguished, that comprise 1) computation services, 2) data services, 3) application services, 4) information services, and 5) knowledge services. The general structures and functions of a Grid are described, and their potential implementation into virtual tissue-based diagnosis is analyzed. As a result Grid technology offers a new dimension to access distributed information and knowledge and to improving the quality in tissue-based diagnosis and therefore improving the medical quality

How I treat anaplastic glioma without 1p/19q codeletion

Anaplastic astrocytoma without 1p/19q codeletion is a rare primary central nervous system tumour occurring primarily in middle-aged adults and associated with a median survival of 5–10 years. The major corner stone of treatment is maximal safe neurosurgical resection, followed by radiotherapy and chemotherapy. Several clinical trials addressed the optimal adjuvant treatment; however, interpretation has been challenged by the recent molecular marker-based reclassification of tumour. The interim study of the CATNON trial strongly suggests the addition of 12 adjuvant cycles of temozolomide in addition to radiotherapy after maximal safe resection in patients with anaplastic astrocytoma without 1p/19q codeletion. Based on more recently presented data from the second interim analysis of the CATNON trial and from the molecular analysis, benefit from temozolomide during and after radiotherapy is limited to patients with isocitrate dehydrogenase-mutated anaplastic astrocytoma. Given the small patient number in the single subgroups and the so far missing neurocognitive and quality of life data, more mature analyses needs to be awaited to draw final conclusions on the application of concurrent temozolomide treatment for the daily routine in patients who already are scheduled for adjuvant temozolomide. Further molecular analysis is ongoing to define personalised treatment approaches in patients with anaplastic astrocytom

Определение оптимального спектрального состава пучка нейтронов при проведении НЗТ

В данной работе рассматривалось определение оптимального спектрального состава пучка нейтронов при проведении НЗТ. Для проведения исследования были созданы модели частей тела, а также задан источник нейтронов при помощи программного обеспечения MCU-PTR. Основной целью данной работы является достижение оптимального спектрального состава в пучке нейтронов для проведения НЗТ.In current work was considered the determination of the optimal spectral composition of a neutron beam during NCT. For the study, models of body parts were created, and a neutron source was set using the MCU-PTR software. The main goal of this work is to achieve the optimal spectral composition in a neutron beam for conducting NC

Identification of the variant Ala335Val of MED25 as responsible for CMT2B2: molecular data, functional studies of the SH3 recognition motif and correlation between wild-type MED25 and PMP22 RNA levels in CMT1A animal models

Charcot-Marie-Tooth (CMT) disease is a clinically and genetically heterogeneous disorder. All mendelian patterns of inheritance have been described. We identified a homozygous p.A335V mutation in the MED25 gene in an extended Costa Rican family with autosomal recessively inherited Charcot-Marie-Tooth neuropathy linked to the CMT2B2 locus in chromosome 19q13.3. MED25, also known as ARC92 and ACID1, is a subunit of the human activator-recruited cofactor (ARC), a family of large transcriptional coactivator complexes related to the yeast Mediator. MED25 was identified by virtue of functional association with the activator domains of multiple cellular and viral transcriptional activators. Its exact physiological function in transcriptional regulation remains obscure. The CMT2B2-associated missense amino acid substitution p.A335V is located in a proline-rich region with high affinity for SH3 domains of the Abelson type. The mutation causes a decrease in binding specificity leading to the recognition of a broader range of SH3 domain proteins. Furthermore, Med25 is coordinately expressed with Pmp22 gene dosage and expression in transgenic mice and rats. These results suggest a potential role of this protein in the molecular etiology of CMT2B2 and suggest a potential, more general role of MED25 in gene dosage sensitive peripheral neuropathy pathogenesis

Programmed death ligand 1 expression and tumor-infiltrating lymphocytes in glioblastoma

Background Immune checkpoint inhibitors targeting programmed cell death 1 (PD1) or its ligand (PD-L1) showed activity in several cancer types. Methods We performed immunohistochemistry for CD3, CD8, CD20, HLA-DR, phosphatase and tensin homolog (PTEN), PD-1, and PD-L1 and pyrosequencing for assessment of the O6-methylguanine-methyltransferase (MGMT) promoter methylation status in 135 glioblastoma specimens (117 initial resection, 18 first local recurrence). PD-L1 gene expression was analyzed in 446 cases from The Cancer Genome Atlas. Results Diffuse/fibrillary PD-L1 expression of variable extent, with or without interspersed epithelioid tumor cells with membranous PD-L1 expression, was observed in 103 of 117 (88.0%) newly diagnosed and 13 of 18 (72.2%) recurrent glioblastoma specimens. Sparse-to-moderate density of tumor-infiltrating lymphocytes (TILs) was found in 85 of 117 (72.6%) specimens (CD3+ 78/117, 66.7%; CD8+ 52/117, 44.4%; CD20+ 27/117, 23.1%; PD1+ 34/117, 29.1%). PD1+ TIL density correlated positively with CD3+ (P < .001), CD8+ (P < .001), CD20+ TIL density (P < .001), and PTEN expression (P = .035). Enrichment of specimens with low PD-L1 gene expression levels was observed in the proneural and G-CIMP glioblastoma subtypes and in specimens with high PD-L1 gene expression in the mesenchymal subtype (P = 5.966e-10). No significant differences in PD-L1 expression or TIL density between initial and recurrent glioblastoma specimens or correlation of PD-L1 expression or TIL density with patient age or outcome were evident. Conclusion TILs and PD-L1 expression are detectable in the majority of glioblastoma samples but are not related to outcome. Because the target is present, a clinical study with specific immune checkpoint inhibitors seems to be warranted in glioblastom

Прогнозирование гидравлического разрыва пласта низкопроницаемых коллекторов на основе математического моделирования на месторождении Х

Объектом исследования является месторождение нефти с низкой проницаемостью, на котором был проведен гидроразрыв пласта с целью увеличения добычи нефти. Цель работы – разработать имитационную модель гидроразрыва с использованием вариационного подхода к гидроразрыву в качестве механической модели, что позволяет использовать единую расчетную область для представления как трещины, так и коллектора, и устраняет необходимость явной идентификации трещины. и направления распространения. В процессе исследования была рассмотрена группа сложных математических моделей деформации.The object of the study is an oil field with low permeability, where hydraulic fracturing was carried out in order to increase oil production. The aim of the work is to develop a simulation model of hydraulic fracturing using a variational approach to hydraulic fracturing as a mechanical model, which allows using a single computational domain to represent both the fracture and the reservoir, and eliminates the need for explicit fracture identification. and directions of distribution. In the course of the study, a group of complex mathematical models of deformation and fluid flow was considered