New Method and Tool for TEM Samples Preparation

А new tool for TEM sample preparation, which allows preparing a thin lamella with thickness less than 20 nm surrounded by and embedded in bulk material, is presented. The main advantages of this system are low ion milling induced damage (less than 2 nm in depth), low process time (1—2 hours), in situ sample monitoring during ion milling (topography and sample thickness), and large treated area (5—30 μm along the area of interest). Comparison of few kinds of working substance of ion sources as well as schemes or drawings of key components of the tool are presented.Представлено нову методику і технологію виготовлення зразків для ПЕМ, яка уможливлює підготувати зразок завтовшки до 20 нм, оточений об’ємним матеріалом і втілений у нього. Головна перевага системи полягає в малій товщині шару пошкоджень, спричинених йонним обробленням (менше 2 нм), в малому часі оброблення (1—2 години), в моніторинґу зразка під час йонного фрезерування (топографія і товщина зразка) і у великій площі, що обробляється (5—30 мкм вздовж області, яка являє інтерес). Виконано порівняння декількох типів робочої речовини для йонних джерел, наведено схеми або креслення ключових вузлів пристрою.Представлена новая методика и технология приготовления образцов для ПЭМ, позволяющая подготовить образец толщиной до 20 нм, окружённый объёмным материалом и вмурованный в него. Главным преимуществом системы является малая толщина слоя повреждений, индуцированных ионной обработкой (меньше 2 нм), малое время обработки (1—2 часа), мониторинг образца во время ионного фрезерования (топография и толщина образца) и большая обрабатываемая площадь (5—30 мкм вдоль интересующей области). Проведено сравнение нескольких рабочих веществ для ионных источников, приведены схемы или чертежи ключевых узлов устройства.The authors would like to thank the staff of SELA and PETRC of Ukraine for taking part in the development and fabrication of Xact. In particular, D. Viazovsky and T. Krasovsky for electronics development, V. Kontorov and V. Isyanov for technical documentation development, D. Farhana, L. Berner for software development, A. Berner, A. Bekkerman, A. Eizner, V. Kuchik, S. Yakovlev, G. Aharonov, all who made this achievement real by their hard work and talent

Enhancing Resource Management through Prediction-based Policies

Task-based programming models are emerging as a promising alternative to make the most of multi-/many-core systems. These programming models rely on runtime systems, and their goal is to improve application performance by properly scheduling application tasks to cores. Additionally, these runtime systems offer policies to cope with application phases that lack in parallelism to fill all cores. However, these policies are usually static and favor either performance or energy efficiency. In this paper, we have extended a task-based runtime system with a lightweight monitoring and prediction infrastructure that dynamically predicts the optimal number of cores required for each application phase, thus improving both performance and energy efficiency. Through the execution of several benchmarks in multi-/many-core systems, we show that our prediction-based policies have competitive performance while improving energy efficiency when compared to state of the art policies.Comment: Postprint submitted and published at Euro-Par2020: International European Conference on Parallel and Distributed Computing (Springer) (https://link.springer.com/chapter/10.1007%2F978-3-030-57675-2_31

Enhancement of the upper critical field by nonmagnetic impurities in dirty two-gap superconductors

Quasiclassic Uzadel equations for two-band superconductors in the dirty limit with the account of both intraband and interband scattering by nonmagnetic impurities are derived for any anisotropic Fermi surface. From these equations the Ginzburg-Landau equations, and the critical temperature $T_c$ are obtained. An equation for the upper critical field, which determines both the temperature dependence of $H_{c2}(T)$ and the orientational dependence of $H_{c2}(\theta)$ as a function of the angle $\theta$ between ${\bf H}$ and the c-axis is obtained. It is shown that the shape of the $H_{c2}(T)$ curve essentially depends on the ratio of the intraband electron diffusivities $D_1$ and $D_1$, and can be very different from the standard one-gap dirty limit theory. In particular, the value $H_{c2}(0)$ can considerably exceed $0.7T_cdH_{c2}/dT_c$, which can have important consequences for applications of $MgB_2$. A scaling relation is proposed which enables one to obtain the angular dependence of $H_{c2}(\theta)$ from the equation for $H_{c2}$ at ${\bf H}\| c$. It is shown that, depending on the relation between $D_1$ and $D_2$, the ratio of the upper critical field $H_{c2}^\|/H_{c2}^\perp$ for ${\bf H}\| ab$ and ${\bf H}\perp ab$ can both increase and decrease as the temperature decreases. Implications of the obtained results for $MgB_2$ are discussed

Reorganization of the nuclear lamina and cytoskeleton in adipogenesis

A thorough understanding of fat cell biology is necessary to counter the epidemic of obesity. Although molecular pathways governing adipogenesis are well delineated, the structure of the nuclear lamina and nuclear-cytoskeleton junction in this process are not. The identification of the ‘linker of nucleus and cytoskeleton’ (LINC) complex made us consider a role for the nuclear lamina in adipose conversion. We herein focused on the structure of the nuclear lamina and its coupling to the vimentin network, which forms a cage-like structure surrounding individual lipid droplets in mature adipocytes. Analysis of a mouse and human model system for fat cell differentiation showed fragmentation of the nuclear lamina and subsequent loss of lamins A, C, B1 and emerin at the nuclear rim, which coincides with reorganization of the nesprin-3/plectin/vimentin complex into a network lining lipid droplets. Upon 18 days of fat cell differentiation, the fraction of adipocytes expressing lamins A, C and B1 at the nuclear rim increased, though overall lamin A/C protein levels were low. Lamin B2 remained at the nuclear rim throughout fat cell differentiation. Light and electron microscopy of a subcutaneous adipose tissue specimen showed striking indentations of the nucleus by lipid droplets, suggestive for an increased plasticity of the nucleus due to profound reorganization of the cellular infrastructure. This dynamic reorganization of the nuclear lamina in adipogenesis is an important finding that may open up new venues for research in and treatment of obesity and nuclear lamina-associated lipodystrophy

Cortactin Phosphorylated by ERK1/2 Localizes to Sites of Dynamic Actin Regulation and Is Required for Carcinoma Lamellipodia Persistence

Tumor cell motility and invasion is governed by dynamic regulation of the cortical actin cytoskeleton. The actin-binding protein cortactin is commonly upregulated in multiple cancer types and is associated with increased cell migration. Cortactin regulates actin nucleation through the actin related protein (Arp)2/3 complex and stabilizes the cortical actin cytoskeleton. Cortactin is regulated by multiple phosphorylation events, including phosphorylation of S405 and S418 by extracellular regulated kinases (ERK)1/2. ERK1/2 phosphorylation of cortactin has emerged as an important positive regulatory modification, enabling cortactin to bind and activate the Arp2/3 regulator neuronal Wiskott-Aldrich syndrome protein (N-WASp), promoting actin polymerization and enhancing tumor cell movement.In this report we have developed phosphorylation-specific antibodies against phosphorylated cortactin S405 and S418 to analyze the subcellular localization of this cortactin form in tumor cells and patient samples by microscopy. We evaluated the interplay between cortactin S405 and S418 phosphorylation with cortactin tyrosine phosphorylation in regulating cortactin conformational forms by Western blotting. Cortactin is simultaneously phosphorylated at S405/418 and Y421 in tumor cells, and through the use of point mutant constructs we determined that serine and tyrosine phosphorylation events lack any co-dependency. Expression of S405/418 phosphorylation-null constructs impaired carcinoma motility and adhesion, and also inhibited lamellipodia persistence monitored by live cell imaging.Cortactin phosphorylated at S405/418 is localized to sites of dynamic actin assembly in tumor cells. Concurrent phosphorylation of cortactin by ERK1/2 and tyrosine kinases enables cells with the ability to regulate actin dynamics through N-WASp and other effector proteins by synchronizing upstream regulatory pathways, confirming cortactin as an important integration point in actin-based signal transduction. Reduced lamellipodia persistence in cells with S405/418A expression identifies an essential motility-based process reliant on ERK1/2 signaling, providing additional understanding as to how this pathway impacts tumor cell migration

Altered adipocyte differentiation and unbalanced autophagy in type 2 Familial Partial Lipodystrophy: an in vitro and in vivo study of adipose tissue browning

Type-2 Familial Partial Lipodystrophy is caused by LMNA mutations. Patients gradually lose subcutaneous fat from the limbs, while they accumulate adipose tissue in the face and neck. Several studies have demonstrated that autophagy is involved in the regulation of adipocyte differentiation and the maintenance of the balance between white and brown adipose tissue. We identified deregulation of autophagy in laminopathic preadipocytes before induction of differentiation. Moreover, in differentiating white adipocyte precursors, we observed impairment of large lipid droplet formation, altered regulation of adipose tissue genes, and expression of the brown adipose tissue marker UCP1. Conversely, in lipodystrophic brown adipocyte precursors induced to differentiate, we noticed activation of autophagy, formation of enlarged lipid droplets typical of white adipocytes, and dysregulation of brown adipose tissue genes. In agreement with these in vitro results indicating conversion of FPLD2 brown preadipocytes toward the white lineage, adipose tissue from FPLD2 patient neck, an area of brown adipogenesis, showed a white phenotype reminiscent of its brown origin. Moreover, in vivo morpho-functional evaluation of fat depots in the neck area of three FPLD2 patients by PET/CT analysis with cold stimulation showed the absence of brown adipose tissue activity. These findings highlight a new pathogenetic mechanism leading to improper fat distribution in lamin A-linked lipodystrophies and show that both impaired white adipocyte turnover and failure of adipose tissue browning contribute to disease.We thank FPLD2 patients for donating biological samples. We thank the Italian Network for Laminopathies and the European Consortium of Lipodystrophies (ECLip) for support and helpful discussion. We thank Aurelio Valmori for the technical support. The studies were supported by Rizzoli Orthopedic Institute “5 per mille” 2014 project to MC, AIProSaB project 2016 and Fondazione Del Monte di Bologna e Ravenna grant 2015–2016 “New pharmacological approaches in bone laminopathies based on the use of antibodies neutralizing TGF beta 2” to GL. GL is also supported by PRIN MIUR project 2015FBNB5Y.S

Cancer Biomarker Discovery: The Entropic Hallmark

Background: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-throughput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases