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The simulation time of parallel and distributed discrete event simulation is the heart rate for as-fast-as execution schemes. Agreeing upon a global simulation time and distributing it to the simulation processes can be improved by exploiting or redesigning the network hardware. In this paper, we present such an approach that offloads simulation time calculations to network switches in order to speed up the steps where time advance requests are made and time advance grants are waited. By reducing the waiting time for time advancement, we aim to improve the overall performance of the parallel simulations. The measurements from the FPGA-based hardware setup and the results from our network simulations show that overall performance can be improved when time management calculations are offloaded to the network switches. Additionally, the transient message problem is also solved within the network by not allowing the time control messages to bypass the time-dependent events. The network acceleration of the region-based event distribution is also studied, and offloading the region matching tasks to the network switches is found to be feasible to reduce the costs of node-based calculations, especially for fast-moving regions. In this study, we consider High-Level Architecture (HLA) for simulation infrastructure and fat tree topology for high-performance networking.

Protein-based underwater adhesives of marine organisms exhibit extraordinary binding strength in high salinity based on utilizing a variety of molecular interaction mechanisms. These include acid-base interactions, bidentate bindings or complex hydrogen bonding interactions, and electrochemical manipulation of interfacial bonding. In this Perspective, we briefly review recent progress in the field, and we discuss how interfacial electrochemistry can vary interfacial forces by concerted tuning of surface charging, hydration forces, and tuning of the interfacial ion concentration. We further discuss open questions, controversial findings, and new paths into understanding and utilizing redox-proteins and derived polymers for enhancing underwater adhesion in a complex salt environment.

OBJECTIVE Gliomas frequently involve the insula both primarily and secondarily by invasion. Despite the high connectivity of the human insula, gliomas do not spread randomly to or from the insula but follow stereotypical anatomical involvement patterns. In the majority of cases, these patterns correspond to the intrinsic connectivity of the limbic system, except for tumors with aggressive biology. On the basis of these observations, the authors hypothesized that these different involvement patterns may be correlated with distinct outcomes and analyzed these correlations in an institutional cohort. METHODS Fifty-nine patients who had undergone surgery for insular diffuse gliomas and had complete demographic, pre- and postoperative imaging, pathology, molecular genetics, and clinical follow-up data were included in the analysis (median age 37 years, range 21–71 years, M/F ratio 1.68). Patients with gliomatosis and those with only minor involvement of the insula were excluded. The presence of T2-hyperintense tumor infiltration was evaluated in 12 anatomical structures. Hierarchical biclustering was used to identify co-involved structures, and the findings were correlated with established functional anatomy knowledge. Overall survival was evaluated using Kaplan-Meier and Cox proportional hazards regression analysis (17 parameters). RESULTS The tumors involved the anterior insula (98.3%), posterior insula (67.8%), temporal operculum (47.5%), amygdala (42.4%), frontal operculum (40.7%), temporal pole (39%), parolfactory area (35.6%), hypothalamus (23.7%), hippocampus (16.9%), thalamus (6.8%), striatum (5.1%), and cingulate gyrus (3.4%). A mean 4.2 ± 2.6 structures were involved. On the basis of hierarchical biclustering, 7 involvement patterns were identified and correlated with cortical functional anatomy (pure insular [11.9%], olfactocentric [15.3%], olfactoopercular [33.9%], operculoinsular [15.3%], striatoinsular [3.4%], translimbic [11.9%], and multifocal [8.5%] patterns). Cox regression identified hippocampal involvement (p = 0.006) and postoperative tumor volume (p = 0.027) as significant negative independent prognosticators of overall survival and extent of resection (p = 0.015) as a significant positive independent prognosticator. CONCLUSIONS The study findings indicate that insular gliomas primarily involve the olfactocentric limbic girdle and that involvement in the hippocampocentric limbic girdle is associated with a worse prognosis.

Catechol reaction mechanisms form the basis of marine mussel adhesion, allowing for bond formation and cross-linking in wet saline environments. To mimic mussel foot adhesion and develop new bioadhesive underwater glues, it is essential to understand and learn to control their redox activity as well as their chemical reactivity. Here, we study the electrochemical characteristics of functionalized catechols to further understand their reaction mechanisms and find a stable and controllable molecule that we subsequently integrate into a polymer to form a highly adhesive hydrogel. Contradictory to previous hypotheses, 3,4-dihydroxy-L-phenylalanine is shown to follow a Schiff-base reaction whereas dopamine shows an intramolecular ring formation. Dihydrocaffeic acid proved to be stable and was substituted onto a poly(allylamine) backbone and electrochemically cross-linked to form an adhesive hydrogel that was tested using a surface forces apparatus. The hydrogel's compression and dehydration dependent adhesive strength have proven to be higher than in mussel foot proteins (mfp-3 and mfp-5). Controlling catechol reaction mechanisms and integrating them into stable electrochemically depositable macroscopic structures is an important step in designing new biological coatings and underwater and biomedical adhesives.

Time management is an important factor that affects the speed of parallel and distributed simulations. Conservative time management mechanisms advance simulation time after synchronization of logical processes, whereas optimistic time management mechanisms loosen synchronization among processes to speed up simulation. Because of loosened synchronization, the optimistic approaches are vulnerable to causality faults that must be addressed by logical processes during run-time. Repairing a simulation, by means of a rollback mechanism, is one of the most time-consuming processes of optimistic approaches. In this paper, we propose a method that considers precautionary measures against possible future rollbacks for Time Warp mechanism due to Jefferson. Our proposed method, named Predetermined Rollbacks, uses a modified simulation engine that can detect and avoid unnecessary rollbacks. Our experiments demonstrate that the proposed method can significantly improve the speedup of Time Warp in agent-based simulations, where agents communicate in a shared environment.

Resistance of cyathostomins to benzimidazole (BZ) anthelmintics is widespread in horses in many parts of the world. This study compared three methods for the determination of benzimidazole resistance of Cyathostominae in 18 horses from a stud farm in Romania. The horses were treated with Fenbendazole. The resistance test was performed by FECRT, ERP and PCR. On Day 0, larvae of species belonging to the Cyathostominae subfamily, types A, B, C, D and Gyalocephalus, as well as Strongylus vulgaris species of the Strongylinae subfamily, were identified. At 42 days post treatment with fenbendazole only larvae of Cyathostominae, types A and D were identified. Resistance to Fenbendazole was found in one horse, using the FECRT and ERP tests. Both genetic resistance and susceptibility to BZ anthelmintics was observed in 13 samples (72.22%) using the PCR test. However, three samples (16.67%) showed only the BZ-susceptibility gene. In 2 samples, (11.11%) only the resistance gene to BZ anthelmintics was identified. Several inconsistencies in the evidence of resistance to benzimidazole were observed between the PCR test and the other two methods, which indicates that several methods for determining and controlling the resistance should be used in practice.

Preprint of open access article Bilotto, P., Imre, A. M., Dworschak, D., Mears, L. L. E., & Valtiner, M. (2021). Visualization of Ion|Surface Binding and In Situ Evaluation of Surface Interaction Free Energies via Competitive Adsorption Isotherms. ACS Physical Chemistry Au. https://doi.org/10.1021/acsphyschemau.1c00012, Function and properties at biologic as well as technological interfaces are controlled by a complex and concerted competition of specific and unspecific binding with ions and water in the electrolyte. It is not possible to date to directly estimate by experiment the interfacial binding energies of involved species in a consistent approach, thus limiting our understanding of how interactions in complex (physiologic) media are moderated. Here, we employ a model system utilizing polymers with end grafted amines interacting with a negatively charged mica surface. We measure interaction forces as a function of the molecule density and ion concentration in NaCl solutions. The measured adhesion decreases by about 90%, from 0.01 to 1 M electrolyte concentration. We further demonstrate by molecular resolution imaging how ions increasingly populate the binding surface at elevated concentrations, and are effectively competing with the functional group for a binding site. We demonstrate that a competing Langmuir isotherm model can describe this concentration-dependent competition. Further, based on this model we can quantitatively estimate ion binding energies, as well as binding energy relationships at a complex solid|liquid interface. Our approach enables the extraction of thermodynamic interaction energies and kinetic parameters of ionic species during monolayer level interactions at a solid|liquid interface, which to-date is impossible with other techniques.

International audience; The Central Neutron Detector is a scintillator barrel that was designed to detect 0.2-1 GeV neutrons at lab polar angles from 40 ∘ to 120 ∘ in the CLAS12 spectrometer in Hall B at Jefferson Laboratory. The design is based on three radial layers of paddles read out at the upstream end of the barrel by photomultipliers tubes. Neighboring paddles in each layer are coupled together at the downstream end of the barrel by “U-turn” light guides. The components of this detector are presented and the performance of the detector with the first beam data taken by CLAS12 is reported.

A feasibility study has been performed in order to investigate the performance of the HADES detector to measure the electromagnetic decays of the hyperon resonances $\Sigma(1385)^0$, $\Lambda(1405)$ and $\Lambda{\Lambda}(1520)$ as well as the production of double strange baryon systems $\Xi^-$ and $\Lambda\Lambda$ in p+p reactions at a beam kinetic energy of 4.5 GeV. The existing HADES detector will be upgraded by a new Forward Detector, which extends the detector acceptance into a range of polar angles that plays a crucial role for these investigations. The analysis of each channel is preceded by a consideration of the production cross-sections. Afterwards the expected signal count rates using a target consisting of either liquid hydrogen or polyethylene are summarized., Comment: Draft prepared by Rafa{\l} Lalik, James Ritman, Piotr Salabura, 19 pages, 21 figures, 4 tables

Present in many experiments, wire and drift chambers have been used in a large variety of shapes and configurations during the last decades. Nevertheless, their readout elements has not evolved much: tungsten, sometimes gold-plated or aluminum, wires. By taking advantage of the developments in the manufacture of conducting carbon fiber, we could obtain interesting improvements for wire detectors. In this article, we present recent tests and simulations using carbon fibers to readout signal in place of traditional tungsten wires. Unlike metallic wires, their low weight guaranties a reduced quantity of material in the active area.

Background Branched-chain amino acids (BCAAs) are synthesized by plants, fungi, bacteria, and archaea with plants being the major source of these amino acids in animal diets. Acetolactate synthase (ALS) is the first enzyme in the BCAA synthesis pathway. Although the functional contribution of ALS to BCAA biosynthesis has been extensively characterized, a comprehensive understanding of the regulation of this pathway at the molecular level is still lacking. Results To characterize the regulatory processes governing ALS activity we utilized several complementary approaches. Using the ALS catalytic protein subunit as bait we performed a yeast two-hybrid (Y2H) screen which resulted in the identification of a set of interacting proteins, two of which (denoted as ALS-INTERACTING PROTEIN1 and 3 [AIP1 and AIP3, respectively]) were found to be evolutionarily conserved orthologues of bacterial feedback-regulatory proteins and therefore implicated in the regulation of ALS activity. To investigate the molecular role AIPs might play in BCAA synthesis in Arabidopsis thaliana, we examined the functional contribution of aip1 and aip3 knockout alleles to plant patterning and development and BCAA synthesis under various growth conditions. Loss-of-function genetic backgrounds involving these two genes exhibited differential aberrant growth responses in valine-, isoleucine-, and sodium chloride-supplemented media. While BCAA synthesis is believed to be localized to the chloroplast, both AIP1 and AIP3 were found to localize to the peroxisome in addition to the chloroplast. Analysis of free amino acid pools in the mutant backgrounds revealed that they differ in the absolute amount of individual BCAAs accumulated and exhibit elevated levels of BCAAs in leaf tissues. Despite the phenotypic differences observed in aip1 and aip3 backgrounds, functional redundancy between these loci was suggested by the finding that aip1/aip3 double knockout mutants are severely developmentally compromised. Conclusions Taken together the data suggests that the two regulatory proteins, in conjunction with ALS, have overlapping but distinct functions in BCAA synthesis, and also play a role in pathways unrelated to BCAA synthesis such as sodium-ion homeostasis, extending to broader aspects of patterning and development. Electronic supplementary material The online version of this article (doi:10.1186/s12870-017-1022-6) contains supplementary material, which is available to authorized users.

International audience; In this work, we describe the optical properties of the single photoelectron (SPE) calibration system designed for NectarCAM, a camera proposed for the Medium Sized Telescopes (MST) of the Cherenkov Telescope Array (CTA). One of the goals of the SPE system, as integral part of the NectarCAM camera, consists in measuring with high accuracy the gain of its photo-detection chain. The SPE system is based on a white painted screen where light pulses are injected through a fishtail light guide from a dedicated flasher. The screen – placed 15 mm away from the focal plane – is mounted on an XY motorization that allows movements over all the camera plane. This allows in-situ measurements of the SPE spectra via a complete scan of the 1855 photo-multiplier tubes (PMTs) of NectarCAM. This calibration process will enable the reduction of the systematic uncertainties on the energy reconstruction of γ -rays coming from distant astronomical sources and detected by CTA.We discuss the design of the screen used in the calibration system and we present its optical performances in terms of light homogeneity and timing of the signal.

In this paper, a dual-mode routing approach is proposed for routing messages in 2D photonic network on chip (NoC) platforms. The dual-mode routing approach is based on selecting exclusively one of two routing techniques for each stage of a parallel application. Depending on the data exchange requirements of a specific stage of an application, either a conventional per-message-based routing or a collective routing technique is selected, and the network on chip architecture is organized to support that selection. The network on chip architecture that we use is a two-dimensional torus topology built from novel $$8\times 8$$8×8 non-blocking all-port photonic switches. The design of $$8\times 8$$8×8 non-blocking all-port photonic switch empowers each node with simultaneous connections to four other nodes in the network. The rich connectivity provided by the switches helps the collective routing technique to efficiently support collective communication operations by allowing deadlock-free and contention-free dense data exchange among the nodes. Similar dense data exchanges are also required for some commonly known parallel algorithms such as parallel matrix multiplication, linear equation solvers and n-body simulation algorithms, just to name a few. A lightweight electronic network is employed for establishing and tearing down the photonic communication paths (light paths) in per-message-based routing technique. The lightweight electronic network is also used for coordinating the whole network in the collective routing technique.

This paper presents a novel scheduling approach that efficiently schedules the computational and the communicational resources of a Software-Defined Photonic Network-on-Chip (SD-PNoC) Architecture designed for high-performance real-time systems. The proposed scheduling approach extends the conventional cyclic executive scheduling algorithm from the one that schedules solely the computational resources into a general one that schedules both the computational and the communicational resources together in a synchronized manner. The proposed SD-PNoC architecture employs Software Defined Network (SDN) approach by using application specific conflict-free and contention-free communication patterns to solve the routing and wavelength assignment (RWA) problem exists in photonic networks. The implementations of the collective communication primitives such as broadcast and all-to-broadcast are also presented to demonstrate the system as a whole.

In the effort of the AugerPrime scintillator surface detector R&D activity, we investigated the performances of different extruded and cast plastic scintillators that were read out with wavelength-shifting (WLS) optical fibers and then coupled to a PMT. In particular we compared the light yield of eighteen scintillator/fiber configurations, obtained combining eight different scintillator bars with six fiber types, in order to investigate which was satisfying the AugerPrime specifications in terms of light production ( > 12 photoelectrons per minimum ionizing particle). In this paper, we present the results of the study on different scintillator bar geometries, scintillator production techniques, and wavelength-shifting optical fiber types. We also propose an effective way to optically couple the fibers to the PMT entrance window.

International audience; The Central Neutron Detector, a recently constructed scintillator barrel which is used in CLAS12 at Jefferson Lab to detect 0.2–1 GeV neutrons at backwards angles, is here described. The motivations and R&D; tests leading to its final design, based on three radial layers of coupled paddles with one-side light readout by photomultipliers plus “U-turn” lightguides on the other side, are outlined. The performance of the detector, evaluated from cosmic-ray tests and simulations, which satisfies the physics requirements, is reported.

Objectives: Venlafaxine is an antidepressant, categorized as a serotonin-norepinephrine reuptake inhibitor (SNRI) with suspected metabolic side effects. The aim of our study was to assess these metabolic effects in rats, using two different doses of venlafaxine. Materials: Three groups of Wistar rats have been treated with venlafaxine during seven weeks. The rats have received a daily dose of 10mg/kg (D1) and 40 mg/kg (D2) while the control group (Dc) has received no treatment. Rats were given “ad libitum” access to food and water. The rats were weighted at treatment day 0, 7, 14, 21, 28, 35, 42 and 49. After completion of venlafaxine treatment, the rats were sacrificed, blood was harvested and the following biochemical parameters have been determined from the centrifuged plasma: triglycerides, glucose and total cholesterol levels. Results: Both the 10 mg/kg and the 40 mg/kg dose venlafaxine therapy resulted in a highly significant increase of rat’s weight. Compared with the control group the mean weight of D1 group has increased with 130.5 ±21.79 g ( Conclusions: Our results suggest that venlafaxine administrated to rats has unwished dose related metabolic effects such as significant increase in weight and hypertriglyceridemia, however serum cholesterol and plasma glucose levels appears to be decreased by this medication.

Chronic venous insufficiency’s frequency reaches almost 25% in European countries. The aim of this present study was to assess the correlation between sociodemographic characteristics as well as clinical findings and para-clinical findings of aCVI patients. A total number of 2636 patients diagnosed with CVI were evaluated for over an 8 year time period (2006-2013). In case of 795 of them, diagnosis of aCVI (C4-C6) has been established. The following variables have been evaluated: demographic data, etiology, risk factors, chronic diseases as risk factors, signs and symptoms, laboratory findings and even the therapeutic approach. All the assessed data has been evaluated using descriptive statistics, t-Student test, and chi square test. Also the relative risk (RR) and Odds ratio (OR) has been calculated. The mean age of aCVI patients was significantly higher (p=0.001) than the age of patients with stage C1-3 CVI. A positive correlation (p

Reaching the physical boundaries of the electronics-based communication approach has enabled photonic-based systems, which promise high-bandwidth and low power consumption, especially in multiprocessor systems, to be an alternative to electronic systems on chips. Real-time systems are specialized systems where tasks that cannot be completed in time cause high costs, and particularly communication with sensors and actuators have high importance. In this study, a sensor data distribution model is presented for multi-processor real-time systems that communicate with the photonic network on the chip. The study provides the distribution of the sensor data to the processors on the chip with the photonic infrastructure, and the results show that the proposed model is an effective approach for real-time systems.

Objective Clinical characteristics and management of hemangioblastomas of the spinal cord associated with von Hippel-Lindau syndrome have been extensively covered in the literature. This report aims to analyze the characteristics and surgical treatment results of sporadic spinal hemangioblastomas (SSHB). Methods This is a retrospective analysis of 14 patients with SSHB (8 men and 6 women) operated on during a span of 23 years. The median age was 41.5 years (24–70 years). von Hippel Lindau syndrome was excluded by imaging in all patients. The median follow-up was 4 years (1–23 years). We also conducted a meta-analysis of all 271 SSHB cases reported in the English-speaking language literature from 1967 to 2011. Results Nine (64.3%) lesions were cervical, 3 (28.5%) were thoracic, and 1 (7.1%) was lumbar. Eight (57.1%) tumors were dorsal intramedullary, 4 (28.6%) were exophytic, 1 (7.1%) was intradural extramedullary, and 1 (7.1%) was completely extradural. Diffuse segmental cord enlargement was present in 7 patients (50%) and a cyst/syrinx was present in 7 (50%). These 14 patients underwent 15 operations, and gross total resection was achieved in all operations. There was no mortality. Symptoms improved after 8 (53.3%) of 15 operations, remained the same after 5 (33.3%), and worsened after 2 (13.3%). The mean Karnofsky performance score improved from 79.3 (± 17.5) to 87.3 (± 12.2) after 6 months of follow-up. There was one recurrence 15 years after magnetic resonance imaging confirmed total resection. Conclusions The SSHBs occur most often in the upper spinal cord. Excellent surgical results and long-term outcome can be achieved using microsurgery alone with only rare recurrences.

High performance computing (HPC) has great potential to speedup agent-based simulations. In parallel and distributed simulation (PADS) community, a well-known fact is that employing an optimistic time management mechanism instead of a conservative time management mechanism may provide remarkable performance enhancement, because optimistic approach avoids redundant synchronization among logical processes (LPs). In this paper, an existing optimistic time management mechanism, namely Time Warp, by Jefferson, is adapted for a distributed agent based simulation tool. We implemented Time Warp on an open source and distributed agent based modeling and simulation (ABMS) tool, namely Repast for High Performance Computing (Repast HPC), from Argonne National Laboratory, Chicago, IL, USA. We incorporated a simple and self-adaptive technique for adjusting checkpoint intervals. Two case studies have been implemented to compare our optimistic approach and existing Repast HPC's conservative approach. The experiments suggest that optimistic approach is more scalable than conservative approach in agent based simulations.

The aim of this study was to evaluate the computed tomography (CT) and magnetic resonance imaging findings (MRI) of asymptomatic remote cerebellar hemorrhage (RCH) at the preoperative, early postoperative, and postoperative period. A total of 983 consecutive adult patients who underwent supratentorial craniotomies were included in the study. The ethics committee approved the study. The patient's clinical records and radiological examinations were retrospectively analyzed. All patients had preoperative CT and MRI examinations, immediate postoperative CT, and postoperative MRI within 24 h. The patients with the radiological diagnosis of RCH were followed up to 5 years. Eight asymptomatic RCH cases were recruited. The prevalence of asymptomatic RCH was 0.8% in our series. RCH was unilateral in two patients and bilateral in six patients. The postoperative CT was positive in two cases. The hemorrhage presented on MRI as folial linear hypointensities in six cases. In three cases (including one mixed case), punctate hypointense spots were identified at the superior cerebellar folia. Diffuse hemorrhage in the cerebellar tonsil, subarachnoid hemorrhage, and hemorrhage in the cerebellar vermis and the ventricles were also seen. The MRI findings were stable up to 5 years. The prevalence of asymptomatic RCH is higher than previously reported. Immediate postoperative CT is usually unremarkable; however, MRI demonstrates various hemorrhagic patterns at the cerebellum other than classical "zebra sign". This condition is self-limiting and no further investigation or follow-up study is required. In the proper clinical setting, the awareness of different hemorrhagic patterns in patients with RCH would prevent unnecessary investigations.

A new parallel implementation of Strassen's matrix multiplication algorithm is proposed for massively parallel supercomputers with 2D, all-port torus interconnection networks. The proposed algorithm employs a special conflict-free routing pattern for better scalability and is able to yield a performance rate very close to the theoretical bound for many practical network and matrix sizes. It effectively scales up to very large networks typically containing hundreds-of-thousands processors where petaflop or exaflop processing rates are sought.

Collective Communication Algorithms for 2D torus networks have been investigated quite extensively in the literature and two broad approaches, namely direct methods and indirect (message combining) methods are recognized in the field. While direct methods minimize the volume of data, the indirect methods reduce the number of message start-ups. Consequently, either a suite of algorithms must be employed for efficiency over a wide range of message lengths and communication operations or algorithms should be able to adapt themselves to the current case, possibly by switching between direct and indirect routing modes as appropriate. In this paper, we propose adaptive routing algorithms for all-port, wormhole routed, synchronous, 2D torus networks optimized for one-to-all broadcast, gossiping and complete exchange collective communication operations. The proposed algorithms employ completely-connected subnetworks where complete exchange amongst the nodes in the subnetwork can be accomplished in one step only. Combined with suitable 2D plane tiling techniques, the proposed algorithms share the same set of primitive operations and yield superior performance compared to previously proposed methods, either pure or hybridized.

Membrane separations are finding greater use in wastewater treatment because of their efficiency. In order to prove the effectiveness of membrane filtration an applicability study is carried out. Nanofiltration and reverse osmosis membranes are tested under quite different conditions to reduce the chemical oxygen demands (COD) of wastewaters to meet the Council Directive 76/464/EEC release limit. Two kinds of real wastewaters were selected for the investigation. The wastewaters represent extreme different circumstances since the difference between their COD is two orders of magnitude. All of the membranes tested can be applied either to the treatment of wastewater of high COD (pharmaceutical wastewater) or wastewater of low COD (dumpsite leachate), since the different conditions do not change the membrane characteristics. The experimental data show that none of the membranes can decrease the COD to the release limit in one step. However, if two-stage filtrations (nanofiltration followed by reverse osmosis) are accomplished for both of the wastewaters, a total COD reduction of 94% can be achieved. With the application of the two-stage filtration the COD of the wastewater of low COD can be decreased below the release limit but in case of wastewater of the high COD further treatment will be required.

In traditional mutant screening approaches, genetic variants are tested for one or a small number of phenotypes. Once bona fide variants are identified, they are typically subjected to a limited number of secondary phenotypic screens. Although this approach is excellent at finding genes involved in specific biological processes, the lack of wide and systematic interrogation of phenotype limits the ability to detect broader syndromes and connections between genes and phenotypes. It could also prevent detection of the primary phenotype of a mutant. As part of a systems biology approach to understand plastid function, large numbers of Arabidopsis thaliana homozygous T-DNA lines are being screened with parallel morphological, physiological, and chemical phenotypic assays (www.plastid.msu.edu). To refine our approaches and validate the use of this high-throughput screening approach for understanding gene function and functional networks, approximately 100 wild-type plants and 13 known mutants representing a variety of phenotypes were analyzed by a broad range of assays including metabolite profiling, morphological analysis, and chlorophyll fluorescence kinetics. Data analysis using a variety of statistical approaches showed that such industrial approaches can reliably identify plant mutant phenotypes. More significantly, the study uncovered previously unreported phenotypes for these well-characterized mutants and unexpected associations between different physiological processes, demonstrating that this approach has strong advantages over traditional mutant screening approaches. Analysis of wild-type plants revealed hundreds of statistically robust phenotypic correlations, including metabolites that are not known to share direct biosynthetic origins, raising the possibility that these metabolic pathways have closer relationships than is commonly suspected.

Baryon-to-meson Transition Distribution Amplitudes (TDAs) encoding valuable new information on hadron structure appear as building blocks in the collinear factorized description for several types of hard exclusive reactions. In this paper, we address the possibility of accessing nucleon-to-pion ($��N$) TDAs from $\bar{p}p \to e^+e^- ��^0$ reaction with the future PANDA detector at the FAIR facility. At high center of mass energy and high invariant mass squared of the lepton pair $q^2$, the amplitude of the signal channel $\bar{p}p \to e^+e^- ��^0$ admits a QCD factorized description in terms of $��N$ TDAs and nucleon Distribution Amplitudes (DAs) in the forward and backward kinematic regimes. Assuming the validity of this factorized description, we perform feasibility studies for measuring $\bar{p}p \to e^+e^- ��^0$ with the PANDA detector. Detailed simulations on signal reconstruction efficiency as well as on rejection of the most severe background channel, i.e. $\bar{p}p \to ��^+��^- ��^0$ were performed for the center of mass energy squared $s = 5$ GeV$^2$ and $s = 10$ GeV$^2$, in the kinematic regions $3.0 < q^2 < 4.3$ GeV$^2$ and $5 < q^2 < 9$ GeV$^2$, respectively, with a neutral pion scattered in the forward or backward cone $| \cos��_{��^0}| > 0.5 $ in the proton-antiproton center of mass frame. Results of the simulation show that the particle identification capabilities of the PANDA detector will allow to achieve a background rejection factor of $5\cdot 10^7$ ($1\cdot 10^7$) at low (high) $q^2$ for $s=5$ GeV$^2$, and of $1\cdot 10^8$ ($6\cdot 10^6$) at low (high) $q^2$ for $s=10$ GeV$^2$, while keeping the signal reconstruction efficiency at around $40\%$. At both energies, a clean lepton signal can be reconstructed with the expected statistics corresponding to $2$ fb$^{-1}$ of integrated luminosity. (.../...), 19 pages, 7 figures (some multiple), 2 tables (each double), preprint of an article for epj - v2

The High Level Architecture (HLA) as a well-known IEEE standard for developing parallel and distributed simulation systems has been around for many years. In this paper, Runtime Infrastructure (RTI) of HLA is re-evaluated in the light of the current trends in many-core processor architectures. The future many-core processor architectures will contain thousands of cores connected with on chip networks. Such network on chip (NoC) architectures will not only be built as electronic networks but also as photonic networks. The communication links are established by using scalable communication patterns which define how the light paths to be setup in a 2D photonic network. In other words, RTI specific communication patterns orchestrate the underlying photonic network both to guarantee contention-free network operation and to utilize the bisection bandwidth available on the photonic torus. Time and data distribution management related algorithms are especially subject to this paper. Both the Greatest Available Logical Time (GALT) calculation algorithm and timestamp order (TSO) message delivery are carried out in small number of communication steps on 2D photonic torus. The approach taken in this work is based on hardware and software co-design.

This document describes the technical layout and the expected performance of the Straw Tube Tracker (STT), the main tracking detector of the $\bar{P}$ANDA target spectrometer. The STT encloses a Micro-Vertex-Detector (MVD) for the inner tracking and is followed in beam direction by a set of GEM stations. The tasks of the STT are the measurement of the particle momentum from the reconstructed trajectory and the measurement of the specific energy loss for a particle identification. Dedicated simulations with full analysis studies of certain proton-antiproton reactions, identified as being benchmark tests for the whole $\bar{P}$ANDA scientific program, have been performed to test the STT layout and performance. The results are presented, and the time lines to construct the STT are described.

The Chloroplast 2010 Project (http://www.plastid.msu.edu/) identified and phenotypically characterized homozygous mutants in over three thousand genes, the majority of which encode plastid-targeted proteins. Despite extensive screening by the community, no homozygous mutant alleles were available for several hundred genes, suggesting that these might be enriched for genes of essential function. Attempts were made to generate homozygotes in ∼1200 of these lines and 521 of the homozygous viable lines obtained were deposited in the Arabidopsis Biological Resource Center (http://abrc.osu.edu/). Lines that did not yield a homozygote in soil were tested as potentially homozygous lethal due to defects either in seed or seedling development. Mutants were characterized at four stages of development: developing seed, mature seed, at germination, and developing seedlings. To distinguish seed development or seed pigment-defective mutants from seedling development mutants, development of seeds was assayed in siliques from heterozygous plants. Segregating seeds from heterozygous parents were sown on supplemented media in an attempt to rescue homozygous seedlings that could not germinate or survive in soil. Growth of segregating seeds in air and air enriched to 0.3% carbon dioxide was compared to discover mutants potentially impaired in photorespiration or otherwise responsive to CO2 supplementation. Chlorophyll fluorescence measurements identified CO2-responsive mutants with altered photosynthetic parameters. Examples of genes with a viable mutant allele and one or more putative homozygous-lethal alleles were documented. RT-PCR of homozygotes for potentially weak alleles revealed that essential genes may remain undiscovered because of the lack of a true null mutant allele. This work revealed 33 genes with two or more lethal alleles and 73 genes whose essentiality was not confirmed with an independent lethal mutation, although in some cases second leaky alleles were identified.

Parallel and distributed simulations (PADS) realize the distributed execution of a simulation system over multiple physical resources. To realize the execution of PADS, different simulation infrastructures such as HLA, DIS and TENA have been defined. Recently, the Distributed Simulation Engineering and Execution Process (DSEEP) that supports the mapping of the simulations on the infrastructures has been defined. An important recommended task in DSEEP is the evaluation of the performance of the simulation systems at the design phase. In general, the performance of a simulation is largely influenced by the allocation of member applications to the resources. Usually, the deployment of the applications to the resources can be done in many different ways. DSEEP does not provide a concrete approach for evaluating the deployment alternatives. Moreover, current approaches that can be used for realizing various DSEEP activities do not yet provide adequate support for this purpose. We provide a concrete approach for deriving feasible deployment alternatives based on the simulation system and the available resources. In the approach, first the simulation components and the resources are designed. The design is used to define alternative execution configurations, and based on the design and the execution configuration; a feasible deployment alternative can be algorithmically derived. Tool support is developed for the simulation design, the execution configuration definition and the automatic generation of feasible deployment alternatives. The approach has been applied within a large-scale industrial case study for simulating Electronic Warfare systems.

This paper reports on the results of tests for low temperature applications of two commercial optical glues in the electromagnetic calorimeter of PANDA at FAIR. Mechanical, thermal and optical properties are presented, as well as radiation hardness to photon and proton radiation. (C) 2013 Elsevier B.V. All rights reserved.

Date of Conference: September 29 – October 4, 2013 Conference name: International Conference on Model Driven Engineering Languages and Systems 16th International Conference, MODELS 2013 The trend from single processor to parallel computer architectures has increased the importance of parallel computing. To support parallel computing it is important to map parallel algorithms to a computing platform that consists of multiple parallel processing nodes. In general different alternative mappings can be defined that perform differently with respect to the quality requirements for power consumption, efficiency and memory usage. The mapping process can be carried out manually for platforms with a limited number of processing nodes. However, for exascale computing in which hundreds of thousands of processing nodes are applied, the mapping process soon becomes intractable. To assist the parallel computing engineer we provide a model-driven approach to analyze, model, and select feasible mappings. We describe the developed toolset that implements the corresponding approach together with the required metamodels and model transformations. We illustrate our approach for the well-known complete exchange algorithm in parallel computing. © 2013 Springer-Verlag.

The need for high-performance computing together with the increasing trend from single processor to parallel computer architectures has leveraged the adoption of parallel computing. To benefit from parallel computing power, usually parallel algorithms are defined that can be mapped and executed on parallel computing platforms. In general, different alternative mappings can be defined each with different performance. For small computing platforms with a limited number of processing nodes, the mapping process can be carried out manually. However, for large-scale parallel computing platforms in which hundreds of thousands of processing nodes are applied, the number of possible mapping alternatives increases dramatically, and the mapping process becomes intractable for the human engineer. To assist the parallel computing engineer, we provide a systematic approach to derive feasible mapping alternatives of parallel algorithms to parallel computing platforms. The approach includes activities for modeling the parallel algorithm and parallel computing platform, generation of feasible mapping alternatives, generation of the deployment code, and finally the deployment of the generated code to the nodes. We evaluate our approach for deriving feasible mapping alternatives for four well-known parallel algorithms. The evaluation is based on both simulations and real executions of the generated mapping alternatives.

We identified an Arabidopsis thaliana mutant, clumped chloroplasts 1 ( clmp1 ), in which disruption of a gene of unknown function causes chloroplasts to cluster instead of being distributed throughout the cytoplasm. The phenotype affects chloroplasts and nongreen plastids in multiple organs and cell types, but is detectable only at certain developmental stages. In young leaf petioles of clmp1 , where clustering is prevalent, cells lacking chloroplasts are detected, suggesting impaired chloroplast partitioning during mitosis. Although organelle distribution and partitioning are actin-dependent in plants, the actin cytoskeleton in clmp1 is indistinguishable from that in WT, and peroxisomes and mitochondria are distributed normally. A CLMP1-YFP fusion protein that complements clmp1 localizes to discrete foci in the cytoplasm, most of which colocalize with the cell periphery or with chloroplasts. Ultrastructural analysis revealed that chloroplasts within clmp1 clusters are held together by membranous connections, including thin isthmi characteristic of late-stage chloroplast division. This finding suggests that constriction of dividing chloroplasts proceeds normally in clmp1 , but separation is impaired. Consistently, chloroplast size and number, as well as positioning of the plastid division proteins FtsZ and ARC5/DRP5B, are unaffected in clmp1 , indicating that loss of CLMP1-mediated chloroplast separation does not prevent otherwise normal division. CLMP1-like sequences are unique to green algae and land plants, and the CLMP1 sequence suggests that it functions through protein–protein interactions. Our studies identify a unique class of proteins required for plastid separation after the constriction stage of plastid division and indicate that CLMP1 activity is also required for plastid distribution and partitioning during cell division.

The aim of this study was to evaluate the dynamics of the recanalization process (spontaneous fibrinolysis) in completely occlusive deep venous thrombosis (DVT) using duplex ultrasound examination and to investigate the influence of different factors on the evolution of thrombus regression.This longitudinal prospective study was done with 74 consecutive patients with completely occlusive acute multilevel DVT, confirmed by echo duplex scan after 1, 3, 6, and 12 months. At each re-evaluation, the degree and the type of recanalization were determined. Efficacy of tinzaparin (175 IU/kg, s.c., q.d. for 7-14 days) and continued with warfarin (12 months at INR 2-3) as well as patients' compliance with compressive elastic hosiery wearing were carefully followed. Relationship between the degree and pattern of recanalization and patients' age, gender, as well as thrombosis etiology and location were determined.Sixty-four patients completed the study. The mean recanalization rate was 39.7% at 1, 64.8% at 3, 82% at 6, and 90.3% at 12 months. Marginal recanalization was more frequently observed, but recanalization pattern was changing during follow-up.In the case of efficient anticoagulant and compressive therapy, the spontaneous recanalization process of DVT is important from the very first month of evolution, but an almost complete re-permeabilization is observed only after 12 months of treatment. The unilocular, marginal pattern of thrombus lysis is often observed and has better evolution than the multilocular cavernous one. The dynamics of recanalization are characterized by distal-to-proximal extension and in the first 6 months are significantly influenced by patient's gender and thrombosis etiology.