bluuebunny/crossref_metadata_2025 huggingface dataset:
Traditional Chinese Medicine Formulas for Irritable Bowel Syndrome: From Ancient Wisdoms to Scientific Understandings
Authors: Xiao Hai-Tao , Zhong Linda , Tsang Siu-Wai , Lin Ze-Si , Bian Zhao-Xiang
Published: January 2015

Traditional Chinese Medicine (TCM) serves as the most common alternative therapeutic approach for Western medicine and benefits IBS patients globally. Due to the lack of scientific evidence in the past, TCM formulas were not internationally well recognized as promising IBS remedies. In this review, firstly, we present the etiology and therapy of IBS in terms of traditional Chinese medical theory. Secondly, we summarize the clinical randomized controlled trials (RCTs) of TCM formulas for IBS patients that are available in the literature (from 1998 to September 2013), in which 14 RCTs conducted of high quality were discussed in detail. Of the 14 selected trials, 12 of those concluded that TCM formulas provided superior improvement in the global symptoms of IBS patients over the placebo or conventional medicines. As well, all 14 RCTs suggested that TCM formulas have good safety and tolerability. Last but not least, we explore the pharmacological mechanisms of the anti-IBS TCM formulas available in the literature (from 1994 to September, 2013). Collectively, in combating IBS symptoms, most TCM formulas exert multi-targeting actions including the regulation of neurotransmitters and hormones in the enteric nervous system (ENS), modulation of smooth muscle motility in the gastrointestinal (GI) tract, modulation of the hypothalamic–pituitary–adrenal (HPA) axis, attenuation of intestinal inflammation and restoration of intestinal flora, etc. In conclusion, TCM formulas appear to be promising for IBS treatment. This review provides a useful reference for the public in furthering a better understanding and acceptance of TCM formulas as IBS remedies.
Decays of dibaryon sextaquarks in broken SU(3) symmetry
Authors: Gupta V. , Sánchez-Colón G.
Published: January 2015

The SU(3) classification of baryon number B = 2, that is dibaryon sextaquarks, is considered. It is noted that the deuteron belongs to the 10* representation. Sum rules in broken SU(3) are given for the 10* and 10 dibaryons into B(8)+B(8). Finally, the possibility of observing the dibaryons in low energy pp- and e+e--collisions is discussed.
Superconductivity in K- and Na-doped BaFe2As2: What can we learn from heat capacity and pressure dependence of Tc
Authors: Bud'ko Sergey L.
Published: January 2015

A brief overview of changes in the superconducting transition temperature under pressure and evolution of specific heat capacity jump at Tc for two related families of iron-based superconductors, Ba 1-x K x Fe 2 As 2 (0.2 ≤ x ≤ 1.0) and Ba 1-x Na x Fe 2 As 2 (0.2 ≤ x ≤ 0.9) will be given. For Ba 1-x K x Fe 2 As 2 the specific heat capacity jump at Tc measured over the whole extent of the superconducting dome shows clear deviation from the empirical, [Formula: see text], scaling (known as the BNC scaling) for x > 0.7. At the same concentrations range apparent equivalence of effects of pressure and K -substitution on Tc fails. These observations suggests a significant change of the superconducting state for x > 0.7. In contrast, the data for the large portion of Ba 1-x Na x Fe 2 As 2 (0.2 ≤ x ≤ 0.9) series follow the BNC scaling. However, the pressure dependence of Tc (measured up to ~12 kbar) have clear nonlinearities for Na concentration in 0.2–0.25 region, that may be consistent with Tc crossing the phase boundaries of the emergent, narrow, antiferromagnetic/tetragonal phase. Results will be discussed in context other studies of these two related families of iron-based superconductors.
Novel Dispersion Curves Extraction Method for Waveguides Affected by Nonuniform Transient Temperature Field
Authors: Xiao Denghong , He Tian , Liu Xiandong , Shan Yingchun
Published: January 2015

Guided waves sensitivity to environmental and operational conditions, especially temperature fluctuations, is one of the major problems when the method is considered for real engineering applications. The aim of this paper is to propose a novel dispersion curves extraction method for waveguides affected by nonuniform transient temperature field. Essentially, the method is based on a simple and robust approach, consisting in a few series of modal analyses for a representative part of the inspected structure. To consider the effect of temperature, a thermal stress calculation based on finite element method is presented. In this way, for different wave lengths, the mode shapes and corresponding natural frequencies can be obtained by solving some thermal-eigenvalue problems. To test the theoretical thermal effect of the dispersion curves a experiment on an isotropic plate is conducted. Those theoretical dispersion curves, consisting of only dominant modes, are compared with dispersion curves obtained from experiment. Finally, this method is used to extract the dispersion curves of the aero-engine casing considering the nonuniform temperature field. The results not only give us insight to how temperature affects Lamb wave velocities in different frequency ranges but also will help those extracting dispersion curves for waveguides affected by nonuniform transient temperature field.
PEOPLE WATCH
Authors: Lim Rachel
Published: January 2015

Future Healthcare Solutions.
Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates
Authors: Zhang Fan , Wu Min , Li Xue-Juan , Li Xiao-Li , Kwoh Chee Keong , Zheng Jie
Published: January 2015

A major goal of personalized anti-cancer therapy is to increase the drug effects while reducing the side effects as much as possible. A novel therapeutic strategy called synthetic lethality (SL) provides a great opportunity to achieve this goal. SL arises if mutations of both genes lead to cell death while mutation of either single gene does not. Hence, the SL partner of a gene mutated only in cancer cells could be a promising drug target, and the identification of SL pairs of genes is of great significance in pharmaceutical industry. In this paper, we propose a hybridized method to predict SL pairs of genes. We combine a data-driven model with knowledge of signalling pathways to simulate the influence of single gene knock-down and double genes knock-down to cell death. A pair of genes is considered as an SL candidate when double knock-down increases the probability of cell death significantly, but single knock-down does not. The single gene knock-down is confirmed according to the human essential genes database. Our validation against literatures shows that the predicted SL candidates agree well with wet-lab experiments. A few novel reliable SL candidates are also predicted by our model.
Beyond 1Mbps Global Overlay Live Streaming
Authors: Ren Dongni , Xu Yisheng , Chan S.-H. Gary
Published: January 2015

In order to provide live streaming over the global Internet, a content provider often deploys an overlay network consisting of distributed proxies placed close to user pools. Streaming of multi-Mbps video over such an overlay is challenging because of bandwidth bottlenecks in paths. To effectively overcome these bottlenecks, we consider employing proxy
helpers
in the overlay to provide rich path diversity. The helpers do not have any attached users, and hence may forward partial video streams (or not at all) if necessary. In this way, the helpers serve as stepping stones to supply full streams to the servers. The issue is how to involve the helpers in the overlay to achieve low streaming delay meeting a certain high streaming bitrate requirement.

To address the issue, we first formulate the problem which captures various delay and bandwidth components, and show that it is NP-hard. We then propose an efficient algorithm called
Stepping-Stones
(SS) which can be efficiently implemented in a controller. Given the encouraging simulation results, we develop a novel streaming testbed for SS and explore, through sets of Internet experiments, the effectiveness of helpers to achieve high bitrate (multi-Mbps) global live streaming. In our experiments, proxies are deployed with a reasonably wide global footprint. We collect more than a hundred hours of streaming traces with bitrate ranging from 500kbps to a few Mbps. Our experimental data validates that helpers indeed play an important role in achieving high bitrate in today's Internet. Global multi-Mbps streaming is possible due to their
multihop
and
multipath
advantages. Our experimental trials and data also provide valuable insights on the design of a global push-based streaming network. There are strong benefits of using proxy helpers to achieve high bitrate and low delay.
Efficient Computation of Shortest Paths in Time-Dependent Multi-Modal Networks
Authors: Kirchler Dominik , Liberti Leo , Calvo Roberto Wolfler
Published: January 2015

We consider shortest paths on time-dependent multimodal transportation networks in which restrictions or preferences on the use of certain modes of transportation may arise. We model restrictions and preferences by means of regular languages. Methods for solving the corresponding problem (called the
regular language constrained shortest path problem
) already exist. We propose a new algorithm, called State Dependent ALT (SDALT), which runs considerably faster in many scenarios. Speed-up magnitude depends on the type of constraints. We present different versions of SDALT, including unidirectional and bidirectional search. We also provide extensive experimental results on realistic multimodal transportation networks.
Mitigation of Radiation Effects in SRAM-Based FPGAs for Space Applications
Authors: Siegle Felix , Vladimirova Tanya , Ilstad Jørgen , Emam Omar
Published: January 2015

The use of static random access memory (SRAM)-based field programmable gate arrays (FPGAs) in harsh radiation environments has grown in recent years. These types of programmable devices require special mitigation techniques targeting the configuration memory, the user logic, and the embedded RAM blocks. This article provides a comprehensive survey of the literature published in this rich research field during the past 10 years. Furthermore, it can also serve as a tutorial for space engineers, scientists, and decision makers who need an introduction to this topic.
Architectural Support for Data-Driven Execution
Authors: Matheou George , Evripidou Paraskevas
Published: January 2015

The exponential growth of sequential processors has come to an end, and thus, parallel processing is probably the only way to achieve performance growth. We propose the development of parallel architectures based on data-driven scheduling. Data-driven scheduling enforces only a partial ordering as dictated by the true data dependencies, which is the minimum synchronization possible. This is very beneficial for parallel processing because it enables it to exploit the maximum possible parallelism. We provide architectural support for data-driven execution for the Data-Driven Multithreading (DDM) model. In the past, DDM has been evaluated mostly in the form of virtual machines. The main contribution of this work is the development of a highly efficient hardware support for data-driven execution and its integration into a multicore system with eight cores on a Virtex-6 FPGA. The DDM semantics make barriers and cache coherence unnecessary, which reduces the synchronization latencies significantly and makes the cache simpler. The performance evaluation has shown that the support for data-driven execution is very efficient with negligible overheads. Our prototype can support very small problem sizes (matrix 16×16) and ultra-lightweight threads (block of 4x4) that achieve speedups close to linear. Such results cannot be achieved by software-based systems.
Fast Crown Scheduling Heuristics for Energy-Efficient Mapping and Scaling of Moldable Streaming Tasks on Manycore Systems
Authors: Melot Nicolas , Kessler Christoph , Keller Jörg , Eitschberger Patrick
Published: January 2015

Exploiting effectively massively parallel architectures is a major challenge that stream programming can help facilitate. We investigate the problem of generating energy-optimal code for a collection of streaming tasks that include parallelizable or moldable tasks on a generic manycore processor with dynamic discrete frequency scaling. Streaming task collections differ from classical task sets in that all tasks are running concurrently, so that cores typically run several tasks that are scheduled round-robin at user level in a data-driven way. A stream of data flows through the tasks and intermediate results may be forwarded to other tasks, as in a pipelined task graph. In this article, we consider
crown scheduling
, a novel technique for the combined optimization of resource allocation, mapping, and discrete voltage/frequency scaling for moldable streaming task collections in order to optimize energy efficiency given a throughput constraint. We first present optimal offline algorithms for separate and integrated crown scheduling based on integer linear programming (ILP). We make no restricting assumption about speedup behavior. We introduce the fast heuristic
Longest Task, Lowest Group
(LTLG) as a generalization of the Longest Processing Time (LPT) algorithm to achieve a load-balanced mapping of parallel tasks, and the
Height
heuristic for crown frequency scaling. We use them in feedback loop heuristics based on binary search and simulated annealing to optimize crown allocation.

Our experimental evaluation of the ILP models for a generic manycore architecture shows that at least for small and medium-sized streaming task collections even the integrated variant of crown scheduling can be solved to optimality by a state-of-the-art ILP solver within a few seconds. Our heuristics produce makespan and energy consumption close to optimality within the limits of the phase-separated crown scheduling technique and the crown structure. Their optimization time is longer than the one of other algorithms we test, but our heuristics consistently produce better solutions.
Oxygen Sensing and Signaling
Authors: van Dongen Joost T. , Licausi Francesco
Published: January 2015

Oxygen is an indispensable substrate for many biochemical reactions in plants, including energy metabolism (respiration). Despite its importance, plants lack an active transport mechanism to distribute oxygen to all cells. Therefore, steep oxygen gradients occur within most plant tissues, which can be exacerbated by environmental perturbations that further reduce oxygen availability. Plants possess various responses to cope with spatial and temporal variations in oxygen availability, many of which involve metabolic adaptations to deal with energy crises induced by low oxygen. Responses are induced gradually when oxygen concentrations decrease and are rapidly reversed upon reoxygenation. A direct effect of the oxygen level can be observed in the stability, and thus activity, of various transcription factors that control the expression of hypoxia-induced genes. Additional signaling pathways are activated by the impact of oxygen deficiency on mitochondrial and chloroplast functioning. Here, we describe the molecular components of the oxygen-sensing pathway.
Form Follows Function: The Importance of Endoplasmic Reticulum Shape
Authors: Westrate L.M. , Lee J.E. , Prinz W.A. , Voeltz G.K.
Published: January 2015

The endoplasmic reticulum (ER) has a remarkably complex structure, composed of a single bilayer that forms the nuclear envelope, along with a network of sheets and dynamic tubules. Our understanding of the biological significance of the complex architecture of the ER has improved dramatically in the last few years. The identification of proteins and forces required for maintaining ER shape, as well as more advanced imaging techniques, has allowed the relationship between ER shape and function to come into focus. These studies have also revealed unexpected new functions of the ER and novel ER domains regulating alterations in ER dynamics. The importance of ER structure has become evident as recent research has identified diseases linked to mutations in ER-shaping proteins. In this review, we discuss what is known about the maintenance of ER architecture, the relationship between ER structure and function, and diseases associated with defects in ER structure.
Chronic Traumatic Encephalopathy: Historical Origins and Current Perspective
Authors: Montenigro Philip H. , Corp Daniel T. , Stein Thor D. , Cantu Robert C. , Stern Robert A.
Published: January 2015

Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease that is most often identified in postmortem autopsies of individuals exposed to repetitive head impacts, such as boxers and football players. The neuropathology of CTE is characterized by the accumulation of hyperphosphorylated tau protein in a pattern that is unique from that of other neurodegenerative diseases, including Alzheimer's disease. The clinical features of CTE are often progressive, leading to dramatic changes in mood, behavior, and cognition, frequently resulting in debilitating dementia. In some cases, motor features, including parkinsonism, can also be present. In this review, the historical origins of CTE are revealed and an overview of the current state of knowledge of CTE is provided, including the neuropathology, clinical features, proposed clinical and pathological diagnostic criteria, potential in vivo biomarkers, known risk factors, and treatment options.
Depression and Cognition in the Elderly
Authors: Wang Sophia , Blazer Dan G.
Published: January 2015

This review provides an overview of the relationship between depression and cognition in the elderly, with an emphasis on psychotherapies and nonpharmacologic approaches. We first review the clinical presentation of late-life depression and comorbid cognitive impairment, as well as the epidemiology and risk factors for cognitive impairment in late-life depression and the temporal relationship between depression and cognitive impairment. Next, we discuss the salient topic of elderly suicide and cognitive impairment. We then touch briefly on the neuropsychological deficits, biomarkers, and neuroimaging findings in late-life depression with comorbid cognitive impairment. We then focus most of this review on psychotherapies and nontraditional treatments for late-life depression with comorbid cognitive impairment and examine what evidence, if any, exists of the cognitive and functional benefits of these treatments. Finally, we examine the cognitive effects of pharmacologic treatments and brain stimulation therapies.
Group Affect
Authors: Barsade Sigal G. , Knight Andrew P.
Published: January 2015

Over two decades of research has indicated that group affect is an important factor that shapes group processes and outcomes. We review and synthesize research on group affect, encompassing trait affect, moods, and emotions at a collective level in purposive teams. We begin by defining group affect and examining four major types of collective affective constructs: (a) convergence in group affect; (b) affective diversity, that is, divergence in group affect; (c) emotional culture; and (d) group affect as a dynamic process that changes over time. We describe the nomological network of group affect, examining both its group-level antecedents and group-level consequences. Antecedents include group leadership, group member attributes, and interactions between and relationships among group members. Consequences of group affect include attitudes about the group and group-level cooperation and conflict, creativity, decision making, and performance. We close by discussing current research knowns, research needs, and what lies on the conceptual and methodological frontiers of this domain.
Beyond Lewin: Toward a Temporal Approximation of Organization Development and Change
Authors: Bartunek Jean M. , Woodman Richard W.
Published: January 2015

We describe the new dialogic organization development (OD) fleshed out by Bushe & Marshak (2009) . In comparing this approach with the old diagnostic OD, we explore the limitations of Lewin’s (1947) unfreeze-change-freeze model for depicting organizational change over time. We develop an approach that more fully approximates an adequate temporal model of change by incorporating attention to sequence, timing, pacing, rhythm, and polyphonic dimensions present in change. We use this approach to explore longitudinally how the new OD came to be, as well as how it is now entrained with the old OD, and show that our approach reveals a number of dimensions of change that are masked by Lewin’s model. We illustrate the use of our approach beyond OD to depict the temporal dimensions of Tushman & Romanelli’s (1985) model of convergence and reorientation. Finally, we suggest next steps for theory, research, and practice.
The Dynamics of Molecular Interactions and Chemical Reactions at Metal Surfaces: Testing the Foundations of Theory
Authors: Golibrzuch Kai , Bartels Nils , Auerbach Daniel J. , Wodtke Alec M.
Published: January 2015

We review studies of molecular interactions and chemical reactions at metal surfaces, emphasizing progress toward a predictive theory of surface chemistry and catalysis. For chemistry at metal surfaces, a small number of central approximations are typically made: (a) the Born-Oppenheimer approximation of electronic adiabaticity, (b) the use of density functional theory at the generalized gradient approximation level, (c) the classical approximation for nuclear motion, and (d) various reduced-dimensionality approximations. Together, these approximations constitute a provisional model for surface chemical reactivity. We review work on some carefully studied examples of molecules interacting at metal surfaces that probe the validity of various aspects of the provisional model.
Unintentional Home Injuries Across the Life Span: Problems and Solutions
Authors: Gielen Andrea C. , McDonald Eileen M. , Shields Wendy
Published: January 2015

Home injuries cause more than 30,000 deaths and 12 million nonfatal injuries annually in the United States. They generate an estimated $222 billion in lifetime costs annually. Despite some data limitations in documenting home as the location of an injury, much progress has been made in identifying effective prevention strategies that reduce injury or mitigate risk behaviors.

The current interest in public health in the role of housing in health offers unparalleled opportunities for injury prevention professionals concerned with home injuries. Sharing the science of injury prevention with the wide array of professionals—such as architects, home builders, home visitors, and fire and emergency medical services providers—who create home environments and interact with residents could be a useful approach. A collaborative national effort to reduce the burden of home injuries is needed.
C++ and Massively Parallel Computers
Authors: Lickly Daniel J. , Hatcher Philip J.
Published: January 2015

Our goal is to apply the software engineering advantages of object‐oriented programming to the raw power of massively parallel architectures. To do this we have constructed a hierarchy of C++ classes to support the data‐parallel paradigm. Feasibility studies and initial coding can be supported by any serial machine that has a C++ compiler. Parallel execution requires an extended Cfront, which understands the data‐parallel classes and generates C* code. (C* is a data‐parallel superset of ANSI C developed by Thinking Machines Corporation). This approach provides potential portability across parallel architectures and leverages the existing compiler technology for translating data‐parallel programs onto both SIMD and MIMD hardware.
Parallel Object‐Oriented Computation Applied to a Finite Element Problem
Authors: Weissman Jon B. , Grimshaw Andrew S. , Ferraro R.D.
Published: January 2015

The conventional wisdom in the scientific computing community is that the best way to solve large‐scale numerically intensive scientific problems on today′s parallel MIMD computers is to use Fortran or C programmed in a data‐parallel style using low‐level message‐passing primitives. This approach inevitably leads to nonportable codes and extensive development time, and restricts parallel programming to the domain of the expert programmer. We believe that these problems are not inherent to parallel computing but are the result of the programming tools used. We will show that comparable performance can be achieved with little effort if better tools that present higher level abstractions are used. The vehicle for our demonstration is a 2D electromagnetic finite element scattering code we have implemented in Mentat, an object‐oriented parallel processing system. We briefly describe the application. Mentat, the implementation, and present performance results for both a Mentat and a hand‐coded parallel Fortran version.
Using Naming Strategies to Make Massively Parallel Systems Work
Authors: Schmidt Henning
Published: January 2015

To handle massively parallel systems and make them usable, an adaptive, application‐oriented operating system is required. The application orientedness is represented by the family concept of parallel operating systems. Incremental loading of operating system services supports the family character by automatically extending the system′s active object structure when it is necessary. This way, also the switching between different operating system family members may be realized. A new active object will be incrementally loaded if its invocation fails because it does not yet exist. This is noticed during object binding while using the naming services. The use of the naming system is exploited and extended to get a flexible and configurable mechanism for triggering incremental loading. This mechanism is built by the freely definable naming strategies and exceptions that result again in a family, namely a family of naming services.
HeNCE: A Heterogeneous Network Computing Environment
Authors: Beguelin Adam , Dongarra Jack J. , Geist George Al , Manchek Robert , Moore Keith
Published: January 2015

Network computing seeks to utilize the aggregate resources of many networked computers to solve a single problem. In so doing it is often possible to obtain supercomputer performance from an inexpensive local area network. The drawback is that network computing is complicated and error prone when done by hand, especially if the computers have different operating systems and data formats and are thus heterogeneous. The heterogeneous network computing environment (HeNCE) is an integrated graphical environment for creating and running parallel programs over a heterogeneous collection of computers. It is built on a lower level package called parallel virtual machine (PVM). The HeNCE philosophy of parallel programming is to have the programmer graphically specify the parallelism of a computation and to automate, as much as possible, the tasks of writing, compiling, executing, debugging, and tracing the network computation. Key to HeNCE is a graphical language based on directed graphs that describe the parallelism and data dependencies of an application. Nodes in the graphs represent conventional Fortran or C subroutines and the arcs represent data and control flow. This article describes the present state of HeNCE, its capabilities, limitations, and areas of future research.
On the Parallel Elliptic Single/Multigrid Solutions about Aligned and Nonaligned Bodies Using the Virtual Machine for Multiprocessors
Authors: Averbuch A. , Gabber E. , Itzikowitz S. , Shoham B.
Published: January 2015

Parallel elliptic single/multigrid solutions around an aligned and nonaligned body are presented and implemented on two multi‐user and single‐user shared memory multiprocessors (Sequent Symmetry and MOS) and on a distributed memory multiprocessor (a Transputer network). Our parallel implementation uses the Virtual Machine for Muli‐Processors (VMMP), a software package that provides a coherent set of services for explicitly parallel application programs running on diverse multiple instruction multiple data (MIMD) multiprocessors, both shared memory and message passing. VMMP is intended to simplify parallel program writing and to promote portable and efficient programming. Furthermore, it ensures high portability of application programs by implementing the same services on all target multiprocessors. The performance of our algorithm is investigated in detail. It is seen to fit well the above architectures when the number of processors is less than the maximal number of grid points along the axes. In general, the efficiency in the nonaligned case is higher than in the aligned case. Alignment overhead is observed to be up to 200% in the shared‐memory case and up to 65% in the message‐passing case. We have demonstrated that when using VMMP, the portability of the algorithms is straightforward and efficient.
POLYSHIFT Communications Software for the Connection Machine System CM‐200
Authors: George William , Brickner Ralph G. , Johnsson S. Lennart
Published: January 2015

We describe the use and implementation of a polyshift function PSHIFT for circular shifts and end‐offs shifts. Polyshift is useful in many scientific codes using regular grids, such as finite difference codes in several dimensions, and multigrid codes, molecular dynamics computations, and in lattice gauge physics computations, such as quantum chromodynamics (QCD) calculations. Our implementation of the PSHIFT function on the Connection Machine systems CM‐2 and CM‐200 offers a speedup of up to a factor of 3–4 compared with CSHIFT when the local data motion within a node is small. The PSHIFT routine is included in the Connection Machine Scientific Software Library (CMSSL).
A Parallel Processing Approach to Transition Prediction for Laminar Flow Control System Design
Authors: Ford R. W. , Poll D. I. A.
Published: January 2015

The performance of transport aircraft can be considerably improved if the process by which the wing boundary layer becomes turbulent can be controlled and extensive areas of laminar flow maintained. In order to design laminar flow control systems, it is necessary to be able to predict the movement of the transition location in response to changes in control variables, e.g., surface suction. At present, the technique which is available to industry requires excessively long computational time – so long that it is not suitable for use in the "design process." Therefore, there is a clear need to produce a system which delivers results in near realtime, i.e., in seconds rather than hours. This article details how parallel computing techniques on a KSR‐1 produce these performance improvements.
Data‐Parallel Numerical Weather Forecasting
Authors: Wolters Lex , Cats Gerard , Gustafsson Nils
Published: January 2015

In this article we describe the implementation of a numerical weather forecast model on a massively parallel computer system. This model is a production code used for routine weather forecasting at the meteorological institutes of several European countries. The modifications needed to achieve a data‐parallel version of this model without explicit message passing are outlined. The achieved performance of different numerical solution methods within this model is presented and compared.
ObjectMath – An Object‐Oriented Language and Environment for Symbolic and Numerical Processing in Scientific Computing
Authors: Viklund Lars , Fritzson Peter
Published: January 2015

ObjectMath is a language for scientific computing that integrates object‐oriented constructs with features for symbolic and numerical computation. Using ObjectMath, complex mathematical models may be implemented in a natural way. The ObjectMath programming environment provides tools for generating efficient numerical code from such models. Symbolic computation is used to rewrite and simplify equations before code is generated. One novelty of the ObjectMath approach is that it provides a comman language and an integrated environment for this kind of mixed symbolic/numerical computation. The motivation for this work is the current low‐level state of the art in programming for scientific computing. Much numerical software is still being developed the traditional way in Fortran. This is especially true in application areas such as machine elements analysis, where complex nonlinear problems are the norm. We believe that tools like ObjectMath can increase productivity and quality, thus enabling users to solve problems that are too complex to handle with traditional tools.
Image Analysis Based Grading of Bladder Carcinoma. Comparison of Object, Texture and Graph Based Methods and Their Reproducibility
Authors: Choi Heung‐Kook , Jarkrans Torsten , Bengtsson Ewert , Vasko Janos , Wester Kenneth , Malmström Per-Uno , Busch Christer
Published: January 2015

The possibility that computerized image analysis could increase the reproducibility of grading of bladder carcinoma as compared to conventional subjective grading made by pathologists was investigated. Object, texture and graph based analysis were carried out from Feulgen stained histological tissue sections. The object based features were extracted from gray scale images, binary images obtained by thresholding the nuclei and several other images derived through image processing operations. The textural features were based on the spatial gray‐tone co‐occurrence probability matrices and the graph based features were extracted from the minimum spanning trees connecting all nuclei. The large numbers of extracted features were evaluated in relation to subjective grading and to factors related to prognosis using multivariate statistical methods and multilayer backpropagation neural networks. All the methods were originally developed and tested on material from one patient and then tested for reproducibility on entirely different patient material. The results indicate reasonably good reproducibility for the best sets of features. In addition, image analysis based grading showed almost identical correlation to mitotic density and expression of p53 protein as subjective grading. It should thus be possible to use this kind of image analysis as a prognostic tool for bladder carcinoma.
Identification of Type VI Collagen Synthesizing Cells in Human Diabetic Glomerulosclerosis Using Renal Biopsy Sections
Authors: Razzaque Mohammed Shawkat , Koji Takehiko , Harada Takashi , Taguchi Takashi
Published: January 2015

Although the role of extracellular matrices in the development of glomerulosclerosis has been discussed widely, the cellular origin of type VI collagen in diabetic nephropathy (DN) has remained relatively unexplored. This study reports the distribution and cellular origin of type VI collagen in DN. Type VI collagen‐specific oligonucleotide probes and monoclonal antibody were used to assess the relative expression of mRNA for \alpha1 (VI) chain and its translated protein in paraffin‐embedded renal biopsy sections of DN. By immunohistochemistry, compared to the control, increased deposition of type VI collagen was noted in the diffuse and nodular lesions of diabetic glomeruli. For cellular localization of type VI collagen mRNA, paraffin‐embedded renal sections of the control and DN were hybridized in situ with digoxigenin (Dig)‐labeled antisense oligo‐DNA probe complementary to a part of \alpha1 (VI) mRNA. In comparison to the control kidney sections, increased numbers of intraglomerular cells (both mesangial and epithelial cells) were positive for α1 (VI) mRNA in renal biopsy sections of DN. From the results, we conclude that overexpression of type VI collagen by intraglomerular cells with its increased deposition might significantly contribute to the glomerulosclerosis found in DN.
Cytometric DNA Analysis and Prognostic Biomarkers in Breast Carcinoma. Expression of P53 Product in the Different Ploidy Classes
Authors: Leonardi Elena , Cristofori Antonella , Caffo Orazio , Dalla Palma Paolo
Published: January 2015

The aim of the study was to correlate the DNA Index (DI) and S‐phase fraction (SPF) values determined by multiparametric flow cytometry in breast cancer (mainly T1 and T2 stages) with several clinico‐pathologic variables and other biological parameters. For this purpose, a total of 136 breast cancers were submitted to flow cytometry and to several types of immunohistochemical analyses. Among clinico‐pathologic data we considered pT, pN and grade and among immunohistochemical markers, hormonal receptors, P53, c‐erbB‐2 and MIB‐1. We found that DNA aneuploidy was strongly correlated with high tumoral grade, absence of hormonal receptors, high proliferation, as shown by high MIB‐1 (≥36%) and SPF values (≥13.3%), and P53 positivity. Grouping the tumours according to their DI values, we observed a relative significantly higher correlation of the near‐triploid range carcinomas (DI 1.40–1.60) with immunohistochemical expression of P53 (p=0.0001). Near‐triploid DI was also associated with a high proliferative activity, expressed both by SPF (p=0.0001) and MIB‐1 reactivity (p=0.0001), high tumoral grade (p=0.0001) and presence of axillary metastases (p=0.03). These data suggest that DNA near‐triploid tumours in breast cancer may have a more aggressive behaviour in comparison with other DI classes.
Performance Issues in High Performance Fortran Implementations of Sensor‐Based Applications
Authors: O′hallaron David R. , Webb Jon , Subhlok Jaspal
Published: January 2015

Applications that get their inputs from sensors are an important and often overlooked application domain for High Performance Fortran (HPF). Such sensor‐based applications typically perform regular operations on dense arrays, and often have latency and through put requirements that can only be achieved with parallel machines. This article describes a study of sensor‐based applications, including the fast Fourier transform, synthetic aperture radar imaging, narrowband tracking radar processing, multibaseline stereo imaging, and medical magnetic resonance imaging. The applications are written in a dialect of HPF developed at Carnegie Mellon, and are compiled by the Fx compiler for the Intel Paragon. The main results of the study are that (1) it is possible to realize good performance for realistic sensor‐based applications written in HPF and (2) the performance of the applications is determined by the performance of three core operations: independent loops (i.e., loops with no dependences between iterations), reductions, and index permutations. The article discusses the implications for HPF implementations and introduces some simple tests that implementers and users can use to measure the efficiency of the loops, reductions, and index permutations generated by an HPF compiler.
Sequential Assessment of Cell Cycle S Phase in Flow Cytometry: A Non‐Isotopic Method to Measure Lymphocyte Activation In Vitro
Authors: Kohler Ch. , Kolopp‐Sarda M. N. , De March‐Kennel A. , Barbaud A. , Béné M. C. , Faure G. C.
Published: January 2015

Lymphocyte multiplication can be induced in vitro by mitogens or specific antigens, and is usually measured using isotopic methods involving tritiated thymidine. Cellular proliferation can also be analyzed by flow cytometry techniques based on cell cycle analysis through the measurement of DNA content. We applied this method to lymphocytes from 113 individuals, to evaluate lymphocyte proliferation after stimulation in vitro by a mitogen (phytohaemagglutinin, PHA) or a recall antigen (tetanus toxoid), using a kinetic approach with four points sequential measurements of the S and G2 phases over six days of culture. The proportion of cells in S phase after PHA stimulation was significantly higher than in controls overall and as early as on day three of the culture. Activation with a recall antigen significantly induced increasing S phase cell proportions up to day six. These data suggest that flow cytometric assessment of the S phase could be a useful alternative to isotopic methods measuring lymphocyte reactivity in vitro.
Questions and Answers about BSP
Authors: Skillicorn D.B. , Hill Jonathan M.D. , McColl W.F.
Published: January 2015

Bulk Synchronous Parallelism (BSP) is a parallel programming model that abstracts from low‐level program structures in favour of supersteps. A superstep consists of a set of independent local computations, followed by a global communication phase and a barrier synchronisation. Structuring programs in this way enables their costs to be accurately determined from a few simple architectural parameters, namely the permeability of the communication network to uniformly‐random traffic and the time to synchronise. Although permutation routing and barrier synch ronisations are widely regarded as inherently expensive, this is not the case. As a result, the structure imposed by BSP does not reduce performance, while bringing considerable benefits for application building. This paper answers the most common questions we are asked about BSP and justifies its claim to be a major step forward in parallel programming.
DNA Measurement of Overlapping Cell Nuclei in Thick Tissue Sections
Authors: Ji Liang , Tucker James
Published: January 2015

The paper describes an improved image analysis procedure for measuring the DNA content of cell nuclei in thick sections of liver tissue by absorption densitometry. Whereas previous methods only permitted the analysis of isolated nuclei, the new technique enables both isolated and overlapping nuclei to be measured. A 3D segmentation procedure determines whether each object is an isolated nucleus or a pair of overlapping nuclei; in the latter case the combined optical density is redistributed to the individual nuclei. A selection procedure ensures that only complete nuclei are measured.

The method has been tested on specially‐prepared Feulgen‐stained 20μ sections of normal liver tissue. The overall distribution of the nuclear DNA measurements shows well‐defined diploid and tetraploid peaks, with coefficient of variations of less than 10%. Similar distributions were obtained from both the isolated nuclei and overlapped nuclei sub‐populations.
How to Express C++ Concepts in Fortran90
Authors: Decyk Viktor K. , Norton Charles D. , Szymanski Boleslaw K.
Published: January 2015

This paper summarizes techniques for emulating in Fortran90 the most important objectoriented concepts of C++: classes (including abstract data types, encapsulation and function overloading), inheritance and dynamic dispatching.
Quantitative Comparison of Immunohistochemical Staining Intensity in Tissues Fixed in Formalin and Histochoice
Authors: Vince D. Geoffrey , Tbakhi Abdelghani , Gaddipati Ajeetkumar , Cothren Robert M. , Cornhill J. Fredrick , Tubbs Raymond R.
Published: January 2015

Formaldehyde fixatives have traditionally been used to preserve tissues as they impart excellent morphological preservation. Formaldehyde fixes tissue by cross linking, a process which can reduce the antigenicity of tissue and weakens the intensity of immunohistochemical stains. Preliminary studies have shown that Histochoice tissue fixative offers equal or greater staining intensity than neutral buffered formalin (NBF). This study compares these fixatives quantitatively and presents the results in unambiguous statistical terms.

Tissue samples were collected, bisected, and fixed in NBF or Histochoice. The sections were stained with a total of 21 antibodies, and color images were collected. The hue, saturation, and value were determined for each positive pixel and an ANOVA performed. Small differences in hue were noted in 8 of 21 cases. Histochoice‐fixed tissue gave a greater mean saturation than NBF with 57.1% of the antibodies tested. No significant difference in the saturation was detected in 28.6% of the cases; NBF gave higher mean saturation levels with only 14.3% of the antibodies. Histochoice‐fixed tissue was found to give lower values in 66.7% of cases than those prepared with NBF, indicating darker staining. These results show that Histochoice produces staining intensity that is comparable, and in many cases superior, to formalin.
Is Rhodamine 123 an Appropriate Fluorescent Probe to Assess P‐Glycoprotein Mediated Multidrug Resistance in Vinblastine‐Resistant CHO Cells?
Authors: Pétriz Jordi , O’Connor José Enrique , Carmona Mercè , García‐López Joan
Published: January 2015

Cellular drug resistance, which involves several mechanisms such as P‐glycoprotein (P‐gp) overexpression, kinetic and metabolic quiescence, or the increase in the intracellular levels of glutathione, limits the effectiveness of cancer treatment. It has been reported that functional assessment of the cationic dye rhodamine 123 (Rho123) efflux reveals accurately the drug‐resistant phenotype. To study cellular drug resistance, we have obtained a CHO‐K1 derived cell line resistant to vinblastine by means of multistep selection. This cell line (CHOVBR) displays high reactivity with a monoclonal antibody (MAb) (C219) directed against an internal domain of P‐gp, and an active Rho123 efflux, as shown by parallel flow cytometric and fluorometric assays. However, under similar experimental conditions, the drug‐sensitive parental cell line CHO‐K1 (as well as the myeloblastic KG1 and KG1a cell lines), was also able to pump Rho123 out. These parental CHO‐K1 cells had a very low reactivity against the C219 Mab, as confirmed by Western blot analysis. Both vinblastine and verapamil inhibited Rho123 efflux in CHO‐K1 cells, but had no effect on CHOVBR cultures. Also, deprivation of vinblastine for one month did not affect Rho123 efflux in these cells. Our results suggest that the activity of P‐gp appears to be essential, but not sufficient to confer drug resistance, and that Rho123‐based functional assays of drug resistance should be evaluated for each cellular experimental model.
PGHPF – An Optimizing High Performance Fortran Compiler for Distributed Memory Machines
Authors: Bozkus Zeki , Meadows Larry , Nakamoto Steven , Schuster Vincent , Young Mark
Published: January 2015

High Performance Fortran (HPF) is the first widely supported, efficient, and portable parallel programming language for shared and distributed memory systems. HPF is realized through a set of directive‐based extensions to Fortran 90. It enables application developers and Fortran end‐users to write compact, portable, and efficient software that will compile and execute on workstations, shared memory servers, clusters, traditional supercomputers, or massively parallel processors. This article describes a production‐quality HPF compiler for a set of parallel machines. Compilation techniques such as data and computation distribution, communication generation, run‐time support, and optimization issues are elaborated as the basis for an HPF compiler implementation on distributed memory machines. The performance of this compiler on benchmark programs demonstrates that high efficiency can be achieved executing HPF code on parallel architectures.