bluuebunny/crossref_metadata_2025 huggingface dataset:
Standard Operational Procedures for Low Sexual Desire in Men
Authors: Rubio-Aurioles Eusebio , Bivalacqua Trinity J.
Published: September 2012

Introduction

Low sexual desire in men is a condition that has received little attention; nevertheless it occurs with high frequency. Clinicians are in need of clear guidelines to address this problem.

Aim

To develop standardized operational procedures to be implemented with men presenting low sexual desire/interest (LSD/I).

Methods

Review of relevant evidence-based literature and published guidelines, integrated with expert opinion.

Main Outcome

Operational procedures for LSD/I that are recommended for clinical practice with various degrees of support from published evidence.

Results

A new classification scheme is proposed; LSD/I is proposed as an umbrella term for which hypoactive sexual desire disorder (HSDD) is only a subtype. The following standard operational procedures are described: (i) Detection of LSD/I: screening for LSD/I, screening for LSD/I in patients with other sexual dysfunctions; (ii) Diagnosis and assessment of etiology: diagnostic criteria for LSD/I, assessment of depression status, assessment of relationship status, assessment of endocrinologic status, diagnostic criteria for HSDD in men; (iii) Treatment: treatment of LSD/I secondary to low testosterone, treatment of LSD/I secondary to elevated prolactin, treatment of LSD/I secondary to other endocrinologic disorders, treatment of LSD/I secondary to depressive illness and or anxiety disorders, treatment of LSD/I secondary to relationship conflict and treatment of HSDD. A diagnostic and treatment algorithm is presented.

Conclusions

LSD/I is a common condition that should be identified in patients; it is recommended that this condition be actively investigated by the clinician. Once the diagnosis of LSD/I in men is confirmed, a thorough search for possible causes needs to include both biological and psychological causes. Treatment should be etiologically oriented.
Standard Operating Procedures for Female Orgasmic Disorder: Consensus of the International Society for Sexual Medicine
Authors: Laan Ellen , Rellini Alessandra H. , Barnes Tricia
Published: September 2012

Introduction

As the field of sexual medicine evolves, it is important to continually improve patient care by developing contemporary “standard operating procedures” (SOPs), reflecting the consensus view of experts in sexual medicine. Few, if any, consensus SOPs have been developed for the diagnosis and treatment of Female Orgasmic Disorder (FOD).

Aim

The objective is to provide standard operating procedures for FOD.

Methods

The SOP Committee was composed of a chair, selected by the International Society for the Study of Sexual Medicine, and two additional experts. To inform its key recommendations, the Committee used systematic reviews of available evidence and discussions during a group meeting, conference calls and e-mail communications. The Committee received no corporate funding or remuneration.

Results

A total of 12 recommendations for the assessment and treatment of FOD were generated, including suggestions for further research.

Conclusions

Evidence-based, practice recommendations for the treatment of FOD are provided that will hopefully inform clinical decision making for those treating this common condition.
Three‐dimensional analysis of lip and perioral soft tissue changes after debonding of labial brackets
Authors: Jeon H , Lee S. J. , Kim T. W. , Donatelli R. E.
Published: September 2012

Jeon H., Lee S. J., Kim T. W., Donatelli R. E. Three‐dimensional analysis of lip and perioral soft tissue changes after debonding of labial brackets  Orthod Craniofac Res 2013; 16: 65–74. © 2012 John Wiley & Sons A/S

Structured Abstract

Objectives –  To evaluate the possible soft tissue changes after debonding of labial brackets using three‐dimensional (3D) images acquired by a laser scanner.

Methods –  On the same day, 3D facial scans were taken immediately before debonding (T1) and immediately after debonding (T2) from 53 patients, and follow‐up scans were taken 3 months after debonding (T3) from 31 patients. To compare the scans, superimpositions were performed and shell‐to‐shell deviations were used for quantitative analysis.

Results –  Shell‐to‐shell deviation map showing warm colors in lip and perioral tissue represented the retrusion of soft tissue after bracket removal. Soft tissue retrusion was significant for all landmarks immediately after debonding (T1–T2) and 3 months after debonding (T1–T3). Gender, bracket type, and the lip thickness variables did not show a clinically significant influence on the amount of soft tissue retrusion at the T1–T3 period. Lip corners and vermilion borders were significantly retruded at the T1–T3 period more than other perioral areas. A negative linear relationship was found in the amount of soft tissue retrusion immediately after debonding (T1–T2) and from debonding to 3 months after debonding (T2–T3).

Conclusion –  Three‐dimensional imaging showed significant changes in lip and perioral soft tissue after debonding of labial brackets. Clinically significant changes, approximately 2 mm of retrusion, occurred in the mouth corners bilaterally. Vermilion border landmarks also demonstrated significant changes in more than 1 mm. However, it was not possible to predict the soft tissue changes. A wide range of individual variability in the response to treatment and soft tissue adaptation was noted.
Highlights of Roy Smith’s Career at General Electric
Authors: Koch C. C.
Published: September 2012

Dr. Leroy H. (Roy) Smith, Jr. of General Electric (GE) was honored at a special session of the ASME Turbo Expo 2009 in recognition of his 55 years of contributions to the gas turbine industry. Although best known to his ASME and International Gas Turbine Institute (IGTI) colleagues for his many publications on compressor aerodynamic design theory, analysis methods, and research, he has made equally impressive contributions to GE’s jet engine product line. This paper gives a brief chronology of his career, then focuses on the many outstanding fan and compressor aero designs he has created for several major GE engine families.
Scanned-spot-array extreme ultraviolet imaging for high-volume maskless lithography
Authors: Johnson Kenneth C.
Published: September 2012

High-volume maskless lithography systems typically operate by raster-scanning a large array of focused radiation spots across an exposure surface while the spot intensities are modulated. This paper outlines a design concept and optical simulation results for a spot-scanning extreme ultraviolet (EUV) system using a 10×-reduction, flat-image Schwarzschild projection system consisting of only two mirrors. The spots are generated in the system's object space by means of blazed, multilevel zone-plate microlenses configured as Schupmann achromatic doublets, which are highly efficient and are designed to nullify geometric aberration in the projection system. Coherent proximity effects are eliminated by partitioning the exposure radiation into discrete, diffraction-limited image spots, which have convergence cones of numerical aperture 0.3 at the 13.5-nm operating wavelength. The image spot separation is 2.5 μm, and the spot array covers a 10-mm square image field, sufficient to achieve printing throughput of order 30 (300-mm) wafers per hour. For simplicity, the spot intensities are all controlled by a single source modulator, allowing printing of 2.5 -μm periodic patterns without a spatial light modulator. The microlens manufacturing technology would be similar to that used for EUV mirrors and phase-shift masks, but with dramatically less stringent tolerance requirements.
Correlation of free‐response and receiver‐operating‐characteristic area‐under‐the‐curve estimates: Results from independently conducted FROC/ROC studies in mammography
Authors: Zanca Federica , Hillis Stephen L. , Claus Filip , Van Ongeval Chantal , Celis Valerie , Provoost Veerle , Yoon Hong‐Jun , Bosmans Hilde
Published: September 2012

Purpose:

From independently conducted free‐response receiver operating characteristic (FROC) and receiver operating characteristic (ROC) experiments, to study fixed‐reader associations between three estimators: the area under the alternative FROC (AFROC) curve computed from FROC data, the area under the ROC curve computed from FROC highest rating data, and the area under the ROC curve computed from confidence‐of‐disease ratings.

Methods:

Two hundred mammograms, 100 of which were abnormal, were processed by two image‐processing algorithms and interpreted by four radiologists under the FROC paradigm. From the FROC data,inferred‐ROC datawere derived, using the highest rating assumption. Eighteen months afterwards, the images were interpreted by the same radiologists under the conventional ROC paradigm;conventional‐ROC data(in contrast toinferred‐ROC data) were obtained. FROC and ROC (inferred, conventional) data were analyzed using the nonparametric area‐under‐the‐curve (AUC), (AFROC and ROC curve, respectively). Pearson correlation was used to quantify the degree of association between the modality‐specific AUC indices and standard errors were computed using the bootstrap‐after‐bootstrap method. The magnitude of the correlations was assessed by comparison with computed Obuchowski‐Rockette fixed reader correlations.

Results:

Average Pearson correlations (with 95% confidence intervals in square brackets) were: Corr(FROC, inferred ROC) = 0.76[0.64, 0.84] > Corr(inferred ROC, conventional ROC) = 0.40[0.18, 0.58] > Corr (FROC, conventional ROC) = 0.32[0.16, 0.46].

Conclusions:

Correlation between FROC and inferred‐ROC data AUC estimates was high. Correlation between inferred‐ and conventional‐ROC AUC was similar to the correlation between two modalities for a single reader using one estimation method, suggesting that the highest rating assumption might be questionable.
Reduction of prostate intrafraction motion using gas‐release rectal balloons
Authors: Su Zhong , Zhao Tianyu , Li Zuofeng , Hoppe Brad , Henderson Randy , Mendenhall William , Nichols R. Charles , Marcus Robert , Mendenhall Nancy
Published: September 2012

Purpose:

To analyze prostate intrafraction motion using both non‐gas‐release (NGR) and gas‐release (GR) rectal balloons and to evaluate the ability of GR rectal balloons to reduce prostate intrafraction motion.

Methods:

Twenty‐nine patients with NGR rectal balloons and 29 patients with GR balloons were randomly selected from prostate patients treated with proton therapy at the University of Florida Proton Therapy Institute (Jacksonville, FL). Their pretreatment and post‐treatment orthogonal radiographs were analyzed, and both pretreatment setup residual error and intrafraction‐motion data were obtained. Population histograms of intrafraction motion were plotted for both types of balloons. Population planning target‐volume (PTV) margins were calculated with the van Herk formula of 2.5Σ + 0.7σ to account for setup residual errors and intrafraction motion errors.

Results:

Pretreatment and post‐treatment radiographs indicated that the use of gas‐release rectal balloons reduced prostate intrafraction motion along superior–inferior (SI) and anterior–posterior (AP) directions. Similar patient setup residual errors were exhibited for both types of balloons. Gas‐release rectal balloons resulted in PTV margin reductions from 3.9 to 2.8 mm in the SI direction, 3.1 to 1.8 mm in the AP direction, and an increase from 1.9 to 2.1 mm in the left–right direction.

Conclusions:

Prostate intrafraction motion is an important uncertainty source in radiotherapy after image‐guided patient setup with online corrections. Compared to non‐gas‐release rectal balloons, gas‐release balloons can reduce prostate intrafraction motion in the SI and AP directions caused by gas buildup.
Magnetic Braking: A Video Analysis
Authors: Molina-Bolívar J. A. , Abella-Palacios A. J.
Published: September 2012

This paper presents a laboratory exercise that introduces students to the use of video analysis software and the Lenz's law demonstration. Digital techniques have proved to be very useful for the understanding of physical concepts. In particular, the availability of affordable digital video offers students the opportunity to actively engage in kinematics in introductory-level physics.1,2 By using digital videos frame advance features and “marking” the position of a moving object in each frame, students are able to more precisely determine the position of an object at much smaller time increments than would be possible with common time devices. Once the student collects data consisting of positions and times, these values may be manipulated to determine velocity and acceleration. There are a variety of commercial and free applications that can be used for video analysis. Because the relevant technology has become inexpensive, video analysis has become a prevalent tool in introductory physics courses.
Analyzing simple pendulum phenomena with a smartphone acceleration sensor
Authors: Vogt Patrik , Kuhn Jochen
Published: September 2012

This paper describes a further experiment using the acceleration sensor of a smartphone. For a previous column on this topic, including the description of the operation and use of the acceleration sensor, see Ref. 1. In this contribution we focus on analyzing simple pendulum phenomena. A smartphone is used as a pendulum bob, and SPARKvue2 software is used in conjunction with an iPhone or an iPod touch, or the Accelogger3 app for an Android device. As described in Ref. 1, the values measured by the smartphone are subsequently exported to a spreadsheet application (e.g., MS Excel) for analysis.
Energy- and wave-based beam-tracing prediction of room-acoustical parameters using different boundary conditions
Authors: Yousefzadeh Behrooz , Hodgson Murray
Published: September 2012

A beam-tracing model was used to study the acoustical responses of three empty, rectangular rooms with different boundary conditions. The model is wave-based (accounting for sound phase) and can be applied to rooms with extended-reaction surfaces that are made of multiple layers of solid, fluid, or poroelastic materials—the acoustical properties of these surfaces are calculated using Biot theory. Three room-acoustical parameters were studied in various room configurations: sound strength, reverberation time, and RApid Speech Transmission Index. The main objective was to investigate the effects of modeling surfaces as either local or extended reaction on predicted values of these three parameters. Moreover, the significance of modeling interference effects was investigated, including the study of sound phase-change on surface reflection. Modeling surfaces as of local or extended reaction was found to be significant for surfaces consisting of multiple layers, specifically when one of the layers is air. For multilayers of solid materials with an air-cavity, this was most significant around their mass-air-mass resonance frequencies. Accounting for interference effects made significant changes in the predicted values of all parameters. Modeling phase change on reflection, on the other hand, was found to be relatively much less significant.
The simulation of Lamb waves in a cracked plate using the scaled boundary finite element method
Authors: Gravenkamp Hauke , Prager Jens , Saputra Albert A. , Song Chongmin
Published: September 2012

The scaled boundary finite element method is applied to the simulation of Lamb waves for ultrasonic testing applications. With this method, the general elastodynamic problem is solved, while only the boundary of the domain under consideration has to be discretized. The reflection of the fundamental Lamb wave modes from cracks of different geometry in a steel plate is modeled. A test problem is compared with commercial finite element software, showing the efficiency and convergence of the scaled boundary finite element method. A special formulation of this method is utilized to calculate dispersion relations for plate structures. For the discretization of the boundary, higher-order elements are employed to improve the efficiency of the simulations. The simplicity of mesh generation of a cracked plate for a scaled boundary finite element analysis is illustrated.
A non-spectrogram-correlation method of automatically detecting minke whale boings
Authors: Ou Hui , Au Whitlow W. L. , Oswald Julie N.
Published: September 2012

This letter introduces an algorithm for automatic detection of minke whale boing sounds. This method searches for frequency features of boings without calculating the continuous spectrogram of the data, thereby reducing computational time. The detector has been tested on 8 h of acoustic data recorded at the Station ALOHA Cabled Observatory in March 2007. This dataset was previously analyzed using the cross-correlation detector of xbat and was verified by a human listener, as reported in Oswald et al. [(2011). J. Acoust. Soc. Am. 129, 3353–3360]. A comparison of results indicates that the detector introduced here generates fewer false alarms, and it recognizes low-SNR calls that are missed by xbat.
Revisiting the Nucleolus: From Marker to Dynamic Integrator of Cancer Signaling
Authors: Ruggero Davide
Published: September 2012

Deregulations in ribosome biogenesis contribute to tumorigenesis and could be targeted to treat cancer.
Sinus Microbiome Diversity Depletion and
Corynebacterium tuberculostearicum
Enrichment Mediates Rhinosinusitis
Authors: Abreu Nicole A. , Nagalingam Nabeetha A. , Song Yuanlin , Roediger Frederick C. , Pletcher Steven D. , Goldberg Andrew N. , Lynch Susan V.
Published: September 2012

Enrichment of
Corynebacterium tuberculostearicum
caused by depletion of the sinus microbiome contributes to chronic rhinosinusitis.
QUASI-TOPOLOGICAL QUANTUM FIELD THEORIES AND ℤ2 LATTICE GAUGE THEORIES
Authors: FERREIRA MIGUEL J. B. , PEREIRA VICTOR A. , TEOTONIO-SOBRINHO PAULO
Published: September 2012

We consider a two-parameter family of ℤ2 gauge theories on a lattice discretization [Formula: see text] of a three-manifold [Formula: see text] and its relation to topological field theories. Familiar models such as the spin-gauge model are curves on a parameter space Γ. We show that there is a region Γ0 ⊂ Γ where the partition function and the expectation value 〈WR(γ)〉 of the Wilson loop can be exactly computed. Depending on the point of Γ0, the model behaves as topological or quasi-topological. The partition function is, up to a scaling factor, a topological number of [Formula: see text]. The Wilson loop on the other hand, does not depend on the topology of γ. However, for a subset of Γ0, 〈WR(γ)〉 depends on the size of γ and follows a discrete version of an area law. At the zero temperature limit, the spin-gauge model approaches the topological and the quasi-topological regions depending on the sign of the coupling constant.
NONCOMMUTATIVE FIELD THEORY: NUMERICAL ANALYSIS WITH THE FUZZY DISK
Authors: LIZZI FEDELE , SPISSO BERNARDINO
Published: September 2012

The fuzzy disk is a discretization of the algebra of functions on the two-dimensional disk using finite matrices which preserves the action of the rotation group. We define a φ4 scalar field theory on it and analyze numerically three different limits for the rank of the matrix going to infinity. The numerical simulations reveal three different phases: uniform and disordered phases already present in the commutative scalar field theory and a nonuniform ordered phase as noncommutative effects. We have computed the transition curves between phases and their scaling. This is in agreement with studies on the fuzzy sphere, although the speed of convergence for the disk seems to be better. We have also performed the limits for the theory in the cases of the theory going to the commutative plane or commutative disk. In this case the theory behaves differently, showing the intimate relationship between the nonuniform phase and noncommutative geometry.
From brains to bytes
Authors: Peck Evan , Chauncey Krysta , Girouard Audrey , Gulotta Rebecca , Lalooses Francine , Solovey Erin Treacy , Weaver Doug , Jacob Robert
Published: September 2012

Brain-computer interfaces have the potential to change the way we use devices, and there are at least four methods for implementation.
Teaching parallel programming
Authors: Mellor-Crummey John , Gropp William , Herlihy Maurice
Published: September 2012

In this roundtable, three professors of parallel programming share their perspective on teaching and learning the computing technique.
Running the turk
Authors: Zhang Nelson
Published: September 2012

To find out how Amazon.com runs its marketplace for crowdsourced labor, we spoke to the vice president at the company responsible for it.
An interview with Greg Schwartz
Authors: Stanier James
Published: September 2012

The CIO of USAA, a full-service,
branchless
financial services operation, sees much more to banking than e-transactions.
Sustainable sensing for a smarter planet
Authors: Dutta Prabal
Published: September 2012

At what scale is indoor solar harvesting the better primary power source?
GrowFood.org
Authors: Schaffer Ethan
Published: September 2012

New social media is helping connect students to apprenticeships in the practice of organic farming.
Dialogical encounters
Authors: Holmes Tiffany
Published: September 2012

Translating ecological data into arresting images and sound require an artist's touch.
Computational social choice
Authors: Procaccia Ariel D.
Published: September 2012

Making the right decision.
What is computation?
Authors: Horswill Ian
Published: September 2012

Our culture is in the process of renegotiating what it thinks computation and computer really mean.
Want a tenure?
Authors: Sadikov Eldar , Medina Montse
Published: September 2012

Why running a startup is a lot like building a research lab.
Jumping into the water
Authors: Armon Amitai
Published: September 2012

How a Ph.D. graduate went from theoretical computer scientist to water-sensor analyzer.
Big data and internships at Cloudera
Authors: Chen Yanpei , Ferguson Andrew , Martin Brian , Wang Andrew , Wendell Patrick
Published: September 2012

Students working in the big data space get uniquely valuable experiences and perspectives by taking industrial internships, which can help further their research agendas.
Faster topology-aware collective algorithms through non-minimal communication
Authors: Sack Paul , Gropp William
Published: September 2012

Known algorithms for two important collective communication operations, allgather and reduce-scatter, are minimal-communication algorithms; no process sends or receives more than the minimum amount of data. This, combined with the data-ordering semantics of the operations, limits the flexibility and performance of these algorithms. Our novel non-minimal, topology-aware algorithms deliver far better performance with the addition of a very small amount of redundant communication. We develop novel algorithms for Clos networks and single or multi-ported torus networks. Tests on a 32k-node BlueGene/P result in allgather speedups of up to 6x and reduce-scatter speedups of over 11x compared to the native IBM algorithm. Broadcast, reduce, and allreduce can be composed of allgather or reduce-scatter and other collective operations; our techniques also improve the performance of these algorithms.
A GPU implementation of inclusion-based points-to analysis
Authors: Mendez-Lojo Mario , Burtscher Martin , Pingali Keshav
Published: September 2012

Graphics Processing Units (GPUs) have emerged as powerful accelerators for many
regular
algorithms that operate on dense arrays and matrices. In contrast, we know relatively little about using GPUs to accelerate highly
irregular
algorithms that operate on pointer-based data structures such as graphs. For the most part, research has focused on GPU implementations of graph analysis algorithms that do not modify the structure of the graph, such as algorithms for breadth-first search and strongly-connected components.

In this paper, we describe a high-performance GPU implementation of an important graph algorithm used in compilers such as gcc and LLVM: Andersen-style inclusion-based points-to analysis. This algorithm is challenging to parallelize effectively on GPUs because it makes extensive modifications to the structure of the underlying graph and performs relatively little computation. In spite of this, our program, when executed on a 14 Streaming Multiprocessor GPU, achieves an average speedup of 7x compared to a sequential CPU implementation and outperforms a parallel implementation of the same algorithm running on 16 CPU cores.

Our implementation provides general insights into how to produce high-performance GPU implementations of graph algorithms, and it highlights key differences between optimizing parallel programs for multicore CPUs and for GPUs.
A speculation-friendly binary search tree
Authors: Crain Tyler , Gramoli Vincent , Raynal Michel
Published: September 2012

We introduce the first binary search tree algorithm designed for speculative executions. Prior to this work, tree structures were mainly designed for their pessimistic (non-speculative) accesses to have a bounded complexity. Researchers tried to evaluate transactional memory using such tree structures whose prominent example is the red-black tree library developed by Oracle Labs that is part of multiple benchmark distributions. Although well-engineered, such structures remain badly suited for speculative accesses, whose step complexity might raise dramatically with contention.

We show that our
speculation-friendly tree
outperforms the existing transaction-based version of the AVL and the red-black trees. Its key novelty stems from the
decoupling
of update operations: they are split into one transaction that modifies the abstraction state and multiple ones that restructure its tree implementation in the background. In particular, the speculation-friendly tree is shown correct, reusable and it speeds up a transaction-based travel reservation application by up to 3.5x.
Algorithm-based fault tolerance for dense matrix factorizations
Authors: Du Peng , Bouteiller Aurelien , Bosilca George , Herault Thomas , Dongarra Jack
Published: September 2012

Dense matrix factorizations, such as LU, Cholesky and QR, are widely used for scientific applications that require solving systems of linear equations, eigenvalues and linear least squares problems. Such computations are normally carried out on supercomputers, whose ever-growing scale induces a fast decline of the Mean Time To Failure (MTTF). This paper proposes a new hybrid approach, based on Algorithm-Based Fault Tolerance (ABFT), to help matrix factorizations algorithms survive fail-stop failures. We consider extreme conditions, such as the absence of any reliable component and the possibility of loosing both data and checksum from a single failure. We will present a generic solution for protecting the right factor, where the updates are applied, of all above mentioned factorizations. For the left factor, where the panel has been applied, we propose a scalable checkpointing algorithm. This algorithm features high degree of checkpointing parallelism and cooperatively utilizes the checksum storage leftover from the right factor protection. The fault-tolerant algorithms derived from this hybrid solution is applicable to a wide range of dense matrix factorizations, with minor modifications. Theoretical analysis shows that the fault tolerance overhead sharply decreases with the scaling in the number of computing units and the problem size. Experimental results of LU and QR factorization on the Kraken (Cray XT5) supercomputer validate the theoretical evaluation and confirm negligible overhead, with- and without-errors.
Automatic communication optimizations through memory reuse strategies
Authors: Baskaran Muthu Manikandan , Vasilache Nicolas , Meister Benoit , Lethin Richard
Published: September 2012

Modern parallel architectures are emerging with sophisticated hardware consisting of hierarchically placed parallel processors and memories. The properties of memories in a system vary wildly, not only quantitatively (size, latency, bandwidth, number of banks) but also qualitatively (scratchpad, cache). Along with the emergence of such architectures comes the need for effectively utilizing the parallel processors and properly managing data movement across memories to improve memory bandwidth and hide data transfer latency. In this paper, we describe some of the high-level optimizations that are targeted at the improvement of memory performance in the R-Stream compiler, a high-level source-to-source automatic parallelizing compiler. We direct our focus in this paper on optimizing communications (data transfers) by improving memory reuse at various levels of an explicit memory hierarchy. This general concept is well-suited to the hardware properties of GPGPUs, which is the architecture that we concentrate on for this paper. We apply our techniques and obtain performance improvement on various stencil kernels including an important iterative stencil kernel in seismic processing applications where the performance is comparable to that of the state-of-the-art implementation of the kernel by a CUDA expert.
An overview of CMPI
Authors: Gong Yifan , He Bingsheng , Zhong Jianlong
Published: September 2012

Cloud computing enables users to perform distributed computing tasks on many virtual machines, without owning a physical cluster. Recently, various distributed computing tasks such as scientific applications are being moved from supercomputers and private clusters to public clouds. Message passing interface (MPI) is a key and common component in distributed computing tasks. The virtualized computing environment of the public cloud hides the network topology information from the users, and existing topology-aware optimizations for MPI are no longer feasible in the cloud environment. We propose a network performance aware MPI library named CMPI. CMPI embraces a new model for capturing the network performance among different virtual machines in the cloud. Based on the network performance model, we develop novel network performance aware algorithms for communication operations. This poster gives an overview of CMPI design, and presents some preliminary results on collective operations such as broadcast.We demonstrate the effectiveness of our network performance aware optimizations on Amazon EC2.
Portable parallel performance from sequential, productive, embedded domain-specific languages
Authors: Kamil Shoaib , Coetzee Derrick , Beamer Scott , Cook Henry , Gonina Ekaterina , Harper Jonathan , Morlan Jeffrey , Fox Armando
Published: September 2012

Domain-expert
productivity programmers
desire scalable application performance, but usually must rely on
efficiency programmers
who are experts in explicit parallel programming to achieve it. Since such programmers are rare, to maximize reuse of their work we propose encapsulating their strategies in mini-compilers for domain-specific embedded languages (DSELs) glued together by a common high-level host language familiar to productivity programmers. The nontrivial applications that use these DSELs perform up to 98% of peak attainable performance, and comparable to or better than existing hand-coded implementations. Our approach is unique in that each mini-compiler not only performs conventional compiler transformations and optimizations, but includes imperative procedural code that captures an efficiency expert's strategy for mapping a narrow domain onto a specific type of hardware. The result is source- and performance-portability for productivity programmers and parallel performance that rivals that of hand-coded efficiency-language implementations of the same applications. We describe a framework that supports our methodology and five implemented DSELs supporting common computation kernels.

Our results demonstrate that for several interesting classes of problems, efficiency-level parallel performance can be achieved by packaging efficiency programmers' expertise in a reusable framework that is easy to use for both productivity programmers and efficiency programmers.
LHlf
Authors: Zhang Donghui , Larson Per-Åke
Published: September 2012

LHlf is a new hash table designed to allow very high levels of concurrency. The table is lock free and grows and shrinks auto-matically according to the number of items in the table. Insertions, lookups and deletions are never blocked. LHlf is based on linear hashing but adopts recursive split-ordering of the items within a bucket to be able to split and merge lists in a lock free manner. LHlf is as fast as the best previous lock-free design and in addition it offers stable performance, uses less space, and supports both expansions and contractions.
Collective algorithms for sub-communicators
Authors: Mittal Anshul , Jain Nikhil , George Thomas , Sabharwal Yogish , Kumar Sameer
Published: September 2012

Collective communication over a group of processors is an integral and time consuming component in many HPC applications. Many modern day supercomputers are based on torus interconnects. On such systems, for an irregular communicator comprising of a subset of processors, the algorithms developed so far are not contention free in general and hence non-optimal.

In this paper, we present a novel contention-free algorithm to perform collective operations over a subset of processors in a torus network. We also extend previous work on regular communicators to handle special cases of irregular communicators that occur frequently in parallel scientific applications. For the generic case where multiple node disjoint sub-communicators communicate simultaneously in a loosely synchronous fashion, we propose a novel cooperative approach to route the data for individual sub-communicators without contention. Empirical results demonstrate that our algorithms outperform the optimized MPI collective implementation on IBM's Blue Gene/P supercomputer for large data sizes and random node distributions.
Automatic datatype generation and optimization
Authors: Kjolstad Fredrik , Hoefler Torsten , Snir Marc
Published: September 2012

Many high performance applications spend considerable time packing noncontiguous data into contiguous communication buffers. MPI Datatypes provide an alternative by describing noncontiguous data layouts. This allows sophisticated hardware to retrieve data directly from application data structures. However, packing codes in real-world applications are often complex and specifying equivalent datatypes is difficult, time-consuming, and error prone. We present an algorithm that automates the transformation. We have implemented the algorithm in a tool that transforms packing code to MPI Datatypes, and evaluated it by transforming 90 packing codes from the NAS Parallel Benchmarks. The transformation allows easy porting of applications to new machines that benefit from datatypes, thus improving programmer productivity.
OpenMP-style parallelism in data-centered multicore computing with R
Authors: Jiang Lei , Patel Pragneshkumar B. , Ostrouchov George , Jamitzky Ferdinand
Published: September 2012

R
1
is a domain specific language widely used for data analysis by the statistics community as well as by researchers in finance, biology, social sciences, and many other disciplines. As R programs are linked to input data, the exponential growth of available data makes high-performance computing with R imperative. To ease the process of writing parallel programs in R, code transformation from a sequential program to a parallel version would bring much convenience to R users. In this paper, we present our work in semi-automatic parallelization of R codes with user-added OpenMP-style pragmas. While such pragmas are used at the frontend, we take advantage of multiple parallel backends with different R packages. We provide flexibility for importing parallelism with plug-in components, impose built-in MapReduce for data processing, and also maintain code reusability. We illustrate the advantage of the on-the-fly mechanisms which can lead to significant applications in data-centered parallel computing.
Identities on the Bernoulli and Genocchi Numbers and Polynomials
Authors: Rim Seog-Hoon , Jeong Joohee , Lee Sun-Jung
Published: September 2012

We give some interesting identities on the Bernoulli numbers and polynomials, on the Genocchi numbers and polynomials by using symmetric properties of the Bernoulli and Genocchi polynomials.
Polyamine-Induced Rapid Root Abscission in Azolla pinnata
Authors: Gurung Sushma , Cohen Michael F. , Fukuto Jon , Yamasaki Hideo
Published: September 2012

Floating ferns of the genus Azolla detach their roots under stress conditions, a unique adaptive response termed rapid root abscission. We found that Azolla pinnata plants exhibited dose-dependent rapid root abscission in response to the polyamines spermidine and spermine after a substantial time lag (>20 min). The duration of the time lag decreased in response to high pH and high temperature whereas high light intensity increased the time lag and markedly lowered the rate of abscission. The oxidation products of polyamines, 1,3-diaminopropane, β-alanine and hydrogen peroxide all failed to initiate root abscission, and hydroxyethyl hydrazine, an inhibitor of polyamine oxidase, did not inhibit spermine-induced root abscission. Exposure of A. pinnata to the polyamines did not result in detectable release of NO and did not affect nitrite-dependent NO production. The finding of polyamine-induced rapid root abscission provides a facile assay for further study of the mode of action of polyamines in plant stress responses.
On Huygens' Inequalities and the Theory of Means
Authors: Sándor József
Published: September 2012

By using the theory of means, various refinements of Huygens' trigonometric and hyperbolic inequalities will be proved. New Huygens' type inequalities will be provided, too.
Structure and Magnetic Properties of Aerosol Nanoparticles of Fe and Its Alloys
Authors: Petrov Yu. I. , Shafranovsky E. A.
Published: September 2012

Structure and magnetic properties of aerosol nanoparticles of Fe and its alloys (FeMn, FeNi, FeNiMn, FePt, FeCr, FeCo, and FeCu) have been reviewed. It has been shown that, compared to a bulk material, the particles have a number of specific features being of much fundamental and applied interest. The effect of both a quenched high-temperature Fe modification and its oxides on the structure and magnetism of nanoparticles has been considered in detail. Particular attention has been paid to the recently observed fine structure in the hyperfine field distribution at iron nuclei in Mössbauer spectra for pure iron and its alloys both as a bulk and aerosol nanoparticles. This phenomenon makes it possible to reveal very weak magnetic interactions in the system under study. The plausible origin of these magnetic interactions has been also discussed.
The Clinical Features and Emotional Stressors in Korean Patients with Tako-Tsubo Cardiomyopathy
Authors: Song Bong Gun , Oh Ju Hyeon , Park Yong Hwan , Kang Gu Hyun , Chun Woo Jung
Published: September 2012

Background. Tako-tsubo cardiomyopathy (TTC) is typically triggered by an acute emotional or physical stress events. Aim of this study was to investigate the impact of emotional stressors on clinical features, laboratory parameters, electrocardiographic and echocardiographic findings in patients with TTC.
Methods. Of 103 patients enrolled from the TTC registry database, fifteen patients had emotional triggers (E group), and 88 patients had physical triggers or no triggers (other group). Results. Most clinical presentations and in-hospital courses were similar between the groups. However, E group had higher prevalence of chest pain (87 versus 42 %, P=0.001), palpitation (27 versus 6%, P=0.008), whereas other group had higher prevalence of cardiogenic shock (35 versus 7%, P=0.027). E group had significantly higher corrected QT intervals (median, 477.5 versus 438 ms, P=0.001), and left ventricular ejection fraction (LVEF) (mean, 45.7 versus 39.6%, P=0.001), but lower hs-CRP (median, 0.1 versus 3.3 mg/L, P=0.001), CK-MB (median, 5.5 versus 11.9 ng/mL, P=0.047), troponin-I (median, 1.0 versus 3.2 ng/mL, P=0.011), and NT-proBNP levels (median, 2145 versus 4939 pg/mL, P=0.020). Other group required more frequent hemodynamic support and had significantly longer intensive care unit (median, 3 versus 1 days, P=0.005) and in-hospital (median, 17 versus 3 days, P=0.001) durations. Conclusion. The clinical features of TTC are different between groups with and without preceding emotional stressors. The TTC group with preceding emotional stressors was more likely to have preserved cardiovascular reserve and lesser likely to require hemodynamic support than other group although the entire prognosis of TTC is excellent regardless of triggering stressors.
Detection of Merkel Cell Polyomavirus in the Human Tissues from 41 Japanese Autopsy Cases Using Polymerase Chain Reaction
Authors: Matsushita Michiko , Kuwamoto Satoshi , Iwasaki Takeshi , Higaki-Mori Hiromi , Yashima Shoji , Kato Masako , Murakami Ichiro , Horie Yasushi , Kitamura Yukisato , Hayashi Kazuhiko
Published: September 2012

It has recently been shown that approximately 80% of Merkel cell carcinomas harbor a novel polyomavirus named Merkel cell polyomavirus (MCPyV). MCPyV has been detected in human tissue samples. However, detailed distribution of MCPyV in non-neoplastic Japanese human tissues remains unclear. To address this, we used single or real-time quantitative polymerase chain reaction (PCR) for 41 autopsy cases. PCR revealed MCPyV-DNA in non-neoplastic samples: total, 29/41 (71%); adult, 29/39 (74%); fetus or infant, 0/2; men, 24/28 (86%); women, 5/13 (38%); total human tissues, 66/572 (12%); skin, 8/15 (53%); adrenal gland, 9/33 (27%), and other 16 organs (4–25%). This study first reported the presence of MCPyV-DNA in non-neoplastic tissues of thyroid gland, adrenal gland, spleen, bone marrow, stomach, gallbladder, pancreas, heart, and aorta. PCR revealed that viral load ranged from 0.00026 to 0.22 in all MCPyV-positive tissues compared with Merkel cell carcinoma samples. These detailed PCR data showed higher prevalence of MCPyV infection in Japanese men than women (p = 0.004) and broad distribution of MCPyV with low viral load in more non-neoplastic human tissues than in the previous reports. These data provide valuable insights for further studies of MCPyV infection and MCPyV-related diseases.
Steroid Hormones and the Development of Reproductive Organs
Authors: Morohashi K. , Baba T. , Tanaka M.
Published: September 2012

It has been more than 150 years since the physiological function of androgen was reported for the first time in fowl. This finding has served as a basis for many studies focusing on steroid hormones from various aspects. These studies have significantly enhanced our knowledge about the structures of steroid hormones, their synthetic pathways, enzymes involved in the synthetic pathways, steroid hormone-specific receptors, actions of steroid hormones through receptor binding, and the differentiation of steroidogenic cells. However, there are still many attractive and important issues in these areas, some of which are currently being addressed. In this review, we trace the history and findings of the previous studies on steroid hormones, summarize our present understanding in this area, and discuss issues that remain to be elucidated.
A Compartmental Model of Linear Resonance and Signal Transfer in Dendrites
Authors: Schoen Alan , Salehiomran Ali , Larkum Matthew E. , Cook Erik P.
Published: September 2012

Dendrites carry signals between synapses and the soma and play a central role in neural computation. Although they contain many nonlinear ion channels, their signal-transfer properties are linear under some experimental conditions. In experiments with continuous-time inputs, a resonant linear two-port model has been shown to provide a near-perfect fit to the dendrite-to-soma input-output relationship. In this study, we focused on this linear aspect of signal transfer using impedance functions that replace biophysical channel models in order to describe the electrical properties of the dendritic membrane. The membrane impedance model of dendrites preserves the accuracy of the two-port model with minimal computational complexity. Using this approach, we demonstrate two membrane impedance profiles of dendrites that reproduced the experimentally observed two-port results. These impedance profiles demonstrate that the two-port results are compatible with different computational schemes. In addition, our model highlights how dendritic resonance can minimize the location-dependent attenuation of signals at the resonant frequency. Thus, in this model, dendrites function as linear-resonant filters that carry signals between nonlinear computational units.
Information-Geometric Measures for Estimation of Connection Weight Under Correlated Inputs
Authors: Nie Yimin , Tatsuno Masami
Published: September 2012

The brain processes information in a highly parallel manner. Determination of the relationship between neural spikes and synaptic connections plays a key role in the analysis of electrophysiological data. Information geometry (IG) has been proposed as a powerful analysis tool for multiple spike data, providing useful insights into the statistical interactions within a population of neurons. Previous work has demonstrated that IG measures can be used to infer the connection weight between two neurons in a neural network. This property is useful in neuroscience because it provides a way to estimate learning-induced changes in synaptic strengths from extracellular neuronal recordings. A previous study has shown, however, that this property would hold only when inputs to neurons are not correlated. Since neurons in the brain often receive common inputs, this would hinder the application of the IG method to real data. We investigated the two-neuron-IG measures in higher-order log-linear models to overcome this limitation. First, we mathematically showed that the estimation of uniformly connected synaptic weight can be improved by taking into account higher-order log-linear models. Second, we numerically showed that the estimation can be improved for more general asymmetrically connected networks. Considering the estimated number of the synaptic connections in the brain, we showed that the two-neuron IG measure calculated by the fourth- or fifth-order log-linear model would provide an accurate estimation of connection strength within approximately a 10% error. These studies suggest that the two-neuron IG measure with higher-order log-linear expansion is a robust estimator of connection weight even under correlated inputs, providing a useful analytical tool for real multineuronal spike data.
Self-Consistent Learning of the Environment
Authors: Kang Kukjin , Amari Shun-ichi
Published: September 2012

We study the Bayesian process to estimate the features of the environment. We focus on two aspects of the Bayesian process: how estimation error depends on the prior distribution of features and how the prior distribution can be learned from experience. The accuracy of the perception is underestimated when each feature of the environment is considered independently because many different features of the environment are usually highly correlated and the estimation error greatly depends on the correlations. The self-consistent learning process renews the prior distribution of correlated features jointly with the estimation of the environment. Here, maximum a posteriori probability (MAP) estimation decreases the effective dimensions of the feature vector. There are critical noise levels in self-consistent learning with MAP estimation, that cause hysteresis behaviors in learning. The self-consistent learning process with stochastic Bayesian estimation (SBE) makes the presumed distribution of environmental features converge to the true distribution for any level of channel noise. However, SBE is less accurate than MAP estimation. We also discuss another stochastic method of estimation, SBE2, which has a smaller estimation error than SBE without hysteresis.