bluuebunny/crossref_metadata_2025 huggingface dataset:
Size-based approaches to aquatic ecosystems and fisheries science: a symposium in honour of Rob Peters
Authors: Giacomini Henrique C. , Shuter Brian J. , Baum Julia K.
Published: March 2016

This special issue honours Rob Peters’ outstanding contributions to the field of aquatic ecology. It focuses on the size spectrum approach — in which individual organisms, rather than species, are the most basic biological unit — and highlights applications of this approach to fisheries management. The 21 papers in this issue cover three subject areas: (i) the use of size spectra to characterize variation in community structure, (ii) the development of size-based models of ecosystem dynamics to address fisheries questions, and (iii) applications of size-based theory to examine the consequences of variation in predator–prey size relationships, body size – trophic level relationships, and body size – life history relationships. The empirical studies herein demonstrate the utility of size spectra as indicators of population or community structure and for detecting impacts associated with environmental change. Future research focused on refining size-based sampling methods, standardizing metrics and analytical methods, understanding model sensitivity to the underlying assumptions, and comparative studies across ecosystems will enhance our ability to reliably interpret changes in size spectrum characteristics, thus facilitating their use as indicators of ecological change.
Approximation Algorithms for Energy, Reliability, and Makespan Optimization Problems
Authors: Aupy Guillaume , Benoit Anne
Published: March 2016

We consider the problem of scheduling an application on a parallel computational platform. The application is a particular task graph, either a linear chain of tasks, or a set of independent tasks. The platform is made of identical processors, whose speed can be dynamically modified. It is also subject to failures: if a processor is slowed down to decrease the energy consumption, it has a higher chance to fail. Therefore, the scheduling problem requires us to re-execute or replicate tasks (i.e., execute twice the same task, either on the same processor, or on two distinct processors), in order to increase the reliability. It is a tri-criteria problem: the goal is to minimize the energy consumption, while enforcing a bound on the total execution time (the makespan), and a constraint on the reliability of each task. Our main contribution is to propose approximation algorithms for linear chains of tasks and independent tasks. For linear chains, we design a fully polynomial-time approximation scheme. However, we show that there exists no constant factor approximation algorithm for independent tasks, unless P=NP, and we propose in this case an approximation algorithm with a relaxation on the makespan constraint.
Clique Here: On the Distributed Complexity in Fully-Connected Networks
Authors: Applebaum Benny , Kowalski Dariusz R. , Patt-Shamir Boaz , Rosén Adi
Published: March 2016

We consider a message passing model with n nodes, each connected to all other nodes by a link that can deliver a message of B bits in a time unit (typically, B = O(log n)). We assume that each node has an input of size L bits (typically, L = O(n log n)) and the nodes cooperate in order to compute some function (i.e., perform a distributed task). We are interested in the number of rounds required to compute the function.

We give two results regarding this model. First, we show that most boolean functions require ‸ L/B ‹ − 1 rounds to compute deterministically, and that even if we consider randomized protocols that are allowed to err, the expected running time remains [Formula: see text] for most boolean function. Second, trying to find explicit functions that require superconstant time, we consider the pointer chasing problem. In this problem, each node i is given an array Ai of length n whose entries are in [n], and the task is to find, for any [Formula: see text], the value of [Formula: see text]. We give a deterministic O(log n/ log log n) round protocol for this function using message size B = O(log n), a slight but non-trivial improvement over the O(log n) bound provided by standard “pointer doubling.” The question of an explicit function (or functionality) that requires super constant number of rounds in this setting remains, however, open.
Built-in-polarization effect on relaxation time and mean free path of phonons in AlxGa1−xN/GaN heterostructure
Authors: Sahoo Sushant Kumar , Pansari Anju , Sahoo Bijaya Kumar
Published: March 2016

In this paper, we have theoretically investigated the effect of built-in-polarization field on various phonon scattering mechanisms in Al[Formula: see text]Ga[Formula: see text]N/GaN heterostructure. The built-in-polarization field enhances the elastic constant, phonon velocity and Debye frequency of Al[Formula: see text]Ga[Formula: see text]N alloy. As a result, various phonon scattering mechanisms are modified. Important phonon scattering mechanisms such as normal scattering, Umklapp scattering, point defect scattering, dislocation scattering and phonon–electron scattering processes have been considered. The combined relaxation time due to above scattering mechanisms has also been computed as a function of phonon frequency for various Al contents at room temperature. Our result shows that built-in-polarization field suppresses scattering rates leading to enhanced combined relaxation time. Increased relaxation time implies longer phonon mean free path and enhanced optical and thermal transport properties. The result can be used to determine the effect of built-in-polarization field on optical and thermal properties of Al[Formula: see text]Ga[Formula: see text]N/GaN heterostructure and will be useful, particularly, for improvement of thermoelectric performance of Al[Formula: see text]Ga[Formula: see text]N/GaN heterostructure through polarization engineering.
A Second Law for Open Markov Processes
Authors: Pollard Blake S.
Published: March 2016

In this paper we define the notion of an open Markov process. An open Markov process is a generalization of an ordinary Markov process in which populations are allowed to flow in and out of the system at certain boundary states. We show that the rate of change of relative entropy in an open Markov process is less than or equal to the flow of relative entropy through its boundary states. This can be viewed as a generalization of the Second Law for open Markov processes. In the case of a Markov process whose equilibrium obeys detailed balance, this inequality puts an upper bound on the rate of change of the free energy for any non-equilibrium distribution.
Entanglement Generation in Two-Mode Gaussian Systems in a Thermal Environment
Authors: Isar Aurelian
Published: March 2016

We describe the evolution of the quantum entanglement in a system composed of two interacting bosonic modes immersed in a thermal reservoir, in the framework of the theory of open systems based on completely positive quantum dynamical semigroups. The evolution of entanglement is described in terms of the covariance matrix for Gaussian initial states. We calculate the logarithmic negativity and show that for separable initial squeezed thermal states entanglement generation may take place, for definite values of squeezing parameter, average photon numbers, temperature of the thermal bath, dissipation constant and the strength of interaction between the two modes. After its generation one can observe temporary suppressions and revivals of the entanglement. For entangled initial squeezed thermal states, entanglement suppression takes place, for all temperatures of the reservoir, and temporary revivals and suppressions of entanglement can be observed too. In the limit of infinite time the system evolves asymptotically to an equilibrium state which may be entangled or separable.
Fracture Criterion of Woven Glass-Epoxy Composite Using a New Modified Mixed-Mode Loading Fixture
Authors: Shameli Moharram , Choupani Naghdali
Published: March 2016

In this study, experimental and numerical investigation of the interlaminar fracture behavior of woven glass-epoxy composite was performed under static mixed-mode loading conditions. A new modified mixed-mode loading fixture was employed for this purpose. Woven glass-epoxy composite sheet was produced by hand lay-up method and post-cured in an autoclave set. Butterfly samples were prepared by saw water machine. Mixed-mode fracture tests from pure mode-I to pure mode-II were performed. A finite element analysis was performed and nondimensional stress intensity factors of butterfly samples were computed and a polynomial fit was proposed to evaluate the stress intensity factors of an interlaminar crack subjected to various mixed-mode loadings using new designed fixture. The results indicated that the composite material used in this study is tougher in shear loading conditions and weaker in tensile loadings. For studied composite material, the interlaminar mixed-mode fracture data were according to the strain energy release rates by power-law criterion with the exponents [Formula: see text], [Formula: see text]
Fatigue Failure Risk Assessment for a Maintained Stiffener-Frame Welded Structure with Multiple Site Cracks
Authors: Huang Wei , Sridhar N.
Published: March 2016

A probabilistic approach is proposed here for the failure risk assessment of a welded ship structure with respect to fatigue damage caused by multiple site cracks. The initiation and propagation of fatigue cracks often occurs at weld toes while a welded structure is subjected to alternating loading. To account for the interaction of multiple fatigue cracks and inherent uncertainties in fatigue crack growth process, a probabilistic model for fatigue crack growth is developed based on the Paris law. The probabilities of fatigue failure of multiple cracks in the welded structure are estimated by using the reliability analysis. Then, the failure risk assessment for the welded structure with multiple site cracks is performed based on the fatigue reliability estimation. As the service life of ship structures is usually very long, in-service maintenance activities for the locations of critical fatigue damage in ship structures are actually necessary to ensure the integrity of structures. The failure risk associated with fatigue crack growth can be updated through inspections and repairs based on the probabilistic model of damage detection. The effects of in-service inspection quality and frequency are investigated with respect to the risk assessment of structural fatigue failure.
Experimental and Theoretical Investigation on Dynamic Properties of Metal Foam
Authors: Luo G. , Xue P. , Li L. , Lu G.
Published: March 2016

In this study, two kinds of dynamic compression tests were conducted using direct-impact Hopkinson pressure bar (DHPB) facilities, i.e., the bullet with foam specimen was shot on the transmission bar, or the foam specimen was mounted at the end surface of the transmission bar and was hit by a bullet directly. Stress enhancement and localized deformation, as two mainly dynamic properties of metal foam, were observed in the experiments. Then, dynamic locking strain is proposed in order to better describe the feature of foam’s localized deformation field during the impact process. A rigid- perfectly-plastic-dynamic-locking strain model (R-P-P-D-L model) is developed to study the dynamic properties of the foams. The parameters included in this model are determined by 3D numerical Voronoi model and experiments. Comparing the predictions from R-P-P-D-L model with numerical results and experimental results, it is found that the R-P-P-D-L model can capture the main deformation mechanisms of the foam in dynamic compression, and provide a more precise prediction than R-P-P-L model. Furthermore, the stress enhancement of foam with the relative density and the impact velocity are discussed using the R-P-P-D-L model.
Dynamic Memory Balancing for Virtualization
Authors: Wang Zhigang , Wang Xiaolin , Hou Fang , Luo Yingwei , Wang Zhenlin
Published: March 2016

Allocating memory dynamically for virtual machines (VMs) according to their demands provides significant benefits as well as great challenges. Efficient memory resource management requires knowledge of the memory demands of applications or systems at runtime. A widely proposed approach is to construct a miss ratio curve (MRC) for a VM, which not only summarizes the current working set size (WSS) of the VM but also models the relationship between its performance and the target memory allocation size. Unfortunately, the cost of monitoring and maintaining the MRC structures is nontrivial. This article first introduces a low-cost WSS tracking system with effective optimizations on data structures, as well as an efficient mechanism to decrease the frequency of monitoring. We also propose a Memory Balancer (MEB), which dynamically reallocates guest memory based on the predicted WSS. Our experimental results show that our prediction schemes yield a high accuracy of 95.2% and low overhead of 2%. Furthermore, the overall system throughput can be significantly improved with MEB, which brings a speedup up to 7.4 for two to four VMs and 4.54 for an overcommitted system with 16 VMs.
Hardware Performance Counter-Based Malware Identification and Detection with Adaptive Compressive Sensing
Authors: Wang Xueyang , Chai Sek , Isnardi Michael , Lim Sehoon , Karri Ramesh
Published: March 2016

Hardware Performance Counter-based (HPC) runtime checking is an effective way to identify malicious behaviors of malware and detect malicious modifications to a legitimate program’s control flow. To reduce the overhead in the monitored system which has limited storage and computing resources, we present a “sample-locally-analyze-remotely” technique. The sampled HPC data are sent to a remote server for further analysis. To minimize the I/O bandwidth required for transmission, the fine-grained HPC profiles are compressed into much smaller vectors with Compressive Sensing. The experimental results demonstrate an 80% I/O bandwidth reduction after applying Compressive Sensing, without compromising the detection and identification capabilities.
A Compiler Approach for Exploiting Partial SIMD Parallelism
Authors: Zhou Hao , Xue Jingling
Published: March 2016

Existing vectorization techniques are ineffective for loops that exhibit little loop-level parallelism but some limited superword-level parallelism (SLP). We show that effectively vectorizing such loops requires partial vector operations to be executed correctly and efficiently, where the degree of partial SIMD parallelism is smaller than the SIMD datapath width. We present a simple yet effective SLP compiler technique called P
aver
(PArtial VEctorizeR), formulated and implemented in LLVM as a generalization of the traditional SLP algorithm, to optimize such partially vectorizable loops. The key idea is to maximize SIMD utilization by widening vector instructions used while minimizing the overheads caused by memory access, packing/unpacking, and/or masking operations, without introducing new memory errors or new numeric exceptions. For a set of 9 C/C++/Fortran applications with partial SIMD parallelism, P
aver
achieves significantly better kernel and whole-program speedups than LLVM on both Intel’s AVX and ARM’s NEON.
Building Heterogeneous Unified Virtual Memories (UVMs) without the Overhead
Authors: Koukos Konstantinos , Ros Alberto , Hagersten Erik , Kaxiras Stefanos
Published: March 2016

This work proposes a novel scheme to facilitate heterogeneous systems with unified virtual memory. Research proposals implement coherence protocols for sequential consistency (SC) between central processing unit (CPU) cores and between devices. Such mechanisms introduce severe bottlenecks in the system; therefore, we adopt the heterogeneous-race-free (HRF) memory model. The use of HRF simplifies the coherency protocol and the graphics processing unit (GPU) memory management unit (MMU). Our protocol optimizes CPU and GPU demands separately, with the GPU part being simpler while the CPU is more elaborate and latency aware. We achieve an average 45% speedup and 45% energy-delay product reduction (20% energy) over the corresponding SC implementation.
Thread-Aware Adaptive Prefetcher on Multicore Systems
Authors: Liu Peng , Yu Jiyang , Huang Michael C.
Published: March 2016

Most processors employ hardware data prefetching techniques to hide memory access latencies. However, the prefetching requests from different threads on a multicore processor can cause severe interference with prefetching and/or demand requests of others. The data prefetching can lead to significant performance degradation due to shared resource contention on shared memory multicore systems. This article proposes a thread-aware data prefetching mechanism based on low-overhead runtime information to tune prefetching modes and aggressiveness, mitigating the resource contention in the memory system. Our solution has three new components: (1) a self-tuning prefetcher that uses runtime feedback to dynamically adjust data prefetching modes and arguments of each thread, (2) a filtering mechanism that informs the hardware about which prefetching request can cause shared data invalidation and should be discarded, and (3) a limiter thread acceleration mechanism to estimate and accelerate the critical thread which has the longest completion time in the parallel region of execution. On a set of multithreaded parallel benchmarks, our thread-aware data prefetching mechanism improves the overall performance of 64-core system by 13% over a multimode prefetch baseline system with two-level cache organization and conventional modified, exclusive, shared, and invalid-based directory coherence protocol. We compare our approach with the feedback directed prefetching technique and find that it provides 9% performance improvement on multicore systems, while saving the memory bandwidth consumption.
GCMA
Authors: Park SeongJae , Kim Minchan , Yeom Heon Y.
Published: March 2016

While demand for physically contiguous memory allocation is still alive, especially in embedded system, existing solutions are insufficient. The most adapted solution is reservation technique. Though it serves allocation well, it could severely degrade memory utilization. There are hardware solutions like Scatter/Gather DMA and IOMMU. However, cost of these additional hardware is too excessive for low-end devices. CMA is a software solution of Linux that aims to solve not only allocation but also memory utilization problem. However, in real environment, CMA could incur unpredictably slow latency and could often fail to allocate contiguous memory due to its complex design.

We introduce a new solution for the above problem, GCMA (Guaranteed Contiguous Memory Allocator). It guarantees not only memory space efficiency but also fast latency and success by using reservation technique and letting only immediately discardable to use the area efficiently. Our evaluation on Raspberry Pi 2 shows 15 to 130 times faster and more predictable allocation latency without system performance degradation compared to CMA.
Autonomic thread scaling library for QoS management
Authors: Durelli Gianluca C. , Santambrogio Marco D.
Published: March 2016

Over the last years embedded system industry faced a revolution thanks to the introduction of multicores and heterogeneous devices. The availability of these new platforms opens new paths for these devices that can be nowadays used for more high demand tasks, exploiting the parallelism made available by the muticore processors. Nonetheless the progresses of the HW technology are not backed up by improvements of the SW side, and runtime mechanisms to manage resource allocation and contention on resources are still lacking the proper effectiveness. This paper tackles the problem of dynamic resource management from the application point of view and presents a user space library to control application performance. The control knob exploited by the library is the possibility of scaling the number of threads used by an application and seamlessly integrates with OpenMP. A case study illustrates the benefits that this library has in a classic embedded system scenario, introducing an overhead of less than 0.5%.
Abstract timers and their implementation onto the ARM Cortex-M family of MCUs
Authors: Lindgren Per , Fresk Emil , Lindner Marcus , Lindner Andreas , Pereira David , Pinho Luís Miguel
Published: March 2016

Real-Time For the Masses (RTFM) is a set of languages and tools being developed to facilitate embedded software development and provide highly efficient implementations geared to static verification. The RTFM-kernel is an architecture designed to provide highly efficient and predicable Stack Resource Policy based scheduling, targeting bare metal (single-core) platforms.

We contribute by introducing a platform independent timer abstraction that relies on existing RTFM-kernel primitives. We develop two alternative implementations for the ARM Cortex-M family of MCUs: a generic implementation, using the ARM defined SysTick/DWT hardware; and a target specific implementation, using the match compare/free running timers. While sacrificing generality, the latter is more flexible and may reduce overall overhead. Invariants for correctness are presented, and methods to static and run-time verification are discussed. Overhead is bound and characterized. In both cases the critical section from release time to dispatch is less than 2us on a 100MHz MCU. Queue and timer mechanisms are directly implemented in the RTFM-core language (
-core
in the following) and can be included in system-wide scheduling analysis.
Making Sense of Antisense
Authors: Yacyshyn Bruce R , Shanahan William R
Published: March 2016

Since the identification of the DNA double‐stranded helix, the gene as a target of therapy and, moreover, the use of DNA as a drug have been possibilities. ‘Antisense’ is used by some living organisms, specifically viruses, to control gene replication. Only recently, the use of antisense DNA as a mechanism to control human gene translation has been appreciated. A recent report on the use of systemically administered oligonucleotides in human Crohn’s disease is reviewed. DNA antisense oligonucleotides offer a technology capable of unique use at the laboratory bench as well as for highly specific therapeutic drugs. The conceptualization and possible future directions of these exciting compounds are reviewed.
Small Bowel Review: Part II
Authors: Thomson ABR , Hasan J , Keelan M , Wild G
Published: March 2016

In the past year there have been many advances in the area of small bowel physiology and pathology. In preparation for this review, over 500 papers were assessed; some have been selected and reviewed, with a particular focus on presenting clinically useful information for the practising gastroenterologist.
Xenotransplantation: A Potential Solution to the Critical Organ Donor Shortage
Authors: Sim K Howe , Marinov Anton , Levy Gary A
Published: March 2016

The success of allotransplantation as a treatment for end‐stage organ failure has resulted in the need for an increasing number of organ donors. Attempts to meet this need include the use of organs from living related and unrelated donors, financial or other incentives for the donor family, and even the reuse of transplanted organs. Despite these initiatives, the supply of organs for transplantation still falls far short of the demand, as evidenced by longer waiting times for transplantation and decreasing transplantation rates. Even if Canada were able to increase its organ donor rate to that of Spain (40 to 50/million), where organ donation is governed by ‘presumed consent’ legislation, this would not alleviate the problem of donor shortage. Interest in xenotransplantation stems from the need to overcome this increasingly severe shortage of human organs. Indeed, some argue that xenotransplantation is the only potential way of addressing this shortage. As immunological barriers to xenotransplantation are better understood, those hurdles are being addressed through genetic engineering of donor animals and the development of new drug therapies. However, before xenotransplantation can be fully implemented, both the scientific/medical communities and the general public must seriously consider and attempt to resolve the many complex ethical, social and economic issues that it presents.
Novel Diagnostic Tests to DetectHelicobacter pyloriInfection: A Pediatric Perspective
Authors: Snyder John D , van Zanten Sander Veldhuyzen
Published: March 2016

Because of the widespread problem ofHelicobacter pyloriinfections, there is an increased need for rapid, reliable and inexpensive diagnostic tests. Five recently developed tests that offer potential advantages because they are less invasive or permit easier acquisition of samples than available tests are assessed. The tests assessed are whole blood, saliva and urine assays that measure systemic antibody response toH pylori, stool tests that measureH pyloriantigens and string tests that recoverH pyloriorganisms.
Systematic Approach toward the Clinical Diagnosis of Functional Dyspepsia
Authors: Paré Pierre
Published: March 2016

Functional dyspepsia (FD) is the most common condition in patients consulting with upper gastrointestinal tract symptoms, resulting in up to 5% of visits to family physicians. By definition, patients with FD have no clinical, biochemical or endoscopic evidence of an organic disease that is likely to explain their symptoms. The process to be used in a structured interview for establishing a clinical diagnosis of FD is presented. The steps are as follows: determine the duration and the course of the disease; characterize the current syndrome and review the alarm symptoms; elicit the patient‐perceived dominant symptom and/or condition; and identify the patient’s reason for consulting and address the psychosocial factors. According to the clinical characteristics of the three most frequent causes of dyspepsia (peptic ulcer, gastroesophageal reflux and FD) and acknowledging that these conditions may coexist rather than overlap in some patients, an algorithm is suggested for establishing a working diagnosis of FD and indications for investigation, and initiating a management strategy.
The Epidemiology of Nonsteroidal Anti‐Inflammatory Drugs
Authors: Tenenbaum Jerry
Published: March 2016

Nonsteroidal anti‐inflammatory drug (NSAID) use has increased dramatically in the past two decades. A large proportion of the elderly population (more than 65 years of age) holds a current or recent NSAID prescription, accounting for approximately 90% of all NSAID prescriptions. Despite studies that advise finding alternatives for NSAIDs for the management of osteoarthritis, physicians often prescribe NSAIDs first for such common musculoskeletal conditions. Despite being identified as risk factors for gastrointestinal complications, the simultaneous use of two NSAIDs and the coadministration of NSAIDs with corticosteroids and with coumadin continue to occur. The point prevalence of NSAID‐induced ulcers is 10% to 30%, and 15% to 35% of all peptic ulcer complications are caused by NSAIDs. The increased risk of gastrointestinal complications when NSAIDs are used is 3% to 5%. This risk increases with other identified risk factors (eg, older age, previous gastrointestinal history, comorbid diseases and poor health). Gastrointestinal causes of hospitalization (eg, gastrointestinal hemorrhage and perforation) and death have increased in parallel to increased NSAID use. ‘Antiulcer’ agents are prescribed twice as often in NSAID users, and the economic impact (eg, diagnostic tests and hospitalization) is that about one‐third of the arthritis budget has been dedicated to deal with gastrointestinal side effects of NSAIDs. Misoprostol and omeprazole have been shown to be cytoprotective for the gastroduodenal mucosa when NSAIDs are used, and misoprostol has been shown to reduce the risk of gastroduodenal ulcer complications. Economic evaluations have suggested that these agents are a cost effective means of dealing with such NSAID‐associated problems. Although no NSAID is totally safe, a number of studies have demonstrated that NSAIDs may be ranked according to relative gastrointestinal toxicity. The role of Helicobacter pylori in NSAID‐associated problems remains uncertain.
East Meets West: What Is Early Cancer?
Authors: Riddell Robert H
Published: March 2016

It has become increasingly apparent that the Japanese and Western systems of classifying dysplasia and carcinoma in the gastrointestinal tract are not the same. The implication of these differences is that in an article in a Western journal on gastrointestinal ‘cancer’ originating from Japan, it is often impossible to repeat the study to confirm or refute it because of these differences in definitions. ‘Carcinoma’ is diagnosed in Japan by virtue of its structural and cytological features but by invasion in the Western system. Adenoma does not mean a dysplastic lump in the Japanese system (although it can), but in most cases is similar to low grade dysplasia irrespective of the macroscopic and/or endoscopic appearances (hence flat and depressed adenomas in the Japanese system); however, most examples of high grade dysplasia in the Western system, as well as some low grade dysplasia, are ‘cancer’ in the Japanese system. Conversely, both have conceptual areas that are useful in the other’s system.
Role of Endoscopy in the Investigation of Upper Gastrointestinal Symptoms in HIV‐Infected Patients
Authors: Wilcox C Mel
Published: March 2016

Endoscopy plays a pivotal role in the management of patients with the acquired immunodeficiency syndrome (AIDS), because tissue documentation of opportunistic processes is often necessary to establish a definitive diagnosis. With progression of immunodeficiency, endoscopy becomes more important because the predisposition to opportunistic disorders of the gastrointestinal tract is greatly increased. The yield of upper endoscopy in human immunodeficiency virus (HIV)‐infected patients is dependent upon the indication for the procedure, including the clinical presentation and the stage of immunodeficiency. Indications for which endoscopy has a high yield include AIDS with esophageal symptoms refractory to empirical antifungal therapy, small bowel biopsy for chronic severe diarrhea and upper gastrointestinal bleeding. Although processes can be identified, a diagnosis is less likely in patients who present with nausea and vomiting or nonspecific abdominal pain. By tailoring the use of endoscopy to the presenting symptoms and CD4 lymphocyte count, the diagnostic benefit can be increased.
The Crohn’s Disease Activity Index, Its Derivatives and the Inflammatory Bowel Disease Questionnaire: A Review of Instruments to Assess in Crohn’s Disease
Authors: Yoshida Eric M
Published: March 2016

The Crohn’s Disease Activity Index (CDAI) has been used to measure Crohn’s activity for over a quarter of a century. The development of the CDAI is reviewed and its reliability and validity are examined. Instruments used to assess Crohn’s disease that were developed subsequent to the CDAI, including the Harvey-Bradshaw Index, the Cape Town Index and a three-variable version of the CDAI (modified for survey research), are similarly reviewed. The most recent instrument to assess Crohn’s disease, the Inflammatory Bowel Disease Questionnaire, which assesses patients in the domains of bowel, systemic, emotional and social function, is also discussed.
Determinants of Disease Outcome followingHelicobacter pyloriInfection in Children
Authors: Jones Nicola L , Day Andrew S , Sherman Philip M
Published: March 2016

Helicobacter pyloriinfection is primarily acquired during childhood, causes chronic, active gastritis and peptic ulcer disease, and is associated with the development of gastric malignancies. However, only a small number of infected individuals ever develop the more severe sequelae of peptic ulcer disease and gastric cancers. Therefore, the identification of bacterial and host factors that play a role in determining the outcomes and pathophysiology of infection is a major focus of current research. Recent advances in the understanding of disease pathogenesis are critically considered, with particular reference to the paediatric population.
Hyperbilirubinemia: Does It Matter?
Authors: Okolicsanyi Lajos , Cavestro Giulia Martina , Guatti-Zuliani Claudia
Published: March 2016

Serum bilirubin concentrations are increased in several hematological and hepatic disorders; however, hyperbilirubinemia, often of familial origin, may occur without overt signs of hemolysis or evident liver disease. The authors review briefly the main steps of hepatic bilirubin metabolism, then discuss the pathogenetic mechanisms of the different forms of familial hyperbilirubinemia. The knowledge of these conditions is increasingly important because orthotopic liver transplantation may be a therapeutic choice for some severe forms. Furthermore, early diagnosis is necessary to avoid unnecessary medical investigations for the otherwise relatively common, benign unconjugated hyperbilirubinemia. Finally, individuals with unmasked defective bilirubin handling may be potential liver donors; thus, unexplained jaundice occurring after orthotopic liver transplantation may be related to this disorder.
Role of Laparoscopic Antireflux Surgery in the Management of Chronic GERD Symptoms
Authors: Anvari Mehran
Published: March 2016

Since the application of minimally invasive techniques to antireflux surgery eight years ago, there has been a rapid increase in the use of laparoscopic antireflux surgery. It is increasingly used as an alternative to long term medical therapy with proton pump inhibitors. The factors responsible for the rapid popularity of this procedure are reviewed, and the choice of techniques, current indications and available literature on the outcomes of these procedures are discussed.
Influence of Sex and Disease on Illness‐Related Concerns in Inflammatory Bowel Disease
Authors: Maunder R , Toner B , de Rooy E , Moskovitz D
Published: March 2016

OBJECTIVE: Identifying the normal concerns of people with ulcerative colitis and Crohn’s disease (CD) facilitates a comprehensive approach to their medical care. Clinically, it can be easily appreciated that the concerns of men and women with inflammatory bowel disease (IBD) may differ and that this may have a substantial impact on both coping and treatment decisions. However, sex differences have received little empirical study.

METHODS: Significant differences between the sexes on the 25 items of the Rating Form of IBD Patient Concerns (RFIPC) were determined in 343 subjects by univariate ANOVA with disease type and sex as factors, correcting for multiple comparisons and covarying for IBD symptom severity.

RESULTS: Compared with men, women reported higher levels of IBD symptom severity and higher overall RFIPC scores. Women were more concerned than men about feelings related to their bodies, attractiveness, feeling alone and having children. There was an interaction between disease and sex regarding concern about sexual performance and intimacy. In both cases, men with CD reported less concern than each other comparison group. The illness concerns that differ between sexes are not the most intense concerns in either sex.

DISCUSSION: These results confirm that sex has a significant influence on a number of illness concerns, particularly concerns related to self‐image and relationships. The interaction of disease type and sex with respect to concern over sexual performance and intimacy is open to several potential explanations and requires further research. Sex differences should be considered in the treatment of IBD. Specific inquiry into sex‐specific concerns may be useful for the clinician. Further research is required to replicate these retrospective findings.
Spots and Clots – Leave Them or Treat Them? Why and How to Treat
Authors: Jensen Dennis M
Published: March 2016

The clinical indication for urgent endoscopy with combined diagnosis and treatment is bleeding that is severe enough to seek medical attention. The author uses stigmata of ulcer hemorrhage as a guide to endoscopic therapy. Active arterial bleeding, nonbleeding visible vessels and adherent nonbleeding clots are always treated endoscopically. In randomized trials, patients have demonstrated better outcomes from endoscopic therapies than from medical therapies. Flat spots, grey or black sloughs, and clear ulcer bases are not treated endoscopically. The clinical condition and the endoscopic appearance of the ulcer (ie, stigmata of hemmorrhage) of the patient with upper gastrointestinal bleeding are used to determine the subsequent level of care (discharge, ward or intensive care).
Survey of Current Practices among Members of CAG in the Follow-Up of Patients Diagnosed with Gastric Ulcer
Authors: Breslin Niall P , Sutherland Lloyd R
Published: March 2016

INTRODUCTION: Guidelines recommend a policy of endoscopic follow-up of all gastric ulcers until healing. Analysis of data from the Alberta Endoscopy Project indicates that fewer than 50% of patients diagnosed with benign gastric ulcer had undergone a repeat procedure. The practice and attitudes of physician members of the Canadian Association of Gastroenterology (CAG) on the follow-up of such patients were assessed.

METHODS: A self-administered questionnaire was mailed to members of CAG. Respondents were asked to indicate their practice setting and to estimate the proportion of gastric ulcer patients in whom they perform follow-up endoscopy. They were also asked to indicate factors influencing this choice, including the role ofHelicobacter pylori.

RESULTS: Fifty-seven per cent of 220 respondents indicated that they perform repeat endoscopy in 95% to 100% of individuals with benign gastric ulcer. The most common reasons influencing this choice were to ensure healing (86.3%) and to confirm the benign nature of the lesion (79.5%). Nonsteroidal anti-inflammatory drug (NSAID) use (83.2%) and patient ill health (62.9%) were the most common reasons for not repeating the endoscopy. Twenty per cent of individuals indicated thatH pylorihad influenced a change in their practice.

DISCUSSION: Physicians vary widely in their follow-up of benign gastric ulcer. Studies on the occurrence of gastric cancer in this setting are not unanimous in their conclusions. Subgroups of patients with NSAID exposure and successfully eradicatedH pyloriinfection may have a lower risk of malignancy. Studies to confirm this are warranted, and modified guidelines may be appropriate.
Pathogenesis of Nonsteroidal Anti‐Inflammatory Drug Gastropathy: Clues to Preventative Therapy
Authors: Bastaki Salim MA , Wallace John L
Published: March 2016

Gastric ulceration and bleeding are major impediments to the chronic use of nonsteroidal anti‐inflammatory drugs (NSAIDs). The development of effective therapies for prevention of these adverse effects requires better understanding of their pathogenesis. Several features of NSAIDs contribute to the development of damage in the stomach, including the topical irritant effects of these drugs on the epithelium, impairment of the barrier properties of the mucosa, suppression of gastric prostaglandin synthesis, reduction of gastric mucosal blood flow and interference with the repair of superficial injury. The presence of acid in the lumen of the stomach also contributes to the pathogenesis of NSAID‐induced ulcers and bleeding in a number of ways. Acid impairs the restitution process, interferes with hemostasis and can inactivate several growth factors that are important in mucosal integrity and repair. Profound suppression of gastric acid secretion has been shown to be effective in preventing NSAID‐induced ulceration. There is a strong possibility that new NSAIDs entering the market will have greatly reduced toxicity in the gastrointestinal tract.
Preventing Ulcer Rebleeding: The Role of Second‐Look Endoscopy
Authors: Chung SC Sydney
Published: March 2016

Whether a second‐look endoscopy after initial endoscopic hemostasis is of value is controversial. Routine surveillance endoscopy on the next day and treatment of any remaining stigmata may provide marginal benefit, but existing studies are not large enough to demonstrate significant differences. Endoscopic retreatment when patients develop rebleeding may allow emergency surgery to be avoided if successful but may endanger life if further bleeding occurs. Early data indicate that surgery can be avoided in about 75% of patients by retreatment without an increase in mortality.
Tissue Staining (Chromoscopy) of the Gastrointestinal Tract
Authors: Fennerty M Brian
Published: March 2016

Tissue staining, or chomoscopy, is used as an adjunctive technique during gastrointestinal endoscopy. Chemical agents are applied to the gastrointestinal mucosal surface to identify specific epithelia or to enhance the mucosal surface characteristics of the gastrointestinal epithelium. This aids in the recognition of subtle lesions (ie, polyps) or allows directed targeting of biopsies (ie, sprue or Barrett’s esophagus) to increase the yield of endoscopic diagnostic accuracy. The four endoscopic tissue‐staining techniques in use are vital staining, contrast staining (chromoscopy), reactive staining and tattooing. Some of the agents used for endoscopic tissue staining and the uses of chromoscopy in identifying pathology of the esophagus, stomach, small bowel and colon during endoscopy are discussed.
Antibiotic Resistance Mechanisms ofHelicobacter pylori
Authors: Hoffman Paul S
Published: March 2016

Infection withHelicobacter pyloriis most frequently associated with gastritis and peptic ulcer disease. Antimicrobial intervention, together with proton pump inhibitors, has become the standard therapy for treating this disease. Resistance to clarithromycin and metronidazole, two of the most commonly used antimicrobials for treatment ofH pyloriinfections, is often associated with treatment failures and relapse of infection. Clarithromycin resistance arises through mutations leading to base changes in 23S ribosomal RNA subunits, while resistance to metronidazole is due to mutations in therdxAgene, which encodes a novel nitroreductase that is responsible for reductive activation of the drug. Products of metronidazole activation are mutagenic and can be demonstrated to increase both the mutation frequency and the frequency at which antibiotic resistance arises inH pylori.
Helicobacter pylori-Epithelial Cell Interactions: From Adhesion to Apoptosis
Authors: Jones Nicola L , Sherman Philip M
Published: March 2016

Studies suggest that host cell signal transduction cascades are manipulated during infection with microbes, including the gastric pathogenHelicobacter pylori. Several putative adhesins have been proposed to mediate the attachment ofH pylorito gastric epithelial cells. Following bacterial binding, a series of signalling pathways are activated in the infected gastric epithelial cell. These signals include both cytoplasmic (such as vacuolization, tyrosine phosphorylation and elevation of cytosolic calcium) and nuclear (proliferation, apoptosis and chemokine transcription) events. Research aimed at elucidating the interactions that occur between the host cell and the bacterium during infection should improve the limited knowledge of disease pathogenesis.
Evaluation of the Isoflavone Genistein as Reversible Human Monoamine Oxidase‐A and ‐B Inhibitor
Authors: Zarmouh Najla O. , Messeha Samia S. , Elshami Faisel M. , Soliman Karam F. A.
Published: March 2016

Monoamine oxidases inhibitors (MAOIs) are effective therapeutic drugs for managing Parkinson’s disease (PD) and depression. However, their irreversibility may lead to rare but serious side effects. As finding safer and reversible MAOIs is our target, we characterized the recombinant human (h) MAO‐A and MAO‐B inhibition potentials of two common natural isoflavones, genistein (GST) and daidzein (DZ) using luminescence assay. The results obtained showed that DZ exhibits partial to no inhibition of the isozymes examined while GST inhibited hMAO‐B (IC50 of 6.81 μM), and its hMAO‐A inhibition was more potent than the standard deprenyl. Furthermore, the reversibility, mode of inhibition kinetics, and tyramine oxidation of GST were examined. GST was a time‐independent reversible and competitive hMAO‐A and hMAO‐B inhibitor with a lower Ki of hMAO‐B (1.45 μM) than hMAO‐A (4.31 μM). GST also inhibited hMAO‐B tyramine oxidation and hydrogen peroxide production more than hMAO‐A. Docking studies conducted indicated that the GST reversibility and hMAO‐B selectivity of inhibition may relate to C5‐OH effects on its orientation and its interactions with the threonine 201 residue of the active site. It was concluded from this study that the natural product GST has competitive and reversible MAOs inhibitions and may be recommended for further investigations as a useful therapeutic agent for Parkinson’s disease.
Sleep Spindles as Facilitators of Memory Formation and Learning
Authors: Ulrich Daniel
Published: March 2016

Over the past decades important progress has been made in understanding the mechanisms of sleep spindle generation. At the same time a physiological role of sleep spindles is starting to be revealed. Behavioural studies in humans and animals have found significant correlations between the recall performance in different learning tasks and the amount of sleep spindles in the intervening sleep. Concomitant neurophysiological experiments showed a close relationship between sleep spindles and other sleep related EEG rhythms as well as a relationship between sleep spindles and synaptic plasticity. Together, there is growing evidence from several disciplines in neuroscience for a participation of sleep spindles in memory formation and learning.
Time Irreversibility from Time Series for Analyzing Oil-in-Water Flow Transition
Authors: Meng Du , Xiao-yan Chen , Hong-ying Liu , Qing He , Rui-xiang Bai , Weixin Liu , Zewei Li
Published: March 2016

We first experimentally collect conductance fluctuation signals of oil-in-water two-phase flow in a vertical pipe. Then we detect the flow pattern asymmetry character from the collected signals with multidimensional time irreversibility and multiscale time irreversibility index. Moreover, we propose a novel criterion, that is, AMSI (average of multiscale time irreversibility), to quantitatively investigate the oil-in-water two-phase flow pattern dynamics. The results show that AMSI is sensitive to the flow pattern evolution that can be used to predict the flow pattern transition and bubble coalescence.
Simplified Information Maximization for Improving Generalization Performance in Multilayered Neural Networks
Authors: Kamimura Ryotaro
Published: March 2016

A new type of information-theoretic method is proposed to improve prediction performance in supervised learning. The method has two main technical features. First, the complicated procedures used to increase information content are replaced by the direct use of hidden neuron outputs. Information is controlled by directly changing the outputs of the hidden neurons. In addition, to simultaneously increase information content and decrease errors between targets and outputs, the information acquisition and use phases are separated. In the information acquisition phase, the autoencoder tries to acquire as much information content on input patterns as possible. In the information use phase, information obtained in the acquisition phase is used to train supervised learning. The method is a simplified version of actual information maximization and directly deals with the outputs from neurons. The method was applied to the three data sets, namely, Iris, bankruptcy, and rebel participation data sets. Experimental results showed that the proposed simplified information acquisition method was effective in increasing the real information content. In addition, by using the information content, generalization performance was greatly improved.