bluuebunny/crossref_metadata_2025 huggingface dataset:
The α-Glucan Phosphorylase MalP of Corynebacterium glutamicum Is Subject to Transcriptional Regulation and Competitive Inhibition by ADP-Glucose
Authors: Clermont Lina , Macha Arthur , Müller Laura M. , Derya Sami M. , von Zaluskowski Philipp , Eck Alexander , Eikmanns Bernhard J. , Seibold Gerd M.
Published: February 2015

α-Glucan phosphorylases contribute to degradation of glycogen and maltodextrins formed in the course of maltose metabolism in bacteria. Accordingly, bacterial α-glucan phosphorylases are classified as either glycogen or maltodextrin phosphorylase, GlgP or MalP, respectively. GlgP and MalP enzymes follow the same catalytic mechanism, and thus their substrate spectra overlap; however, they differ in their regulation: GlgP genes are constitutively expressed and the enzymes are controlled on the activity level, whereas expression of MalP genes are transcriptionally controlled in response to the carbon source used for cultivation. We characterize here the modes of control of the α-glucan phosphorylase MalP of the Gram-positive
Corynebacterium glutamicum
. In accordance to the proposed function of the
malP
gene product as MalP, we found transcription of
malP
to be regulated in response to the carbon source. Moreover,
malP
transcription is shown to depend on the growth phase and to occur independently of the cell glycogen content. Surprisingly, we also found MalP activity to be tightly regulated competitively by the presence of ADP-glucose, an intermediate of glycogen synthesis. Since the latter is considered a typical feature of GlgPs, we propose that
C. glutamicum
MalP acts as both maltodextrin and glycogen phosphorylase and, based on these findings, we question the current system for classification of bacterial α-glucan phosphorylases.

IMPORTANCE
Bacterial α-glucan phosphorylases have been classified conferring to their purpose as either glycogen or maltodextrin phosphorylases. We found transcription of
malP
in
C. glutamicum
to be regulated in response to the carbon source, which is recognized as typical for maltodextrin phosphorylases. Surprisingly, we also found MalP activity to be tightly regulated competitively by the presence of ADP-glucose, an intermediate of glycogen synthesis. The latter is considered a typical feature of GlgPs. These findings, taken together, suggest that
C. glutamicum
MalP is the first α-glucan phosphorylase that does not fit into the current system for classification of bacterial α-glucan phosphorylases and exemplifies the complex mechanisms underlying the control of glycogen content and maltose metabolism in this model organism.
The Bifunctional Alcohol and Aldehyde Dehydrogenase Gene,
adhE
, Is Necessary for Ethanol Production in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum
Authors: Lo Jonathan , Zheng Tianyong , Hon Shuen , Olson Daniel G. , Lynd Lee R.
Published: February 2015

Thermoanaerobacterium saccharolyticum
and
Clostridium thermocellum
are anaerobic thermophilic bacteria being investigated for their ability to produce biofuels from plant biomass. The bifunctional alcohol and aldehyde dehydrogenase gene,
adhE
, is present in these bacteria and has been known to be important for ethanol formation in other anaerobic alcohol producers. This study explores the inactivation of the
adhE
gene in
C. thermocellum
and
T. saccharolyticum
. Deletion of
adhE
reduced ethanol production by >95% in both
T. saccharolyticum
and
C. thermocellum
, confirming that
adhE
is necessary for ethanol formation in both organisms. In both
adhE
deletion strains, fermentation products shifted from ethanol to lactate production and resulted in lower cell density and longer time to reach maximal cell density. In
T. saccharolyticum
, the
adhE
deletion strain lost >85% of alcohol dehydrogenase (ADH) activity. Aldehyde dehydrogenase (ALDH) activity did not appear to be affected, although ALDH activity was low in cell extracts. Adding ubiquinone-0 to the ALDH assay increased activity in the
T. saccharolyticum
parent strain but did not increase activity in the
adhE
deletion strain, suggesting that ALDH activity was inhibited. In
C. thermocellum
, the
adhE
deletion strain lost >90% of ALDH and ADH activity in cell extracts. The
C. thermocellum
adhE
deletion strain contained a point mutation in the lactate dehydrogenase gene, which appears to deregulate its activation by fructose 1,6-bisphosphate, leading to constitutive activation of lactate dehydrogenase.

IMPORTANCE
Thermoanaerobacterium saccharolyticum
and
Clostridium thermocellum
are bacteria that have been investigated for their ability to produce biofuels from plant biomass. They have been engineered to produce higher yields of ethanol, yet questions remain about the enzymes responsible for ethanol formation in these bacteria. The genomes of these bacteria encode multiple predicted aldehyde and alcohol dehydrogenases which could be responsible for alcohol formation. This study explores the inactivation of
adhE
, a gene encoding a bifunctional alcohol and aldehyde dehydrogenase. Deletion of
adhE
reduced ethanol production by >95% in both
T. saccharolyticum
and
C. thermocellum
, confirming that
adhE
is necessary for ethanol formation in both organisms. In strains without
adhE
, we note changes in biochemical activity, product formation, and growth.
Nodular fasciitis of the masseter
Authors: Babu Satish , Nash Robert , Shenoy Ravikiran , Weir Justin
Published: February 2015

A 73-year-old man presented to ENT clinic with a painless, smooth lump overlying his right cheek. Fine needle aspiration wrongly diagnosed necrotising malignancy with squamous differentiation. MRI showed a lesion overlying the right masseter, and positron emission tomography scanning incorrectly suggested this was a metabolically active lymph node. After surgical excision, immunohistochemical analysis showed this was in fact nodular fasciitis of the masseter. Nodular fasciitis is a rare, benign, proliferative lesion whose clinical and histological features make it difficult to distinguish from malignancies such as sarcoma. Immunohistochemical analysis for markers including vimentin and actin is crucial for diagnosis. Without this, misdiagnoses are common and patients are at risk of unnecessarily aggressive treatment. This case report summarises the epidemiological, aetiological and clinical features of nodular fasciitis, explores the pitfalls of investigation modalities and describes its management.
Single-stage management of a neglected radial club hand deformity in an adult
Authors: Vaishya Raju , Agarwal Amit Kumar , Vijay Vipul , Mancha David Ghorau
Published: February 2015

Radial club hand is an intercalary congenital deformity involving the forearm, wrist and hand. A congenital absence of radius (partial or complete) and ulnar bowing are classical radiographic abnormalities seen in this condition. This deformity is usually treated surgically in infants and young children but the management of this problem in an adult is complex and challenging. We present a neglected case of an adult with severe and rigid deformity that was successfully treated by one-stage correction involving ulnar osteotomy and wrist arthrodesis, simultaneously.
Violence, self-harm and drug or alcohol misuse in adolescents admitted to hospitals in England for injury: a retrospective cohort study
Authors: Herbert Annie , Gilbert Ruth , González-Izquierdo Arturo , Li Leah
Published: February 2015

Objectives

Of adolescents in the general population in England, we aimed to determine (1) the proportion that has an emergency admission to hospital for injury related to adversity (violence, self-harm or drug or alcohol misuse) and (2) the risk of recurrent emergency admissions for injury in adolescents admitted with adversity-related injury compared with those admitted with accident-related injury only.

Design

We used longitudinally linked administrative hospital data (Hospital Episode Statistics) to identify participants aged 10–19 years with emergency admissions for injury (including day cases lasting more than 4 h) in England in 1998–2011. We used the Office for National Statistics mid-year estimates for population denominators.

Results

Approximately 4.3% (n=141 248) of adolescents in the general population (n=3 254 046) had one or more emergency admissions for adversity-related injury (girls 4.6%, boys 4.1%), accounting for 50% of all emergency admissions for injury in girls and 29.1% in boys. Admissions for self-harm or drug or alcohol misuse commonly occurred in the same girls and boys. Recurrent emergency admissions for injury were more common in adolescents with adversity-related injury (girls 17.3%, boys 16.5%) than in those with accident-related injury only (girls 4.7%, boys 7.4%), particularly for adolescents with adversity-related injury related to multiple types of adversity (girls 21.1%, boys 24.2%).

Conclusions

Hospital-based interventions should be developed to reduce the risk of future injury in adolescents admitted for adversity-related injury.
Mental health trajectories from childhood to young adulthood affect the educational and employment status of young adults: results from the TRAILS study
Authors: Veldman Karin , Reijneveld Sijmen A , Almansa Ortiz Josue , Verhulst Frank C , Bültmann Ute
Published: February 2015

Background

Young adults at work without basic educational level (BEL), and young adults in Neither Employment, Education nor Training (NEET) are at high risk of adverse employment outcomes. Evidence lacks on the impact of mental health problems during childhood, adolescence and young adulthood on employment outcomes of young adults. Therefore, the aims of this study were to (1) identify trajectories of mental health problems from childhood to young adulthood and (2) investigate the relation between these trajectories and the educational or employment status of young adults.

Methods

Data were used from the Tracking Adolescents’ Individual Lives Survey (TRAILS), a Dutch prospective cohort study with 9-year follow-up. Trajectories of mental health problems measured at ages 11, 13.5, 16 and 19 years were identified in 1711 young adults with latent class growth models.

Results

Young adults with high-stable trajectories of total problems, from childhood to young adulthood, were more likely to work without BEL or be in NEET at age 19, than to be at school or to work with BEL (28.0% vs 16.0%, p=0.01). The same was found for externalising problems (35.3% vs 23.2%, p=0.02). For internalising and attention problems, no statistically significant differences were found.

Conclusions

Young adults with high-stable trajectories of mental health problems from age 11 to 19, were at risk of adverse employment outcomes. Interventions reducing mental health problems in childhood may improve the educational or employment status of young adults and their chances for successfully entering the labour market.
Intravenous thrombolysis of large vessel occlusions is associated with higher hospital costs than small vessel strokes: a rationale for developing stroke severity-based financial models
Authors: Rai Ansaar T , Evans Kim , Riggs Jack E , Hobbs Gerald R
Published: February 2015

Background

Owing to their severity, large vessel occlusion (LVO) strokes may be associated with higher costs that are not reflected in current coding systems. This study aimed to determine whether intravenous thrombolysis costs are related to the presence or absence of LVO.

Methods

Patients who had undergone intravenous thrombolysis over a 9-year period were divided into LVO and no LVO (nLVO) groups based on admission CT angiography. The primary outcome was hospital cost per admission. Secondary outcomes included admission duration, 90-day clinical outcome, and discharge destination.

Results

119 patients (53%) had LVO and 104 (47%) had nLVO. Total mean±SD cost per LVO patient was $18 815±14 262 compared with $15 174±11 769 per nLVO patient (p=0.04). Hospital payments per admission were $17 338±13 947 and $15 594±16 437 for LVO and nLVO patients, respectively (p=0.4). A good outcome was seen in 33 LVO patients (27.7%) and in 69 nLVO patients (66.4%) (OR 0.2, 95% CI 0.1 to 0.3, p<0.0001). Hospital mortality occurred in 31 LVO patients (26.1%) and in 7 nLVO patients (6.7%) (OR 0.2, 95% CI 0.08 to 0.5, p<0.0001). 31 LVO patients (32.6%) were discharged to home versus 64 nLVO patients (61.5%) (OR 4.5, 95% CI 2.6 to 8, p<0.0001). Admission duration was 7.5±6.9 days in LVO patients versus 4.9±4.2 days in nLVO patients (p=0.0009). Multivariate regression analysis after controlling for comorbidities showed the presence of LVO to be an independent predictor of higher total hospital costs.

Conclusions

The presence or absence of LVO is associated with significant differences in hospital costs, outcomes, admission duration, and home discharge. These differences can be important when developing systems of care models for acute ischemic stroke.
Effects of DHA-rich fish oil supplementation on the lipid profile, markers of muscle damage, and neutrophil function in wheelchair basketball athletes before and after acute exercise
Authors: Marques Camila Garcia , Santos Vinicius Coneglian , Levada-Pires Adriana Cristina , Jacintho Thiago Manzoni , Gorjão Renata , Pithon-Curi Tânia Cristina , Cury-Boaventura Maria Fernanda
Published: February 2015

We investigated the effects of docosahexaenoic acid (DHA)-rich fish oil (FO) supplementation on the lipid profile, levels of plasma inflammatory mediators, markers of muscle damage, and neutrophil function in wheelchair basketball players before and after acute exercise. We evaluated 8 male basketball wheelchair athletes before and after acute exercise both prior to (S0) and following (S1) FO supplementation. The subjects were supplemented with 3 g of FO daily for 30 days. The following components were measured: the plasma lipid profile (total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides), plasma inflammatory mediators (C-reactive protein, interleukin (IL)-1β, IL-1ra, IL-4, IL-6, IL-8, and tumor necrosis factor-α), markers of muscle damage (creatine kinase and lactate dehydrogenase (LDH)), and neutrophil function (cytokine production, phagocytic capacity, loss of membrane integrity, mitochondrial membrane potential, neutral lipid accumulation, phosphatidylserine externalization, DNA fragmentation, and production of reactive oxygen species (ROS)). Acute exercise increased the plasma levels of total cholesterol, LDH, IL1ra, and IL-6, led to the loss of membrane integrity, ROS production, and a high mitochondrial membrane potential in neutrophils, and reduced the phagocytic capacity and IL-6 production by the neutrophils (S0). However, supplementation prevented the increases in the plasma levels of LDH and IL-6, the loss of membrane integrity, and the alterations in ROS production and mitochondrial membrane potential in the neutrophils that were induced by exercise (S1). In conclusion, DHA-rich FO supplementation reduces the markers of muscle damage, inflammatory disturbances, and neutrophil death induced by acute exercise in wheelchair athletes.
Iron supplementation prevents a decline in iron stores and enhances strength performance in elite female volleyball players during the competitive season
Authors: Mielgo-Ayuso Juan , Zourdos Michael C. , Calleja-González Julio , Urdampilleta Aritz , Ostojic Sergej
Published: February 2015

The primary aim of this study was to examine the effects of 11 weeks of iron supplementation on hematological and strength markers in elite female volleyball players. Twenty-two volleyball players (aged 27.0 ± 5.6 years) from 2 Spanish First National League teams participated and were counterbalanced into 1 of 2 groups based upon iron status: (i) control group (CG, n = 11); or (ii) iron treatment group (ITG, n = 11), which received 325 mg/day of ferrous sulphate daily. Subjects performed their team’s regimen of training or match play every day. Both groups were tested for hematological and strength levels at 2 points: (i) baseline (T0, before preseason) and (ii) 11 weeks later (T11, post-testing). Hematological parameters were serum iron (sFe), serum ferritin (FER), transferrin saturation index (TSI), and hemoglobin (Hb); strength assessments were bench press, military press, half-squat, power clean, clean and jerk, and pull-over. CG experienced a significant decrease (p < 0.05) for sFe (T0, 112.7 ± 31.5; T11, 69.0 ± 20.5 μg·dL−1; –33.9%), FER (T0, 60.2 ± 28.6; T11, 38.2 ± 16.4 ng·mL−1; –34.6%), TSI (T0, 29.4% ± 9.5%; T11, 17.4% ± 5.1%; –35.3%), and Hb (T0, 14.1 ± 1.0; T11, 13.0 ± 0.8 g·L−1; –7.44%); however, ITG experienced no changes (p > 0.05). Consequently, in ITG all hematological parameters were significantly greater (p < 0.05) than CG at T11. There was greater (p < 0.05) percent increase in the clean and jerk (CG: +5.1% ± 20.9 vs. ITG: +29.0% ± 21.3%), power clean (CG: –5.8% ± 30.3% vs. ITG: +44.6% ± 56.6%), and total mean strength (CG: +10.9% ± 3.2% vs. ITG: +26.2% ± 3.6%) in ITG. Our findings suggest that oral iron supplementation prevents iron loss and enhances strength in female volleyball players during the competitive season.
Can different combinations of natural tags identify river herring natal origin at different levels of stock structure?
Authors: Turner Sara M. , Limburg Karin E. , Palkovacs Eric P.
Published: February 2015

We compared the accuracy of different combinations of natural markers, specifically otolith elemental (Sr:Ca and Ba:Ca) and isotopic ratios (87:86Sr) with and without genetic stock constraints to evaluate their ability to distinguish among anadromous river herring (i.e., alewife, Alosa pseudoharengus, and blueback herring, Alosa aestivalis) populations from their US ranges. Model accuracy increased when constrained to a regional level by genetic stocks. Both species were misclassified to sites up to 1000 km from their collection location when only otolith chemistry was used. The inclusion of genetic constraints improved reclassification rates, and the longer time scale of genetic variation makes this method less sensitive to interannual variation. We recommend the combined approach of otolith chemistry and genetics as a means to trace river herring in marine bycatch back to river of origin.
Bidirectional connectivity in rivers and implications for watershed stability and management
Authors: Moore Jonathan W.
Published: February 2015

River networks are connected in both upstream and downstream directions on large spatial scales by movement of water, materials, and animals. Here I examine the implications of these linkages for the stability, productivity, and management of watersheds and their migratory fishes. I use simple simulations of watershed alteration to illustrate that degradation can erode the productivity and stability of both upstream and downstream fisheries. Through analysis of an existing global dataset on rivers, I found that larger rivers tend to be more fragmented than smaller rivers. I offer three challenges and opportunities for the future management of watersheds. First, given that human impacts can spread up and down rivers, there is a need to align the scales of impact assessments with the natural scale of river systems. Second, free-flowing rivers naturally dampen variability; thus, the conservation of connectivity, habitat, and biodiversity represents a key opportunity to sustain the processes that confer stability. Third, watersheds represent natural units of social–ecological systems; watershed governance would facilitate reciprocal feedbacks between people and ecosystems and enable more social–ecological resilience.
In situ investigation of M/CuO interface (M is Ti, V, Cr or Mn) by X-ray photoelectron spectroscopy
Authors: Chourasia A. R. , Stahl Jacob
Published: February 2015

The technique of X-ray photoelectron spectroscopy has been used to investigate the chemical reactivity at the metal/ CuO interfaces. Thin films of the metallic overlayer (0.5 nm, 1.0 nm and 2.0 nm thickness) were deposited on copper oxide substrates at room temperature. In situ characterization of the interfaces has been performed. The 2p core level regions of the metals have been investigated. The spectral features show considerable reactivity at the interfaces. The core level peaks of the metal are observed to be shifted to the high BE energy side with the appearance of satellites. The spectral data confirm the formation of the metallic oxide at the interface. The satellite structure in the copper region is observed to disappear and the spectral features are found to approach those of elemental copper. The room temperature deposition of the metal on copper oxide therefore results in the reduction of copper oxide to elemental copper followed by the oxidation of the metal. The interface is found to consist of a mixture of metal oxide and elemental copper. The 2.0 nm samples were annealed. These samples show the diffusion of copper oxide through the overlayer. The metal reacts with this diffusing oxide to form metallic oxide. The interface is found to consist of a mixture of unreacted metal, the metal oxide, and elemental copper. The amount of the unreacted metal varied between 0% and 40% and can be controlled by the processing conditions. The investigation shows room temperature chemical reactivity at the metal/ CuO interface and provides a new method of preparing sub-nano-oxide films.
Preferences and Motivating Factors for Knowledge Sharing by Students
Authors: Majid Shaheen , Idio Cendana Desiree , Liang Shuang , Zhang Wen
Published: February 2015

The main objective of this study was to explore students' perceptions of knowledge sharing, their preference for participation in face-to-face and online discussion boards, motivating factors, and barriers to knowledge sharing. A questionnaire was used for data collection and 154 graduate students from two public universities in Singapore participated in this study. It was found that over one-half of the students preferred face-to-face knowledge sharing, 26% preferred participation in study-related online discussion boards (ODBs) and the rest expressed an equal preference for both communication channels. The major motivator for face-to-face knowledge sharing received immediate feedback from peers while the major motivator for online discussion boards was the availability of enough time to conceptualise and express ideas. The major barriers to face-to-face knowledge sharing were shyness and poor language skills, whereas lack of time to read multiple threads was a barrier to participation over study-related online discussion boards.
Meso-N-arylamino- and N, N-diarylaminoporphyrinoids: Syntheses, properties and applications
Authors: Sakamoto Ryota , Mustafar Suzaliza , Nishihara Hiroshi
Published: February 2015

This review is devoted to porphyrinoids with N-arylamino groups tethered directly to their meso positions, the study of which has significantly progressed in the past two decades. After a brief introductory description, various synthetic procedures for these compounds are described. The third section focuses on their photochemical and electrochemical properties, and reviews the synergetic effects that arise between the porphyrinoids and the N-arylamino groups. Potential applications are then discussed, focusing on dye-sensitized solar cells (DSSCs).
High Energy Colliding Beams; What Is Their Future?
Authors: Richter Burton
Published: February 2015

The success of the first few years of LHC operations at CERN, and the expectation of more to come as the LHC's performance improves, are already leading to discussions of what should be next for both proton–proton and electron–positron colliders. In this discussion I see too much theoretical desperation caused by the so-far-unsuccessful hunt for what is beyond the Standard Model, and too little of the necessary interaction of the accelerator, experimenter, and theory communities necessary for a scientific and engineering success. Here, I give my impressions of the problem, its possible solution, and what is needed to have both a scientifically productive and financially viable future.
Proton–Proton and Proton–Antiproton Colliders
Authors: Scandale Walter
Published: February 2015

In the last five decades, proton–proton and proton–antiproton colliders have been the most powerful tools for high energy physics investigations. They have also deeply catalyzed innovation in accelerator physics and technology. Among the large number of proposed colliders, only four have really succeeded in becoming operational: the ISR, the SppbarS, the Tevatron and the LHC. Another hadron collider, RHIC, originally conceived for ion–ion collisions, has also been operated part-time with polarized protons. Although a vast literature documenting them is available, this paper is intended to provide a quick synthesis of their main features and key performance.
Muon Colliders
Authors: Palmer R. B.
Published: February 2015

After an introduction, the projected performances are presented for muon colliders with a range of energies from 126 GeV (the Higgs mass) to 6 TeV. Estimates of potential wall power consumption are also given. It is noted that a merit factor, the number of simultaneously operated detectors times the luminosity divided by the power consumption, rises rapidly above 1.5 TeV. At 6 TeV it is projected to be almost two orders of magnitude higher than that for an e+e- linear collider. The reason for this is discussed. The physics potential of these machines is then outlined, including the 126 GeV collider's unique ability to measure the Higgs width, and the potential for a high energy machine's study of any structure seen in a hadron collider. The design and simulations of the different components are then reviewed, followed by a discussion of the supporting experiments and technology R&D.
Andy Sessler: The Full Life of an Accelerator Physicist
Authors: Kim Kwang-Je , Budnitz Robert J. , Winick Herman
Published: February 2015

This article describes the distinguished career of Andrew M. Sessler, the visionary former director of the Lawrence Berkeley National Laboratory (LBNL), one of the most influential accelerator physicists, and a strong, dedicated human-rights activist. Andy died on 17 April 2014 from cancer at age 85. He grew up in New York City, and attended Harvard (BA in Mathematics, 1949) and then Columbia (PhD in Physics, 1953.) After an NSF postdoc at Cornell with Hans Bethe and a stint on the faculty at the Ohio State University in 1954–59, he joined the Lawrence Radiation Laboratory (now LBNL) in 1959, and spent the remainder of his career there. Although Andy left his mark on several areas of physics, including nuclear structure theory, elementary-particle physics, and many-body problems, his lasting and most important contributions came from his efforts in accelerator physics and engineering, to which he devoted most of his life's work. In collaboration with his colleagues of the legendary Midwestern Universities Research Association, he developed theories for the RF acceleration process and the collective instability phenomena, helping to realize the colliding-beam accelerators with which most of the high-energy-physics discoveries of the last few decades have been made. His work in connection with the free-electron-laser (FEL) amplifier for high-power microwave generation constructed at the Lawrence Livermore National Laboratory anticipated the optical-guiding and the self-amplified spontaneous-emission principles, upon which the success of the X-ray FELs as the fourth-generation light sources is based. Throughout his career Andy made major contributions to issues related to the impact of science and technology on society. He helped usher in a new era of research on energy efficiency and sustainable-energy technology and was instrumental in building the research agendas in those areas for the Atomic Energy Commission (AEC) and later the Department of Energy. With a lifelong interest in promoting the human rights of scientists, Andy was instrumental in initiating the American Physical Society's Committee on International Freedom of Scientists and in raising funds to endow the APS Andrei Sakharov Prize. He and Moishe Pripstein cofounded Scientists for Sakharov, Orlov, and Sharansky; the group's protests along with those of other groups led to the release of the three Soviet dissidents. More importantly, Andy's voice and example became a major force in helping call the world's attention to the plight of scientists trapped in places where their human rights and their ability to do science were severely compromised. Andy received many honors, including the AEC's Ernest Orlando Lawrence Award in 1970, the APS's Dwight Nicholson Medal in 1994, and the Enrico Fermi Award from the US Department of Energy in 2014.
Solving Boundary Integral Problems with BEM++
Authors: Śmigaj Wojciech , Betcke Timo , Arridge Simon , Phillips Joel , Schweiger Martin
Published: February 2015

Many important partial differential equation problems in homogeneous media, such as those of acoustic or electromagnetic wave propagation, can be represented in the form of integral equations on the boundary of the domain of interest. In order to solve such problems, the boundary element method (BEM) can be applied. The advantage compared to domain-discretisation-based methods such as finite element methods is that only a discretisation of the boundary is necessary, which significantly reduces the number of unknowns. Yet, BEM formulations are much more difficult to implement than finite element methods. In this article, we present BEM++, a novel open-source library for the solution of boundary integral equations for Laplace, Helmholtz and Maxwell problems in three space dimensions. BEM++ is a C++ library with Python bindings for all important features, making it possible to integrate the library into other C++ projects or to use it directly via Python scripts. The internal structure and design decisions for BEM++ are discussed. Several examples are presented to demonstrate the performance of the library for larger problems.
TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator
Authors: Si Hang
Published: February 2015

TetGen is a C++ program for generating good quality tetrahedral meshes aimed to support numerical methods and scientific computing. The problem of quality tetrahedral mesh generation is challenged by many theoretical and practical issues. TetGen uses Delaunay-based algorithms which have theoretical guarantee of correctness. It can robustly handle arbitrary complex 3D geometries and is fast in practice. The source code of TetGen is freely available.

This article presents the essential algorithms and techniques used to develop TetGen. The intended audience are researchers or developers in mesh generation or other related areas. It describes the key software components of TetGen, including an efficient tetrahedral mesh data structure, a set of enhanced local mesh operations (combination of flips and edge removal), and filtered exact geometric predicates. The essential algorithms include incremental Delaunay algorithms for inserting vertices, constrained Delaunay algorithms for inserting constraints (edges and triangles), a new edge recovery algorithm for recovering constraints, and a new constrained Delaunay refinement algorithm for adaptive quality tetrahedral mesh generation. Experimental examples as well as comparisons with other softwares are presented.
Image Enhancement in Encrypted Domain over Cloud
Authors: Lathey Ankita , Atrey Pradeep K.
Published: February 2015

Cloud-based multimedia systems are becoming increasingly common. These systems offer not only storage facility, but also high-end computing infrastructure which can be used to process data for various analysis tasks ranging from low-level data quality enhancement to high-level activity and behavior identification operations. However, cloud data centers, being third party servers, are often prone to information leakage, raising security and privacy concerns. In this article, we present a Shamir's secret sharing based method to enhance the quality of encrypted image data over cloud. Using the proposed method we show that several image enhancement operations such as noise removal, antialiasing, edge and contrast enhancement, and dehazing can be performed in encrypted domain with near-zero loss in accuracy and minimal computation and data overhead. Moreover, the proposed method is proven to be information theoretically secure.
Achieving Effective Test Suites for Reactive Systems using Specification Mining and Test Suite Reduction Techniques
Authors: Bokil Prasad , Krishnan Padmanabhan , Venkatesh R.
Published: February 2015

Failures in reactive embedded systems are often unacceptable. Moreover, effective testing of such systems to detect potential critical failures is a difficult task.

We present an automated black box test suite generation technique for reactive systems. The technique is based on dynamic mining of specifications, in form of a finite state machine (FSM), from initial runs. The set of test cases thus produced contain several redundant test cases, many of which are eliminated by a simple greedy test suite reduction algorithm to give the final test suite. The effectiveness of tests generated by our technique was evaluated using five case studies from the reactive embedded domain. Results indicate that a test suite generated by our technique is promising in terms of effectiveness and scalability. While the test suite reduction algorithm removes redundant test cases, the change in effectiveness of test suites due to this reduction is examined in the experimentation.

We present our specification mining based test suite generation technique, the test suite reduction technique and results on industrial case studies.
Programming Languages shouldn't be "too Natural"
Authors: Mandrioli Dino , Pradella Matteo
Published: February 2015

Despite much research on programming language principles, most often the design of modern languages ignores such principles which results in cumbersome, hard to understand, and error-prone code. We substantiate our claim through a short sampling of the features of some widely used languages and by referring to other criticisms widely publicized in the literature. We argue that a major reason of such an unpleasant state of the art is that programming languages evolve in a way that too much resembles that of natural languages. We advocate a different attitude in programming language design, going back to essentiality and rigorous application of few basic, well-chosen principles.
Modeling of Safety-Critical Systems Using Petri Nets
Authors: Sunanda B. Esther , Seetharamaiah P.
Published: February 2015

Safety plays a crucial role in the development of complex computer systems in the relevant areas like railway transport, process industry, power plants, etc. In the design phase of safety-critical systems, various methods are used to make the system work correctly. Due to advancements in technology, safety-critical systems are equipped with the necessary safety precautions but not completely. The malfunctioning of systems may lead to catastrophic accidents. Compared to commonly used safety-analysis approaches like Failure Mode and Effects Analysis, Fault Tree Analysis, Event Tree Analysis, etc., Petri Nets are more suitable for hazard analysis as they can specify data flow and stochastic interdependencies. An example safety-critical system, Railroad Crossing Junction has been modeled using Petri Nets for hazard analysis to detect the occurrences of possible hazards in the system. The proposed modeling framework provides a flexible graphical representation allowing a qualitative analysis based on the safe and unsafe state representations and a quantitative analysis based on the reachability graph that in turn leads to an effective safety analysis. The result of careful and rigorous safety analysis is to identify unsafe states. The results of safety analysis can be used by the designer for re-designing the system to improve safety. The designer of the system needs to repeat the process to detect the unsafe states.
Software Development Roles
Authors: Yilmaz Murat , O'Connor Rory V. , Clarke Paul
Published: February 2015

In our earlier research work, we developed a conceptual framework that identifies the di?erent types of roles that can exist in contemporary software development projects (including both agile and traditional software development approaches). The purpose of the framework is to assist software project managers when tuning software development project roles to the demands of individual projects, with our previous research indicating that there is a need to tailor software development roles to individual projects. In this work, we extend the earlier research through the use of a series of semi-structured interviews within seven Turkish software companies. The results, which are consistent with previous findings, offer further evidence of the usefulness of the framework, while also identifying possible areas for future work in this space.
Concurrent Bounded Model Checking
Authors: Phan Quoc-Sang , Malacaria Pasquale , Pǎsǎreanu Corina S.
Published: February 2015

We introduce a methodology, based on symbolic execution, for Concurrent Bounded Model Checking. In our approach, we translate a program into a formula in a disjunctive form. This design enables concurrent verification, with a main thread running symbolic execution, without any constraint solving, to build subformulas, and a set of worker threads running a decision procedure for satisfiability checks.

We have implemented this methodology in a tool called JCBMC, the first bounded model checker for Java. JCBMC is built as an extension of Java Pathfinder, an open-source verification platform developed by NASA. JCBMC uses Symbolic PathFinder (SPF) for the symbolic execution, Z3 as the solver and implements concurrency with multi-threading.

For evaluation, we compare JCBMC against SPF and the Bounded Model Checker CBMC. The results of the experiments show that we can achieve significant advantages of performance over these two tools.
Minimizing the Size of Path Conditions Using Convex Polyhedra Abstract Domain
Authors: Lloyd Justin , Sherman Elena
Published: February 2015

Symbolic execution (SE) is a path-sensitive program analysis technique widely used in program verification. As it interprets a program path on symbolic inputs, SE generates a set of constraints called a path condition (PC). A PC describes possible concrete values that can traverse the same path during program execution. In order to determine whether such a set is non-empty, symbolic execution utilizes constraint solvers to determine whether a PC is satisfiable.

The further SE explores a program path, the more constraints are added to PCs. This raises the issue of the scalability of the approach since SE needs more memory to store large PCs and a solver needs additional time to decide them. Approaches such as,slicing and decomposition of a PC addresses the latter but not the former issue.

In this work we propose an orthogonal to the previous efforts technique that minimizes the number of constraints in a PC. The idea is to identify in the PC a set of linear constraints describing a polyhedron and use effiocient techniques to remove the redundant constraints in that set. In this work, we outsource this task to Parma Polyhedra Library (PPL). Our experiments have shown that this approach reduced the size of PCs and if a solver is insensitive to the PPL's constraint format the solver's time to decide PCs is reduced also.
JPF Verification of Habanero Java Programs using Gradual Type Permission Regions
Authors: Anderson Peter , Vrvilo Nick , Mercer Eric , Sarkar Vivek
Published: February 2015

The Habanero Java Library (HJ-lib) is a Java 8 library implementation of the Habanero Java (HJ) programming model. Calls into this pure Java library provide support for all HJ primitives, including async, finish, and phasers. In previous work, we presented VR, a custom verification run-time designed to be used within Java Pathfinder (JPF) to verify a subset of HJ programs. In this work, we present VR-lib, a library implementation of HJ, which supports verification of a larger subset of programs than VR. Additionally, we present the implementation of gradually typed permission regions (GPRs). PRs provide a building block for dynamically detecting violations of conditions sufficient to guarantee race-freedom. Lastly, we present results for benchmarks using PRs in combination with VR-lib to verify HJ programs.
Verification of Architectural Constraints on Sequences of Method Invocations
Authors: Siroky Stuart , Podorozhny Rodion , Yang Guowei
Published: February 2015

The importance of correspondence between the architectural prescription and implementation has been long recognized. This paper presents an approach to verification of constraints on method invocation chains prescribed by an architectural style. It consists of two key steps. One, static backward and forward search is applied on the call graph of the system, to find all potential paths between the initial method and the final method prescribed in the architecture. Two, symbolic execution is applied to check the feasibility of those potential paths and generate tests for all feasible ones to check the correspondence. We implement our approach in a prototype based on Soot and Symbolic PathFinder (SPF), and demonstrate the usefulness of our approach using a case study.
The Dart, the Psyco, and the Doop
Authors: Dimjašević Marko , Giannakopoulou Dimitra , Howar Falk , Isberner Malte , Rakamarić Zvonimir , Raman Vishwanath
Published: February 2015

JDart is a concolic execution extension for Java PathFinder. Concolic execution executes programs with concrete values while recording symbolic constraints. In this way, it combines the benefits of fast concrete execution, with the possibility of generating new concrete values, triggered by symbolic constraints, in order to exercise additional, potentially rare, program behaviors. As is typical with concolic execution engines, JDart can be used for test-case generation. Beyond this basic mode, it has also been used as a component of other tools. In this paper, we describe the main features of JDart, provide usage examples, and give an overview of applications that use JDart. We particularly concentrate on our efforts into making JDart robust enough to handle large, complex systems.
Boosted Multifeature Learning for Cross-Domain Transfer
Authors: Yang Xiaoshan , Zhang Tianzhu , Xu Changsheng , Yang Ming-Hsuan
Published: February 2015

Conventional learning algorithm assumes that the training data and test data share a common distribution. However, this assumption will greatly hinder the practical application of the learned model for cross-domain data analysis in multimedia. To deal with this issue, transfer learning based technology should be adopted. As a typical version of transfer learning, domain adaption has been extensively studied recently due to its theoretical value and practical interest. In this article, we propose a boosted multifeature learning (BMFL) approach to iteratively learn multiple representations within a boosting procedure for unsupervised domain adaption. The proposed BMFL method has a number of properties. (1) It reuses all instances with different weights assigned by the previous boosting iteration and avoids discarding labeled instances as in conventional methods. (2) It models the instance weight distribution effectively by considering the classification error and the domain similarity, which facilitates learning new feature representation to correct the previously misclassified instances. (3) It learns multiple different feature representations to effectively bridge the source and target domains. We evaluate the BMFL by comparing its performance on three applications: image classification, sentiment classification and spam filtering. Extensive experimental results demonstrate that the proposed BMFL algorithm performs favorably against state-of-the-art domain adaption methods.
INSTRE
Authors: Wang Shuang , Jiang Shuqiang
Published: February 2015

Over the last several decades, researches on visual object retrieval and recognition have achieved fast and remarkable success. However, while the category-level tasks prevail in the community, the instance-level tasks (especially recognition) have not yet received adequate focuses. Applications such as content-based search engine and robot vision systems have alerted the awareness to bring instance-level tasks into a more realistic and challenging scenario. Motivated by the limited scope of existing instance-level datasets, in this article we propose a new benchmark for INSTance-level visual object REtrieval and REcognition (INSTRE). Compared with existing datasets, INSTRE has the following major properties: (1) balanced data scale, (2) more diverse intraclass instance variations, (3) cluttered and less contextual backgrounds, (4) object localization annotation for each image, (5) well-manipulated double-labelled images for measuring multiple object (within one image) case. We will quantify and visualize the merits of INSTRE data, and extensively compare them against existing datasets. Then on INSTRE, we comprehensively evaluate several popular algorithms to large-scale object retrieval problem with multiple evaluation metrics. Experimental results show that all the methods suffer a performance drop on INSTRE, proving that this field still remains a challenging problem. Finally we integrate these algorithms into a simple yet efficient scheme for recognition and compare it with classification-based methods. Importantly, we introduce the realistic multiobjects recognition problem. All experiments are conducted in both single object case and multiple objects case.
Progressive Motion Vector Clustering for Motion Estimation and Auxiliary Tracking
Authors: Chen Ke , Zhou Zhong , Wu Wei
Published: February 2015

The motion vector similarity between neighboring blocks is widely used in motion estimation algorithms. However, for nonneighboring blocks, they may also have similar motions due to close depths or belonging to the same object inside the scene. Therefore, the motion vectors usually have several kinds of patterns, which reveal a clustering structure. In this article, we propose a progressive clustering algorithm, which periodically counts the motion vectors of the past blocks to make incremental clustering statistics. These statistics are used as the motion vector predictors for the following blocks. It is proved to be much more efficient for one block to find the best-matching candidate with the predictors. We also design the clustering based search with CUDA for GPU acceleration. Another interesting application of the clustering statistics is persistent static object tracking. Based on the statistics, several auxiliary tracking areas are created to guide the object tracking. Even when the target object has significant changes in appearance or it disappears occasionally, its position still can be predicted. The experiments on Xiph.org Video Test Media dataset illustrate that our clustering based search algorithm outperforms the mainstream and some state-of-the-art motion estimation algorithms. It is 33 times faster on average than the full search algorithm with only slightly higher mean-square error values in the experiments. The tracking results show that the auxiliary tracking areas help to locate the target object effectively.