bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Persistence of Infectious Human Noroviruses on Food Surfaces by Using Real-Time Nucleic Acid Sequence-Based Amplification
Authors: Lamhoujeb Safaa , Fliss Ismail , Ngazoa Solange E. , Jean Julie 
Published: April 2008

ABSTRACT
Noroviruses (NoV) are the major cause of nonbacterial gastroenteritis. However, there is no published study to ascertain their survival on foodstuffs which are directly related to human health risk. In the present study, we developed a rapid, simple, and sensitive real-time nucleic acid sequence-based amplification (NASBA) combined with an enzymatic treatment for distinguishing infectious from noninfectious human NoV. The developed method was validated using spiked ready-to-eat food samples. When feline calicivirus (FCV) was used as a NoV surrogate in the preliminary assays, it appeared more sensitive to heat inactivation and enzymatic pretreatment than the human NoV. This suggests that FCV may not be an ideal model for studying NoV. Our results reveal clearly that the developed enzymatic pretreatment/real-time NASBA combination successfully distinguished the infectious from heat-inactivated NoV. Moreover, we demonstrate that NoV survived for at least 10 days on refrigerated ready-to-eat foods, such as lettuce and turkey. However, the survival rate was higher on turkey than on lettuce, probably because of their different surface natures. The approach developed in this study may be suitable for more in-depth studies of the persistence and inactivation of human NoV and may be applied to other nonculturable RNA viruses. Moreover, the evaluation of infectious NoV survival provided valuable information concerning its persistence on ready-to-eat food.
Identification and Characterization of a Repeat-in-Toxin Gene Cluster in
Vibrio anguillarum
Authors: Li Ling , Rock Jessica L. , Nelson David R. 
Published: April 2008

ABSTRACT

Vibrio anguillarum
is the causative agent of vibriosis in fish. Hemolysins of
V. anguillarum
have been considered virulence factors during infection. One hemolysin gene,
vah1
, has been previously identified but does not account for all hemolytic activity. The mini-Tn
10
Km mutagenesis performed with a
vah1
mutant resulted in a hemolysin-negative mutant. The region surrounding the mutation was cloned and sequenced, revealing a putative
rtx
operon with six genes (
rtxACHBDE
), where
rtxA
encodes an exotoxin,
rtxC
encodes an RtxA activator,
rtxH
encodes a conserved hypothetical protein, and
rtxBDE
encode the ABC transporters. Single mutations in
rtx
genes did not result in a hemolysin-negative phenotype. However, strains containing a mutation in
vah1
and a mutation in an
rtx
gene resulted in a hemolysin-negative mutant, demonstrating that the
rtx
operon is a second hemolysin gene cluster in
V. anguillarum
M93Sm. Reverse transcription-PCR analysis revealed that the
rtxC
and
rtxA
genes are cotranscribed, as are the
rtxBDE
genes. Additionally, Vah1 and RtxA each have cytotoxic activity against Atlantic salmon kidney (ASK) cells. Single mutations in
vah1
or
rtxA
attenuate the cytotoxicity of
V. anguillarum
M93Sm. A
vah1 rtxA
double mutant is no longer cytotoxic. Moreover, Vah1 and RtxA each have a distinct cytotoxic effect on ASK cells, Vah1 causes cell vacuolation, and RtxA causes cell rounding. Finally, wild-type and mutant strains were tested for virulence in juvenile Atlantic salmon. Only strains containing an
rtxA
mutation had reduced virulence, suggesting that RtxA is a major virulence factor for
V. anguillarum
.
Distinct Roles for MyD88 and Toll-Like Receptors 2, 5, and 9 in Phagocytosis ofBorrelia burgdorferiand Cytokine Induction
Authors: Shin Ok S. , Isberg Ralph R. , Akira Shizuo , Uematsu Satoshi , Behera Aruna K. , Hu Linden T. 
Published: April 2008

ABSTRACTThe contribution of Toll-like receptors (TLRs) to phagocytosis ofBorrelia burgdorferihas not been extensively studied. We show that bone marrow-derived macrophages (BMDM) from MyD88−/−mice or Raw cells transfected with a dominant-negative MyD88 were unable to efficiently internalizeB. burgdorferi.Knockouts of TLR2 and TLR9 or knockdown of TLR5 by small interfering RNA produced no defects in phagocytosis ofB. burgdorferi. Production of inflammatory cytokines was greatly diminished in MyD88−/−BMDM but only partially affected in TLR2−/−BMDM or knockdown of TLR5 and unaffected in TLR9−/−BMDM. Cytochalasin D reduced cytokine induction, but not to the level of the MyD88−/−BMDM. Addition of cytochalasin D to TLR2−/−BMDM inhibited inflammatory responses toB. burgdorferito the level of MyD88−/−BMDM, consistent with a role for TLR2 in both recognition of extracellular products and lysosomal sampling by TLR2 after processing of the organism. Cytochalasin D had no impact on cytokine production in cells undergoing TLR5 knockdown. These results suggest that MyD88, but not TLR2, TLR5, and TLR9, is important for the uptake ofB. burgdorferiand that MyD88 affects inflammatory responses through both its effects on phagocytosis and its role in transducing signals from TLR2 and TLR5.
Patterns of parasitism and body size in red squirrels (Tamiasciurus hudsonicus)
Authors: Gorrell Jamieson C. , Schulte-Hostedde Albrecht I. 
Published: April 2008

Parasites use their hosts for nutrition, shelter, and even dispersal; the latter can result in sex-biased parasite distribution. Host sex-biased parasitism has been well documented in vertebrates, including mammals, and males are often more parasitized than females. Male-biased parasitism is often attributed to sexual size dimorphism, with larger animals being more parasitized. Here, we used a natural population of red squirrels ( Tamiasciurus hudsonicus (Erxleben, 1777)), a species without sexual size dimorphism, to test for sex-biased parasitism in ectoparasites and intestinal helminth parasites. We also tested for size-dependent parasitism to determine the importance of body size on parasitism. We predicted that males would be more parasitized and that larger individuals would be more parasitized. As well, we predicted a male-biased flea distribution on male squirrels. Parasitism fluctuated over the course of 4 months, with flea infection peaking in August and helminth infection peaking in June. We found evidence of male-biased parasitism in helminth and ectoparasite infections. Flea infection was weakly correlated with body size in females but not in males, while no correlation was found between body size and helminth infection. Lastly, fleas had a female-biased population; however, male fleas were more likely to be found on male squirrels, and this could be to maximize dispersal to avoid inbreeding.
The effects of El Niño on the foraging behavior of lactating California sea lions (Zalophus californianus californianus) during the nonbreeding season
Authors: Melin S. R. , DeLong R. L. , Siniff D. B. 
Published: April 2008

We compared the nonbreeding-season foraging behavior of lactating California sea lions ( Zalophus californianus californianus (Lesson, 1828)) at San Miguel Island, California, during El Niño conditions in 1993 and non-El Niño conditions in 1996. Lactating females were instrumented with satellite-linked time–depth recorders between January and March in 1993 (n = 6) and 1996 (n = 10) and data were collected through May in each year. Females foraged northwest of the colony, up to 367 km from it and 230 km from the California coast. Mean dive depths ranged from 19.5 to 279.3 m, but most females achieved dives deeper than 400 m. Most females fed exclusively in the offshore habitat, traveled farther from the colony, spent more time traveling, made deeper and longer dives, and terminated lactation earlier during the 1993 El Niño. The results suggest that prey were concentrated in the offshore habitat and located farther from the colony and deeper in the water column during El Niño. Females did not change their foraging direction, foraging-trip duration, foraging effort, or prey species consumed.
Comparative swimming effort of migrating gray whales (Eschrichtius robustus) and calf cost of transport along Costa Azul, Baja California, Mexico
Authors: Rodríguez de la Gala-Hernández S. , Heckel G. , Sumich J. L. 
Published: April 2008

Swimming velocities and breathing rates were measured for migrating gray whales ( Eschrichtius robustus (Lilljeborg, 1861)) at Costa Azul, Baja California, to compare swimming effort of southbound whales, northbound whales without calves, and northbound mothers and calves. From December 2004 to May 2005, whales were followed using a theodolite to determine swimming velocity. Binoculars were used to count whale blows and their timings were recorded to determine breathing rates. Individual whale breathing rates (BR) were divided by their swimming velocity (V) to derive a comparative index of swimming effort in units of breaths per kilometre. There were significant differences in mean BR, V, and swimming effort among the three migrating groups (p < 0.05). Southbound migrating whales averaged a swimming effort of 7.4 breaths·km–1(V = 1.9 m·s–1, BR = 0.8 breaths·min–1). Northbound whales without calves showed the lowest swimming effort of the three migrating groups (4.7 breaths·km–1, V = 1.8 m·s–1, BR = 0.5 breaths·min–1). Northbound mothers and calves had the same swimming velocity (V = 1.2 m·s–1), but BR and swimming effort were calculated separately yielding a swimming effort of 7.6 breaths·km–1(BR = 0.5 breaths·min–1) for mothers and 10.1 breaths·km–1(BR = 0.7 breaths·min–1) for calves. Cost of transport was calculated for northbound calves, yielding a range based on 1.5% and 3% tidal volumes of 0.25–0.34 and 0.51–0.58 J·kg–1·m–1, respectively.
Physiological analysis of the lymphatic system in the eastern painted turtle (Chrysemys picta picta)
Authors: Walker Mary E. , Wolfe Deanna C. , Toews Daniel P. 
Published: April 2008

Examination into the anuran lymphatic system has led to a comprehensive understanding of lymphatics, including the importance of synchrony in fluid-balance maintenance. However, little research has been conducted on the lymphatics of turtles and other reptilian vertebrates. Using pressure-peak recordings created through cannulation of both lymph hearts of the eastern painted turtle, Chrysemys picta picta (Schneider, 1783), the lymph heart contraction rate was verified and the interbeat interval patterns were examined using Poincaré plots. The lymph heart beating rate was determined to be 38.2 beats·min–1with a mean pulse pressure of 2.40 ± 1.44 mm Hg (1 mm Hg at 0 °C = 133.3224 Pa). Poincaré plots are useful in displaying nonlinear sequential data and are often given descriptive names related to the overall pattern. The Poincaré plot resembled a garden hose nozzle spray, indicating a large variability in interbeat time intervals with periods of multiple-beat patterns. The degree of bilateral lymph heart synchrony was determined in the turtle using the mean time difference between right and left lymph heart systoles. Results show that chelonian lymph hearts do in fact beat in synchrony, with over 50% of contractions occurring within 100 ms of each other. This indicates shared neuronal control and may suggest an energetic advantage to fluid homeostasis.
Six Sigma Implementation at Bharti Infotel
Authors: Shukla Archana , Srinivasan R. 
Published: April 2008

Bharti Airtel Limited was a leading private sector provider of telecommunication services in India, with a customer base of 8.73 million as of July 2004. The company had two branch companies — Bharti Infotel (that dealt with fixed line, long distance, and enterprise services) and Bharti Cellular (that dealt with mobile telephone services). This case is about the six sigma implementation at Bharti Infotel. The case briefly discusses the business imperatives in the fast changing Indian telecommunications industry. The industry was a monopoly for over half a century after independence and had recently been deregulated with the private players competing with the state-owned BSNL. The industry had exploded in the recent years with increasing number of players, falling tariffs, and improving technology. Stiff competition in the industry meant that any competitive action by a company was immediately imitated by others. Therefore the only sources of competitive advantage in the industry were “quality of service” and “speed”. This case discusses the various steps in the implementation of six sigma quality management system in the company. The company had already implemented Business Process Management Systems (BPMS) and had begun monitoring their performance on the Non-Financial Parameters (NFPs). The six sigma initiative was expected to leverage on these initiatives. Following the six sigma initiative was the Knowledge Management (KM) initiative that was intended to help share the best practices and learning from the six sigma projects across the entire organization. This case highlights the contribution of the six sigma quality management initiative to the company's business strategy, and helps students analyze the process of implementing and institutionalizing the six sigma initiative. The case enables the readers to appreciate the business benefits of six sigma implementation and how it fosters innovation.
A study of the development of students' visualizations of program state during an elementary object-oriented programming course
Authors: Sajaniemi Jorma , Kuittinen Marja , Tikansalo Taina 
Published: April 2008

Students' understanding of object-oriented (OO) program execution was studied by asking students to draw a picture of a program state at a specific moment. Students were given minimal instructions on what to include in their drawings in order to see what they considered to be central concepts and relationships in program execution. Three drawing tasks were given at different phases of an elementary OO programming course where two animation tools were used for program visualization. The drawings were analyzed for their overall approaches and their detailed contents.
There was a large variability in the overall approaches and the popularity of various approaches changed during the course. The results indicate that students' mental representations of OO concepts and program execution not only grow as new material is covered in teaching, but they also change. The first drawings treat methods as having primarily a static existence; later methods are seen as dynamic invocations that call each other. The role of classes in program execution fluctuates during learning, indicating problems in locating the notion of class with respect to, for example, objects. Two major sources of problems that manifested in many different forms were the relationship between object and method, and the role of the main method with respect to program state. Other problems were caused by overly simplistic understanding of object identification and improper use of application domain knowledge.
Interview with Wendy Hall
Authors: Atzenbeck Claus 
Published: April 2008

Wendy Hall is Professor of Computer Science at the University of Southampton, UK, and was Head of the School of Electronics and Computer Science from 2002 to 2007. Her team invented the ground-breaking Microcosm hypermedia system, which pre-dated the Web, and for which a patent was granted.
Her research interests now include the development of web technologies (particularly the Semantic Web), hypermedia systems and link services, advanced knowledge technologies, digital libraries, decentralized information systems, and human computer interaction. She has published over 350 papers in areas such as hypermedia, multimedia, digital libraries, and distributed information systems.
She is founding director, along with Professor Sir Tim Berners-Lee, Professor Nigel Shadbolt, and Daniel J. Weitzner, of the Web Science Research Initiative, which was launched in 2006 as a long-term research collaboration between the University of Southampton and MIT.
She holds a number of prestigious leadership roles. She is currently senior Vice President of the Royal Academy of Engineering, and was President of the British Computer Society (2003-2004). She is a member of the Institute of Engineering and Technology (IET) Council and Publications Board and also Vice-President of the Association for Computing Machinery (ACM). She is a member of IW3C2 and was executive chair of the 15th International WWW conference in Edinburgh in May 2006. In April 2007 she joined the Board of the British Library.
Hardbound
Authors: Devietti Joe , Blundell Colin , Martin Milo M. K. , Zdancewic Steve 
Published: April 2008

The C programming language is at least as well known for its absence of spatial memory safety guarantees (i.e., lack of bounds checking) as it is for its high performance. C's unchecked pointer arithmetic and array indexing allow simple programming mistakes to lead to erroneous executions, silent data corruption, and security vulnerabilities. Many prior proposals have tackled enforcing spatial safety in C programs by checking pointer and array accesses. However, existing software-only proposals have significant drawbacks that may prevent wide adoption, including: unacceptably high run-time overheads, lack of completeness, incompatible pointer representations, or need for non-trivial changes to existing C source code and compiler infrastructure.
Inspired by the promise of these software-only approaches, this paper proposes a hardware bounded pointer architectural primitive that supports cooperative hardware/software enforcement of spatial memory safety for C programs. This bounded pointer is a new hardware primitive datatype for pointers that leaves the standard C pointer representation intact, but augments it with bounds information maintained separately and invisibly by the hardware. The bounds are initialized by the software, and they are then propagated and enforced transparently by the hardware, which automatically checks a pointer's bounds before it is dereferenced. One mode of use requires instrumenting only malloc, which enables enforcement of perallocation spatial safety for heap-allocated objects for existing binaries. When combined with simple intraprocedural compiler instrumentation, hardware bounded pointers enable a low-overhead approach for enforcing complete spatial memory safety in unmodified C programs.
Communication optimizations for global multi-threaded instruction scheduling
Authors: Ottoni Guilherme , August David I. 
Published: April 2008

The recent shift in the industry towards chip multiprocessor (CMP) designs has brought the need for multi-threaded applications to mainstream computing. As observed in several limit studies, most of the parallelization opportunities require looking for parallelism beyond local regions of code. To exploit these opportunities, especially for sequential applications, researchers have recently proposed global multi-threaded instruction scheduling techniques, including DSWP and GREMIO. These techniques simultaneously schedule instructions from large regions of code, such as arbitrary loop nests or whole procedures, and have been shown to be effective at extracting threads for many applications. A key enabler of these global instruction scheduling techniques is the Multi-Threaded Code Generation (MTCG) algorithm proposed in [16], which generates multi-threaded code for any partition of the instructions into threads. This algorithm inserts communication and synchronization instructions in order to satisfy all inter-thread dependences.
In this paper, we present a general compiler framework, COCO, to optimize the communication and synchronization instructions inserted by the MTCG algorithm. This framework, based on thread-aware data-flow analyses and graph min-cut algorithms, appropriately models andoptimizes all kinds of inter-thread dependences, including register, memory, and control dependences. Our experiments, using a fully automatic compiler implementation of these techniques, demonstrate significant reductions (about 30% on average) in the number of dynamic communication instructions in code parallelized with DSWP and GREMIO. This reduction in communication translates to performance gains of up to 40%.
Xoc, an extension-oriented compiler for systems programming
Authors: Cox Russ , Bergan Tom , Clements Austin T. , Kaashoek Frans , Kohler Eddie 
Published: April 2008

Today's system programmers go to great lengths to extend the languages in which they program. For instance, system-specific compilers find errors in Linux and other systems, and add support for specialized control flow to Qt and event-based programs. These compilers are difficult to build and cannot always understand each other's language changes. However, they can greatly improve code understandability and correctness, advantages that should be accessible to all programmers.
We describe an extension-oriented compiler for C called xoc. An extension-oriented compiler, unlike a conventional extensible compiler, implements new features via many small extensions that are loaded together as needed. Xoc gives extension writers full control over program syntax and semantics while hiding many compiler internals. Xoc programmers concisely define powerful compiler extensions that, by construction, can be combined; even some parts of the base compiler, such as GNU C compatibility, are structured as extensions.
Xoc is based on two key interfaces. Syntax patterns allow extension writers to manipulate language fragments using concrete syntax. Lazy computation of attributes allows extension writers to use the results of analyses by other extensions or the core without needing to worry about pass scheduling.
Extensions built using xoc include xsparse, a 345-line extension that mimics Sparse, Linux's C front end, and xlambda, a 170-line extension that adds function expressions to C. An evaluation of xoc using these and 13 other extensions shows that xoc extensions are typically more concise than equivalent extensions written for conventional extensible compilers and that it is possible to compose extensions.
Understanding the propagation of hard errors to software and implications for resilient system design
Authors: Li Man-Lap , Ramachandran Pradeep , Sahoo Swarup Kumar , Adve Sarita V. , Adve Vikram S. , Zhou Yuanyuan 
Published: April 2008

With continued CMOS scaling, future shipped hardware will be increasingly vulnerable to in-the-field faults. To be broadly deployable, the hardware reliability solution must incur low overheads, precluding use of expensive redundancy. We explore a cooperative hardware-software solution that watches for anomalous software behavior to indicate the presence of hardware faults. Fundamental to such a solution is a characterization of how hardware faults indifferent microarchitectural structures of a modern processor propagate through the application and OS.
This paper aims to provide such a characterization, resulting in identifying low-cost detection methods and providing guidelines for implementation of the recovery and diagnosis components of such a reliability solution. We focus on hard faults because they are increasingly important and have different system implications than the much studied transients. We achieve our goals through fault injection experiments with a microarchitecture-level full system timing simulator. Our main results are: (1) we are able to detect 95% of the unmasked faults in 7 out of 8 studied microarchitectural structures with simple detectors that incur zero to little hardware overhead; (2) over 86% of these detections are within latencies that existing hardware checkpointing schemes can handle, while others require software checkpointing; and (3) a surprisingly large fraction of the detected faults corrupt OS state, but almost all of these are detected with latencies short enough to use hardware checkpointing, thereby enabling OS recovery in virtually all such cases.