bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct Compartmentalization of NF-κB Activity in Crypt and Crypt-Denuded Lamina Propria Precedes and Accompanies Hyperplasia and/or Colitis following Bacterial Infection
Authors: Chandrakesan Parthasarathy , Ahmed Ishfaq , Chinthalapally Anisha , Singh Pomila , Awasthi Shanjana , Anant Shrikant , Umar Shahid 
Published: December 2011

ABSTRACTCitrobacter rodentiuminduces transmissible murine colonic hyperplasia (TMCH) and variable degrees of inflammation and necrosis depending upon the genetic background. UtilizingC. rodentium-induced TMCH in C3H/HeNHsd inbred mice, we observed significant crypt hyperplasia on days 3 and 7 preceding active colitis. NF-κB activity in the crypt-denuded lamina propria (CLP) increased within 24 h postinfection, followed by its activation in the crypts at day 3, which peaked by day 7. Increases in interleukin-α1 (IL-1α), IL-12(p40), and macrophage inflammatory protein 1α (MIP-1α) paralleled NF-κB activation, while increases in IL-1α/β, IL-6/IL-12(p40)/granulocyte colony-stimulating factor (G-CSF)/keratinocyte-derived chemokine (KC)/monocyte chemotactic protein 1 (MCP-1), and MIP-1α followed NF-κB activation leading to significant recruitment of neutrophils to the colonic mucosa and increased colonic myeloperoxidase (MPO) activity. Phosphorylation of the crypt cellular and nuclear p65 subunit at serines 276 and 536 led to functional NF-κB activation that facilitated expression of its downstream target, CXCL-1/KC, during TMCH. Distinct compartmentalization of phosphorylated extracellular signal-regulated kinase 1 and 2 ([ERK1/2] Thr180/Tyr182) and p38 (Thr202/Tyr204) in the CLP preceded increases in the crypts. Inhibition of ERK1/2 and p38 suppressed NF-κB activity in both crypts and the CLP. Dietary administration of 6% pectin or 4% curcumin inC. rodentium-infected mice also inhibited NF-κB activity and blocked CD3, F4/80, IL-1α/β, G-CSF/MCP-1/KC, and MPO activity in the CLP while not affecting NF-κB activity in the crypts. Thus, distinct compartmentalization of NF-κB activity in the crypts and the CLP regulates crypt hyperplasia and/or colitis, and dietary intervention may be a novel strategy to modulate NF-κB-dependent protective immunity to facilitate crypt regeneration followingC. rodentium-induced pathogenesis.
Free Lipid A Isolated from Porphyromonas gingivalis Lipopolysaccharide Is Contaminated with Phosphorylated Dihydroceramide Lipids: Recovery in Diseased Dental Samples
Authors: Nichols Frank C. , Bajrami Bekim , Clark Robert B. , Housley William , Yao Xudong 
Published: December 2011

ABSTRACT

Recent reports indicate that
Porphyromonas gingivalis
mediates alveolar bone loss or osteoclast modulation through engagement of Toll-like receptor 2 (TLR2), though the factors responsible for TLR2 engagement have yet to be determined. Lipopolysaccharide (LPS) and lipid A, lipoprotein, fimbriae, and phosphorylated dihydroceramides of
P. gingivalis
have been reported to activate host cell responses through engagement of TLR2. LPS and lipid A are the most controversial in this regard because conflicting evidence has been reported concerning the capacity of
P. gingivalis
LPS or lipid A to engage TLR2 versus TLR4. In the present study, we first prepared
P. gingivalis
LPS by the Tri-Reagent method and evaluated this isolate for contamination with phosphorylated dihydroceramide lipids. Next, the lipid A prepared from this LPS was evaluated for the presence of phosphorylated dihydroceramide lipids. Finally, we characterized the lipid A by the matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and electrospray-MS methods in order to quantify recovery of lipid A in lipid extracts from diseased teeth or subgingival plaque samples. Our results demonstrate that both the LPS and lipid A derived from
P. gingivalis
are contaminated with phosphorylated dihydroceramide lipids. Furthermore, the lipid extracts derived from diseased teeth or subgingival plaque do not contain free lipid A constituents of
P. gingivalis
but contain substantial amounts of phosphorylated dihydroceramide lipids. Therefore, the free lipid A of
P. gingivalis
is not present in measurable levels at periodontal disease sites. Our results also suggest that the TLR2 activation of host tissues attributed to LPS and lipid A of
P. gingivalis
could actually be mediated by phosphorylated dihydroceramides.
Early change in thermal perception is not a driver of anticipatory exercise pacing in the heat
Authors: Barwood Martin James , Corbett Jo , White Danny , James Jason 
Published: December 2011

AimInitial power output declines significantly during exercise in hot conditions on attaining a rapid increase in skin temperature when exercise commences. It is unclear whether this initial reduced power is mediated consciously, through thermal perceptual cues, or is a subconscious process. The authors tested the hypothesis that improved thermal perception (feeling cooler and more comfortable) in the absence of a change in thermal state (ie, similar deep-body and skin temperatures between spray conditions) would alter pacing and 40 km cycling time trial (TT) performance.MethodEleven trained participants (mean (SD): age 30 (8.1) years; height 1.78 (0.06) m; mass 76.0 (8.3) kg) completed three 40 km cycling TTs in standardised conditions (32°C, 50% RH) with thermal perception altered prior to exercise by application of cold-receptor-activating menthol spray (MENTHOL SPRAY), in contrast to a separate control spray (CONTROL SPRAY) and no spray control (CON). Thermal perception, perceived exertion, thermal responses and cycling TT performance were measured.ResultsMENTHOL SPRAY induced feelings of coolness and improved thermal comfort before and during exercise. Skin temperature profile at the start of exercise was similar between sprays (CON-SPRAY 33.3 (1.1)°C and MENTHOL SPRAY 33.4 (0.4)°C, but different to CON 34.5 (0.5)°C), but there was no difference in the pacing strategy adopted. There was no performance benefit using MENTHOL SPRAY; cycling TT completion time for CON is 71.58 (6.21) min, for CON-SPRAY is 70.94 (6.06) min and for MENTHOL SPRAY is 71.04 (5.47) min.ConclusionThe hypothesis is rejected. Thermal perception is not a primary driver of early pacing during 40 km cycling TT in hot conditions in trained participants.
Risk management: FIFA's approach for protecting the health of football players
Authors: Fuller Colin W , Junge Astrid , Dvorak Jiri 
Published: December 2011

BackgroundSport and exercise have long-term health benefits, but there is also a risk that participants will sustain injuries and/or ill health from these activities. For this reason, international sports governing bodies have a responsibility to identify the risks that exist within their sport and to provide guidance to participants and other stakeholders on how these risks can be controlled within acceptable levels.PurposeTo demonstrate how Fédération Internationale de Football Association (FIFA), as football's governing body, uses a risk management framework to identify, quantify, mitigate and communicate the risks of injury and ill health in football for men, women and children in all environments.MethodAll the research papers published by FIFA's Medical Assessment and Research Centre (F-MARC) during the period 1994 to 2011 were reviewed and categorised according to an established sport-related risk management framework.ConclusionsF-MARC investigated and mitigated 17 areas of risk to footballers' health in a coherent and consistent approach through the process of risk management.
Mechanical thrombectomy as first-line treatment for venous sinus thrombosis: technical considerations and preliminary results using the AngioJet device
Authors: Dashti Shervin R , Hu Yin C , Yao Tom , Fiorella David , Mitha Alim P , Albuquerque Felipe C , McDougall Cameron G 
Published: December 2011

BackgroundCerebral venous sinus thrombosis (CVT) is an uncommon cause of stroke that is usually treated medically with intravenous heparin therapy followed by long-term anticoagulation therapy. A series of patients with CVT who underwent rheolytic thrombectomy with the AngioJet as a first-line adjunctive treatment in addition to standard anticoagulation therapy is presented.MethodsProspectively maintained endovascular databases at two institutions were retrospectively reviewed. The available clinical and imaging data were compiled at each institution and combined for analysis.ResultsOver 18 months, 13 patients (seven women and six men; age range 17–73 years, median age 45 years) with CVT were treated with rheolytic thrombectomy. Immediate (partial or complete) recanalization of the thrombosed intracranial sinuses was achieved in all patients. At a median radiographic follow-up of 7 months there was continued patency of all recanalized sinuses. Clinical follow-up was available on nine patients: modified Rankin score of 0 in four patients, 1 in three patients and 6 in two patients.ConclusionThis series demonstrates the feasibility of performing mechanical thrombectomy as a first-line treatment for acute CVT. This technique facilitates the prompt restoration of intracranial venous outflow, which may result in rapid neurological and symptomatic improvement.
Deflexed didymograptids from the Lower Ordovician Skiddaw Group of northern England
Authors: Rushton A. W. A. 
Published: December 2011

SUMMARY

The type species of
Corymbograptus
,
Didymograptus v-fractus
, is discussed and a neotype is proposed. The zonal graptolites
Didymograptus varicosus
and
D. deflexus
, mainly from the Loweswater Formation of the Skiddaw Group succession, are discussed and illustrated as species of
Baltograptus
. Study of their proximal structure shows that the identification of
D. varicosus
in the Loweswater Formation is not correct, and the English specimens are here assigned to
Baltograptus jacksoni
sp. nov.
Scandinavian Isograptids (Graptolithina, Isograptidae): Biostratigraphy and Taxonomy
Authors: Maletz Jörg 
Published: December 2011

SUMMARY

The Lower–Middle Ordovician of Scandinavia is largely dominated by endemic Atlantic Province graptolite faunas, which are useful only for local biostratigraphy and paleoecology, but are difficult for correlation on an inter-continental scale. Isograptids, regarded as essential for inter-continental biostratigraphic correlations in the Lower–Middle Ordovician due to their wide palaeobiogeographic distribution, have rarely been recorded from the region. The Scandinavian Tøyen Shale and Bogo Shale formations bear a number of isograptids that range in age from the late Floian to the early Darriwilian, and these provide a good tool for inter-continental correlations of this interval.
Isograptus caduceus norvegicus
Monsen and
Isograptus spinosus
Spjeldnaes are interpreted as possible tetragraptid species. The following biostratigraphically important
Isograptus
species from Scandinavia are described as new:
Isograptus spjeldnaesi
n. sp.,
Isograptus rigidus
n. sp.
Isograptus mobergi
n. sp. and Scandinavian zonal names in the Dapingian are revised accordingly.
GrapEl – a simple spreadsheet application for managing and disseminating graptolite biozonal range chart data
Authors: Howe Michael P. A. 
Published: December 2011

SUMMARY
Biostratigraphical data frequently consist of tables indicating the presence, absence or relative abundance of taxa in a sequence of rock units or time units such as biozones or various chronostratigraphic units. Spreadsheet programs provide a simple means for managing this data and can be used for archiving and disseminating it, in addition to manipulating it. A simple spreadsheet (‘GrapEl’) is used to link the biozonal ranges of graptolite taxa to illustrations of representative or type specimens. Use of the filtering function enables the rapid selection of species from particular biozones, or species belonging to particular genera, and is intended to assist workers with a limited working knowledge of the faunas concerned. This approach is briefly compared to other uses of spreadsheets and databases in the management, analysis and distribution of graptolite biostratigraphical data.

Supplementary material:
‘GrapEl’ spreadsheets are available at
http://www.geolsoc.org.uk/SUP18504
The evolutionary lineage of
Petalolithus
to
Cephalograptus
: evidence from Coalpit Bay, Northern Ireland
Authors: Snelling Andrea M. , Zalasiewicz Jan A. 
Published: December 2011

SUMMARY

The evolution of graptolites is the basis upon which much of the Lower Palaeozoic is subdivided. Amongst the clearest evolutionary lineages within graptolites are those that show seemingly unidirectional trends in morphology, such as the sequence of stratigraphically successive taxa of
Petalolithus
and
Cephalograptus
, discussed here. Graptolite specimens collected in the 1960s from Coalpit Bay, Northern Ireland are consistent with the succession established in the Czech Republic by
Bouček & Přibyl (1941)
and
Štorch (1998)
, and include the first UK records of
P
. aff
. krizi
. We recognise other intermediate forms within this lineage that may enable further subdivision of the
convolutus
Biozone.
Safe parallel programming using dynamic dependence hints
Authors: Ke Chuanle , Liu Lei , Zhang Chao , Bai Tongxin , Jacobs Bryan , Ding Chen 
Published: December 2011

Speculative parallelization divides a sequential program into possibly parallel tasks and permits these tasks to run in parallel if and only if they show no dependences with each other. The parallelization is safe in that a speculative execution always produces the same output as the sequential execution.
In this paper, we present the dependence hint, an interface for a user to specify possible dependences between possibly parallel tasks. Dependence hints may be incorrect or incomplete but they do not change the program output. The interface extends Cytron's do-across and recent OpenMP ordering primitives and makes them safe and safely composable. We use it to express conditional and partial parallelism and to parallelize large-size legacy code. The prototype system is implemented as a software library. It is used to improve performance by nearly 10 times on average on current multicore machines for 8 programs including 5 SPEC benchmarks.
Sprint
Authors: Raman Arun , Yorsh Greta , Vechev Martin , Yahav Eran 
Published: December 2011

Remote data access latency is a significant performance bottleneck in many modern programs that use remote databases and web services. We present Sprint - a run-time system for optimizing such programs by prefetching and caching data from remote sources in parallel to the execution of the original program. Sprint separates the concerns of exposing potentially-independent data accesses from the mechanism for executing them efficiently in parallel or in a batch. In contrast to prior work, Sprint can efficiently prefetch data in the presence of irregular or input-dependent access patterns, while preserving the semantics of the original program.
We used Sprint to automatically improve the performance of several real-world Java programs that access remote databases (MySQL, DB2) and web services (Facebook, IBM's Yellow Pages). Sprint achieves speedups ranging 2.4x to 15.8x over sequential execution, which are comparable to those achieved by manually modifying the program for asynchronous and batch execution of data accesses. Sprint provides a simple interface that allows a programmer to plug in support for additional data sources without modifying the client program.
Asynchronous assertions
Authors: Aftandilian Edward E. , Guyer Samuel Z. , Vechev Martin , Yahav Eran 
Published: December 2011

Assertions are a familiar and widely used bug detection technique. Traditional assertion checking, however, is performed synchronously, imposing its full cost on the runtime of the program. As a result, many useful kinds of checks, such as data structure invariants and heap analyses, are impractical because they lead to extreme slowdowns. We present a solution that decouples assertion evaluation from program execution: assertions are checked asynchronously by separate checking threads while the program continues to execute. Our technique guarantees that asynchronous evaluation always produces the same result as synchronous evaluation, even if the program concurrently modifies the program state. The checking threads evaluate each assertion on a consistent snapshot of the program state as it existed at the moment the assertion started.
We implemented our technique in a system called Strobe, which supports asynchronous assertion checking in both single-and multi-threaded Java applications. Strobe runs inside the Java virtual machine and uses copy-on-write to construct snapshots incrementally, on-the-fly. Our system includes all necessary synchronization to support multiple concurrent checking threads, and to prevent data races with the main program threads. We find that asynchronous checking significantly outperforms synchronous checking, incurring tolerable overheads -- in the range of 10% to 50% over no checking at all -- even for heavy-weight assertions that would otherwise result in crushing slowdowns.
Efficiently speeding up sequential computation through the n-way programming model
Authors: Cledat Romain E. , Kumar Tushar , Pande Santosh 
Published: December 2011

With core counts on the rise, the sequential components of applications are becoming the major bottleneck in performance scaling as predicted by Amdahl's law. We are therefore faced with the simultaneous problems of occupying an increasing number of cores and speeding up sequential sections. In this work, we reconcile these two seemingly incompatible problems with a novel programming model called N-way. The core idea behind N-way is to benefit from the algorithmic diversity available to express certain key computational steps. By simultaneously launching in parallel multiple ways to solve a given computation, a runtime can just-in-time pick the best (for example the fastest) way and therefore achieve speedup.
Previous work has demonstrated the benefits of such an approach but has not addressed its inherent waste. In this work, we focus on providing a mathematically sound learning-based statistical model that can be used by a runtime to determine the optimal balance between resources used and benefits obtainable through N-way. We further describe a dynamic culling mechanism to further reduce resource waste.
We present abstractions and a runtime support to cleanly encapsulate the computational-options and monitor their progress. We demonstrate a low-overhead runtime that achieves significant speedup over a range of widely used kernels. Our results demonstrate super-linear speedups in certain cases.
Delegated isolation
Authors: Lublinerman Roberto , Zhao Jisheng , Budimlić Zoran , Chaudhuri Swarat , Sarkar Vivek 
Published: December 2011

Isolation---the property that a task can access shared data without interference from other tasks---is one of the most basic concerns in parallel programming. In this paper, we present Aida, a new model of isolated execution for parallel programs that perform frequent, irregular accesses to pointer-based shared data structures. The three primary benefits of Aida are dynamism, safety and liveness guarantees, and programmability. First, Aida allows tasks to dynamically select and modify, in an isolated manner, arbitrary fine-grained regions in shared data structures, all the while maintaining a high level of concurrency. Consequently, the model can achieve scalable parallelization of regular as well as irregular shared-memory applications. Second, the model offers freedom from data races, deadlocks, and livelocks. Third, no extra burden is imposed on programmers, who access the model via a simple, declarative isolation construct that is similar to that for transactional memory. The key new insight in Aida is a notion of delegation among concurrent isolated tasks (known in Aida as assemblies). Each assembly A is equipped with a region in the shared heap that it owns---the only objects accessed by A are those it owns, guaranteeing race-freedom. The region owned by A can grow or shrink flexibly---however, when A needs to own a datum owned by B, A delegates itself, as well as its owned region, to B. From now on, B has the responsibility of re-executing the task A set out to complete. Delegation as above is the only inter-assembly communication primitive in Aida. In addition to reducing contention in a local, data-driven manner, it guarantees freedom from deadlocks and livelocks.
We offer an implementation of Aida on top of the Habanero Java parallel programming language. The implementation employs several novel ideas, including the use of a union-find data structure to represent tasks and the regions that they own. A thorough evaluation using several irregular data-parallel benchmarks demonstrates the low overhead and excellent scalability of Aida, as well as its benefits over existing approaches to declarative isolation. Our results show that Aida performs on par with the state-of-the-art customized implementations of irregular applications and much better than coarse-grained locking and transactional memory approaches.
Freedom before commitment
Authors: Summers Alexander J. , Mueller Peter 
Published: December 2011

One of the main purposes of object initialisation is to establish invariants such as a field being non-null or an immutable data structure containing specific values. These invariants are then implicitly assumed by the rest of the implementation, for instance, to ensure that a field may be safely dereferenced or that immutable data may be accessed concurrently. Consequently, letting an object escape from its constructor is dangerous; the escaping object might not yet satisfy its invariants, leading to errors in code that relies on them. Nevertheless, preventing objects entirely from escaping from their constructors is too restrictive; it is often useful to call auxiliary methods on the object under initialisation or to pass it to another constructor to set up mutually-recursive structures.
We present a type system that tracks which objects are fully initialised and which are still under initialisation. The system can be used to prevent objects from escaping, but also to allow safe escaping by making explicit which objects might not yet satisfy their invariants. We designed, formalised and implemented our system as an extension to a non-null type system, but it is not limited to this application. Our system is conceptually simple and requires little annotation overhead; it is sound and sufficiently expressive for many common programming idioms. Therefore, we believe it to be the first such system suitable for mainstream use.