bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hamstring muscle injuries in professional football: the correlation of MRI findings with return to play
Authors: Ekstrand Jan , Healy Jeremiah C , Waldén Markus , Lee Justin C , English Bryan , Hägglund Martin 
Published: December 2011

BackgroundHamstring injury is the single most common injury in professional football. MRI is commonly used to confirm the diagnosis and provide a prognosis of lay-off time.ObjectiveTo evaluate the use of MRI as a prognostic tool for lay-off after hamstring injuries in professional football players and to study the association between MRI findings and injury circumstances.MethodsProspective cohort study where 23 European professional teams, were followed between 2007 and 2011. Team medical staffs recorded individual player exposure and time-loss injuries. Radiological grading was performed using a modified Peetrons classification into four grades where grades 2 and 3 represent fibre disruption.ResultsIn total, 516 hamstring injuries occurred and 58% of these were examined by MRI. Thirteen per cent were grade 0 injuries, 57% grade 1, 27% of grade 2 and 3% of grade 3. Grade 0 and 1 injuries accounted for 56% (2141/3830 days) of the total lay-off. The lay-off time differed between all four radiological grades of injury (8±3, 17±10, 22±11 and 73±60 days, p<0.0001). Eighty-three per cent of injuries affected the biceps femoris while 11% and 5% occurred to the semimembranosus and semitendinosus, respectively. Re-injuries (N=34/207) constituted 16% of injuries. All re-injuries occurred to the biceps femoris.ConclusionMRI can be helpful in verifying the diagnosis of a hamstring injury and to prognosticate lay-off time. Radiological grading is associated with lay-off times after injury. Seventy per cent of hamstring injuries seen in professional football are of radiological grade 0 or 1, meaning no signs of fibre disruption on MRI, but still cause the majority of absence days.
Excessive thickening of the cortical layer in graptolites
Authors: Bates Denis , Kozłowska Anna , Chmielarz Dagmara , Lenz Alfred 
Published: December 2011

SUMMARY

A number of graptolites with thickened periderm, both dendroids and graptoloids, have been examined with the SEM. The thickening is by the deposition of layers of ectocortical tissue, clearly as bandages in the graptoloids. In
Colonograptus colonus
and some ‘diplograptids’, the thickening is most pronounced in the proximal regions of the rhabdosome, and can lead to the partial or complete occlusion of the aperture of the sicula and proximal thecae, as well as thickening the virgella. This thickening is interpreted as an adaptation connected with an extra gerontic production of cortex, which might have served as a reinforcement of the rhabdosome, or as an adaptation to modify or retain, the centre of gravity in the water column, or both. In
Amphigraptus
sp. the thickening appears to be common, and is concentrated on the dorsal side of the stipes. In
Dendrograptus
sp. thickening is also common: the main branches become excessively thickened, uniformly around the stipes, the side branches less thickened. In
Cyrtograptus
, thickening is rare, and appears to be gerontic, with the exception of a new form tentatively identified as
Cyrtograptus
in which thickening is uniform throughout the rhabdosome, and may have been formed initially. In
Colonograptus
and several ‘diplograptids’, the thickened proximal part shows it is much heavier than the distal part, suggesting a downwards vertical direction of the proximal end. In
Amphigraptus
the asymmetrical thickening suggests an orientation with the ventral side uppermost.
Biogeography and Mass Extinction: Extirpation and re-invasion of
Normalograptus
species (Graptolithina) in the Late Ordovician Palaeotropics
Authors: Goldman Daniel , Mitchell Charles E. , Melchin Michael J. , Fan Junxuan , Wu Shuang-Ye , Sheets H. David 
Published: December 2011

SUMMARY

Normalograptids constitute a distinctive but not easily identified group of derived axonophorans. A new study of
Normalograptus
morphology indicates that many Late Ordovician taxa previously identified as
Normalograptus
are actually referable to
Styracograptus
and related climacograptoids. These re-identifications have led to the recognition of a complex biogeographic history among normalograptids and their descendants, including an interesting pattern that had previously been overlooked – a late Katian disappearance of
Normalograptus
from the palaeotropics. Normalograptid palaeogeographic distribution in the Ordovician appears to comprise 5 main phases: (1) evolutionary origin probably in relatively high palaeolatitudes in the early to mid Darriwilian; (2) spread to global distribution in later Darriwilian time; (3) retreat from most low palaeolatitude regions during the early Katian, with perhaps a slightly delayed retreat from Laurentia; (4) a complete extirpation from the low palaeolatitudes by the mid Katian (Ea4); (5) reinvasion of the low palaeolatitudes that accompanies the remarkable ecological and evolutionary replacement of the Diplograptina by species of
Normalograptus
and their descendants during the latest Katian–early Hirnantian. We propose two sets of hypotheses to explain Late Ordovician
Normalograptus
distribution. First, given the low species diversity of
Normalograptus
, we suggest as a null hypothesis that the disappearance of normalograptids from low palaeolatitudes during the late Sandbian and early Katian as simply a stochastic outcome – a small clade simply went extinct by chance alone. The alternative is that the loss of
Normalograptus
species reflects some form of extinction for cause, either: (1) competitive exclusion; or (2) an inability to adapt to changing environmental conditions. In the case of the competitive exclusion hypothesis, the most likely competitors are species of the Diplograptina.
Phylogeny and Adaptive Radiation of the Neograptina (Graptoloida) During the Hirnantian Mass Extinction and Silurian Recovery
Authors: Melchin M. J. , Mitchell C. E. , Naczk-Cameron A. , Fan J. X. , Loxton J. 
Published: December 2011

SUMMARY

Cladistic analysis of some Hirnantian (latest Ordovician) and Rhuddanian–Aeronian (early Silurian) biserial graptolites and basal monograptids has been undertaken in order to test hypotheses of the relationships among the Neograptina (‘normalograptids’ and their descendents) and to provide a phylogenetic framework for understanding the early Silurian adaptive radiation of graptoloids. It is clear that Silurian graptolite faunas are dominated by two major clades, here named the superfamilies Retiolitoidea and Monograptoidea. Several other lineages whose basal relationships are unresolved, including
Normalograptus
and
Metaclimacograptus
, persisted through much of the Llandovery. The Retiolitoidea includes some taxa previously assigned to the Normalograptidae, as well as petalolithids and retiolitids. The Monograptoidea includes akidograptids, dimorphograptids, the uniserial monograptids, as well as stem taxa previously regarded as normalograptids. Both of these major clades had their origins in Late Ordovician time and began their diversification within the Hirnantian–early Rhuddanian, in step with the two main phases of the Hirnantian Mass Extinction. The Neograptina also exhibit an additional interval of accelerated turnover in the Rhuddanian during which the characteristic Silurian fauna largely replaced the Hirnantian Neograptina. One new family, Neodiplograptidae, and four new genera are described:
Avitograptus
,
Rickardsograptus
,
Korenograptus
and
Paramplexograptus
.
The systematic relationship of the monograptid species
acinaces
Törnquist, 1899 and
rheidolensis
Jones, 1909
Authors: Zalasiewicz Jan , Russell Catherine , Snelling Andrea , Williams Mark 
Published: December 2011

SUMMARY

The relationship between the early Silurian (Rhuddanian) monograptid species
rheidolensis
Jones, 1909 and
acinaces
Törnquist, 1899 has been contentious, with debate as regards both their possible synonymy and their generic assignation. We have re-examined the type and associated material of
rheidolensis
, and conclude that this taxon is almost certainly a junior synonym of
acinaces
. Lacking ventral apertural processes,
acinaces
does not belong within
Lagarograptus
, as previously thought, but may be placed within
Huttagraptus
, as proposed by Koren' & Bjerreskov (1997). The confusion between these two taxa arose because the material that Jones assigned to
rheidolensis
includes two taxa, one representing non-topotype (and probably mis-localized) specimens of an undoubted
Neolagarograptu
s. This is morphologically very similar to, and probably referable to, the late Aeronian species
Neolagarograptus tenuis
, the type material of which we show here to be tectonically distorted.
Computing the volume of a union of balls
Authors: Cazals Frederic , Kanhere Harshad , Loriot Sébastien 
Published: December 2011

Balls and spheres are amongst the simplest 3
D
modeling primitives, and computing the volume of a union of balls is an elementary problem. Although a number of strategies addressing this problem have been investigated in several communities, we are not aware of any robust algorithm, and present the first such algorithm.

Our calculation relies on the decomposition of the volume of the union into convex regions, namely the restrictions of the balls to their regions in the power diagram. Theoretically, we establish a formula for the volume of a restriction, based on Gauss' divergence theorem. The proof being constructive, we develop the associated algorithm. On the implementation side, we carefully analyse the predicates and constructions involved in the volume calculation, and present a certified implementation relying on interval arithmetic. The result is certified in the sense that the exact volume belongs to the interval computed.
Experimental results are presented on hand-crafted models illustrating various difficulties, as well as on the 58,898 models found in the tenth of July 2009 release of the Protein Data Bank.
SHERIFF
Authors: Liu Tongping , Berger Emery D. 
Published: December 2011

False sharing is an insidious problem for multithreaded programs running on multicore processors, where it can silently degrade performance and scalability. Previous tools for detecting false sharing are severely limited: they cannot distinguish false sharing from true sharing, have high false positive rates, and provide limited assistance to help programmers locate and resolve false sharing.
This paper presents two tools that attack the problem of false sharing: Sheriff-Detect and Sheriff-Protect. Both tools leverage a framework we introduce here called Sheriff. Sheriff breaks out threads into separate processes, and exposes an API that allows programs to perform per-thread memory isolation and tracking on a per-page basis. We believe Sheriff is of independent interest.
Sheriff-Detect finds instances of false sharing by comparing updates within the same cache lines by different threads, and uses sampling to rank them by performance impact. Sheriff-Detect is precise (no false positives), runs with low overhead (on average, 20%), and is accurate, pinpointing the exact objects involved in false sharing. We present a case study demonstrating Sheriff-Detect's effectiveness at locating false sharing in a variety of benchmarks.
Rewriting a program to fix false sharing can be infeasible when source is unavailable, or undesirable when padding objects would unacceptably increase memory consumption or further worsen runtime performance. Sheriff-Protect mitigates false sharing by adaptively isolating shared updates from different threads into separate physical addresses, effectively eliminating most of the performance impact of false sharing. We show that Sheriff-Protect can improve performance for programs with catastrophic false sharing by up to 9×, without programmer intervention.
Kind analysis for MATLAB
Authors: Doherty Jesse , Hendren Laurie , Radpour Soroush 
Published: December 2011

MATLAB is a popular dynamic programming language used for scientific and numerical programming. As a language, it has evolved from a small scripting language intended as an interactive interface to numerical libraries, to a very popular language supporting many language features and libraries. The overloaded syntax and dynamic nature of the language, plus the somewhat organic addition of language features over the years, makes static analysis of modern MATLAB quite challenging. A fundamental problem in MATLAB is determining the kind of an identifier. Does an identifier refer to a variable, a named function or a prefix? Although this is a trivial problem for most programming languages, it was not clear how to do this properly in MATLAB. Furthermore, there was no simple explanation of kind analysis suitable for MATLAB programmers, nor a publicly-available implementation suitable for compiler researchers.
This paper explains the required background of MATLAB, clarifies the kind assignment program, and proposes some general guidelines for developing good kind analyses. Based on these foundations we present our design and implementation of a variety of kind analyses, including an approach that matches the intended behaviour of modern MATLAB 7 and two potentially better alternatives.
We have implemented all the variations of the kind analysis in McLab, our extensible compiler framework, and we present an empirical evaluation of the various analyses on a large set of benchmark programs.
Trustworthy numerical computation in Scala
Authors: Darulova Eva , Kuncak Viktor 
Published: December 2011

Modern computing has adopted the floating point type as a default way to describe computations with real numbers. Thanks to dedicated hardware support, such computations are efficient on modern architectures, even in double precision. However, rigorous reasoning about the resulting programs remains difficult. This is in part due to a large gap between the finite floating point representation and the infinite-precision real-number semantics that serves as the developers' mental model. Because programming languages do not provide support for estimating errors, some computations in practice are performed more and some less precisely than needed.
We present a library solution for rigorous arithmetic computation. Our numerical data type library tracks a (double) floating point value, but also a guaranteed upper bound on the error between this value and the ideal value that would be computed in the real-value semantics. Our implementation involves a set of linear approximations based on an extension of affine arithmetic. The derived approximations cover most of the standard mathematical operations, including trigonometric functions, and are more comprehensive than any publicly available ones. Moreover, while interval arithmetic rapidly yields overly pessimistic estimates, our approach remains precise for several computational tasks of interest. We evaluate the library on a number of examples from numerical analysis and physical simulations. We found it to be a useful tool for gaining confidence in the correctness of the computation.
A step towards transparent integration of input-consciousness into dynamic program optimizations
Authors: Tian Kai , Zhang Eddy , Shen Xipeng 
Published: December 2011

Dynamic program optimizations are critical for the efficiency of applications in managed programming languages and scripting languages. Recent studies have shown that exploitation of program inputs may enhance the effectiveness of dynamic optimizations significantly. However, current solutions for enabling the exploitation require either programmers' annotations or intensive offline profiling, impairing the practical adoption of the techniques.
This current work examines the basic feasibility of transparent integration of input-consciousness into dynamic program optimizations, particularly in managed execution environments. It uses transparent learning across production runs as the basic vehicle, and investigates the implications of cross-run learning on each main component of input-conscious dynamic optimizations. It proposes several techniques to address some key challenges for the transparent integration, including randomized inspection-instrumentation for cross-user data collection, a sparsity-tolerant algorithm for input characterization, and selective prediction for efficiency protection. These techniques make it possible to automatically recognize the relations between the inputs to a program and the appropriate ways to optimize it. The whole process happens transparently across production runs; no need for offline profiling or programmer intervention. Experiments on a number of Java programs demonstrate the effectiveness of the techniques in enabling input-consciousness for dynamic optimizations, revealing the feasibility and potential benefits of the new optimization paradigm in some basic settings.
Kismet
Authors: Jeon Donghwan , Garcia Saturnino , Louie Chris , Taylor Michael Bedford 
Published: December 2011

Software engineers now face the difficult task of refactoring serial programs for parallel execution on multicore processors. Currently, they are offered little guidance as to how much benefit may come from this task, or how close they are to the best possible parallelization. This paper presents Kismet, a tool that creates parallel speedup estimates for unparallelized serial programs. Kismet differs from previous approaches in that it does not require any manual analysis or modification of the program. This difference allows quick analysis of many programs, avoiding wasted engineering effort on those that are fundamentally limited. To accomplish this task, Kismet builds upon the hierarchical critical path analysis (HCPA) technique, a recently developed dynamic analysis that localizes parallelism to each of the potentially nested regions in the target program. It then uses a parallel execution time model to compute an approximate upper bound for performance, modeling constraints that stem from both hardware parameters and internal program structure.
Our evaluation applies Kismet to eight high-parallelism NAS Parallel Benchmarks running on a 32-core AMD multicore system, five low-parallelism SpecInt benchmarks, and six medium-parallelism benchmarks running on the finegrained MIT Raw processor. The results are compelling. Kismet is able to significantly improve the accuracy of parallel speedup estimates relative to prior work based on critical path analysis.
JIT compilation policy for modern machines
Authors: Kulkarni Prasad A. 
Published: December 2011

Dynamic or Just-in-Time (JIT) compilation is crucial to achieve acceptable performance for applications (written in managed languages, such as Java and C#) distributed as intermediate language binary codes for a virtual machine (VM) architecture. Since it occurs at runtime, JIT compilation needs to carefully tune its compilation policy to make effective decisions regarding 'if' and 'when' to compile different program regions to achieve the best overall program performance. Past research has extensively tuned JIT compilation policies, but mainly for VMs with a single compiler thread and for execution on single-processor machines.
This work is driven by the need to explore the most effective JIT compilation strategies in their modern operational environment, where (a) processors have evolved from single to multi/many cores, and (b) VMs provide support for multiple concurrent compiler threads. Our results confirm that changing 'if' and 'when' methods are compiled have significant performance impacts. We construct several novel configurations in the HotSpot JVM to facilitate this study. The new configurations are necessitated by modern Java benchmarks that impede traditional static whole-program discovery, analysis and annotation, and are required for simulating future many-core hardware that is not yet widely available. We study the effects on performance of increasing compiler aggressiveness for VMs with multiple compiler threads running on existing single/multi-core and future many-core machines. Our results indicate that although more aggressive JIT compilation policies show no benefits on single-core machines, these can often improve program performance for multi/many-core machines. However, accurately prioritizing JIT method compilations is crucial to realize such benefits.
Reducing trace selection footprint for large-scale Java applications without performance loss
Authors: Wu Peng , Hayashizaki Hiroshige , Inoue Hiroshi , Nakatani Toshio 
Published: December 2011

When optimizing large-scale applications, striking the balance between steady-state performance, start-up time, and code size has always been a grand challenge. While recent advances in trace compilation have significantly improved the steady-state performance of trace JITs for large-scale Java applications, the size control aspect of a trace compilation system remains largely overlooked. For instance, using the DaCapo 9.12 benchmarks, we observe that 40% of traces selected by a state-of-the-art trace selection algorithm are short-lived and, on average, each selected basic block is replicated 13 times in the trace cache.
This paper studies the size control problem for a class of commonly used trace selection algorithms and proposes six techniques to reduce the footprint of trace selection without incurring any performance loss. The crux of our approach is to target redundancies in trace selection in the form of either short-lived traces or unnecessary trace duplication.
Using one of the best performing selection algorithms as the baseline, we demonstrate that, on the DaCapo 9.12 benchmarks and DayTrader 2.0 on WebSphere Application Server 7.0, our techniques reduce the code size and compilation time by 69% and the start-up time by 43% while retaining the steady-state performance. On DayTrader 2.0, an example of large-scale application, our techniques also improve the steady-state performance by 10%.
Safe and atomic run-time code evolution for Java and its application to dynamic AOP
Authors: Würthinger Thomas , Ansaloni Danilo , Binder Walter , Wimmer Christian , Mössenböck Hanspeter 
Published: December 2011

Dynamic updates to running programs improve development productivity and reduce downtime of long-running applications. This feature is however severely limited in current virtual machines for object-oriented languages. In particular, changes to classes often apply only to methods invoked after a class change, but not to active methods on the call stack of threads. Additionally, adding and removing methods as well as fields is often not supported.
We present a novel programming model for safe and atomic code updates of Java programs that also updates methods that are currently executed. We introduce safe update regions and pause threads only there before an update. We automatically convert the stack frames to suit the new versions of the methods. Our implementation is based on a production-quality Java virtual machine.
Additionally, we present SafeWeave, a dynamic aspect-oriented programming system that exposes the atomic code updates through a high-level programming model. AspectJ advice can be added to and removed from a running application.Changes are atomic and correctness is guaranteed even though weaving happens in parallel to program execution, and the system fully supports the dynamic class loading of Java. We show that the enhanced evolution features do not incur any performance penalty before and after version changes.