bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical and Technical Demands of Rugby League 9s Tournament Match Play: A Preliminary Study
Authors: Kempton Thomas , Coutts Aaron J. 
Published: September 2014

Purpose:To describe the physical and technical demands of rugby league 9s (RL9s) match play for positional groups.Methods:Global positioning system data were collected during 4 games from 16 players from a team competing in the Auckland RL9s tournament. Players were classified into positional groups (pivots, outside backs, and forwards). Absolute and relative physical-performance data were classified as total high-speed running (HSR; >14.4 km/h), very-high-speed running (VHSR; >19.0 km/h), and sprint (>23.0 km/h) distances. Technical-performance data were obtained from a commercial statistics provider. Activity cycles were coded by an experienced video analyst.Results:Forwards (1088 m, 264 m) most likely completed less overall and high-speed distances than pivots (1529 m, 371 m) and outside backs (1328 m, 312 m). The number of sprint efforts likely varied between positions, although differences in accelerations were unclear. There were no clear differences in relative total (115.6−121.3 m/min) and HSR (27.8−29.8 m/min) intensities, but forwards likely performed less VHSR (7.7 m/min) and sprint distance (1.3 m/min) per minute than other positions (10.2−11.8 m/min, 3.7−4.8 m/min). The average activity and recovery cycle lengths were ~50 and ~27 s, respectively. The average longest activity cycle was ~133 s, while the average minimum recovery time was ~5 s. Technical involvements including tackles missed, runs, tackles received, total collisions, errors, off-loads, line breaks, and involvements differed between positions.Conclusions:Positional differences exist for both physical and technical measures, and preparation for RL9s play should incorporate these differences.
Draft Genome Sequence of a Streptococcus agalactiae Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland
Authors: Kropp K. A. , Lucid A. , Carroll J. , Belgrudov V. , Walsh P. , Kelly B. , Smith C. , Dickinson P. , O'Driscoll A. , Templeton K. , Ghazal P. , Sleator R. D. 
Published: September 2014

ABSTRACT

Herein, we report the draft genome sequence of
Streptococcus agalactiae
ED-NGS-1000, cultivated from a blood sample taken from a preterm neonate blood sepsis patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
Draft Genome Sequence of a Staphylococcus warneri Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland
Authors: Kropp K. A. , Lucid A. , Carroll J. , Belgrudov V. , Walsh P. , Kelly B. , Smith C. , Dickinson P. , O'Driscoll A. , Templeton K. , Ghazal P. , Sleator R. D. 
Published: September 2014

ABSTRACT

Herein, we report the draft genome sequence of
Staphylococcus warneri
ED-NGS-1001, cultivated from a blood sample taken from a preterm neonate blood sepsis patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
Complete Genome Sequence of Actinobaculum schaalii Strain CCUG 27420
Authors: Kristiansen Rikke , Dueholm Morten S. , Bank Steffen , Nielsen Per Halkjær , Karst Søren M. , Cattoir Vincent , Lienhard Reto , Grisold Andrea J. , Olsen Anne Buchhave , Reinhard Mark , Søby Karen Marie , Christensen Jens Jørgen , Prag Jørgen , Thomsen Trine R. 
Published: September 2014

ABSTRACT

Complete genome sequencing of the emerging uropathogen
Actinobaculum schaalii
indicates that an important mechanism of its virulence is attachment pili, which allow the organism to adhere to the surface of animal cells, greatly enhancing the ability of this organism to colonize the urinary tract.
Genome-Wide Association Studies of Virulent and Avirulent Haemophilus parasuis Serotype 4 Strains
Authors: Lawrence Paulraj K. , Wiener Brittanny L. , Kolander-Bremer Tammy , Bey Russell F. , Stine Douglas L. , Kittichotirat Weerayuth , Bumgarner Roger E. 
Published: September 2014

ABSTRACTHaemophilus parasuisis a normal commensal of the upper respiratory tract of healthy pigs. However, in conjunction with stress and/or viral infections, or in immunocompromised animals,H. parasuiscan transform into a pathogen causing Glasser's disease, which is typically characterized by fibrinous polyserositis, polyarthritis, meningitis, and sometimes acute pneumonia and septicemia.H. parasuisserotype 5 is highly virulent and more frequently isolated from respiratory and systemic infection in pigs. Recently Newport Laboratories isolated highly virulentH. parasuisserotype 4 strains from the tissues of diseased pigs. This study was undertaken to identify the genes responsible forH. parasuisserotype 4 virulence. To achieve this objective we performed genome-wide association studies (GWAS) across two virulent and three avirulentH. parasuisserotype 4 strains.
Anticipated significant work limitation in primary care consulters with osteoarthritis: a prospective cohort study
Authors: Wilkie Ross , Phillipson Chris , Hay Elaine M , Pransky Glenn 
Published: September 2014

ObjectiveTo describe the prevalence of expected work limitations (EWL) prior to future retirement age in osteoarthritis consulters, and the associated health, sociodemographic and workplace factors.DesignPopulation-based prospective cohort study.SettingGeneral practices in Staffordshire, England.Participants297 working adults aged 50–65, who had consulted primary care for osteoarthritis.OutcomeEWL was defined using a single question, “Do you think joint pain will limit your ability to work before you reach 69 years old?”Results51 (17.2%) indicated that joint pain would not limit their ability to work until 69, 79 (26.6%) indicated EWL and 167 (56.2%) did not know if joint pain would limit work before 69. In bivariate analysis, physical function (OR 0.93; 95% CI 0.91 to 0.96), depression (4.51; 1.81 to 11.3), cognitive symptom (3.84; 1.81 to 8.18), current smoker (2.75; 1.02 to 7.38), age (0.69; 0.58 to 0.82), physically demanding job (3.18; 1.50 to 6.72), no opportunities to retrain (3.01; 1.29 to 7.05) and work dissatisfaction (3.69; 1.43 to 9.49) were associated with EWL. The final multivariate model included physical function and age.ConclusionsOnly one in five osteoarthritis consulters expected that joint pain would not limit their work participation before 69 years of age. Given the expectation for people to work until they are older, the results highlight the increasing need for clinicians to include work participation in their consultation and implement strategies to address work loss/limitation. Targeting pain-related functional limitation and effective communication with employers to manage workplace issues could reduce EWL.
The IDEAL DVT study, individualised duration elastic compression therapy against long-term duration of therapy for the prevention of post-thrombotic syndrome: protocol of a randomised controlled trial
Authors: ten Cate-Hoek Arina J , Bouman Annemieke C , Joore Manuela A , Prins Martin , ten Cate Hugo 
Published: September 2014

IntroductionPost-thrombotic syndrome (PTS) is a serious complication of deep vein thrombosis (DVT) of the leg that affects 20–50% of patients. Once a patient experiences PTS there is no treatment that effectively reduces the debilitating complaints. Two randomised controlled trials showed that elastic compression stocking (ECS) therapy after DVT for 24 months can reduce the incidence of PTS by 50%. However, it is unclear whether all patients benefit to the same extent from ECS therapy or what the optimal duration of therapy for individual patients should be. ECS therapy is costly, inconvenient, demanding and sometimes even debilitating. Tailoring therapy to individual needs could save substantial costs. The objective of the IDEAL DVT study, therefore, is to evaluate whether tailoring the duration of ECS therapy on signs and symptoms of the individual patient is a safe and effective method to prevent PTS, compared with standard ECS therapy.Methods and analysisA multicentre, single-blinded, allocation concealed, randomised, non-inferiority trial. A total of 864 consecutive patients with acute objectively documented proximal DVT of the leg are randomised to either standard duration of 24 months or tailored duration of ECS therapy following an initial therapeutic period of 6 months. Signs and symptoms of PTS are recorded at regular clinic visits. Furthermore, quality of life, costs, patient preferences and compliance are measured. The primary outcome is the proportion of patients with PTS at 24 months.Ethics and disseminationBased on current knowledge the standard application of ECS therapy is questioned. The IDEAL DVT study will address the central questions that remain unanswered: Which individual patients benefit from ECS therapy and what is the optimal individual treatment duration? Primary ethics approval was received from the Maastricht University Medical Centre.ResultsResults of the study will be disseminated via peer-reviewed publications and presentations at scientific conferences.Trial registration numberNCT01429714 and NTR 2597.
Association between HTR2C gene variants and suicidal behaviour: a protocol for the systematic review and meta-analysis of genetic studies
Authors: Thelma Beatriz González-Castro , Isela Juárez-Rojop , Alma Genis , María Lilia López-Narváez , Carlos Alfonso Tovilla-Zárate 
Published: September 2014

IntroductionSuicide is an important public health problem and one of the most common causes of death throughout the world. Suicidal behaviour is complex, and its causes are multifactorial. Case–control studies have reported an association between an alteration of the serotonin system and suicidal behaviour. Recently, it has been suggested that the 5-HTRC2 serotonin receptor gene is involved in the pathogenesis of suicidal behaviour.Methods and analysisTo evaluate the role of the 5-HTR2C gene in suicidal behaviour, we will perform a systematic review and a meta-analysis of worldwide reports that have investigated the association between the serotonin system and suicidal behaviour. This analysis will be reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) criteria. Studies deemed fit for inclusion in the systematic review will be scored for methodological quality using the Newcastle-Ottawa Assessment Scale (NOS). The inclusion criteria will be to present independent data, to be case–control studies and to be published in journal peer reviews. To generate more accurate analyses, we will grade the reports using the GRADES scale procedures.Ethics and disseminationThis study will describe the association between the HTR2C gene and suicidal behaviour. The results will be reported in a peer-reviewed publication and in scientific presentations in Mexico and throughout the world.Trial registration numberPROSPERO CRD42014009213.
Illustrating the AADL error modeling annex (v.2) using a simple safety-critical medical device
Authors: Larson Brian , Hatcliff John , Fowler Kim , Delange Julien 
Published: September 2014

Developing and certifying safety-critical and highly reliable systems almost always includes significant emphasis on hazard analysis and risk assessment. There have been substantial improvements in automation and formalization of other aspects of critical system engineering including model-driven development, analysis of source code and models, and verification techniques. However, hazard analysis and risk assessment are still largely manual and informal activities, tool support is limited (which for both development and auditing, increases time and effort and reduces accuracy and correctness), and artifacts are not integrated with architectural descriptions, system interfaces, high-level behavioral descriptions or code.
The Error Model annex of the Architecture Analysis and Design Language (AADL) provides formal and automated support for a variety of forms of hazard analysis and risk assessment activities. Specifically, it enables engineers to formally specify errors, error propagation, error mitigation -- using annotations that are integrated with formal architecture and behavioral descriptions written in AADL. Plug-ins to the Open-Source AADL Tool Environment (OSATE) process these annotations to provide various forms of (semi)-automated support for reliability predication and tasks necessary to support common hazard analysis and risk assessment techniques such as Failure Modes and Effects Analysis (FMEA), Fault Tree Analysis (FTA), and Functional Hazard Analysis (FHA).
In this paper, we illustrate basic aspects of Error Modeling in AADL using a simple safety-critical medical system -- an infant incubator called "Isolette". We summarize standard tasks involved in FMEA and FTA, we illustrate the principal steps involved in AADL Error Modeling for the Isolette, and we describe how those steps relate to FMEA and FTA. We give a brief survey of emerging automated analysis tools implemented as plug-ins to the AADL OSATE environment that process error modeling annotations. We believe this introduction to Error Modeling in AADL can expose engineers of high-integrity systems to techniques and tools that can provide a more rigorous, automated, and integrated approach to important risk management activities.
SAW
Authors: Carter Kyle , Foltzer Adam , Hendrix Joe , Huffman Brian , Tomb Aaron 
Published: September 2014

Galois has developed a suite of symbolic simulation and formal analysis tools, collectively called the Software Analysis Workbench (SAW). SAW provides security analysts and engineers with the ability to generate formal models from C and Java programs and prove properties of those programs using several automated verification tools. SAW is primarily used to verify the correctness of cryptographic implementations, and is able to import specifications written in Cryptol, a language developed by Galois for specifying cryptographic primitives.
In this short paper, we describe the main components of SAW. We then given an overview of the cryptographic implementations that have been verified.
Engineering domain-specific languages with formula 2.0
Authors: Jackson Ethan K. 
Published: September 2014

Domain-specific languages (DSLs) are useful for capturing and reusing engineering expertise. They can formalize industrial patterns and practices while increasing the scalability of verification, because input programs are written at a higher level of abstraction. However, engineering new DSLs with custom verification is a non-trivial task in its own right, and usually requires programming language, formal methods, and automated theorem proving expertise.
In this tutorial we present FORMULA 2.0, which is formal framework for developing DSLs. FORMULA specifications are succinct descriptions of DSLs, and specifications can be immediately connected to state-of-the-art analysis engines without additional expertise. FORMULA provides: (1) succinct specifications of DSLs and compilers, (2) efficient compilation and execution of input programs, (3) program synthesis and compiler verification.
We take a unique approach to provide these features: Specifications are written as strongly-typed open-world logic programs. These specifications are highly declarative and easily express rich synthesis / verification problems. Automated reasoning is enabled by efficient symbolic execution of logic programs into quantifier-free sub-problems, which are dispatched to the state-of-the-art SMT solver Z3. FORMULA has been applied within Microsoft to develop DSLs for verifiable device drivers and protocols. It has been used by the automotive / embedded systems industries for software / hardware co-design and design-space exploration under hard resource allocation constraints. It is being used to develop semantic specifications for complex cyber-physical systems.
Up and out
Authors: Whalen Michael W. 
Published: September 2014

Systems are naturally constructed in hierarchies in which design choices made at higher levels of abstraction ``flow down'' to requirements on system components at lower levels of abstraction. Thus, whether an aspect of the system is a design choice or a requirement depends largely on one's vantage point within the hierarchy of system components. Furthermore, systems are often constructed middle-out rather than top-down; compatibility with existing systems and architectures, or availability of specific components influences high-level requirements. We believe that requirements and architectural design should be more closely aligned: that requirements models must account for hierarchical system construction, and that architectural design notations must better support specification of requirements for system components.
In this presentation, I describe tools supporting iterative development of architecture and verification based on software models. We represent the hierarchical composition of the system in the Architecture Analysis & Design Language (AADL), and use an extension to the AADL language to describe requirements at different levels of abstraction for compositional verification. To describe and verify component-level behavior, we use Simulink and Stateflow and multiple analysis tools.
Commutativity race detection
Authors: Dimitrov Dimitar , Raychev Veselin , Vechev Martin , Koskinen Eric 
Published: September 2014

This paper introduces the concept of a commutativity race. A commutativity race occurs in a given execution when two library method invocations can happen concurrently yet they do not commute. Commutativity races are an elegant concept enabling reasoning about concurrent interaction at the library interface.
We present a dynamic commutativity race detector. Our technique is based on a novel combination of vector clocks and a structural representation automatically obtained from a commutativity specification. Conceptually, our work can be seen as generalizing classical read-write race detection.
We also present a new logical fragment for specifying commutativity conditions. This fragment is expressive, yet guarantees a constant number of comparisons per method invocation rather than linear with unrestricted specifications.
We implemented our analyzer and evaluated it on real-world applications. Experimental results indicate that our analysis is practical: it discovered harmful commutativity races with overhead comparable to state-of-the-art, low-level race detectors.
A personal perspective on concurrency
Authors: Misra Jayadev 
Published: September 2014

This talk will describe a view of concurrency, the author's own, as it has evolved since the late 1970s. Early notions of concurrency were intimately tied with physical hardware and speeding up of computations, which proved to be an impediment to the development of a logical theory of concurrency. In collaboration with K. Mani Chandy, the author developed a theory called UNITY that combined a programming notation with a verification logic to describe a large class of fundamental concurrent algorithms arising in operating systems, communication protocols and distributed systems. Several model checkers, including Murphi, developed by David Dill, are based on UNITY.
A limitation of UNITY was a lack of adequate structuring mechanism. While this was not a major problem in low-level applications, the current wide-spread use of concurrency requires theories that go beyond managing infrastructure to the level of massive applications. Our current research, a programming model called Orc, introduces mechanisms to organize the communication, synchronization and coordination in programs that run on wide-area networks. Orc includes constructs to orchestrate the concurrent invocation of services to achieve a goal -- while managing time-outs, priorities, and failure of sites or communication.
Loss of Keratinocytic RXRα Combined with Activated CDK4 or Oncogenic NRAS Generates UVB-Induced Melanomas via Loss of p53 and PTEN in the Tumor Microenvironment
Authors: Coleman Daniel J. , Chagani Sharmeen , Hyter Stephen , Sherman Anna M. , Löhr Christiane V. , Liang Xiaobo , Ganguli-Indra Gitali , Indra Arup K. 
Published: September 2014

Abstract
Understanding the molecular mechanisms behind formation of melanoma, the deadliest form of skin cancer, is crucial for improved diagnosis and treatment. One key is to better understand the cross-talk between epidermal keratinocytes and pigment-producing melanocytes. Here, using a bigenic mouse model system combining mutant oncogenic NRASQ61K (constitutively active RAS) or mutant activated CDK4R24C/R24C (prevents binding of CDK4 by kinase inhibitor p16INK4A) with an epidermis-specific knockout of the nuclear retinoid X receptor alpha (RXRαep−/−) results in increased melanoma formation after chronic ultraviolet-B (UVB) irradiation compared with control mice with functional RXRα. Melanomas from both groups of bigenic RXRαep−/− mice are larger in size with higher proliferative capacity, and exhibit enhanced angiogenic properties and increased expression of malignant melanoma markers. Analysis of tumor adjacent normal skin from these mice revealed altered expression of several biomarkers indicative of enhanced melanoma susceptibility, including reduced expression of tumor suppressor p53 and loss of PTEN, with concomitant increase in activated AKT. Loss of epidermal RXRα in combination with UVB significantly enhances invasion of melanocytic cells to draining lymph nodes in bigenic mice expressing oncogenic NRASQ61K compared with controls with functional RXRα. These results suggest a crucial role of keratinocytic RXRα to suppress formation of UVB-induced melanomas and their progression to malignant cancers in the context of driver mutations such as activated CDK4R24C/R24C or oncogenic NRASQ61K.
Implications: These findings suggest that RXRα may serve as a clinical diagnostic marker and therapeutic target in melanoma progression and metastasis. Mol Cancer Res; 13(1); 186–96. ©2014 AACR.
RSK Promotes Prostate Cancer Progression in Bone through ING3, CKAP2, and PTK6-Mediated Cell Survival
Authors: Yu Guoyu , Lee Yu-Chen , Cheng Chien-Jui , Wu Chuan-Fen , Song Jian H. , Gallick Gary E. , Yu-Lee Li-Yuan , Kuang Jian , Lin Sue-Hwa 
Published: September 2014

AbstractProstate cancer has a proclivity to metastasize to bone. The mechanism by which prostate cancer cells are able to survive and progress in the bone microenvironment is not clear. Identification of molecules that play critical roles in the progression of prostate cancer in bone will provide essential targets for therapy. Ribosomal S6 protein kinases (RSK) have been shown to mediate many cellular functions critical for cancer progression. Whether RSK plays a role in the progression of prostate cancer in bone is unknown. IHC analysis of human prostate cancer specimens showed increased phosphorylation of RSK in the nucleus of prostate cancer cells in a significant fraction of human prostate cancer bone metastasis specimens, compared with the primary site or lymph node metastasis. Expression of constitutively active myristylated RSK in C4-2B4 cells (C4-2B4/RSK) increased their survival and anchorage-independent growth compared with C4-2B4/vector cells. Using an orthotopic bone injection model, it was determined that injecting C4-2B4/RSK cells into mouse femurs enhanced their progression in bone compared with control cells. In PC3-mm2 cells, knockdown of RSK1 (RPS6KA1), the predominant RSK isoform, but not RSK2 (RPS6KA2) alone, decreased anchorage-independent growth in vitro and reduced tumor progression in bone and tumor-induced bone remodeling in vivo. Mechanistic studies showed that RSK regulates anchorage-independent growth through transcriptional regulation of factors that modulate cell survival, including ING3, CKAP2, and PTK6. Together, these data provide strong evidence that RSK is an important driver in prostate cancer progression in bone.Implications: RSK, an important driver in prostate cancer progression in bone, has promising potential as a therapeutic target for prostate cancer bone metastasis. Mol Cancer Res; 13(2); 348–57. ©2014 AACR.