bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not
Authors: Hedge Jessica , Wilson Daniel J. 
Published: November 2014

ABSTRACT
Phylogenetic inference in bacterial genomics is fundamental to understanding problems such as population history, antimicrobial resistance, and transmission dynamics. The field has been plagued by an apparent state of contradiction since the distorting effects of recombination on phylogeny were discovered more than a decade ago. Researchers persist with detailed phylogenetic analyses while simultaneously acknowledging that recombination seriously misleads inference of population dynamics and selection. Here we resolve this paradox by showing that phylogenetic tree topologies based on whole genomes robustly reconstruct the clonal frame topology but that branch lengths are badly skewed. Surprisingly, removing recombining sites can exacerbate branch length distortion caused by recombination.

IMPORTANCE
Phylogenetic tree reconstruction is a popular approach for understanding the relatedness of bacteria in a population from differences in their genome sequences. However, bacteria frequently exchange regions of their genomes by a process called homologous recombination, which violates a fundamental assumption of phylogenetic methods. Since many researchers continue to use phylogenetics for recombining bacteria, it is important to understand how recombination affects the conclusions drawn from these analyses. We find that whole-genome sequences afford great accuracy in reconstructing evolutionary relationships despite concerns surrounding the presence of recombination, but the branch lengths of the phylogenetic tree are indeed badly distorted. Surprisingly, methods to reduce the impact of recombination on branch lengths can exacerbate the problem.
Sports Injury and Illness Epidemiology: Great Britain Olympic Team (TeamGB) surveillance during the Sochi 2014 Winter Olympic Games
Authors: Palmer-Green Debbie , Elliott Niall 
Published: November 2014

BackgroundSports injury and illness surveillance is the first step in injury and illness prevention, and is important for the protection of both athlete health and performance in major competitions.AimTo identify the prevalence, severity nature and causes of athlete injuries and illnesses in the Great Britain Olympic Team (TeamGB) during the Sochi 2014 Winter Olympic Games.MethodsThe observational prospective cohort study followed the Great Britain Injury/Illness Performance Project surveillance methodology and obtained information on injuries and illnesses that occurred during the Games between 30 January and 23 February 2014 in TeamGB athletes (n=56).ResultsAmong the 56 TeamGB athletes, there were 27 injuries and 11 illnesses during the Olympic Games period. This equated to 39% sustaining at least one injury and 18% at least one illness, with an incidence of 48.2 injuries and 19.6 illnesses per 100 athletes, respectively. Of all injuries and illnesses, 9% and 7%, respectively, resulted in time loss. The risk of sustaining an injury was highest for freestyle skiing, skeleton and snowboarding; and lowest for curling, biathlon and Alpine skiing (with no reported injuries); with the lower limb being the most commonly injured location. Respiratory system illnesses were most frequently reported overall, and older female athletes were the ones most affected by illness.ConclusionsThe risk of injury was double the risk of illness for TeamGB athletes. Overall, the rate of time-loss issues was low. Methodological considerations are important when interpreting data, and prevention strategies should focus on those issues causing the greatest risk, in terms of prevalence and severity, to athlete health and performance.
Molecular Pathways: Targeting the Dependence of Mutant RAS Cancers on the DNA Damage Response
Authors: Grabocka Elda , Commisso Cosimo , Bar-Sagi Dafna 
Published: November 2014

Abstract
Of the genes mutated in cancer, RAS remains the most elusive to target. Recent technological advances and discoveries have greatly expanded our knowledge of the biology of oncogenic Ras and its role in cancer. As such, it has become apparent that a property that intimately accompanies RAS-driven tumorigenesis is the dependence of RAS-mutant cells on a number of nononcogenic signaling pathways. These dependencies arise as a means of adaptation to Ras-driven intracellular stresses and represent unique vulnerabilities of mutant RAS cancers. A number of studies have highlighted the dependence of mutant RAS cancers on the DNA damage response and identified the molecular pathways that mediate this process, including signaling from wild-type Ras isoforms, ATR/Chk1, and DNA damage repair pathways. Here, we review these findings, and we discuss the combinatorial use of DNA-damaging chemotherapy with blockade of wild-type H- and N-Ras signaling by farnesyltransferase inhibitors, Chk1 inhibitors, or small-molecule targeting DNA damage repair as potential strategies through which the dependence of RAS cancers on the DNA damage response can be harnessed for therapeutic intervention. Clin Cancer Res; 21(6); 1243–7. ©2014 AACR.
Study on Related Courses to Help Undergraduate Students Write Research Reports: A Curriculum Evaluation
Authors: Winarti Eny 
Published: November 2014

From the experience of joining the boards in the studentsâ€™ research report defence, teaching education research methodology, and classroom action research, the researcher indicated that students had challenges related with the logic of research methods and academic research writing.Â These findings encouraged the researcher to study the courses that have potential in helping students writing their research reports.Â To study the courses, the researcher analysed related documents, such as syllabi and lesson plans.Â The researcher also interviewed teachers and students to clarify the relevance of the syllabi and the classroom learning.Â The results of the study indicated that logic, academic writing, statistics, research methodology, and classroom action research had the potential of helping the students write their research report.Â The researcher also indicated that the content of the courses should have been more helpful.Â The fact, however, was that the students still had challenges understanding the materials after taking the courses.Â Further study about this fact is then recommended.
Pedagogical competence-based Training Needs Analysis for Natural Science Teachers
Authors: Febrianis Irma , Muljono Pudji , Susanto Djoko 
Published: November 2014

This study offers an effective approach in determining the needs of training of the teachers using the Training Needs Analysis (TNA). The objectives of the study were to obtain evidence an actual pedagogic competence of the natural sciences teachers, to obtain needs and training priorities, and proposing recommendations on the effectiveness of training method. Surveys, interviews, and FGD were conducted to get primary data. Survey was carried on 165 natural science teachers of SMP Negeri Pekanbaru using self-evaluation questionnaire. Results showed that actual pedagogic competence of the teachers was below the ideal competence. There were five priorities of training program, namely : training of ICT, classroom action research, theory and principles of learning on integrated natural science, curriculum development, and understanding of pupilsâ€™ characteristics. It is suggested that In House Training, specific training, and short courses are worth applied as effective training methods to improve pedagocical competence of the teachers.Â Â
Readiness of Makassar Public High School Counsellors in Coping Organizational Change
Authors: Dasmawati Andi , Boon Yusof 
Published: November 2014

This study aims to determine the readiness of State High School counsellors in the city of Makassar who are confronted with organizational change. The assessment is viewed from the aspect of preparedness of counsellors that includes self-esteem, optimism and perceived control. A mixed method was used in this study that was simultaneously embedded. Survey questionnaires were distributed to 68 counsellors of State High Schools in Makassar for purposes of quantitative analysis, while an interview was conducted to five counsellor-coordinators for purposes of qualitative analysis.Â Both descriptive and inferential statistics were employed to best analyze the quantitative data, while the qualitative data was analyzed manually. The study revealed that the level of readiness of the 68 counsellorsâ€™ performance was low in coping with organizational change. This implies that there is a need for the counsellors to improve their performance in the future. Through the qualitative analysis, it was found out that the counsellors have numerous difficulties in their ability to cope with organizational change, while the result of good performance was noted in the quantitative analysis that was conducted.
Compare Unidimensional & Multidimensional Rasch Model for Test with Multidimensional Construct and Items Local Dependence
Authors: Hasmy Ali 
Published: November 2014

Test in education, generally, constructed based on multi contents. If every contents viewed as a dimension, hence the test also have multi-dimension too, so that the analysis must be done with the multidimensional model. In reality at some selected tests, we can see that dependence exist between items in different contents. Dependence as referred, make assumption about multidimensional test is not valid anymore so that gives us the opportunity to apply unidimensional models in its analysis, including by using Rasch Model. This matter motivated me to do write this paper with aim to: get Unidimensional Rasch Model based on logistics function, get the item parameter estimation and testee parameter estimation together using the Joint Maximum Likelihood Method, and prove that Unidimensional Rasch Model is the better choice than Multidimensional Rasch Model in condition like this.
Pre-Service Teachers’ Internet Usage a Function of Demographic Factors: The Case of a Nigerian College of Education
Authors: Onwuagboke Bede Blaise Chukwunyere , Singh Termit Kaur Ranjit , Fook Fong Soon 
Published: November 2014

With the overreaching acceptance of ICT in education and access to Internet occasioned by advancement in technology, this paper investigates pre-service teachers’ use of Internet in a college of education. The study was a descriptive survey. Data was collected using a researcher designed instrument tagged “Student Internet Use Scale” (SIUS). The population comprised of all NCE pre-service teachers in Alvan Ikoku Federal College of Education Owerri Nigeria. Findings show that mobile phones remains the most widely used mode of internet access with social networking, searching for information on school assignments, chatting forming the major reasons why they surf the net. Social networking is the major purpose for Internet use by female pre-service teachers while school related activities are of priority to males. The difference in purpose of internet use according to gender is however not statistically significant; similarly, there is no statically significant difference between male and female pre-service teachers in the frequency of Internet usage. The result has far reaching implication for provision and use of Internet facilities to enhance teaching and learning in the College and colleges of education in Nigeria.
Angiogenic Microvascular Endothelial Cells Release Microparticles Rich in Tissue Factor That Promotes Postischemic Collateral Vessel Formation
Authors: Arderiu Gemma , Peña Esther , Badimon Lina 
Published: November 2014

Objective—
Therapeutic angiogenesis is a promising strategy for treating ischemia. Our previous work showed that endogenous endothelial tissue factor (TF) expression induces intracrine signaling and switches-on angiogenesis in microvascular endothelial cells (mECs). We have hypothesized that activated mECs could exert a further paracrine regulation through the release of TF-rich microvascular endothelial microparticles (mEMPs) and induce neovascularization of ischemic tissues.

Approach and Results—
Here, we describe for the first time that activated mECs are able to induce reparative neovascularization in ischemic zones by releasing TF-rich microparticles. We show in vitro and in vivo that mEMPs released by both wild-type and TF-upregulated-mECs induce angiogenesis and collateral vessel formation, whereas TF-poor mEMPs derived from TF-silenced mECs are not able to trigger angiogenesis. Isolated TF-bearing mEMPs delivered to nonperfused adductor muscles in a murine hindlimb ischemia model enhance collateral flow and capillary formation evidenced by MRI. TF-bearing mEMPs increase angiogenesis operating via paracrine regulation of neighboring endothelial cells, signaling through the β1-integrin pathway Rac1–ERK1/2–ETS1 and triggering CCL2 (chemokine [C-C motif] ligand 2) production to form new and competent mature neovessels.

Conclusions—
These findings demonstrate that TF-rich mEMPs released by microvascular endothelial cells can overcome the consequences of arterial occlusion and tissue ischemia by promoting postischemic neovascularization and tissue reperfusion.
Who is the ‘Son of God’ in 4Q246? An Overlooked Example of Early Biblical Interpretation
Authors: Segal Michael 
Published: November 2014

The Aramaic Apocalypse of Daniel (4Q246) has been the subject of intense debate among scholars, primarily surrounding the enigmatic epithets ברה די אל “son of God” and בר עליון “son of the Most High.” Previous interpreters have suggested either that this character is a human sovereign with divine pretensions or that he is a divine messianic figure. The current study posits a new identification of this figure based upon the analysis of the biblical texts underlying this Qumran scroll: in addition to its dependence upon Dan 7 (which has been previously recognized), 4Q246 also contains a hitherto overlooked allusion to Ps 82. In light of the relationship to these biblical passages, it is proposed that the character described as “son of God/the Most High” should be taken as the heavenly representative of the penultimate kingdom in Dan 7.
The identification of the allusion to Ps 82 within 4Q246 also enriches our analysis of Dan 7 itself, since the Qumran scroll demonstrates that early readers of the apocalyptic vision posited a literary-theological connection between Dan 7 and Ps 82. These texts together formed a cluster of related biblical passages that were read and interpreted in concert by ancient authors.
Divergences within the Lǎozǐ: A Study of Chapters 67-81
Authors: Perkins Franklin 
Published: November 2014

It is well known that the three bundles of bamboo strips found at Guōdiàn containing versions of materials appearing in the Lǎozǐ included no passages from the last fifteen chapters of the received text. This article examines closely those final ­fifteen chapters, arguing that they articulate a coherent philosophical position funda­mentally different from and even opposed to that of the Guōdiàn materials. The foundation of the last fifteen chapters is an anthropomorphic conception of heaven that supports the good, a view explicitly rejected in the rest of the Lǎozǐ. These last fifteen chapters support the use of punishments, show no awareness of skepticism about language or moralizing categories, and they have no concern with internal practices of self-cultivation. The article concludes with some reflections on the background of the last fifteen chapters and on the significance of this argument for interpreting the Lǎozǐ, particularly the split between so-called “religious” and “philosophical” readings. Il est bien connu que les trois faisceaux de fiches de bambou découverts à Guodian portant des recensions de matériaux figurant dans le Laozi ne contiennent aucun ­passage des quinze derniers chapitres du texte reçu. Cet article propose un examen soigneux de ces quinze derniers chapitres et affirme qu’ils énoncent une position philo­sophique cohérente, fondamentalement différente de celle des textes de Guodian, voire en opposition avec eux. Les quinze derniers chapitres se fondent sur une conception anthropomorphique d’un Ciel encourageant le bien. Or cette vue est explicitement rejetée par le reste du Laozi. Ils encouragent le recours aux châtiments, ne manifestent aucun scepticisme au regard du langage et des catégories morales, et se désintéressent des pratiques internes du perfectionnement de soi. L’article se conclut par quelques réflexions sur l’arrière-plan des quinze derniers chapitres et sur la portée des arguments de l’auteur pour l’interprétation du Laozi, notamment la coupure entre les lectures dites “religieuses” et “philosophiques”.
Lagrangian Investigation of the Precipitation Efficiency of Convective Clouds
Authors: Langhans Wolfgang , Yeo Kyongmin , Romps David M. 
Published: November 2014

Abstract
The precipitation efficiency of cumulus congestus clouds is investigated with a new Lagrangian particle framework for large-eddy simulations. The framework is designed to track particles representative of individual water molecules. A Monte Carlo approach facilitates the transition of particles between the different water classes (e.g., vapor, rain, or graupel). With this framework, it is possible to reconstruct the pathways of water as it moves from vapor at a particular altitude to rain at the surface. By tracking water molecules through both physical and microphysical space, the precipitation efficiency can be studied in detail as a function of height.
Large-eddy simulations of individual cumulus congestus clouds show that the clouds convert entrained vapor to surface precipitation with an efficiency of around 10%. About two-thirds of all vapor that enters the cloud does so by entrainment in the free troposphere, but free-tropospheric vapor accounts for only one-third to one-half of the surface rainfall, with the remaining surface rainfall originating as vapor entrained through the cloud base. The smaller efficiency with which that laterally entrained water is converted into surface precipitation results from the smaller efficiencies with which it condenses, forms precipitating hydrometeors, and reaches the surface.
Changes in Global Ocean Bottom Properties and Volume Transports in CMIP5 Models under Climate Change Scenarios
Authors: Heuzé Céline , Heywood Karen J. , Stevens David P. , Ridley Jeff K. 
Published: November 2014

AbstractChanges in bottom temperature, salinity, and density in the global ocean by 2100 for CMIP5 climate models are investigated for the climate change scenarios RCP4.5 and RCP8.5. The mean of 24 models shows a decrease in density in all deep basins, except the North Atlantic, which becomes denser. The individual model responses to climate change forcing are more complex: regarding temperature, the 24 models predict a warming of the bottom layer of the global ocean; in salinity, there is less agreement regarding the sign of the change, especially in the Southern Ocean. The magnitude and equatorward extent of these changes also vary strongly among models. The changes in properties can be linked with changes in the mean transport of key water masses. The Atlantic meridional overturning circulation weakens in most models and is directly linked to changes in bottom density in the North Atlantic. These changes are the result of the intrusion of modified Antarctic Bottom Water, made possible by the decrease in North Atlantic Deep Water formation. In the Indian, Pacific, and South Atlantic Oceans, changes in bottom density are congruent with the weakening in Antarctic Bottom Water transport through these basins. The authors argue that the greater the 1986–2005 meridional transports, the more changes have propagated equatorward by 2100. However, strong decreases in density over 100 yr of climate change cause a weakening of the transports. The speed at which these property changes reach the deep basins is critical for a correct assessment of the heat storage capacity of the oceans as well as for predictions of future sea level rise.
Interannual Variability of the Mixed Layer Winter Convection and Spice Injection in the Eastern Subtropical North Atlantic
Authors: Kolodziejczyk Nicolas , Reverdin Gilles , Lazar Alban 
Published: November 2014

AbstractThe Argo dataset is used to study the winter upper-ocean conditions in the northeastern subtropical (NEA) Atlantic during 2006–12. During late winter 2010, the mixed layer depth is abnormally shallow and a negative anomaly of density-compensated salinity, the so-called spiciness, is generated in the permanent pycnocline. This is primarily explained by unusual weak air–sea buoyancy flux during the late winter 2010, in contrast with the five other studied winters. Particularly deep mixed layers and strong spiciness anomalies are observed during late winter 2012. The 2010 winter conditions appear to be related to historically low North Atlantic Oscillation (NAO) and high tropical North Atlantic index (TNA). Interannual variability of the eastern subtropical mixed layer is further investigated using a simple 1D bulk model of mean temperature and salinity linear profiles, based on turbulent kinetic energy conservation in the upper-ocean layer, and forced only with seasonal air–sea buoyancy forcing corresponding to fall–winter 2006–12. It suggests that year-to-year variability of the winter convective mixing driven by atmospheric buoyancy flux is able to generate interannual variability of both late winter mixed layer depth and spiciness in a strongly compensated layer at the base of the mixed layer and in the permanent pycnocline.
Sensitivity of Idealized Hurricane Intensity and Structures under Varying Background Flows and Initial Vortex Intensities to Different Vertical Resolutions in HWRF
Authors: Zhang Da-Lin , Zhu Lin , Zhang Xuejin , Tallapragada Vijay 
Published: November 2014

Abstract
A series of 5-day numerical simulations of idealized hurricane vortices under the influence of different background flows is performed by varying vertical grid resolution (VGR) in different portions of the atmosphere with the operational version of the Hurricane Weather Research and Forecasting Model in order to study the sensitivity of hurricane intensity forecasts to different distributions of VGR. Increasing VGR from 21 to 43 levels produces stronger hurricanes, whereas increasing it further to 64 levels does not intensify the storms further, but intensity fluctuations are much reduced. Moreover, increasing the lower-level VGRs generates stronger storms, but the opposite is true for increased upper-level VGRs. On average, adding mean flow increases intensity fluctuations and variability (between the strongest and weakest hurricanes), whereas adding vertical wind shear (VWS) delays hurricane intensification and then causes more rapid growth in intensity variability. The stronger the VWS, the larger intensity variability and bifurcation rate occur at later stages. These intensity differences are found to be closely related to inner-core structural changes, and they are attributable to how much latent heat could be released in higher-VGR layers, followed by how much moisture content in nearby layers is converged. Hurricane intensity with higher VGRs is shown to be much less sensitive to varying background flows, and stronger hurricane vortices at the model initial time are less sensitive to the vertical distribution of VGR; the opposite is true for relatively uniform VGRs or weaker hurricane vortices. Results reveal that higher VGRs with a near-parabolic or Ω shape tend to produce smoother intensity variations and more typical inner-core structures.