bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards understanding wild boar Sus scrofa movement: a synthetic movement ecology approach
Authors: Morelle Kevin , Podgórski Tomasz , Prévot Céline , Keuling Oliver , Lehaire François , Lejeune Philippe 
Published: September 2014

Abstract
In recent decades, the wild boar Sus scrofa has simultaneously increased its population size and colonized new habitats, causing more ecological and socio‐economic concern than perhaps any other ungulate species. However, the drivers and mechanisms of the species' spatial ecology remain poorly understood. Thanks to a recently developed framework, the movement ecology of any organism can now be tackled within a consistent and unified theoretical approach.
Based on this framework, we reviewed the literature on wild boar movement ecology to assess current knowledge and to identify important gaps.
By using important navigational (e.g. olfactory sense) and cognitive (e.g. spatial memory, learning from conspecifics) abilities, wild boar have developed complex movement strategies to cope with external factors. However, there is a lack of detailed information on the role played by the internal state (motivation) and motion capacity in shaping the spatial ability of the species.
Specific aspects of the movement ecology of the wild boar, together with its high diet plasticity and its high prolificacy, are probably the most important causes of the rapid spread of wild boar worldwide.
We hope our review will inspire other scientists to apply their biological models to the movement ecology paradigms. Furthermore, we suggest that future researchers dealing with the movement ecology of any species should explicitly state the components and interactions of the framework investigated to facilitate further understanding and comparison among studies.
Genome scans and elusive candidate genes: detecting the variation that matters for speciation
Authors: Sætre Glenn‐Peter 
Published: September 2014

Next‐generation sequencing is providing us with vast amounts of genetic data, yet we are currently struggling in our attempts to make sense of them. In particular, it has proven difficult to link phenotypic divergence and speciation to genome level divergence. In the current issue of Molecular Ecology, Ruegg et al. () present new empirical results from two closely related bird taxa. They use a promising approach combining genome scan and candidate gene analysis. Their results suggest that we may have been looking in vain for candidate speciation genes by focusing only on genes found within genomic islands of divergence. This is because genes important in divergence and speciation may not be detected by genome scans and because features of the genomic architecture per se may have a large effect on the pattern of genome divergence.
Patristic Exegetical Theory and Practice in De Lubac and Congar
Authors: Wright William M. 
Published: September 2014

AbstractThis article examines the retrieval of patristic exegesis in two major figure in Catholic Ressourcement theology: Henri de Lubac and Yves Congar. Henri de Lubac's driving concern in his biblical writings is not so much to chronicle the history of interpretation as it is to explicate the great theological synthesis, which underlies the doctrine of the fourfold sense of Scripture. For de Lubac, this synthesis, wherein the totality of Christian doctrine and practice is centered in Christ and grounded in the reading of Scripture, is an essential component of Christianity. De Lubac encourages the integration of this theological vision with modern biblical studies, but he does not offer much as to what such an integration might look like in practice. Congar, building upon de Lubac's work, goes beyond de Lubac in making concrete efforts to integrate some of the theory and practice of patristic interpretation with modern exegesis. Important here is Congar's notion of “typological tradition” whereby the divine mystery concealed and revealed in the realities presented by the biblical text, unfold in the tradition, doctrine, and practice of the Church.
A hybrid approach for forecasting of oil prices volatility
Authors: Komijani Akbar , Naderi Esmaeil , Gandali Alikhani Nadiya 
Published: September 2014

AbstractThis study aims to introduce an ideal model for forecasting crude oil price volatility. For this purpose, the ‘predictability’ hypothesis was tested using the variance ratio test, BDS test and the chaos analysis. Structural analyses were also carried out to identify possible non‐linear patterns in this series. On this basis, Lyapunov exponents confirmed that the return series of crude oil price is chaotic. Moreover, according to the findings, the rate of return series has the long memory property rejecting the efficient market hypothesis and affirming the fractal markets hypothesis. The results of the Geweke and Porter‐Hudak test verified that both the rate of return and volatility series of crude oil price have the long memory property. Besides, according to both mean square error (MSE) and root mean square error (RMSE) criteria, wavelet‐decomposed data improve the performance of the model significantly. Therefore, a hybrid model was introduced based on the long memory property which uses wavelet decomposed data as the most relevant model.
Genetic variation and structure in the Mediterranean shrubs Myrtus communis and Pistacia lentiscus in different landscape contexts
Authors: Nora S. , Albaladejo R. G. , Aparicio A. 
Published: September 2014

AbstractStudies concerning different habitat configurations can provide insights into the complex interactions between species’ life‐history traits and the environment and can help to predict patterns in population genetics. In this study, we compared patterns of genetic variation in two Mediterranean shrub species (Myrtus communis and Pistacia lentiscus) that co‐occur in populations within three contrasting landscape contexts: continuous, fragmented‐connected and fragmented‐isolated populations. Analysing variation at microsatellites loci, our results revealed weak responses to the landscape contexts. We rather found a population‐specific response in both study species. However, despite both study species sharing similar levels of genetic diversity, Myrtus displayed higher levels of homozygosity and genetic differentiation among populations, stronger patterns of within‐population spatial genetic structure, lower values of mutation‐scaled effective population size and stronger evidence for recent genetic bottlenecks than Pistacia. This result highlights the influence of past events (e.g. historical connectivity, fluctuations in population size) and local factors (e.g. microhabitat availability for recruitment, habitat quality, plant density, native fauna) and that the landscape configuration per se (i.e. fragment size and/or isolation) might not completely determine the species’ genetic patterns.
Religions Policies During the Allied Occupation of Japan, 1945–1952
Authors: Thomas Jolyon 
Published: September 2014

AbstractReligion played a prominent role in the Allied Occupation of Japan (1945–1952) that followed the brutal Pacific War (1941–1945). Officially, the occupiers were to promulgate religious freedom, separate religion from the state, and encourage the Japanese people to develop a ‘desire for religious freedom’. Promulgating religious freedom was the easy part. Separating religion from the state without infringing on religious freedom was far more challenging, and the ambiguous objective of instilling a desire for religious freedom in the Japanese populace was nearly impossible to measure. This review article provides a brief overview of trends in Occupation research, traces historical changes and paradoxes in Occupation religions policy and examines the unexpected and frequently ironic outcomes of that policy. It provides a cursory look into the postwar efflorescence of ‘new religions’ and the politically fraught category of ‘State Shintō’. It closes with an overview of archives and records on the Occupation.Video abstract (click to view)https://www.youtube.com/watch?v=Oyzjk8AaCP8
A Convex Pseudolikelihood Framework for High Dimensional Partial Correlation Estimation with Convergence Guarantees
Authors: Khare Kshitij , Oh Sang-Yun , Rajaratnam Bala 
Published: September 2014

SummarySparse high dimensional graphical model selection is a topic of much interest in modern day statistics. A popular approach is to apply l 1-penalties to either parametric likelihoods, or regularized regression/pseudolikelihoods, with the latter having the distinct advantage that they do not explicitly assume Gaussianity. As none of the popular methods proposed for solving pseudolikelihood-based objective functions have provable convergence guarantees, it is not clear whether corresponding estimators exist or are even computable, or if they actually yield correct partial correlation graphs. We propose a new pseudolikelihood-based graphical model selection method that aims to overcome some of the shortcomings of current methods, but at the same time retain all their respective strengths. In particular, we introduce a novel framework that leads to a convex formulation of the partial covariance regression graph problem, resulting in an objective function comprised of quadratic forms. The objective is then optimized via a co-ordinatewise approach. The specific functional form of the objective function facilitates rigorous convergence analysis leading to convergence guarantees; an important property that cannot be established by using standard results, when the dimension is larger than the sample size, as is often the case in high dimensional applications. These convergence guarantees ensure that estimators are well defined under very general conditions and are always computable. In addition, the approach yields estimators that have good large sample properties and also respect symmetry. Furthermore, application to simulated and real data, timing comparisons and numerical convergence is demonstrated. We also present a novel unifying framework that places all graphical pseudolikelihood methods as special cases of a more general formulation, leading to important insights.
Germination ecology of Emex spinosa and Emex australis, invasive weeds of winter crops
Authors: Javaid M M , Tanveer A 
Published: September 2014

SummaryEmex spinosa and Emex australis are invasive dicotyledonous weeds. The effects of various environmental factors on the germination of these weeds were investigated under laboratory and glasshouse conditions. Germination response of both species was lower at warmer temperature, and maximum germination was recorded at 20/12°C (day/night). Light stimulated germination in both species, but considerable germination also occurred under darkness. More than 80% of E. spinosa seeds germinated at pH between 6 and 9, whereas E. australis seeds germination was considerably decreased at pH 9. Emex spinosa was fairly tolerant to salinity as compared with E. australis and germination (21%) of E. spinosa occurred even at 200 mm NaCl. Both species were sensitive to osmotic stress, but E. spinosa tolerated more osmotic stress than E. australis. Temperature above 20/12°C (day/night) and low osmotic potential increased time to start germination and mean germination time (MGT), as well as decreased germination index (GI) of both species. Darkness resulted in increased MGT and decreased GI in both species when compared with 10 h photoperiod. Salt stress strongly increased time to obtain 50% germination and reduced GI of both species. In both species, an increasing burial depth decreased emergence percentage and emergence index and increased time to start emergence, although some seed emerged even at 10 cm burial depth. It was concluded that both species can germinate over a wide range of environmental conditions. However, E. australis was more sensitive under adverse environmental conditions compared with E. spinosa. This information on germination ecology may aid in developing tools and strategies for management.
Misinterpretation of the mouse ECG: ‘musing the waves of Mus musculus’
Authors: Boukens Bastiaan J. , Rivaud Mathilde R. , Rentschler Stacey , Coronel Ruben 
Published: September 2014

AbstractThe ECG is a primary diagnostic tool in patients suffering from heart disease, underscoring the importance of understanding factors contributing to normal and abnormal electrical patterns. Over the past few decades, transgenic mouse models have been increasingly used to study pathophysiological mechanisms of human heart diseases. In order to allow extrapolation of insights gained from murine models to the human condition, knowledge of the similarities and differences between the mouse and human ECG is of crucial importance. In this review, we briefly discuss the physiological mechanisms underlying differences between the baseline ECG of humans and mice, and provide a framework for understanding how these inherent differences are relevant to the interpretation of the mouse ECG during pathology and to the translation of the results from the mouse to man.
Sci—Thur AM: YIS ‐ 01: Dosimetric Analysis of Respiratory Induced Cardiac Intrafraction Motion in Left‐sided Breast Cancer Radiotherapy
Authors: El‐Sherif O , Xhaferllari I , Patrick J , Yu E , Gaede S 
Published: September 2014

Introduction:Long‐term cardiac side effects in left‐sided breast cancer patients (BREL) after post‐operative radiotherapy has become one of the most debated issues in radiation oncology. Through breathing‐adapted radiotherapy the volume of the heart exposed to radiation can be significantly reduced by delivering the radiation only at the end of inspiration phase of the respiratory cycle, this is referred to as inspiration gating (IG).The purpose of this study is to quantify the potential reduction in cardiac exposure during IG compared to conventional BREL radiotherapy and to assess the dosimetric impact of cardiac motion due to natural breathing.Methods:24 BREL patients treated with tangential parallel opposed photon beams were included in this study. All patients received a standard fast helical planning CT (FH‐CT) and a 4D‐CT. Treatment plans were created on the FH‐CT using a clinical treatment planning system. The original treatment plan was then superimposed onto the end of inspiration CT and all 10 phases of the 4D‐CT to quantify the dosimetric impact of respiratory motion and IG through 4D dose accumulation.Results:Through IG the mean dose to the heart, left ventricle, and left anterior descending artery (LAD) can be reduced in comparison to the clinical standard BREL treatment by as much as 8.39%, 10.11%, and 13.71% respectively (p < 0.05).Conclusion:Failure to account for respiratory motion can lead to under or overestimation in the calculated DVH for the heart, and it's sub‐structures. IG can reduce cardiac exposure especially to the LAD during BREL radiotherapy.
Poster — Thur Eve — 32: Stereotactic Body Radiation Therapy for Peripheral Lung Lesion: Treatment Planning and Quality Assurance
Authors: Wan Shuying , Oliver Michael , Wang Xiaofang 
Published: September 2014

Stereotactic body radiation therapy (SBRT), due to its high precision for target localizing, has become widely used to treat tumours at various locations, including the lungs.Lung SBRT program was started at our institution a year ago. Eighteen patients with peripheral lesions up to 3 cm diameter have been treated with 48 Gy in 4 fractions.Based on four‐dimensional computed tomography (4DCT) simulation, internal target volume (ITV) was delineated to encompass the respiratory motion of the lesion. A margin of 5 mm was then added to create the planning target volume (PTV) for setup uncertainties. There was no expansion from gross tumour volume (GTV) to clinical target volume (CTV). Pinnacle 9.6 was used as the primary treatment planning system. Volumetric modulated arc therapy (VMAT) technique, with one or two coplanar arcs, generally worked well. For quality assurance (QA), each plan was exported to Eclipse 10 and dose calculation was repeated. Dose volume histograms (DVHs) of the targets and organs at risk (OARs) were then compared between the two treatment planning systems.Winston‐Lutz tests were carried out as routine machine QA. Patient‐specific QA included ArcCheck measurement with an insert, where an ionization chamber was placed at the centre to measure dose at the isocenter. For the first several patients, and subsequently for the plans with extremely strong modulation, Gafchromic film dosimetry was also employed.For each patient, a mock setup was scheduled prior to treatments. Daily pre‐ and post‐CBCT were acquired for setup and assessment of intra‐fractional motion, respectively.
Poster — Thur Eve — 06: Dose assessment of cone beam CT imaging protocols as part of SPECT/CT examinations
Authors: Tonkopi E , Ross AA 
Published: September 2014

Purpose:To assess radiation dose from the cone beam CT (CBCT) component of SPECT/CT studies and to compare with other CT examinations performed in our institution.Methods:We used an anthropomorphic chest phantom and the 6 cc ion chamber to measure entrance breast dose for several CBCT and diagnostic CT acquisition protocols. The CBCT effective dose was calculated with ImPACT software; the CT effective dose was evaluated from the DLP value and conversion factor, dependent on the anatomic region. The RADAR medical procedure radiation dose calculator was used to assess the nuclear medicine component of exam dose.Results:The entrance dose to the breast measured with the anthropomorphic phantom was 0.48 mGy and 9.41 mGy for cardiac and chest CBCT scans; and 4.59 mGy for diagnostic thoracic CT. The effective doses were 0.2 mSv, 3.2 mSv and 2.8 mSv respectively. For a small patient represented by the anthropomorphic phantom, the dose from the diagnostic CT was lower than from the CBCT scan, as a result of the exposure reduction options available on modern CT scanners. The CBCT protocols used the same fixed scanning techniques. The diagnostic CT dose based on the patient data was 35% higher than the phantom dose. For most SPECT/CT studies the dose from the CBCT component was comparable with the dose from the radiopharmaceutical.Conclusions:The patient radiation dose from the cone beam CT scan can be higher than that from a diagnostic CT and should be taken into consideration in evaluating total SPECT/CT patient dose.
Draft Genome Assembly of Klebsiella pneumoniae Type Strain ATCC 13883
Authors: Daligault H. E. , Davenport K. W. , Minogue T. D. , Bishop-Lilly K. A. , Bruce D. C. , Chain P. S. , Coyne S. R. , Frey K. G. , Jaissle J. , Koroleva G. I. , Ladner J. T. , Lo C.-C. , Meincke L. , Munk A. C. , Palacios G. F. , Redden C. L. , Johnson S. L. 
Published: September 2014

ABSTRACT

Klebsiella pneumoniae
is a common cause of antibiotic-resistant bacterial infections in immunocompromised individuals. Here, we present the 5.54-Mb scaffolded assembly of the type strain
K. pneumoniae
type strain ATCC 13883, as deposited in GenBank under accession no. JOOW00000000.
Draft Genome Sequence of “
Candidatus
Phytoplasma asteris” Strain OY-V, an Unculturable Plant-Pathogenic Bacterium
Authors: Kakizawa Shigeyuki , Makino Ayaka , Ishii Yoshiko , Tamaki Hideyuki , Kamagata Yoichi 
Published: September 2014

ABSTRACT

Phytoplasmas are unculturable plant-pathogenic bacteria causing devastating damage to agricultural production worldwide. Here, we report the draft genome sequence of “
Candidatus
Phytoplasma asteris” strain OY-V. Most of the known virulence factors and host-interacting proteins were conserved in OY-V. This genome furthers our understanding of genetic diversity and pathogenicity of phytoplasmas.
Draft Genome Sequence of the Flagellated Xanthomonas fuscans subsp.
fuscans
Strain CFBP 4884
Authors: Indiana A. , Briand M. , Arlat M. , Gagnevin L. , Koebnik R. , Noël L. D. , Portier P. , Darrasse A. , Jacques M. A. 
Published: September 2014

ABSTRACT

We report the draft genome sequence of the flagellated strain CFBP 4884 of
Xanthomonas fuscans
subsp.
fuscans
, which was isolated in an outbreak of common bacterial blight of beans along with non-flagellated strains. Comparative genomics will allow one to decipher the genomic diversity of strains cohabiting in epidemics.
Genome Assembly of Serratia marcescens Type Strain ATCC 13880
Authors: Daligault H. E. , Davenport K. W. , Minogue T. D. , Broomall S. M. , Bruce D. C. , Chain P. S. , Coyne S. R. , Gibbons H. S. , Jaissle J. , Rosenzweig C. N. , Scholz M. , Teshima H. , Johnson S. L. 
Published: September 2014

ABSTRACT

Serratia marcescens
ATCC 13880 is the type strain of the species and a commonly used quality control strain. Here, we present the annotated genome assembly of 5.13 Mbp (59.8% G+C content) as submitted to NCBI under accession no. JOVM00000000.
Complete Genome Assembly of Enterococcus faecalis 29212, a Laboratory Reference Strain
Authors: Minogue T. D. , Daligault H. E. , Davenport K. W. , Broomall S. M. , Bruce D. C. , Chain P. S. , Coyne S. R. , Chertkov O. , Freitas T. , Gibbons H. S. , Jaissle J. , Koroleva G. I. , Ladner J. T. , Palacios G. F. , Rosenzweig C. N. , Xu Y. , Johnson S. L. 
Published: September 2014

ABSTRACT

Enterococcus faecalis
is a nonmotile Gram-positive coccus, found both as a commensal organism in healthy humans and animals and as a causative agent of multiple diseases, in particular endocarditis. We sequenced the genome of
E. faecalis
ATCC 29212, a commonly used reference strain in laboratory studies, to complete “finished” annotated assembly (3 Mb).
Complete Genome Assembly of Escherichia coli ATCC 25922, a Serotype O6 Reference Strain
Authors: Minogue T. D. , Daligault H. A. , Davenport K. W. , Bishop-Lilly K. A. , Broomall S. M. , Bruce D. C. , Chain P. S. , Chertkov O. , Coyne S. R. , Freitas T. , Frey K. G. , Gibbons H. S. , Jaissle J. , Redden C. L. , Rosenzweig C. N. , Xu Y. , Johnson S. L. 
Published: September 2014

ABSTRACT

We present the complete genome assembly of
Escherichia coli
ATCC 25922 as submitted to NCBI under accession no. CP009072. This strain was originally isolated from a clinical sample in Seattle, Washington (1946), and is often used in quality control testing. The assembled genome is 5.20 Mb (50.4% G+C content) and includes two plasmids.
Whole-Genome Sequence of Listeria monocytogenes Type Strain 53 XXIII
Authors: Davenport K. W. , Daligault H. E. , Minogue T. D. , Bishop-Lilly K. A. , Bruce D. C. , Chain P. S. , Coyne S. R. , Frey K. G. , Jaissle J. , Koroleva G. I. , Ladner J. T. , Li P.-E. , Palacios G. F. , Redden C. L. , Scholz M. B. , Teshima H. , Johnson S. L. 
Published: September 2014

ABSTRACT

Listeria monocytogenes
causes the food-borne illness listeriosis that primarily infects “vulnerable” groups (e.g., elderly adults, pregnant women, very young children, and the immunocompromised). We sequenced the genome of
L. monocytogenes
XXIII (ATCC 15313) and assembled it into a single scaffold (three contigs) and deposited the annotated assembly into GenBank as accession no. JOOX00000000.