bluuebunny/crossref_metadata_2025_split huggingface dataset:
Femtosecond phase-transition in hard x-ray excited bismuth
Authors: Makita M. , Vartiainen I. , Mohacsi I. , Caleman C. , Diaz A. , Jönsson H. O. , Juranić P. , Medvedev N. , Meents A. , Mozzanica A. , Opara N. L. , Padeste C. , Panneels V. , Saxena V. , Sikorski M. , Song S. , Vera L. , Willmott P. R. , Beaud P. , Milne C. J. , Ziaja-Motyka B. , David C. 
Published: January 2019

AbstractThe evolution of bismuth crystal structure upon excitation of its A1g phonon has been intensely studied with short pulse optical lasers. Here we present the first-time observation of a hard x-ray induced ultrafast phase transition in a bismuth single crystal at high intensities (~1014 W/cm2). The lattice evolution was followed using a recently demonstrated x-ray single-shot probing setup. The time evolution of the (111) Bragg peak intensity showed strong dependence on the excitation fluence. After exposure to a sufficiently intense x-ray pulse, the peak intensity dropped to zero within 300 fs, i.e. faster than one oscillation period of the A1g mode at room temperature. Our analysis indicates a nonthermal origin of a lattice disordering process, and excludes interpretations based on electron-ion equilibration process, or on thermodynamic heating process leading to plasma formation.
Metal artifacts with dental implants: Evaluation using a dedicated CT/MR oral phantom with registration of the CT and MR images
Authors: Lee Min-Young , Song Kyu-Ho , Lee Jeong-Woo , Choe Bo-Young , Suh Tae Suk 
Published: January 2019

AbstractThe aims of this study were to develop a computed tomography/magnetic resonance (CT/MR) oral phantom with insertable dental implants and to register CT/MR images to generate artifact-free MR images for patients undergoing teeth restorations. All measurements were done using a human MR scanner with spin echo (SE) and gradient echo (GRE) sequences image scan together with CT image. The metal regions and normal teeth parts are extracted with a suitable threshold from an initial image reconstructed with artifact from the CT images. Corrected metal projection regions of MR images and CT images are fused to produce artifact-free MR image that include dental restorations. After CT/MR registration, artifact size presented differences on the x- (SE, 12.0 mm; GRE, 18.0 mm) and y- (SE, 24.0 mm; GRE, 36.6 mm). When comparing the dental restoration with normal teeth, the structural similarity index metric (SSIM) of GRE 50 was lower than for the GRE 8 sequence and the SSIM of SE 145 shown higher than for the SE 490 sequence. The dedicated phantom provides a useful tool in head and neck research for multi-modality images. Therefore, CT/MR image-based approach for ground truth and registration offers visualization in diagnostic system and radiation treatment planning system.
Positively interacting strains that co-circulate within a network structured population induce cycling epidemics of Mycoplasma pneumoniae
Authors: Zhang Xu-Sheng , Zhao Hongxin , Vynnycky Emilia , Chalker Vicki 
Published: January 2019

AbstractMycoplasma pneumoniae(MP) is considered a common cause of pneumonia, causing about 15–20% of adult community-acquired pneumonia (CAP) and up to 40% of cases in children. It has often been observed that MP epidemics last approximately 1–2 years and occur every 3–7 years, with the dominant strains alternating between epidemics. However, the underlying mechanism by which these cycles and changes in the dominant strains occur remains unclear. The traditional models for the periodicity of MP epidemics neglected two phenomena: structured contact patterns among people and co-circulating strains of MP. We also believe that the two distinctive aspects of MP epidemics: prevalent serotype shifts among epidemics and incidence cycling of MP, are interconnected. We propose a network transmission model that assumes two strains of MP are transmitted within a network structured population and they can interact as secondary infections with primary infections. Our studies show that multiple strains that co-circulate within a network structured population and interact positively generate the observed patterns of recurrent epidemics of MP. Hence our study provides a possible mechanism for the cycling epidemics of MP, and could provide useful information for future vaccine design and vaccine evaluation/monitoring processes.
Collaborative efforts to forecast seasonal influenza in the United States, 2015–2016
Authors: McGowan Craig J. , Biggerstaff Matthew , Johansson Michael , Apfeldorf Karyn M. , Ben-Nun Michal , Brooks Logan , Convertino Matteo , Erraguntla Madhav , Farrow David C. , Freeze John , Ghosh Saurav , Hyun Sangwon , Kandula Sasikiran , Lega Joceline , Liu Yang , Michaud Nicholas , Morita Haruka , Niemi Jarad , Ramakrishnan Naren , Ray Evan L. , Reich Nicholas G. , Riley Pete , Shaman Jeffrey , Tibshirani Ryan , Vespignani Alessandro , Zhang Qian , Reed Carrie ,   The Influenza Forecasting Working Group, Rosenfeld Roni , Ulloa Nehemias , Will Katie , Turtle James , Bacon David , Riley Steven , Yang Wan 
Published: January 2019

AbstractSince 2013, the Centers for Disease Control and Prevention (CDC) has hosted an annual influenza season forecasting challenge. The 2015–2016 challenge consisted of weekly probabilistic forecasts of multiple targets, including fourteen models submitted by eleven teams. Forecast skill was evaluated using a modified logarithmic score. We averaged submitted forecasts into a mean ensemble model and compared them against predictions based on historical trends. Forecast skill was highest for seasonal peak intensity and short-term forecasts, while forecast skill for timing of season onset and peak week was generally low. Higher forecast skill was associated with team participation in previous influenza forecasting challenges and utilization of ensemble forecasting techniques. The mean ensemble consistently performed well and outperformed historical trend predictions. CDC and contributing teams will continue to advance influenza forecasting and work to improve the accuracy and reliability of forecasts to facilitate increased incorporation into public health response efforts.
TaCAMTA4, a Calmodulin-Interacting Protein, Involved in Defense Response of Wheat to Puccinia triticina
Authors: Wang Yuelin , Wei Fengju , Zhou Hui , Liu Na , Niu Xiaonan , Yan Chao , Zhang Lifeng , Han Shengfang , Hou Chunyan , Wang Dongmei 
Published: January 2019

AbstractLeaf rust caused by Puccinia triticina is one of the main diseases affecting wheat (Triticum aestivum) production worldwide. Calmodulin (CaM) was found involved in the early stage of signal transduction pathway in response to P. triticina in wheat. To study the function and molecular mechanism of calmodulin (CaM) in signal transduction of wheat against P. triticina, we cloned a putative calmodulin-binding transcription activator (TaCAMTA4), and characterized its molecular structure and functions by using the CaM-encoding gene (TaCaM4-1) as a bait to screen the cDNA library from P. triticina infected wheat leaves. The open reading frame of TaCAMTA4 was 2505 bp encoding a protein of 834 aa, which contained all the four conserved domains of family (CG-1 domain, TIG domain, ANK repeats and CaM-binding domain). TaCaM4-1 bound to TaCAMTA4 by the C-terminal CaM-binding domain in Ca2+-dependent manner in the electrophoretic mobility shift assay (EMSA). Bimolecular fluorescence complementation (BiFC) analysis indicated that the interaction of TaCAMTA4 and TaCaM4-1 took place in the cytoplasm and nucleus of epidermal leaf cells in N. benthamiana. The expression level of TaCAMTA4 genes was down-regulated in incompatible combination after P. triticina infection. Furthermore, virus-induced gene silencing (VIGS)-based knockdown of TaCAMTA4 and disease assays verified that silencing of TaCAMTA4 resulted in enhanced resistance to P. triticina race 165. These results suggested that TaCAMTA4 function as negative regulator of defense response against P. triticina.
Design factors for determining the radula shape of Euhadra Peliomphala
Authors: Miura Satoshi , Saito Rikako , Parque Victor , Miyashita Tomoyuki 
Published: January 2019

AbstractBiomimetics present useful ideas for various product designs. However, most biomimetics only mimic the features of living organisms. It has not been clarified how a given shape is attained through natural selection. This paper presents the design factors that optimize the radula shape of Euhadra peliomphala. Clarifying the important design factors would help designers in solving several problems simultaneously in order to adapt to complicated and multi-functionalized design mechanisms. We measured the radula of Euhadra peliomphala by using a microscope and modeled the grinding/cutting force using the finite element analysis (FEA). We reproduced the natural selection using multi-objective genetic algorithm (MOGA). We compared the solutions when optimizing the radula shape using objective functions of each combination of stress, cutting force, abrasion, or volume. The results show that the solution obtained through two-objective optimization with stress and cutting force was the closest to the actual radula shape.
Molecular ontogeny of the stomach in the catshark Scyliorhinus canicula
Authors: Gonçalves Odete , Freitas Renata , Ferreira Patrícia , Araújo Mafalda , Zhang GuangJun , Mazan Sylvie , Cohn Martin J. , Castro L. Filipe C. , Wilson Jonathan M. 
Published: January 2019

AbstractThe origin of extracellular digestion in metazoans was accompanied by structural and physiological alterations of the gut. These adaptations culminated in the differentiation of a novel digestive structure in jawed vertebrates, the stomach. Specific endoderm/mesenchyme signalling is required for stomach differentiation, involving the growth and transcription factors: 1) Shh and Bmp4, required for stomach outgrowth; 2) Barx1, Sfrps and Sox2, required for gastric epithelium development and 3) Cdx1 and Cdx2, involved in intestinal versus gastric identity. Thus, modulation of endoderm/mesenchyme signalling emerges as a plausible mechanism linked to the origin of the stomach. In order to gain insight into the ancient mechanisms capable of generating this structure in jawed vertebrates, we characterised the development of the gut in the catshark Scyliorhinus canicula. As chondrichthyans, these animals retained plesiomorphic features of jawed vertebrates, including a well-differentiated stomach. We identified a clear molecular regionalization of their embryonic gut, characterised by the expression of barx1 and sox2 in the prospective stomach region and expression of cdx1 and cdx2 in the prospective intestine. Furthermore, we show that gastric gland development occurs close to hatching, accompanied by the onset of gastric proton pump activity. Our findings favour a scenario in which the developmental mechanisms involved in the origin of the stomach were present in the common ancestor of chondrichthyans and osteichthyans.
An inverse free electron laser acceleration-driven Compton scattering X-ray source
Authors: Gadjev I. , Sudar N. , Babzien M. , Duris J. , Hoang P. , Fedurin M. , Kusche K. , Malone R. , Musumeci P. , Palmer M. , Pogorelsky I. , Polyanskiy M. , Sakai Y. , Swinson C. , Williams O. , Rosenzweig J. B. 
Published: January 2019

AbstractThe generation of X-rays and γ-rays based on synchrotron radiation from free electrons, emitted in magnet arrays such as undulators, forms the basis of much of modern X-ray science. This approach has the drawback of requiring very high energy, up to the multi-GeV-scale, electron beams, to obtain the required photon energy. Due to the limit in accelerating gradients in conventional particle accelerators, reaching high energy typically demands use of instruments exceeding 100’s of meters in length. Compact, less costly, monochromatic X-ray sources based on very high field acceleration and very short period undulators, however, may enable diverse, paradigm-changing X-ray applications ranging from novel X-ray therapy techniques to active interrogation of sensitive materials, by making them accessible in energy reach, cost and size. Such compactness and enhanced energy reach may be obtained by an all-optical approach, which employs a laser-driven high gradient accelerator based on inverse free electron laser (IFEL), followed by a collision point for inverse Compton scattering (ICS), a scheme where a laser is used to provide undulator fields. We present an experimental proof-of-principle of this approach, where a TW-class CO2 laser pulse is split in two, with half used to accelerate a high quality electron beam up to 84 MeV through the IFEL interaction, and the other half acts as an electromagnetic undulator to generate up to 13 keV X-rays via ICS. These results demonstrate the feasibility of this scheme, which can be joined with other techniques such as laser recirculation to yield very compact photon sources, with both high peak and average brilliance, and with energies extending from the keV to MeV scale. Further, use of the IFEL acceleration with the ICS interaction produces a train of high intensity X-ray pulses, thus enabling a unique tool synchronized with a laser pulse for ultra-fast strobe, pump-probe experimental scenarios.
Bacteriophage biodistribution and infectivity from honeybee to bee larvae using a T7 phage model
Authors: Ribeiro Henrique G. , Correia Rossana , Moreira Tiago , Vilas Boas Diana , Azeredo Joana , Oliveira Ana 
Published: January 2019

AbstractBacteriophages (phages) or viruses that specifically infect bacteria have widely been studied as biocontrol agents against animal and plant bacterial diseases. They offer many advantages compared to antibiotics. The American Foulbrood (AFB) is a bacterial disease affecting honeybee larvae caused byPaenibacillus larvae. Phages can be very significant in fighting it mostly due to European restrictions to the use of antibiotics in beekeeping. New phages able to controlP. larvaein hives have already been reported with satisfactory results. However, the efficacy and feasibility of administering phages indirectly to larvae through their adult workers only by providing phages in bees’ feeders has never been evaluated. This strategy is considered herein the most feasible as far as hive management is concerned. Thisin vivostudy investigated the ability of a phage to reach larvae in an infective state after oral administration to honeybees. The screening (by direct PFU count) and quantification (by quantitative PCR) of the phage in bee organs and in larvae after ingestion allowed us to conclude that despite 104phages reaching larvae only an average of 32 were available to control the spread of the disease. The fast inactivation of many phages in royal jelly could compromise this therapeutic approach. The protection of phages from hive-derived conditions should be thus considered in further developments for AFB treatment.
Exposure to Pb impairs breeding success and is associated with longer lifespan in urban European blackbirds
Authors: Fritsch Clémentine , Jankowiak Łukasz , Wysocki Dariusz 
Published: January 2019

AbstractAlthough several factors have been highlighted to explain the influence of urbanization on bird fitness and survival, the role of persistent toxicants such as lead (Pb), which is typically present in urban areas worldwide, has seldom been studied despite the ecological importance of such a widespread stressor. Studying free-living European blackbirds (Turdus merula) in city parks, we tested the hypothesis that low-dose chronic exposure to Pb could shape the life-history traits of urban birds. The feather concentrations of Pb and cadmium were typical of urban areas and low-to-moderate contamination of sites. Although the lifetime breeding success of females decreased with increasing exposure to Pb, the lifespan and survival probabilities of blackbirds increased with Pb contamination regardless of gender. Breeding effort-dependent patterns in the relationship between lifespan and Pb levels were highlighted. No significant relationships were detected between cadmium and life-history traits. The results suggest a possible trade-off between self-maintenance and reproduction, with the most affected birds redirecting allocations towards their own survival, which is consistent with the “stress hormone hypothesis”. These findings suggest that Pb pollution in urban environments may shape avian ecological features and be one of the drivers of wildlife responses to urbanization and that some urban areas may function as ecological traps driven by pollutants.
Mechanisms for lyssavirus persistence in non-synanthropic bats in Europe: insights from a modeling study
Authors: Colombi Davide , Serra-Cobo Jordi , Métras Raphaëlle , Apolloni Andrea , Poletto Chiara , López-Roig Marc , Bourhy Hervé , Colizza Vittoria 
Published: January 2019

AbstractBats are natural reservoirs of the largest proportion of viral zoonoses among mammals, thus understanding the conditions for pathogen persistence in bats is essential to reduce human risk. Focusing on the European Bat Lyssavirus subtype 1 (EBLV-1), causing rabies disease, we develop a data-driven spatially explicit metapopulation model to investigate EBLV-1 persistence inMyotis myotisandMiniopterus schreibersiibat species in Catalonia. We find that persistence relies on host spatial structure through the migratory nature ofM. schreibersii, on cross-species mixing withM. myotis, and on survival of infected animals followed by temporary immunity. The virus would not persist in the single colony ofM. myotis. Our study provides for the first time epidemiological estimates for EBLV-1 progression inM. schreibersii. Our approach can be readily adapted to other zoonoses of public health concern where long-range migration and habitat sharing may play an important role.
Gibbsian Thermodynamic Study of Capillary Meniscus Depth
Authors: Eslami Fatemeh , Elliott Janet A. W. 
Published: January 2019

AbstractIn the presence of gravity or other external fields, liquid surface curvature deviates from a spherical shape and the surface configuration can be found by numerical integration of the Young–Laplace equation and the typical initial point for integration is the apex of the interface. The meniscus shape in large Bond number systems, which have the central portion of the interface flattened, cannot be determined with the apex as the initial point for integration. Here we find the depth of capillary menisci by considering an initial point for integration to be at the three-phase-contact-line (TPCL) and evaluate the curvature at the TPCL by free energy analysis and inspect the effect of different parameters on the interface shape. A new parameter—which is the deviation of equilibrium curvature at the TPCL from the spherical shape (SR)—is introduced and inspected and it was found that at a Bond number of 13 the maximum deviation, approximately 0.8 of spherical curvature, takes place while for large enough Bond numbers the curvature at the three-phase contact line is near the spherical shape (0.95 < SR < 1). A potential application of this approach is to measure the capillary rise at the TPCL to find the surface tension in high Bond number systems such as those with low surface/interfacial tensions.
Molecular Characterization of Carbapenem Resistant Klebsiella pneumoniae and Klebsiella quasipneumoniae Isolated from Lebanon
Authors: Arabaghian Harout , Salloum Tamara , Alousi Sahar , Panossian Balig , Araj George F. , Tokajian Sima 
Published: January 2019

AbstractKlebsiella pneumoniae is a Gram-negative organism and a major public health threat. In this study, we used whole-genome sequences to characterize 32 carbapenem-resistant K. pneumoniae (CRKP) and two carbapenem-resistant K. quasipneumoniae (CRKQ). Antimicrobial resistance was assessed using disk diffusion and E-test, while virulence was assessed in silico. The capsule type was determined by sequencing the wzi gene. The plasmid diversity was assessed by PCR-based replicon typing to detect the plasmid incompatibility (Inc) groups. The genetic relatedness was determined by multilocus sequence typing, pan-genome, and recombination analysis. All of the isolates were resistant to ertapenem together with imipenem and/or meropenem. Phenotypic resistance was due to blaOXA-48,blaNDM-1, blaNDM-7, or the coupling of ESBLs and outer membrane porin modifications. This is the first comprehensive study reporting on the WGS of CRKP and the first detection of CRKQ in the region. The presence and dissemination of CRKP and CRKQ, with some additionally having characteristics of hypervirulent clones such as the hypermucoviscous phenotype and the capsular type K2, are particularly concerning. Additionally, mining the completely sequenced K. pneumoniae genomes revealed the key roles of mobile genetic elements in the spread of antibiotic resistance and in understanding the epidemiology of these clinically significant pathogens.
Smoothelin-like 1 deletion enhances myogenic reactivity of mesenteric arteries with alterations in PKC and myosin phosphatase signaling
Authors: Turner Sara R. , Chappellaz Mona , Popowich Brittany , Wooldridge Anne A. , Haystead Timothy A. J. , Cole William C. , MacDonald Justin A. 
Published: January 2019

AbstractThe role of the smoothelin-like 1 (SMTNL1) protein in mediating vascular smooth muscle contractile responses to intraluminal pressure was examined in resistance vessels. Mesenteric arterioles from wild type (WT) and SMTNL1 global knock-out (KO) mice were examined with pressure myography. SMTNL1 deletion was associated with enhanced myogenic tone in vessels isolated from male, but not female, mice. Intraluminal pressures greater than 40 mmHg generated statistically significant differences in myogenic reactivity between WT and KO vessels. No overt morphological differences were recorded for vessels dissected from KO animals, but SMTNL1 deletion was associated with loss of myosin phosphatase-targeting protein MYPT1 and increase in the myosin phosphatase inhibitor protein CPI-17. Additionally, we observed altered contractile responses of isolated arteries from SMTNL1 KO mice to phenylephrine, KCl-dependent membrane depolarization and phorbol 12,13-dibutyrate (PDBu). Using pharmacological approaches, myogenic responses of both WT and KO vessels were equally affected by Rho-associated kinase (ROCK) inhibition; however, augmented protein kinase C (PKC) signaling was found to contribute to the increased myogenic reactivity of SMTNL1 KO vessels across the 60–120 mmHg pressure range. Based on these findings, we conclude that deletion of SMTNL1 contributes to enhancement of pressure-induced contractility of mesenteric resistance vessels by influencing the activity of myosin phosphatase.