bluuebunny/crossref_metadata_2025_split huggingface dataset:
The potential role of modern radiotherapy techniques in the treatment of malignant spinal cord compression: a dose planning study
Authors: Fog Lotte S. , Schut Deborah , Sjøgren Per , Aznar Marianne C. 
Published: September 2015

AbstractAimTo investigate the doses given to the kidneys and the small intestines for three radiation therapy techniques [anterior–posterior (APPA) fields, three fields and volumetric-modulated arc therapy (VMAT)] for spinal cord compression (SCC) patients with metastatic disease in the lower thoracic or lumbar spine and to monitor the time spent by clinicians and dose planners.IntroductionRadiation therapy is one of the main treatment modalities for SCC. Typical palliative radiation therapy techniques have used APPA fields or a three-field technique.However, as delivery techniques have evolved dramatically over the past decades, VMAT has gained wide acceptance. VMAT allows for a dose reduction in the organs at risk. Such a dose reduction may result in less toxicity.The use of the VMAT technique may require more time for contouring and planning compared with the APPA and three-field techniques. Any potential dosimetric benefit of VMAT must not be outweighed by large amounts of extra time spent by clinicians and dose planners.Materials and methodsFor 20 patients treated with radiation therapy for SCC at our hospital, we created a VMAT plan, and the more traditionally used APPA and three-field plans. The mean kidney doses and the volume of bowel, which received 20 Gy, were extracted for each plan. The correlations between parameters for three techniques were determined.Furthermore, the time required for contouring targets for five patients; and the time required to plan five patients, was recorded.ResultsVMAT lead to the most conformal distributions: the high-dose areas were restricted to the target volume, whereas the healthy tissue, especially the bowel, received a lower dose. In contrast, the APPA plan lead to a larger volume of bowel being irradiated, whereas the three-field technique spared the bowel at the expense of a higher dose to the kidneys.The average contouring time was 16 minutes, the average planning time was 38 minutes.ConclusionPatients treated for SCC in the lower thoracic or lumbar region may benefit from VMAT treatment, as it reduces the dose to the bowel and kidneys compared with APPA or three-field treatments.
Conservation agriculture and drought-tolerant germplasm: Reaping the benefits of climate-smart agriculture technologies in central Mozambique
Authors: Thierfelder Christian , Rusinamhodzi Leonard , Setimela Peter , Walker Forbes , Eash Neal S. 
Published: September 2015

AbstractConservation agriculture (CA) based on minimum soil disturbance, crop residue retention and crop rotations is considered as a soil and crop management system that could potentially increase soil quality and mitigate the negative effects of climate variability. When CA is combined with drought-tolerant (DT) maize varieties, farmers can reap the benefits of both—genetic improvement and sustainable land management. New initiatives were started in 2007 in Mozambique to test the two climate-smart agriculture technologies on farmers' fields. Long-term trends showed that direct seeded manual CA treatments outyielded conventional tillage treatments in up to 89% of cases on maize and in 90% of cases on legume in direct yield comparisons. Improved DT maize varieties outyielded the traditional control variety by 26–46% (695–1422 kg ha−1) on different tillage treatment, across sites and season. However a direct interaction between tillage treatment and variety performance could not be established. Maize and legume grain yields on CA plots in this long-term dataset did not increase with increased years of practice due to on-site variability between farmer replicates. It was evident from the farmers' choice that, beside taste and good milling quality, farmers in drought-prone environments considered the potential of a variety to mature faster more important than larger potential yields of long season varieties. Population growth, labor shortage to clear new land areas and limited land resources in future will force farmers to change toward more permanent and sustainable cropping systems and CA is a viable option to improve their food security and livelihoods.
Subducting seamounts control interplate coupling and seismic rupture in the 2014 Iquique earthquake area
Authors: Geersen Jacob , Ranero César R. , Barckhausen Udo , Reichert Christian 
Published: September 2015

AbstractTo date, the parameters that determine the rupture area of great subduction zone earthquakes remain contentious. On 1 April 2014, the Mw 8.1 Iquique earthquake ruptured a portion of the well-recognized northern Chile seismic gap but left large highly coupled areas un-ruptured. Marine seismic reflection and swath bathymetric data indicate that structural variations in the subducting Nazca Plate control regional-scale plate-coupling variations, and the limited extent of the 2014 earthquake. Several under-thrusting seamounts correlate to the southward and up-dip arrest of seismic rupture during the 2014 Iquique earthquake, thus supporting a causal link. By fracturing of the overriding plate, the subducting seamounts are likely further responsible for reduced plate-coupling in the shallow subduction zone and in a lowly coupled region around 20.5°S. Our data support that structural variations in the lower plate influence coupling and seismic rupture offshore Northern Chile, whereas the structure of the upper plate plays a minor role.
Towards a table-top microscope for nanoscale magnetic imaging using picosecond thermal gradients
Authors: Bartell J. M. , Ngai D. H. , Leng Z. , Fuchs G. D. 
Published: September 2015

AbstractResearch advancement in magnetoelectronics is challenged by the lack of a table-top magnetic measurement technique with the simultaneous temporal and spatial resolution necessary for characterizing magnetization dynamics in devices of interest, such as magnetic memory and spin torque oscillators. Although magneto-optical microscopy provides superb temporal resolution, its spatial resolution is fundamentally limited by optical diffraction. To address this challenge, we study heat rather than light as a vehicle to stroboscopically transduce a local magnetic moment into an electrical signal while retaining picosecond temporal resolution. Using this concept, we demonstrate spatiotemporal magnetic microscopy using the time-resolved anomalous Nernst effect (TRANE). Experimentally and with supporting numerical calculations, we find that TRANE microscopy has temporal resolution below 30 ps and spatial resolution determined by the area of thermal excitation. Based on these findings, we suggest a route to exceed the limits imposed by far-field optical diffraction.
Genetic diversity and evolutionary insights of respiratory syncytial virus A ON1 genotype: global and local transmission dynamics
Authors: Duvvuri Venkata R. , Granados Andrea , Rosenfeld Paul , Bahl Justin , Eshaghi Alireza , Gubbay Jonathan B. 
Published: September 2015

AbstractHuman respiratory syncytial virus (RSV) A ON1 genotype, first detected in 2010 in Ontario, Canada, has been documented in 21 countries to date. This study investigated persistence and transmission dynamics of ON1 by grouping 406 randomly selected RSV-positive specimens submitted to Public Health Ontario from August 2011 to August 2012; RSV-A-positive specimens were genotyped. We identified 370 RSV-A (181 NA1, 135 NA2, 51 ON1 3 GA5) and 36 RSV-B positive specimens. We aligned time-stamped second hypervariable region (330 bp) of G-gene sequence data (global, n = 483; and Ontario, n = 60) to evaluate transmission dynamics. Global data suggests that the most recent common ancestor of ON1 emerged during the 2008–2009 season. Mean evolutionary rate of the global ON1 was 4.10 × 10−3substitutions/site/year (95% BCI 3.1–5.0 × 10−3), not significantly different to that of Ontario ON1. The estimated mean reproductive number (R0 = ∼ 1.01) from global and Ontario sequences showed no significant difference and implies stability among global RSV-A ON1. This study suggests that local epidemics exhibit similar underlying evolutionary and epidemiological dynamics to that of the persistent global RSV-A ON1 population. These findings underscore the importance of continual molecular surveillance of RSV in order to gain a better understanding of epidemics.
Antigen exposure in the late light period induces severe symptoms of food allergy in an OVA-allergic mouse model
Authors: Tanabe Kana , Kitagawa Eri , Wada Misaki , Haraguchi Atsushi , Orihara Kanami , Tahara Yu , Nakao Atsuhito , Shibata Shigenobu 
Published: September 2015

AbstractThe mammalian circadian clock controls many physiological processes that include immune responses and allergic reactions. Several studies have investigated the circadian regulation of intestinal permeability and tight junctions known to be affected by cytokines. However, the contribution of circadian clock to food allergy symptoms remains unclear. Therefore, we investigated the role of the circadian clock in determining the severity of food allergies. We prepared an ovalbumin food allergy mouse model and orally administered ovalbumin either late in the light or late in the dark period under light-dark cycle. The light period group showed higher allergic diarrhea and weight loss than the dark period group. The production of type 2 cytokines, IL-13 and IL-5, from the mesenteric lymph nodes and ovalbumin absorption was higher in the light period group than in the dark period group. Compared to the dark period group, the mRNA expression levels of the tight junction proteins were lower in the light period group. We have demonstrated that increased production of type 2 cytokines and intestinal permeability in the light period induced severe food allergy symptoms. Our results suggest that the time of food antigen intake might affect the determination of the severity of food allergy symptoms.
Targeting substrate-site in Jak2 kinase prevents emergence of genetic resistance
Authors: Kesarwani Meenu , Huber Erika , Kincaid Zachary , Evelyn Chris R. , Biesiada Jacek , Rance Mark , Thapa Mahendra B. , Shah Neil P. , Meller Jarek , Zheng Yi , Azam Mohammad 
Published: September 2015

AbstractEmergence of genetic resistance against kinase inhibitors poses a great challenge for durable therapeutic response. Here, we report a novel mechanism of JAK2 kinase inhibition by fedratinib (TG101348) that prevents emergence of genetic resistance. Using in vitro drug screening, we identified 211 amino-acid substitutions conferring resistance to ruxolitinib (INCB018424) and cross-resistance to the JAK2 inhibitors AZD1480, CYT-387 and lestaurtinib. In contrast, these resistant variants were fully sensitive to fedratinib. Structural modeling, coupled with mutagenesis and biochemical studies, revealed dual binding sites for fedratinib. In vitro binding assays using purified proteins showed strong affinity for the substrate-binding site (Kd = 20 nM) while affinity for the ATP site was poor (Kd = ~8 μM). Our studies demonstrate that mutations affecting the substrate-binding pocket encode a catalytically incompetent kinase, thereby preventing emergence of resistant variants. Most importantly, our data suggest that in order to develop resistance-free kinase inhibitors, the next-generation drug design should target the substrate-binding site.
Unravelling polar lipids dynamics during embryonic development of two sympatric brachyuran crabs (Carcinus maenas and Necora puber) using lipidomics
Authors: Rey Felisa , Alves Eliana , Melo Tânia , Domingues Pedro , Queiroga Henrique , Rosa Rui , Domingues M. Rosário M. , Calado Ricardo 
Published: September 2015

AbstractEmbryogenesis is an important stage of marine invertebrates with bi-phasic life cycles, as it conditions their larval and adult life. Throughout embryogenesis, phospholipids (PL) play a key role as an energy source, as well as constituents of biological membranes. However, the dynamics of PL during embryogenesis in marine invertebrates is still poorly studied. The present work used a lipidomic approach to determine how polar lipid profiles shift during embryogenesis in two sympatric estuarine crabs, Carcinus maenas and Necora puber. The combination of thin layer chromatography, liquid chromatography – mass spectrometry and gas chromatography – mass spectrometry allowed us to achieve an unprecedented resolution on PL classes and molecular species present on newly extruded embryos (stage 1) and those near hatching (stage 3). Embryogenesis proved to be a dynamic process, with four PL classes being recorded in stage 1 embryos (68 molecular species in total) and seven PL classes at stage 3 embryos (98 molecular species in total). The low interspecific difference recorded in the lipidomic profiles of stage 1 embryos appears to indicate the existence of similar maternal investment. The same pattern was recorded for stage 3 embryos revealing a similar catabolism of embryonic resources during incubation for both crab species.
On the thermodynamically stable amorphous phase of polymer-derived silicon oxycarbide
Authors: Yu Liping , Raj Rishi 
Published: September 2015

AbstractA model for the thermodynamic stability of amorphous silicon oxycarbide (SiCO) is presented. It builds upon the reasonably accepted model of SiCO which is conceived as a nanodomain network of graphene. The domains are expected to be filled with SiO2molecules, while the interface with graphene is visualized to contain mixed bonds described as Si bonded to C as well as to O atoms. Normally these SiCO compositions would be expected to crystallize. Instead, calorimetric measurements have shown that the amorphous phase is thermodynamically stable. In this article we employ first-principles calculations to estimate how the interfacial energy of the graphene networks is favorably influenced by having mixed bonds attached to them. We analyze the ways in which this reduction in interfacial energy can stabilize the amorphous phase. The approach highlights how density functional theory computations can be combined with the classical analysis of phase transformations to explain the behavior of a complex material. In addition we discover a two-dimensional lattice structure, with the composition Si2C4O3that is constructed from a single layer of graphene congruent with silicon and oxygen bonds on either side.
Visible-light-accelerated oxygen vacancy migration in strontium titanate
Authors: Li Y. , Lei Y. , Shen B. G. , Sun J. R. 
Published: September 2015

AbstractStrontium titanate is a model transition metal oxide that exhibits versatile properties of special interest for both fundamental and applied researches. There is evidence that most of the attractive properties of SrTiO3 are closely associated with oxygen vacancies. Tuning the kinetics of oxygen vacancies is then highly desired. Here we reported on a dramatic tuning of the electro-migration of oxygen vacancies by visible light illumination. It is found that, through depressing activation energy for vacancy diffusion, light illumination remarkably accelerates oxygen vacancies even at room temperature. This effect provides a feasible approach towards the modulation of the anionic processes. The principle proved here can be extended to other perovskite oxides, finding a wide application in oxide electronics.
The structure of Legionella pneumophila LegK4 type four secretion system (T4SS) effector reveals a novel dimeric eukaryotic-like kinase
Authors: Flayhan Ali , Bergé Célia , Baïlo Nathalie , Doublet Patricia , Bayliss Richard , Terradot Laurent 
Published: September 2015

AbstractBacterial pathogens subvert signalling pathways to promote invasion and/or replication into the host. LegK1-4 proteins are eukaryotic-like serine/threonine kinases that are translocated by the Dot/Icm type IV secretion system (T4SS) of several Legionella pneumophila strains. We present the crystal structures of an active fragment of the LegK4 protein in apo and substrate-bound states. The structure of LegK41–445 reveals a eukaryotic-like kinase domain flanked by a novel cap domain and a four-helix bundle. The protein self-assembles through interactions mediated by helices αF and αG that generate a dimeric interface not previously observed in a protein kinase. The helix αG is displaced compared to previous kinase structures and its role in stabilization of the activation loop is taken on by the dimerisation interface. The apo-form of the protein has an open conformation with a disordered P-loop but a structured activation segment in absence of targeted phosphorylation. The nucleotide-binding site of LegK4 contains an unusual set of residues that mediate non-canonical interactions with AMP-PNP. Nucleotide binding results in limited changes in the active site, suggesting that LegK4 constitutive kinase activity does not depend on phosphorylation of the activation loop but on the stabilizing effects of the dimer.
Quantifying barcodes of dendritic spines using entropy-based metrics
Authors: Viggiano D. , Srivastava D. P. , Speranza L. , Perrone-Capano C. , Bellenchi G. C. , di Porzio U. , Buckley N. J. 
Published: September 2015

AbstractSpine motility analysis has become the mainstay for investigating synaptic plasticity but is limited in its versatility requiring complex, non automatized instrumentations. We describe an entropy-based method for determining the spatial distribution of dendritic spines that allows successful estimation of spine motility from still images. This method has the potential to extend the applicability of spine motility analysis to ex vivo preparations.
Ginkgo biloba leaf extract induces DNA damage by inhibiting topoisomerase II activity in human hepatic cells
Authors: Zhang Zhuhong , Chen Si , Mei Hu , Xuan Jiekun , Guo Xiaoqing , Couch Letha , Dobrovolsky Vasily N. , Guo Lei , Mei Nan 
Published: September 2015

AbstractGinkgo biloba leaf extract has been shown to increase the incidence in liver tumors in mice in a 2-year bioassay conducted by the National Toxicology Program. In this study, the DNA damaging effects of Ginkgo biloba leaf extract and many of its constituents were evaluated in human hepatic HepG2 cells and the underlying mechanism was determined. A molecular docking study revealed that quercetin, a flavonoid constituent of Ginkgo biloba, showed a higher potential to interact with topoisomerase II (Topo II) than did the other Ginkgo biloba constituents; this in silico prediction was confirmed by using a biochemical assay to study Topo II enzyme inhibition. Moreover, as measured by the Comet assay and the induction of γ-H2A.X, quercetin, followed by keampferol and isorhamnetin, appeared to be the most potent DNA damage inducer in HepG2 cells. In Topo II knockdown cells, DNA damage triggered by Ginkgo biloba leaf extract or quercetin was dramatically decreased, indicating that DNA damage is directly associated with Topo II. DNA damage was also observed when cells were treated with commercially available Ginkgo biloba extract product. Our findings suggest that Ginkgo biloba leaf extract- and quercetin-induced in vitro genotoxicity may be the result of Topo II inhibition.
Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR)
Authors: Gallart-Palau Xavier , Serra Aida , Wong Andrew See Weng , Sandin Sara , Lai Mitchell K. P. , Chen Christopher P. , Kon Oi Lian , Sze Siu Kwan 
Published: September 2015

AbstractExtracellular vesicles (EVs) such as exosomes and microvesicles mediate intercellular communication and regulate a diverse range of crucial biological processes. Host cells that are damaged, infected or transformed release biomarker-containing EVs into the peripheral circulation, where they can be readily accessed for use in diagnostic or prognostic testing. However, current methods of EV isolation from blood plasma are complex and often require relatively large sample volumes, hence are inefficient for widespread use in clinical settings. Here, we report a novel and inexpensive method of rapidly isolating EVs from small volumes of human blood plasma by PRotein Organic Solvent PRecipitation (PROSPR). PROSPR encompasses a rapid three-step protocol to remove soluble proteins from plasma via precipitation in cold acetone, leaving the lipid-encapsulated EVs behind in suspension. This generates higher purity EVs that can then be obtained from filtration or classical ultracentrifugation methods. We foresee that PROSPR-based purification of EVs will significantly accelerate the discovery of new disease biomarkers and the characterization of EVs with potential for clinical applications.
Germ plasm localisation of the HELICc of Vasa in Drosophila: analysis of domain sufficiency and amino acids critical for localisation
Authors: Wang Szu-Chieh , Hsu Hao-Jen , Lin Gee-way , Wang Ting-Fang , Chang Chun-che , Lin Ming-Der 
Published: September 2015

AbstractFormation of the germ plasm drives germline specification in Drosophila and some other insects such as aphids. Identification of the DEAD-box protein Vasa (Vas) as a conserved germline marker in flies and aphids suggests that they share common components for assembling the germ plasm. However, to which extent the assembly order is conserved and the correlation between functions and sequences of Vas remain unclear. Ectopic expression of the pea aphid Vas (ApVas1) in Drosophila did not drive its localisation to the germ plasm, but ApVas1 with a replaced C-terminal domain (HELICc) of Drosophila Vas (DmVas) became germ-plasm restricted. We found that HELICc itself, through the interaction with Oskar (Osk), was sufficient for germ-plasm localisation. Similarly, HELICc of the grasshopper Vas could be recruited to the germ plasm in Drosophila. Nonetheless, germ-plasm localisation was not seen in the Drosophila oocytes expressing HELICcs of Vas orthologues from aphids, crickets and mice. We further identified that glutamine (Gln) 527 within HELICc of DmVas was critical for localisation and its corresponding residue could also be detected in grasshopper Vas yet missing in the other three species. This suggests that Gln527 is a direct target of Osk or critical to the maintenance of HELICc conformation.
Mutual positive effects between shrubs in an arid ecosystem
Authors: Tirado Reyes , Bråthen Kari Anne , Pugnaire Francisco I. 
Published: September 2015

AbstractOne-way facilitation in plants has been found in many harsh environments and their role as structural forces governing species composition in plant communities is now well established. However, reciprocal positive effects benefiting two interacting species have seldom been reported and, in recent reviews, conceptually considered merely as facilitation when in fact there is room for adaptive strategies and evolutionary responses. We tested the existence of such reciprocal positive effects in an arid environment in SE Spain using spatial pattern analysis, a species removal experiment and a natural experiment. We found that the spatial association between Maytenus senegalensis and Whitania frutescens, two shrub species of roughly similar size intimately interacting in our community, resulted in mutual benefit for both species. Benefits included improved water relations and nutritional status and protection against browsing and did occur despite simultaneous competition for resources. Our data suggest two-way facilitation or, rather, a facultative mutualism among higher plant species, a process often overlooked which could be a main driver of plant community dynamics allowing for evolutionary processes.