bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Reaction-Diffusion Model for Radiation-Induced Bystander Effects
Authors: Olobatuyi Oluwole , de Vries Gerda , Hillen Thomas 
Published: December 2016

AbstractWe develop and analyze a reaction-diffusion model to investigate the dynamics of the lifespan of a bystander signal emitted when cells are exposed to radiation. Experimental studies by Mothersill and Seymour 1997, using malignant epithelial cell lines, found that an emitted bystander signal can still cause bystander effects in cells even 60h after its emission. Several other experiments have also shown that the signal can persist for months and even years. Also, bystander effects have been hypothesized as one of the factors responsible for the phenomenon of low-dose hyper-radiosensitivity and increased radioresistance (HRS/IRR). Here, we confirm this hypothesis with a mathematical model, which we fit to Joiner’s data on HRS/IRR in a T98G glioma cell line. Furthermore, we use phase plane analysis to understand the full dynamics of the signal’s lifespan. We find that both single and multiple radiation exposure can lead to bystander signals that either persist temporarily or permanently. We also found that, in an heterogeneous environment, the size of the domain exposed to radiation and the number of radiation exposures can determine whether a signal will persist temporarily or permanently. Finally, we use sensitivity analysis to identify those cell parameters that affect the signal’s lifespan and the signal-induced cell death the most.
Diversity patterns across 1,800 chloroplast genomes of wild (Oryza rufipogonGriff.) and cultivated rice (O. sativaL.)
Authors: Civáň Peter , Brown Terence A. 
Published: December 2016

AbstractCultivated Asian rice(O. sativaL.) comprises several groups with distinct ecological requirements and culinary uses. While the two subspecies ofO. sativa–indicaandjaponica– have been subjected to a multitude of genetic and genomic analyses, less is known about the origins and diversity of the agronomically marginal groups –ausand aromatic rice. Here we reconstructed complete chloroplast genomes of over 1,800 accessions of wild and cultivated rice, including 240ausand 73 aromatic varieties, and analysed the haplotype diversity of the taxonomic groups. We confirm the deep phylogenetic divergence between the main chloroplast haplotypes ofjaponicaandindica,and reveal unique profiles of chloroplast diversity inausand aromatic rice. Our results indicate that the latter two groups are not simple derivatives ofindicaandjaponica,respectively, but originated from independent and/or reticulate domestication processes. Absence of phylogeographic patterns in the wild distribution of chloroplast haplogroups did not allow firm conclusions about geographic origins and the role of inter-group gene flow. Nonetheless, our results suggest that the domestication ofindica, japonica, ausand aromatic rice operated on genetically different gene pools and followed different dynamics.
Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation
Authors: Timmins-Schiffman Emma B. , Crandall Grace A. , Vadopalas Brent , Riffle Michael E. , Nunn Brook L. , Roberts Steven B. 
Published: December 2016

AbstractGeoduck clams (Panopea generosa) are an increasingly important fishery and aquaculture product along the eastern Pacific coast from Baja California, Mexico to Alaska. These long-lived clams are highly fecund, though sustainable hatchery production of genetically diverse larvae is hindered by the lack of sexual dimorphism, resulting in asynchronous spawning of broodstock, unequal sex ratios, and low numbers of breeders. Development of assays of gonad physiology could indicate sex and maturation stage, as well as be used to assess the status of natural populations. Proteomic profiles were determined for three reproductive maturation stages in both male and female clams using data dependent acquisition (DDA) of gonad proteins. Gonad proteomes became increasingly divergent between males and females as maturation progressed. The DDA data was used to develop targets analyzed with selected reaction monitoring (SRM) in gonad tissue as well as hemolymph. The SRM assay yielded a suite of indicator peptides that can be used as an efficient assay to determine geoduck gonad maturation status. Application of SRM in hemolymph samples demonstrates this procedure could effectively be used to assess reproductive status in marine mollusks in a non-lethal manner.
Intergenerational social mobility and leisure-time physical activity in adulthood: a systematic review
Authors: Elhakeem Ahmed , Hardy Rebecca , Bann David , Caleyachetty Rishi , Cosco Theodore D , Hayhoe Richard PG , Muthuri Stella G , Wilson Rebecca , Cooper Rachel 
Published: December 2016

AimTo systematically review the association between intergenerational social mobility and leisure-time physical activity (LTPA) in adulthood, in order to assess all published evidence relating to the hypothesis that adults socially mobile between childhood and adulthood will have different levels of LTPA than those in the same socioeconomic group across life.MethodsA systematic review was carried out following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Studies were identified by searching databases (MEDLINE, Embase, PsycINFO) and reference lists. Eligible studies examined associations between any indicator of social mobility, based on at least one measure of parental socioeconomic position (SEP) and one measure of own adult SEP, and LTPA in adulthood.Results13 studies comprising a total of 44 000 participants from the UK, Finland, Sweden, Australia, USA and Brazil were included. Participants were aged 16–70 years and were from population-based surveys, occupational cohorts and primary care registries. Most studies (n=9) used occupational class measures to identify social mobility; education (n=4) and income (n=1) were also used. There was consistent evidence in nine of the 13 studies that stable high socioeconomic groups tended to report the highest levels of participation in LTPA and stable low socioeconomic groups the lowest. Upward and downwardly mobile groups participated in LTPA at levels between these stable groups.ConclusionsCumulative exposure to higher SEP in childhood and adulthood was associated with higher LTPA in adulthood. Thus, a potential outcome of policies and interventions which aim to minimise exposure to socioeconomic adversity may be increased LTPA among adults.Trial registration numberCRD42016036538.
Synthesis and electrical properties of BaBiO3 and high resistivity BaTiO3–BaBiO3 ceramics
Authors: Kumar Nitish , Golledge Stephen L. , Cann David P. 
Published: December 2016

Ceramics of the composition BaBiO3 (BB) were sintered in oxygen to obtain a single phase with monoclinic [Formula: see text]2/[Formula: see text] symmetry as suggested by high-resolution X-ray diffraction. X-ray photoelectron spectroscopy confirmed the presence of bismuth in two valence states — 3[Formula: see text] and 5[Formula: see text]. Optical spectroscopy showed presence of a direct bandgap at [Formula: see text] 2.2[Formula: see text]eV and a possible indirect bandgap at [Formula: see text] 0.9[Formula: see text]eV. This combined with determination of the activation energy for conduction of 0.25[Formula: see text]eV, as obtained from ac impedance spectroscopy, suggested that a polaron-mediated conduction mechanism was prevalent in BB. The BB ceramics were crushed, mixed with BaTiO3 (BT), and sintered to obtain BT–BB solid solutions. All the ceramics had tetragonal symmetry and exhibited a normal ferroelectric-like dielectric response. Using ac impedance and optical spectroscopy, it was shown that resistivity values of BT–BB were orders of magnitude higher than BT or BB alone, indicating a change in the fundamental defect equilibrium conditions. A shift in the site occupancy of Bi to the A-site is proposed to be the mechanism for the increased electrical resistivity.
Old challenges, new developments and new plays in Irish offshore exploration
Authors: Shannon Patrick M. 
Published: December 2016

Abstract
More than 46 years of exploration in the Irish offshore has yielded modest commercial success. However, working petroleum systems have been proven in all the offshore basins. The pace of exploration has been controlled by: (a) data quality and technological advances; (b) geological understanding and plays; (c) fiscal and infrastructural environments; and (d) international conditions. Irish offshore exploration drilling started in the Celtic Sea basins in 1970 and the region has seen a recent renewal of exploration interest, stimulated by new and much improved seismic data. In the Atlantic margin basins west of Ireland, there has been a recent significant improvement in the understanding of the geological evolution and petroleum systems, especially in the hyperextended basins such as the Porcupine and Rockall basins. Here the major targets of current exploration are stratigraphic traps at Lower Cretaceous and Lower Cenozoic levels. The application of new and innovative seismic and other geophysical technologies in a number of the Irish offshore basins has led to significant enhancement in data quality and in resolving imaging challenges. Combined with recent geological learnings, they offer renewed hope for exploration success in the Irish offshore basins.
Shale prospectivity onshore Britain
Authors: Harvey Antoinette L. , Andrews Ian J. , Monaghan Alison A. 
Published: December 2016

Abstract
The UK Department of Energy and Climate Change (DECC) commissioned the British Geological Survey (BGS) to summarize the available geological knowledge, integrate new seismic mapping and well analysis, and make preliminary in-place resource assessments for the three most prospective areas onshore Britain to foster a greater understanding of the unconventional shale resource potential in advance of the 14th Landward Licensing Round.
The first study, published in June 2013, reviewed the Carboniferous Bowland–Hodder shales across central Britain where a large volume of in-place gas was assessed to be present. The second study, of the Jurassic shale of the Weald Basin in southern England, published in May 2014, concluded that owing to insufficient burial there was no significant Jurassic shale gas potential, but there could still be shale oil resources at several levels in the centre of the basin. The third study, published in June 2014, covered the Midland Valley of Scotland where both oil and gas potential in Carboniferous shales was identified.
A large volume of in-place gas and oil resource has been assessed to be present. However, not enough is known at the time of writing to estimate a recovery factor or to estimate potential producible reserves. This paper summarizes the results of the BGS reports and their impact on the subsequent licensing process in England.
Pyroclastic deposits of San Diego maar, central Colombia: an example of a silicic magma-related monogenetic eruption in a hard substrate
Authors: Borrero C. , Murcia H. , Agustin-Flores J. , Arboleda M. T. , Giraldo A. M. 
Published: December 2016

Abstract
The San Diego maar is a volcano located at the middle of the Colombian Central Cordillera that forms part of the dispersed and isolated Samaná Volcanic Field (with at least three volcanoes). San Diego is excavated on Triassic metamorphic rocks and Neogene sub-volcanic andesitic units, and forms approximately 15 m of mostly unconsolidated eruption-related deposits. These deposits were divided into four stratigraphic units (U1–U4) that together define the evolution of the eruption: (1) an unsteady vent-clearing stage; (2) drier to wet pyroclastic base surges; (3) dry base surges; and (4) a final wet stage. At the end of the activity, the crater was enlarged due to a complex set of rock falls and slides in the crater walls. Finally, the volcanic activity switched to a magmatic phase, creating a dacitic dome. The northern dome flank was affected by a gravitational collapse that produced a small-volume debris avalanche.
The eruption style of the San Diego maar was controlled by the stratigraphic, structural and hydrogeological characteristics of the substrate, as well as the surficial environmental condition. In addition, the mountainous terrain around the maar crater controlled the deposit extension. These constraints provide additional information for a hazard assessment related to this type of eruption in the region.
Protective roles of hepatic GABA signaling in acute liver injury of rats
Authors: Wang Shuanglian , Xiang Yun-Yan , Zhu Jianchun , Yi Fan , Li Jingxin , Liu Chuanyong , Lu Wei-Yang 
Published: December 2016

γ-Aminobutyric acid (GABA) is produced by various cells through the catalytic activity of glutamic acid decarboxylase (GAD). Activation of type-A GABA receptor (GABAAR) inhibits stem cell proliferation but protects differentiated cells from injures. The present study investigated hepatic GABA signaling system and the role of this system in liver physiology and pathophysiology. RT-PCR and immunoblot assays identified GAD and GABAAR subunits in rat livers and in HepG2 and Clone 9 hepatocytes. Patch-clamp recording detected GABA-induced currents in Clone 9 hepatocytes and depolarization in WITT cholangiocytes. The function of hepatic GABA signaling system in rats was examined using models of d-galactosamine (GalN)-induced acute hepatocytic injury in vivo and in vitro. The expression of GAD increased whereas GABAAR subunits decreased in the liver of GalN-treated rats. Remarkably, treating rats with GABA or the GABAAR agonist muscimol, but not the GABABR agonist baclofen, protected hepatocytes against GalN toxicity and improved liver function. In addition, muscimol treatment decreased the formation of pseudobile ductules and the enlargement of hepatocytic canaliculi in GalN-treated rats. Our results revealed that a complex GABA signaling system exists in the rat liver. Activation of this intrahepatic GABAergic system protected the liver against toxic injury.NEW & NOTEWORTHY Auto- and paracrine GABAergic signaling systems exist in the rat hepatocytes and cholangiocytes. Activation of GABA signaling protects liver function from d-galactosamine injury by reducing toxic impairment of hepatocytes and by decreasing cholangiocyte proliferation.
Changes in muscle fiber contractility and extracellular matrix production during skeletal muscle hypertrophy
Authors: Mendias Christopher L. , Schwartz Andrew J. , Grekin Jeremy A. , Gumucio Jonathan P. , Sugg Kristoffer B. 
Published: December 2016

Skeletal muscle can adapt to increased mechanical loads by undergoing hypertrophy. Transient reductions in whole muscle force production have been reported during the onset of hypertrophy, but contractile changes in individual muscle fibers have not been previously studied. Additionally, the extracellular matrix (ECM) stores and transmits forces from muscle fibers to tendons and bones, and determining how the ECM changes during hypertrophy is important in understanding the adaptation of muscle tissue to mechanical loading. Using the synergist ablation model, we sought to measure changes in muscle fiber contractility, collagen content, and cross-linking, and in the expression of several genes and activation of signaling proteins that regulate critical components of myogenesis and ECM synthesis and remodeling during muscle hypertrophy. Tissues were harvested 3, 7, and 28 days after induction of hypertrophy, and nonoverloaded rats served as controls. Muscle fiber specific force (sFo), which is the maximum isometric force normalized to cross-sectional area, was reduced 3 and 7 days after the onset of mechanical overload, but returned to control levels by 28 days. Collagen abundance displayed a similar pattern of change. Nearly a quarter of the transcriptome changed over the course of overload, as well as the activation of signaling pathways related to hypertrophy and atrophy. Overall, this study provides insight into fundamental mechanisms of muscle and ECM growth, and indicates that although muscle fibers appear to have completed remodeling and regeneration 1 mo after synergist ablation, the ECM continues to be actively remodeling at this time point.NEW & NOTEWORTHY This study utilized a rat synergist ablation model to integrate changes in single muscle fiber contractility, extracellular matrix composition, activation of important signaling pathways in muscle adaption, and corresponding changes in the muscle transcriptome to provide novel insight into the basic biological mechanisms of muscle fiber hypertrophy.
Modeling Alveolar Soft Part Sarcoma Unveils Novel Mechanisms of Metastasis
Authors: Tanaka Miwa , Homme Mizuki , Yamazaki Yukari , Shimizu Rikuka , Takazawa Yutaka , Nakamura Takuro 
Published: December 2016

Abstract
Alveolar soft part sarcoma (ASPS) is a slowly growing, but highly metastatic, sarcoma that affects adolescents and young adults. Its characteristic alveolar structure is constituted by tumor cell nests and an abundant vascular network that is responsible for metastatic activities at the initial stage. Here, we have generated a new ex vivo mouse model for ASPS that well recapitulates associated angiogenic and metastatic phenotypes. In mouse ASPS, the tumor cells frequently showed tumor intravasation, with the intravascular tumor cells presenting as organoid structures covered with hemangiopericytes, which is also observed in human ASPS. High expression of glycoprotein nmb (GPNMB), a transcriptional target of ASPSCR1-TFE3, was observed at the sites of intravasation. ASPS tumor cells also demonstrated enhanced transendothelial migration activity, which was inhibited by silencing of Gpnmb, indicating that GPNMB plays an important role in tumor intravasation, a key step in cancer metastasis. The present model also enabled the evaluation of TFE/MITF family transcription factor function, which demonstrated that ASPSCR1-TFEB possessed definitive albeit less marked oncogenic activity than that of ASPSCR1-TFE3. Collectively, our mouse model provides a tool to understand oncogenic, angiogenic, and metastatic mechanisms of ASPS. It also identifies important motifs within the ASPSCR1-TFE3 fusion protein and provides a platform for developing novel therapeutic strategies for this disorder. Cancer Res; 77(4); 897–907. ©2016 AACR.
The FA/BRCA Pathway Identified as the Major Predictor of Cisplatin Response in Head and Neck Cancer by Functional Genomics
Authors: Martens-de Kemp Sanne R. , Brink Arjen , van der Meulen Ida H. , de Menezes Renée X. , te Beest Dennis E. , Leemans C. René , van Beusechem Victor W. , Braakhuis Boudewijn J.M. , Brakenhoff Ruud H. 
Published: December 2016

AbstractPatients with advanced stage head and neck squamous cell carcinoma (HNSCC) are often treated with cisplatin-containing chemoradiation protocols. Although cisplatin is an effective radiation sensitizer, it causes severe toxicity and not all patients benefit from the combination treatment. HNSCCs expectedly not responding to cisplatin may better be treated with surgery and postoperative radiation or cetuximab and radiation, but biomarkers to personalize chemoradiotherapy are not available. We performed an unbiased genome-wide functional genetic screen in vitro to identify genes that influence the response to cisplatin in HNSCC cells. By siRNA-mediated knockdown, we identified the Fanconi anemia/BRCA pathway as the predominant pathway for cisplatin response in HNSCC cells. We also identified the involvement of the SHFM1 gene in the process of DNA cross-link repair. Furthermore, expression profiles based on these genes predict the prognosis of radiation- and chemoradiation-treated head and neck cancer patients. This genome-wide functional analysis designated the genes that are important in the response of HNSCC to cisplatin and may guide further biomarker validation. Cisplatin imaging as well as biomarkers that indicate the activity of the Fanconi anemia/BRCA pathway in the tumors are the prime candidates. Mol Cancer Ther; 16(3); 540–50. ©2016 AACR.
Folate-Hapten–Mediated Immunotherapy Synergizes with Vascular Endothelial Growth Factor Receptor Inhibitors in Treating Murine Models of Cancer
Authors: Bandara N. Achini , Bates Cody D. , Lu Yingjuan , Hoylman Emily K. , Low Philip S. 
Published: December 2016

AbstractThe overexpression of folate receptors (FR) on many human cancers has led to the development of folate-linked drugs for the imaging and therapy of FR-expressing cancers. In a recent phase I clinical trial of late-stage renal cell carcinoma patients, folate was exploited to deliver an immunogenic hapten, fluorescein, to FR+ tumor cells in an effort to render the cancer cells more immunogenic. Although &gt;50% of the patients showed prolonged stable disease, all patients eventually progressed, suggesting that the folate-hapten immunotherapy was insufficient by itself to treat the cancer. In an effort to identify a companion therapy that might augment the folate-hapten immunotherapy, we explored coadministration of two approved cancer drugs that had been previously shown to also stimulate the immune system. We report that sunitinib and axitinib (VEGF receptor inhibitors that simultaneously mitigate immune suppression) synergize with the folate-hapten–targeted immunotherapy to reduce tumor growth in three different syngeneic murine tumor models. We further demonstrate that the combination therapy not only enhances tumor infiltration of CD4+ and CD8+ effector cells, but surprisingly reduces tumor neovasculogenesis more than predicted. Subsequent investigation of the mechanism for this unexpected suppression of neovasculogenesis revealed that it is independent of elimination of any tumor cells, but instead likely derives from a reduction in the numbers of FR+ tumor-associated macrophages and myeloid-derived suppressor cells, that is, immunosuppressive cells that release significant quantities of VEGF. These data suggest that a reduction in stromal cells of myeloid origin can inhibit tumor growth by suppressing neovasculogenesis. Mol Cancer Ther; 16(3); 461–8. ©2016 AACR.