bluuebunny/crossref_metadata_2025_split huggingface dataset:
Managing Wicked Herbicide-Resistance: Lessons from the Field
Authors: Schroeder Jill , Barrett Michael , Shaw David R. , Asmus Amy B. , Coble Harold , Ervin David , Jussaume Raymond A. , Owen Micheal D. K. , Burke Ian , Creech Cody F. , Culpepper A. Stanley , Curran William S. , Dodds Darrin M. , Gaines Todd A. , Gunsolus Jeffrey L. , Hanson Bradley D. , Jha Prashant , Klodd Annie E. , Kniss Andrew R. , Leon Ramon G. , McDonald Sandra , Morishita Don W. , Schutte Brian J. , Sprague Christy L. , Stahlman Phillip W. , Steckel Larry E. , VanGessel Mark J. 
Published: August 2018

AbstractHerbicide resistance is ‘wicked’ in nature; therefore, results of the many educational efforts to encourage diversification of weed control practices in the United States have been mixed. It is clear that we do not sufficiently understand the totality of the grassroots obstacles, concerns, challenges, and specific solutions needed for varied crop production systems. Weed management issues and solutions vary with such variables as management styles, regions, cropping systems, and available or affordable technologies. Therefore, to help the weed science community better understand the needs and ideas of those directly dealing with herbicide resistance, seven half-day regional listening sessions were held across the United States between December 2016 and April 2017 with groups of diverse stakeholders on the issues and potential solutions for herbicide resistance management. The major goals of the sessions were to gain an understanding of stakeholders and their goals and concerns related to herbicide resistance management, to become familiar with regional differences, and to identify decision maker needs to address herbicide resistance. The messages shared by listening-session participants could be summarized by six themes: we need new herbicides; there is no need for more regulation; there is a need for more education, especially for others who were not present; diversity is hard; the agricultural economy makes it difficult to make changes; and we are aware of herbicide resistance but are managing it. The authors concluded that more work is needed to bring a community-wide, interdisciplinary approach to understanding the complexity of managing weeds within the context of the whole farm operation and for communicating the need to address herbicide resistance.
Managing Herbicide Resistance: Listening to the Perspectives of Practitioners. Procedures for Conducting Listening Sessions and an Evaluation of the Process
Authors: Schroeder Jill , Barrett Michael , Shaw David R. , Asmus Amy B. , Coble Harold , Ervin David , Jussaume Raymond A. , Owen Micheal D. K. , Burke Ian , Creech Cody F. , Culpepper A. Stanley , Curran William S. , Dodds Darrin M. , Gaines Todd A. , Gunsolus Jeffrey L. , Hanson Bradley D. , Jha Prashant , Klodd Annie E. , Kniss Andrew R. , Leon Ramon G. , McDonald Sandra , Morishita Don W. , Schutte Brian J. , Sprague Christy L. , Stahlman Phillip W. , Steckel Larry E. , VanGessel Mark J. 
Published: August 2018

AbstractSeven half-day regional listening sessions were held between December 2016 and April 2017 with groups of diverse stakeholders on the issues and potential solutions for herbicide-resistance management. The objective of the listening sessions was to connect with stakeholders and hear their challenges and recommendations for addressing herbicide resistance. The coordinating team hired Strategic Conservation Solutions, LLC, to facilitate all the sessions. They and the coordinating team used in-person meetings, teleconferences, and email to communicate and coordinate the activities leading up to each regional listening session. The agenda was the same across all sessions and included small-group discussions followed by reporting to the full group for discussion. The planning process was the same across all the sessions, although the selection of venue, time of day, and stakeholder participants differed to accommodate the differences among regions. The listening-session format required a great deal of work and flexibility on the part of the coordinating team and regional coordinators. Overall, the participant evaluations from the sessions were positive, with participants expressing appreciation that they were asked for their thoughts on the subject of herbicide resistance. This paper details the methods and processes used to conduct these regional listening sessions and provides an assessment of the strengths and limitations of those processes.
Paleoproductivity and Stratification Across the Subarctic Pacific Over Glacial‐Interglacial Cycles
Authors: Costa Kassandra M. , McManus Jerry F. , Anderson Robert F. 
Published: August 2018

AbstractIn the Subarctic Pacific, variability in productivity on glacial‐interglacial timescales is often attributed to changes in stratification and nutrient delivery to the surface, but the mechanisms driving this relationship are poorly constrained. Records extending beyond the last glacial maximum from both the open ocean and the marginal seas are required to investigate the timing and magnitude of different influential processes through the full glacial cycle. In this study we generated 231Pa/230Th over 210,000 years in order to capture two full glacial cycles of paleoproductivity on the Juan de Fuca Ridge in the East Subarctic Pacific. The sedimentary 231Pa/230Th ratios are always equal to or greater than the seawater production ratio (0.093), consistent with enhanced biological scavenging in this region. The temporal pattern of 231Pa/230Th burial is remarkably coherent with changes in climate, with high values (0.20) during peak interglacial periods descending to low values (0.10) during peak glacial conditions, consistent with other long productivity records from this region. We investigate the possible contributions of temperature, sea ice formation, Bering Strait closure, wind strength, upwelling, and subsurface nutrient concentrations as possible mechanisms by which physical and/or chemical stratification emerged during glacial periods. Due to the low sea surface salinity in the North Pacific, cooling actually weakens the density gradient in surface (0–200 m) waters. To create the steep density profiles that characterize physical stratification, additional processes to reduce the salinity of surface waters must occur during glacial periods. We suggest that regional sea ice formation and Bering Strait closure may have contributed to freshening surface waters and enhancing physical stratification during glacial periods. Additionally, simulated weak winds in this region due to the southward shift of the glacial westerlies may have further reduced surface mixing depths in the Subarctic Pacific. Finally, previous model simulations suggest strong glacial wind stress curl in the Subarctic Pacific, but enhanced Ekman divergence of nutrient‐poor subsurface waters would have little impact on stimulating productivity in surface waters of the Subarctic Pacific. We therefore suggest that the combined effects of surface freshening, weak winds, and lower subsurface nutrient concentrations may all have contributed to lower productivity during glacial periods in the Subarctic Pacific.
Notch3 inhibits epithelial–mesenchymal transition in breast cancer via a novel mechanism, upregulation of GATA-3 expression
Authors: Lin Hao-Yu , Liang Yuan-Ke , Dou Xiao-Wei , Chen Chun-Fa , Wei Xiao-Long , Zeng De , Bai Jing-Wen , Guo Yu-Xian , Lin Fang-Fang , Huang Wen-He , Du Cai-Wen , Li Yao-Chen , Chen Min , Zhang Guo-Jun 
Published: August 2018

AbstractNotch3 and GATA binding protein 3 (GATA-3) have been, individually, shown to maintain luminal phenotype and inhibit epithelial–mesenchymal transition (EMT) in breast cancers. In the present study, we report that Notch3 expression positively correlates with that of GATA-3, and both are associated with estrogen receptor-α (ERα) expression in breast cancer cells. We demonstrate in vitro and in vivo that Notch3 suppressed EMT and breast cancer metastasis by activating GATA-3 transcription. Furthermore, Notch3 knockdown downregulated GATA-3 and promoted EMT; while overexpression of Notch3 intracellular domain upregulated GATA-3 and inhibited EMT, leading to a suppression of metastasis in vivo. Moreover, inhibition or overexpression of GATA-3 partially reversed EMT or mesenchymal–epithelial transition induced by Notch3 alterations. In breast cancer patients, high GATA-3 expression is associated with higher Notch3 expression and lower lymph node metastasis, especially for hormone receptor (HR) positive cancers. Herein, we demonstrate a novel mechanism whereby Notch3 inhibit EMT by transcriptionally upregulating GATA-3 expression, at least in part, leading to the suppression of cancer metastasis in breast cancers. Our findings expand our current knowledge on Notch3 and GATA-3's roles in breast cancer metastasis.
Otx2 promotes granule cell precursor proliferation and Shh-dependent medulloblastoma maintenance in vivo
Authors: El Nagar Salsabiel , Chakroun Almahdi , Le Greneur Coralie , Figarella-Branger Dominique , Di Meglio Thomas , Lamonerie Thomas , Billon Nathalie 
Published: August 2018

AbstractThe developmental gene OTX2 is expressed by cerebellar granule cell precursors (GCPs), a cell population which undergoes massive expansion during the early postnatal period in response to sonic hedgehog (Shh). GCPs are thought to be at the origin of most medulloblastomas, a devastating paediatric cancer that arises in the developing cerebellum. OTX2 is overexpressed in all types of medulloblastomas, except in Shh-dependent type 2 medulloblastomas, although it has GCPs as cell-of-origin. This has led to the current view that OTX2 is not involved in tumorigenesis of this subgroup. How OTX2 might contribute to normal or tumoral GCP development in vivo remains unresolved. Here, we have investigated, for the first time, the physiological function of this factor in regulating proliferation and tumorigenesis in the developing mouse cerebellum. We first characterized Otx2-expressing cells in the early postnatal cerebellum and showed that they represent a unique subpopulation of highly proliferative GCPs. We next performed in vivo loss-of-function analysis to dissect out the role of Otx2 in these cells and identified a novel, Shh-independent, function for this factor in controlling postnatal GCP proliferation and cerebellum morphogenesis. Finally, we addressed the function of Otx2 in the context of type 2 medulloblastomas by directing Shh-dependent tumour formation in Otx2+ cells of the developing cerebellum and assessing the effects of Otx2 ablation in this context. We unravel an unexpected, mandatory function for Otx2 in sustaining cell proliferation and long-term maintenance of these tumours in vivo, therefore bringing unpredicted insight into the mechanisms of type 2 medulloblastoma subsistence. Together, these data pinpoint, for the first time, a crucial Shh-independent role for Otx2 in the control of proliferation of normal and tumoral granule cell precursors in vivo and make it an attractive candidate for targeted therapy in Shh-dependent medulloblastomas.
Annotation and functional clustering of circRNA expression in rhesus macaque brain during aging
Authors: Xu Kaiyu , Chen Dong , Wang Zhengbo , Ma Jian , Zhou Jian , Chen Nanhui , Lv Longbao , Zheng Yongtang , Hu Xintian , Zhang Yi , Li Jiali 
Published: August 2018

AbstractThe abundance and function of circular RNAs (circRNAs) in mammalian brain have been reported, but their alterations in the biology of brain aging remain elusive. Here, using deep RNA profiling with linear RNA digestion by RNase R we explored a comprehensive map of changes in circRNA expression in rhesus macaque (macaca mulatta) brain in two age groups from adult (10 y) to aged (20 y) periods. Total 17,050 well expressed, stable circRNAs were identified. Cluster analysis reveals that dynamic changes in circRNA expression show the spatial-, sex- and age-biased specificities. On the basis of separate profiling of the RNAs, age-related circRNAs show differential correlation to host mRNA expression. Furthermore, two voltage-dependent L- and R-type calcium channel gene-derived circCACNA2D1 and circCACNA1E negatively regulate their host mRNA expression. Our results demonstrate the power of changes in circRNA expression to reveal insights into a potentially circRNA-mediated regulatory mechanism underlying the biology of brain aging.
Gene essentiality landscape and druggable oncogenic dependencies in herpesviral primary effusion lymphoma
Authors: Manzano Mark , Patil Ajinkya , Waldrop Alexander , Dave Sandeep S. , Behdad Amir , Gottwein Eva 
Published: August 2018

AbstractPrimary effusion lymphoma (PEL) is caused by Kaposi’s sarcoma-associated herpesvirus. Our understanding of PEL is poor and therefore treatment strategies are lacking. To address this need, we conducted genome-wide CRISPR/Cas9 knockout screens in eight PEL cell lines. Integration with data from unrelated cancers identifies 210 genes as PEL-specific oncogenic dependencies. Genetic requirements of PEL cell lines are largely independent of Epstein-Barr virus co-infection. Genes of the NF-κB pathway are individually non-essential. Instead, we demonstrate requirements for IRF4 and MDM2. PEL cell lines depend on cellular cyclin D2 and c-FLIP despite expression of viral homologs. Moreover, PEL cell lines are addicted to high levels of MCL1 expression, which are also evident in PEL tumors. Strong dependencies on cyclin D2 and MCL1 render PEL cell lines highly sensitive to palbociclib and S63845. In summary, this work comprehensively identifies genetic dependencies in PEL cell lines and identifies novel strategies for therapeutic intervention.
Genome‐wide mapping of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease
Authors: Yao Chen , Chen George , Song Ci , Keefe Joshua , Mendelson Michael , Huan Tianxiao , Sun Benjamin B. , Laser Annika , Maranville Joseph C. , Wu Hongsheng , Ho Jennifer E. , Courchesne Paul , Lyass Asya , Larson Martin G. , Gieger Christian , Graumann Johannes , Johnson Andrew D. , Danesh John , Runz Heiko , Hwang Shih-Jen , Liu Chunyu , Butterworth Adam S. , Suhre Karsten , Levy Daniel 
Published: August 2018

AbstractIdentifying genetic variants associated with circulating protein concentrations (protein quantitative trait loci; pQTLs) and integrating them with variants from genome-wide association studies (GWAS) may illuminate the proteome’s causal role in disease and bridge a knowledge gap regarding SNP-disease associations. We provide the results of GWAS of 71 high-value cardiovascular disease proteins in 6861 Framingham Heart Study participants and independent external replication. We report the mapping of over 16,000 pQTL variants and their functional relevance. We provide an integrated plasma protein-QTL database. Thirteen proteins harbor pQTL variants that match coronary disease-risk variants from GWAS or test causal for coronary disease by Mendelian randomization. Eight of these proteins predict new-onset cardiovascular disease events in Framingham participants. We demonstrate that identifying pQTLs, integrating them with GWAS results, employing Mendelian randomization, and prospectively testing protein-trait associations holds potential for elucidating causal genes, proteins, and pathways for cardiovascular disease and may identify targets for its prevention and treatment.
Distributed natural gas venting offshore along the Cascadia margin
Authors: Riedel M. , Scherwath M. , Römer M. , Veloso M. , Heesemann M. , Spence G. D. 
Published: August 2018

AbstractWidespread gas venting along the Cascadia margin is investigated from acoustic water column data and reveals a nonuniform regional distribution of over 1100 mapped acoustic flares. The highest number of flares occurs on the shelf, and the highest flare density is seen around the nutrition-rich outflow of the Juan de Fuca Strait. We determine ∼430 flow-rates at ∼340 individual flare locations along the margin with instantaneous in situ values ranging from ∼6 mL min−1 to ∼18 L min−1. Applying a tidal-modulation model, a depth-dependent methane density, and extrapolating these results across the margin using two normalization techniques yields a combined average in situ flow-rate of ∼88 × 106 kg y−1. The average methane flux-rate for the Cascadia margin is thus estimated to ∼0.9 g y−1m−2. Combined uncertainties result in a range of these values between 4.5 and 1800% of the estimated mean values.
21st-century modeled permafrost carbon emissions accelerated by abrupt thaw beneath lakes
Authors: Walter Anthony Katey , Schneider von Deimling Thomas , Nitze Ingmar , Frolking Steve , Emond Abraham , Daanen Ronald , Anthony Peter , Lindgren Prajna , Jones Benjamin , Grosse Guido 
Published: August 2018

AbstractPermafrost carbon feedback (PCF) modeling has focused on gradual thaw of near-surface permafrost leading to enhanced carbon dioxide and methane emissions that accelerate global climate warming. These state-of-the-art land models have yet to incorporate deeper, abrupt thaw in the PCF. Here we use model data, supported by field observations, radiocarbon dating, and remote sensing, to show that methane and carbon dioxide emissions from abrupt thaw beneath thermokarst lakes will more than double radiative forcing from circumpolar permafrost-soil carbon fluxes this century. Abrupt thaw lake emissions are similar under moderate and high representative concentration pathways (RCP4.5 and RCP8.5), but their relative contribution to the PCF is much larger under the moderate warming scenario. Abrupt thaw accelerates mobilization of deeply frozen, ancient carbon, increasing 14C-depleted permafrost soil carbon emissions by ~125–190% compared to gradual thaw alone. These findings demonstrate the need to incorporate abrupt thaw processes in earth system models for more comprehensive projection of the PCF this century.
Inhibition of IRE1 RNase activity modulates the tumor cell secretome and enhances response to chemotherapy
Authors: Logue Susan E. , McGrath Eoghan P. , Cleary Patricia , Greene Stephanie , Mnich Katarzyna , Almanza Aitor , Chevet Eric , Dwyer Róisín M. , Oommen Anup , Legembre Patrick , Godey Florence , Madden Emma C. , Leuzzi Brian , Obacz Joanna , Zeng Qingping , Patterson John B. , Jäger Richard , Gorman Adrienne M. , Samali Afshin 
Published: August 2018

AbstractTriple-negative breast cancer (TNBC) lacks targeted therapies and has a worse prognosis than other breast cancer subtypes, underscoring an urgent need for new therapeutic targets and strategies. IRE1 is an endoplasmic reticulum (ER) stress sensor, whose activation is predominantly linked to the resolution of ER stress and, in the case of severe stress, to cell death. Here we demonstrate that constitutive IRE1 RNase activity contributes to basal production of pro-tumorigenic factors IL-6, IL-8, CXCL1, GM-CSF, and TGFβ2 in TNBC cells. We further show that the chemotherapeutic drug, paclitaxel, enhances IRE1 RNase activity and this contributes to paclitaxel-mediated expansion of tumor-initiating cells. In a xenograft mouse model of TNBC, inhibition of IRE1 RNase activity increases paclitaxel-mediated tumor suppression and delays tumor relapse post therapy. We therefore conclude that inclusion of IRE1 RNase inhibition in therapeutic strategies can enhance the effectiveness of current chemotherapeutics.
The role of metal vacancies during high-temperature oxidation of alloys
Authors: Oleksak Richard P. , Kapoor Monica , Perea Daniel. E. , Holcomb Gordon R. , Doğan Ömer N. 
Published: August 2018

AbstractAn improved understanding of high-temperature alloy oxidation is key to the design of structural materials for next-generation energy conversion technologies. An often overlooked, yet fundamental aspect of this oxidation process concerns the fate of the metal vacancies created when metal atoms are ionized and enter the growing oxide layer. In this work, we provide direct experimental evidence showing that these metal vacancies can be inseparably linked to the oxidation process beginning at the very early stages. The coalescence of metal vacancies at the oxide/alloy interface results initially in the formation of low-density metal and eventually in nm-sized voids. The simultaneous and subsequent oxidation of these regions fills the vacated space and promotes adhesion between the growing oxide and the alloy substrate. These structural transformations represent an important deviation from conventional metal oxidation theory, and this improved understanding will aid in the development of new structural alloys with enhanced oxidation resistance.
Differentiating cognitive or motor dimensions associated with the perception of fall-related self-efficacy in Parkinson’s disease
Authors: Chomiak Taylor , Watts Alexander , Burt Jacqueline , Camicioli Richard , Tan Sun Nee , McKeown Martin J. , Hu Bin 
Published: August 2018

AbstractIn Parkinson’s disease (PD), concurrent declines in cognitive and motor domain function can severely limit an individual’s ability to conduct daily tasks. Current diagnostic methods, however, lack precision in differentiating domain-specific contributions of cognitive or motor impairments based on a patients’ clinical manifestation. Fear of falling (FOF) is a common clinical manifestation among the elderly, in which both cognitive and motor impairments can lead to significant barriers to a patients’ physical and social activities. The present study evaluated whether a set of analytical and machine-learning approaches could be used to help delineate boundary conditions and separate cognitive and motor contributions to a patient’s own perception of self-efficacy and FOF. Cognitive and motor clinical scores, in conjunction with FOF, were collected from 57 Parkinson’s patients during a multi-center rehabilitation intervention trial. Statistical methodology was used to extract a subset of uncorrelated cognitive and motor components associated with cognitive and motor predictors, which were then used to independently identify and visualize cognitive and motor dimensions associated with FOF. We found that a central cognitive process, extracted from tests of executive, attentional, and visuoperceptive function, was a unique and significant independent cognitive predictor of FOF in PD. In addition, we provide evidence that the approaches described here may be used to computationally discern specific types of FOF based on separable cognitive or motor models. Our results are consistent with a contemporary model that the deterioration of a central cognitive mechanism that modulates self-efficacy also plays a critical role in FOF in PD.
Remote quantum clock synchronization without synchronized clocks
Authors: Ilo-Okeke Ebubechukwu O. , Tessler Louis , Dowling Jonathan P. , Byrnes Tim 
Published: August 2018

AbstractA major outstanding problem for many quantum clock synchronization protocols is the hidden assumption of a common phase reference between the parties to be synchronized. In general, the definition of the quantum states between two parties do not have consistent phase definitions, which can lead to an unknown systematic error. We show that despite prior arguments to the contrary, it is possible to remove this unknown phase via entanglement purification. This closes the loophole for entanglement based quantum clock synchronization protocols, which is a non-local approach to synchronize two clocks independent of the properties of the intervening medium. Starting with noisy Bell pairs, we show that the scheme produces a singlet state for any combination of (i) differing basis conventions for Alice and Bob; (ii) an overall time offset in the execution of the purification algorithm; and (iii) the presence of a noisy channel. Error estimates reveal that better performance than existing classical Einstein synchronization protocols should be achievable using current technology.