bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure of Electron‐Scale Plasma Mixing Along the Dayside Reconnection Separatrix
Authors: Holmes J. C. , Ergun R. E. , Nakamura R. , Roberts O. , Wilder F. D. , Newman D. L. 
Published: November 2019

AbstractInteractions between magnetic reconnection inflows and outflows can result in a violent mixing process. In Magnetospheric MultiScale observations of asymmetric, low guide‐field reconnection, highly sheared electron flow paired with sharp density and temperature gradients have been found in association with bursts of strong (≥100 mV/m) electric fields parallel to the ambient magnetic field. It is likely that large spikes in E‖ are part of a dynamic, small‐scale structure which results from mixing between plasmas. In this study, a 1‐D Vlasov simulation with parameters directly comparable to the observed plasma environment and interaction timescale is used to demonstrate that mixing at a sharp boundary between magnetospheric and magnetosheath electrons is qualitatively consistent with measured particle distributions and signatures in E‖. Properties of mixing structures such as net electric potential are estimated and found capable of accelerating electron beams toward the electron diffusion region but are not necessarily sufficient to generate the strongest observed jets. Obliquely propagating lower hybrid drift waves are also present and likely provide most of the energy for acceleration. Drift waves may be responsible for cross‐field transport required to begin the mixing process. We conclude that parallel mixing primarily acts to mediate plasma boundaries, thermalizing electron beams contributing to the high anisotropy (Te‖>Te⊥) electron distributions found in the dayside reconnection magnetospheric inflow region.
Role of Iron in the Marquesas Island Mass Effect
Authors: Raapoto Hirohiti , Martinez Elodie , Petrenko Anne , Doglioli Andrea , Gorgues Thomas , Sauzède Raphaëlle , Maamaatuaiahutapu Keitapu , Maes Christophe , Menkes Christophe , Lefèvre Jérôme 
Published: November 2019

AbstractA remarkable chlorophyll‐a concentration (Chl, a proxy of phytoplankton biomass) plume can be noticed on remotely sensed ocean color observations at the boundary separating the equatorial mesotrophic from the subtropical oligotrophic waters in the central South Pacific Ocean. This prominent biological feature is known as the island mass effect of the Marquesas archipelago. Waters surrounding these islands present high macronutrient concentrations but an iron depletion. In this study, the origin of Chl enhancement is investigated using a modeling approach. Four simulations based on identical physical and biogeochemical forcings but with different iron sources are conducted and analyzed. Only simulations considering an iron input from the island sediments present similar patterns (despite being too weak) of vertical and horizontal Chl distributions as compared to biogeochemical‐Argo profiling float and satellite observations. In addition, simulations with no other iron input than the boundary forcings reveal the relative importance of remote processes in modulating the seasonal pattern of Chl around the archipelago through horizontal advection of nutrient‐rich waters from the equator toward the archipelago and vertical mixing uplifting deep nutrient‐rich waters toward the upper lit layer.
Toward a Better Regional Ozone Forecast Over CONUS Using Rapid Data Assimilation of Clouds and Meteorology in WRF‐Chem
Authors: Ryu Young‐Hee , Hodzic Alma , Descombes Gael , Hu Ming , Barré Jérôme 
Published: November 2019

AbstractAccuracy of cloud predictions in numerical weather models can considerably impact ozone (O3) forecast skill. This study assesses the benefits in surface O3 predictions of using the Rapid Refresh (RAP) forecasting system that assimilates clouds as well as conventional meteorological variables at hourly time scales. We evaluate and compare the WRF‐Chem simulations driven by RAP and the Global Forecast System (GFS) forecasts over the Contiguous United States (CONUS) for 2016 summer. The day 1 forecasts of surface O3 and temperature driven by RAP are in better agreements with observations. Reductions of 5 ppb in O3 mean bias error and 2.4 ppb in O3 root‐mean‐square‐error are obtained on average over CONUS with RAP compared to those with GFS. The WRF‐Chem simulation driven by GFS shows a higher probability of capturing O3 exceedances but exhibits more frequent false alarms, resulting from its tendency to overpredict O3. The O3 concentrations are found to respond mainly to the changes in boundary layer height that directly affects the mixing of O3 and its precursors. The RAP data assimilation shows improvements in the cloud forecast skill during the initial forecast hours, which reduces O3 forecast errors at the initial forecast hours especially under cloudy‐sky conditions. Sensitivity simulations utilizing satellite clouds show that the WRF‐Chem simulation with RAP produces too thick low‐level clouds, which leads to O3 underprediction in the boundary layer.
Low‐Latitude Calcareous Nannofossil Response in the Indo‐Pacific Warm Pool Across the Eocene‐Oligocene Transition of Java, Indonesia
Authors: Jones Amy P. , Dunkley Jones Tom , Coxall Helen , Pearson Paul N. , Nala Dominika , Hoggett Murray 
Published: November 2019

AbstractWe reconstruct the calcareous nannofossil response to the Eocene‐Oligocene Transition (EOT)—the most significant climate transition of the Cenozoic—in the Indo‐Pacific Warm Pool. Data from south central Java consist of species relative abundance counts of well‐preserved nannofossil assemblages. From the late middle Eocene to early Oligocene species biodiversity declined, with the most rapid species loss occurring across the latest Eocene rosette‐shaped discoaster extinction event (DEE; ~34.44–34.77 Ma). A decline in abundance of oligotrophic indicator taxa across the DEE indicates increased nutrient supply to the tropical surface ocean in the early stages of the EOT. The mean lith size of reticulofenestrids also increases across the DEE driven by a marked reduction in the abundance of smallReticulofenestramorphotypes (<3.5 μm). There is no preferential loss of largerReticulofenestracell sizes (coccoliths > 8 μm) across the EOT, indicating that coccolith size was apparently not limited by atmospheric CO2concentrations at this time. Overall, the main phase of tropical phytoplankton ecosystem change preceded the interval of rapid Antarctic ice sheet growth and is closely associated with the biotic perturbations that define the start of the EOT. This suggests that enhancement of Southern Ocean controls on tropical ocean biogeochemistry and nutrient pathways may have played a role in triggering the transition to an icehouse climate state.
Groundwater cable bacteria conserve energy by sulfur disproportionation
Authors: Müller Hubert , Marozava Sviatlana , Probst Alexander J , Meckenstock Rainer U 
Published: November 2019

Abstract
Cable bacteria of the family Desulfobulbaceae couple spatially separated sulfur oxidation and oxygen or nitrate reduction by long-distance electron transfer, which can constitute the dominant sulfur oxidation process in shallow sediments. However, it remains unknown how cells in the anoxic part of the centimeter-long filaments conserve energy. We found 16S rRNA gene sequences similar to groundwater cable bacteria in a 1-methylnaphthalene-degrading culture (1MN). Cultivation with elemental sulfur and thiosulfate with ferrihydrite or nitrate as electron acceptors resulted in a first cable bacteria enrichment culture dominated &gt;90% by 16S rRNA sequences belonging to the Desulfobulbaceae. Desulfobulbaceae-specific fluorescence in situ hybridization (FISH) unveiled single cells and filaments of up to several hundred micrometers length to belong to the same species. The Desulfobulbaceae filaments also showed the distinctive cable bacteria morphology with their continuous ridge pattern as revealed by atomic force microscopy. The cable bacteria grew with nitrate as electron acceptor and elemental sulfur and thiosulfate as electron donor, but also by sulfur disproportionation when Fe(Cl)2 or Fe(OH)3 were present as sulfide scavengers. Metabolic reconstruction based on the first nearly complete genome of groundwater cable bacteria revealed the potential for sulfur disproportionation and a chemo-litho-autotrophic metabolism. The presence of different types of hydrogenases in the genome suggests that they can utilize hydrogen as alternative electron donor. Our results imply that cable bacteria not only use sulfide oxidation coupled to oxygen or nitrate reduction by LDET for energy conservation, but sulfur disproportionation might constitute the energy metabolism for cells in large parts of the cable bacterial filaments.
Schizophrenia polygenic risk score and 20-year course of illness in psychotic disorders
Authors: Jonas Katherine G. , Lencz Todd , Li Kaiqiao , Malhotra Anil K. , Perlman Greg , Fochtmann Laura J. , Bromet Evelyn J. , Kotov Roman 
Published: November 2019

AbstractUnderstanding whether and how the schizophrenia polygenic risk score (SZ PRS) predicts course of illness could improve diagnosis and prognostication in psychotic disorders. We tested whether the SZ PRS predicts symptoms, cognition, illness severity, and diagnostic changes over the 20 years following first admission. The Suffolk County Mental Health Project is an inception cohort study of first-admission patients with psychosis. Patients were assessed six times over 20 years, and 249 provided DNA. Geographically- and demographically-matched never psychotic adults were recruited at year 20, and 205 provided DNA. Symptoms were rated using the Schedule for the Assessment of Positive Symptoms and Schedule for the Assessment of Negative Symptoms. Cognition was evaluated with a comprehensive neuropsychological battery. Illness severity and diagnosis were determined by consensus of study psychiatrists. SZ PRS was significantly higher in first-admission than never psychotic groups. Within the psychosis cohort, the SZ PRS predicted more severe negative symptoms (β = 0.21), greater illness severity (β = 0.28), and worse cognition (β = −0.35), across the follow-up. The SZ PRS was the strongest predictor of diagnostic shifts from affective to non-affective psychosis over the 20 years (AUC = 0.62). The SZ PRS predicts persistent differences in cognition and negative symptoms. The SZ PRS also predicts who among those who appear to have a mood disorder with psychosis at first admission will ultimately be diagnosed with a schizophrenia spectrum disorder. These findings show potential for the SZ PRS to become a tool for diagnosis and treatment planning.
Cisplatin exposure causes c-Myc-dependent resistance to CDK4/6 inhibition in HPV-negative head and neck squamous cell carcinoma
Authors: Robinson Anthony M. , Rathore Richa , Redlich Nathan J. , Adkins Douglas R. , VanArsdale Todd , Van Tine Brian A. , Michel Loren S. 
Published: November 2019

AbstractThe loss of p16 is a signature event in Human Papilloma Virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) that leads to increased Cyclin Dependent Kinase 4/6 (CDK) signaling. Palbociclib, a CDK4/6 inhibitor, is active for the treatment of a subset of HNSCC. In this study, we analyzed patient response data from a phase I clinical trial of palbociclib in HNSCC and observed an association between prior cisplatin exposure and CDK inhibitor resistance. We studied the effects of palbociclib on cisplatin-sensitive and -resistant HNSCC cell lines. We found that while palbociclib is highly effective against chemo-naive HNSCC cell lines and tumor xenografts, prior cisplatin exposure induces intrinsic resistance to palbociclib in vivo, a relationship that was not observed in vitro. Mechanistically, in the course of provoking a DNA damage-resistance phenotype, cisplatin exposure upregulates both c-Myc and cyclin E, and combination treatment with palbociclib and the c-Myc bromodomain inhibitor JQ1 exerts a synergistic anti-growth effect in cisplatin-resistant cells. These data show the benefit of exploiting the inherent resistance mechanisms of HNSCC to overcome cisplatin- and palbociclib resistance through the use of c-Myc inhibition.
Targeting melanoma’s MCL1 bias unleashes the apoptotic potential of BRAF and ERK1/2 pathway inhibitors
Authors: Sale Matthew J. , Minihane Emma , Monks Noel R. , Gilley Rebecca , Richards Frances M. , Schifferli Kevin P. , Andersen Courtney L. , Davies Emma J. , Vicente Mario Aladren , Ozono Eiko , Markovets Aleksandra , Dry Jonathan R. , Drew Lisa , Flemington Vikki , Proia Theresa , Jodrell Duncan I. , Smith Paul D. , Cook Simon J. 
Published: November 2019

AbstractBRAF and MEK1/2 inhibitors are effective in melanoma but resistance inevitably develops. Despite increasing the abundance of pro-apoptotic BIM and BMF, ERK1/2 pathway inhibition is predominantly cytostatic, reflecting residual pro-survival BCL2 family activity. Here, we show that uniquely low BCL-XL expression in melanoma biases the pro-survival pool towards MCL1. Consequently, BRAF or MEK1/2 inhibitors are synthetic lethal with the MCL1 inhibitor AZD5991, driving profound tumour cell death that requires BAK/BAX, BIM and BMF, and inhibiting tumour growth in vivo. Combination of ERK1/2 pathway inhibitors with BCL2/BCL-w/BCL-XL inhibitors is stronger in CRC, correlating with a low MCL1:BCL-XL ratio; indeed the MCL1:BCL-XL ratio is predictive of ERK1/2 pathway inhibitor synergy with MCL1 or BCL2/BCL-w/BCL-XL inhibitors. Finally, AZD5991 delays acquired BRAFi/MEKi resistance and enhances the efficacy of an ERK1/2 inhibitor in a model of acquired BRAFi + MEKi resistance. Thus combining ERK1/2 pathway inhibitors with MCL1 antagonists in melanoma could improve therapeutic index and patient outcomes.
Destabilization of NOXA mRNA as a common resistance mechanism to targeted therapies
Authors: Montero Joan , Gstalder Cécile , Kim Daniel J. , Sadowicz Dorota , Miles Wayne , Manos Michael , Cidado Justin R. , Paul Secrist J. , Tron Adriana E. , Flaherty Keith , Stephen Hodi F. , Yoon Charles H. , Letai Anthony , Fisher David E. , Haq Rizwan 
Published: November 2019

AbstractMost targeted cancer therapies fail to achieve complete tumor regressions or attain durable remissions. To understand why these treatments fail to induce robust cytotoxic responses despite appropriately targeting oncogenic drivers, here we systematically interrogated the dependence of cancer cells on the BCL-2 family of apoptotic proteins after drug treatment. We observe that multiple targeted therapies, including BRAF or EGFR inhibitors, rapidly deplete the pro-apoptotic factor NOXA, thus creating a dependence on the anti-apoptotic protein MCL-1. This adaptation requires a pathway leading to destabilization of the NOXA mRNA transcript. We find that interruption of this mechanism of anti-apoptotic adaptive resistance dramatically increases cytotoxic responses in cell lines and a murine melanoma model. These results identify NOXA mRNA destabilization/MCL-1 adaptation as a non-genomic mechanism that limits apoptotic responses, suggesting that sequencing of MCL-1 inhibitors with targeted therapies could overcome such widespread and clinically important resistance.
Hyperpolarized relaxometry based nuclear T1 noise spectroscopy in diamond
Authors: Ajoy A. , Safvati B. , Nazaryan R. , Oon J. T. , Han B. , Raghavan P. , Nirodi R. , Aguilar A. , Liu K. , Cai X. , Lv X. , Druga E. , Ramanathan C. , Reimer J. A. , Meriles C. A. , Suter D. , Pines A. 
Published: November 2019

AbstractThe origins of spin lifetimes in quantum systems is a matter of importance in several areas of quantum information. Spectrally mapping spin relaxation processes provides insight into their origin and motivates methods to mitigate them. In this paper, we map nuclear relaxation in a prototypical system of $${}^{13}{\rm{C}}$$

13

C
nuclei in diamond coupled to Nitrogen Vacancy (NV) centers over a wide field range (1 mT-7 T). Nuclear hyperpolarization through optically pumped NV electrons allows signal measurement savings exceeding million-fold over conventional methods. Through a systematic study with varying substitutional electron (P1 center) and $${}^{13}{\rm{C}}$$

13

C
concentrations, we identify the operational relaxation channels for the nuclei at different fields as well as the dominant role played by $${}^{13}{\rm{C}}$$

13

C
coupling to the interacting P1 electronic spin bath. These results motivate quantum control techniques for dissipation engineering to boost spin lifetimes in diamond, with applications including engineered quantum memories and hyperpolarized $${}^{13}{\rm{C}}$$

13

C
imaging.
Chemokine receptor trafficking coordinates neutrophil clustering and dispersal at wounds in zebrafish
Authors: Coombs Caroline , Georgantzoglou Antonios , Walker Hazel A. , Patt Julian , Merten Nicole , Poplimont Hugo , Busch-Nentwich Elisabeth M. , Williams Sarah , Kotsi Christina , Kostenis Evi , Sarris Milka 
Published: November 2019

AbstractImmune cells congregate at specific loci to fight infections during inflammatory responses, a process that must be transient and self-resolving. Cell dispersal promotes resolution, but it remains unclear how transition from clustering to dispersal is regulated. Here we show, using quantitative live imaging in zebrafish, that differential ligand-induced trafficking of chemokine receptors such as Cxcr1 and Cxcr2 orchestrates the state of neutrophil congregation at sites of tissue damage. Through receptor mutagenesis and biosensors, we show that Cxcr1 promotes clustering at wound sites, but is promptly desensitized and internalized, which prevents excess congregation. By contrast, Cxcr2 promotes bidirectional motility and is sustained at the plasma membrane. Persistent plasma membrane residence of Cxcr2 prolongs downstream signaling and is required for sustained exploratory motion conducive to dispersal. Thus, differential trafficking of two chemokine receptors allows coordination of antagonistic cell behaviors, promoting a self-resolving migratory response.
A thalamocortical pathway for fast rerouting of tactile information to occipital cortex in congenital blindness
Authors: Müller Franziska , Niso Guiomar , Samiee Soheila , Ptito Maurice , Baillet Sylvain , Kupers Ron 
Published: November 2019

AbstractIn congenitally blind individuals, the occipital cortex responds to various nonvisual inputs. Some animal studies raise the possibility that a subcortical pathway allows fast re-routing of tactile information to the occipital cortex, but this has not been shown in humans. Here we show using magnetoencephalography (MEG) that tactile stimulation produces occipital cortex activations, starting as early as 35 ms in congenitally blind individuals, but not in blindfolded sighted controls. Given our measured thalamic response latencies of 20 ms and a mean estimated lateral geniculate nucleus to primary visual cortex transfer time of 15 ms, we claim that this early occipital response is mediated by a direct thalamo-cortical pathway. We also observed stronger directed connectivity in the alpha band range from posterior thalamus to occipital cortex in congenitally blind participants. Our results strongly suggest the contribution of a fast thalamo-cortical pathway in the cross-modal activation of the occipital cortex in congenitally blind humans.
The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype
Authors: Xie Dasen , Xu Yuanchao , Wang Jinpeng , Liu Wenrui , Zhou Qian , Luo Shaobo , Huang Wu , He Xiaoming , Li Qing , Peng Qingwu , Yang Xueyong , Yuan Jiaqing , Yu Jigao , Wang Xiyin , Lucas William J. , Huang Sanwen , Jiang Biao , Zhang Zhonghua 
Published: November 2019

AbstractThe botanical family Cucurbitaceae includes a variety of fruit crops with global or local economic importance. How their genomes evolve and the genetic basis of diversity remain largely unexplored. In this study, we sequence the genome of the wax gourd (Benincasa hispida), which bears giant fruit up to 80 cm in length and weighing over 20 kg. Comparative analyses of six cucurbit genomes reveal that the wax gourd genome represents the most ancestral karyotype, with the predicted ancestral genome having 15 proto-chromosomes. We also resequence 146 lines of diverse germplasm and build a variation map consisting of 16 million variations. Combining population genetics and linkage mapping, we identify a number of regions/genes potentially selected during domestication and improvement, some of which likely contribute to the large fruit size in wax gourds. Our analyses of these data help to understand genome evolution and function in cucurbits.
Pathways to defense metabolites and evading fruit bitterness in genus Solanum evolved through 2-oxoglutarate-dependent dioxygenases
Authors: Cárdenas Pablo D. , Sonawane Prashant D. , Heinig Uwe , Jozwiak Adam , Panda Sayantan , Abebie Bekele , Kazachkova Yana , Pliner Margarita , Unger Tamar , Wolf Dalia , Ofner Itai , Vilaprinyo Ester , Meir Sagit , Davydov Olga , Gal-on Amit , Burdman Saul , Giri Ashok , Zamir Dani , Scherf Tali , Szymanski Jedrzej , Rogachev Ilana , Aharoni Asaph 
Published: November 2019

AbstractThe genus Solanum comprises three food crops (potato, tomato, and eggplant), which are consumed on daily basis worldwide and also producers of notorious anti-nutritional steroidal glycoalkaloids (SGAs). Hydroxylated SGAs (i.e. leptinines) serve as precursors for leptines that act as defenses against Colorado Potato Beetle (Leptinotarsa decemlineata Say), an important pest of potato worldwide. However, SGA hydroxylating enzymes remain unknown. Here, we discover that 2-OXOGLUTARATE-DEPENDENT-DIOXYGENASE (2-ODD) enzymes catalyze SGA-hydroxylation across various Solanum species. In contrast to cultivated potato, Solanum chacoense, a widespread wild potato species, has evolved a 2-ODD enzyme leading to the formation of leptinines. Furthermore, we find a related 2-ODD in tomato that catalyzes the hydroxylation of the bitter α-tomatine to hydroxytomatine, the first committed step in the chemical shift towards downstream ripening-associated non-bitter SGAs (e.g. esculeoside A). This 2-ODD enzyme prevents bitterness in ripe tomato fruit consumed today which otherwise would remain unpleasant in taste and more toxic.
Rice life cycle-based global mercury biotransport and human methylmercury exposure
Authors: Liu Maodian , Zhang Qianru , Cheng Menghan , He Yipeng , Chen Long , Zhang Haoran , Cao Hanlin , Shen Huizhong , Zhang Wei , Tao Shu , Wang Xuejun 
Published: November 2019

AbstractProtecting the environment and enhancing food security are among the world’s greatest challenges. Fish consumption is widely considered to be the single significant dietary source of methylmercury. Nevertheless, by synthesizing data from the past six decades and using a variety of models, we find that rice could be a significant global dietary source of human methylmercury exposure, especially in South and Southeast Asia. In 2013, globalization caused 9.9% of human methylmercury exposure via the international rice trade and significantly aggravated rice-derived exposure in Africa (62%), Central Asia (98%) and Europe (42%). In 2016, 180 metric tons of mercury were generated in rice plants, 14-fold greater than that exported from oceans via global fisheries. We suggest that future research should consider both the joint ingestion of rice with fish and the food trade in methylmercury exposure assessments, and anthropogenic biovectors such as crops should be considered in the global mercury cycle.