bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exposed soil and mineral map of the Australian continent revealing the land at its barest
Authors: Roberts Dale , Wilford John , Ghattas Omar 
Published: November 2019

AbstractMulti-spectral remote sensing has already played an important role in mapping surface mineralogy. However, vegetation – even when relatively sparse – either covers the underlying substrate or modifies its spectral response, making it difficult to resolve diagnostic mineral spectral features. Here we take advantage of the petabyte-scale Landsat datasets covering the same areas for periods exceeding 30 years combined with a novel high-dimensional statistical technique to extract a noise-reduced, cloud-free, and robust estimate of the spectral response of the barest state (i.e. least vegetated) across the whole continent of Australia at 25 m2 resolution. Importantly, our method preserves the spectral relationships between different wavelengths of the spectra. This means that our freely available continental-scale product can be combined with machine learning for enhanced geological mapping, mineral exploration, digital soil mapping, and establishing environmental baselines for understanding and responding to food security, climate change, environmental degradation, water scarcity, and threatened biodiversity.
Taming out-of-equilibrium dynamics on interconnected networks
Authors: Buldú Javier M. , Pablo-Martí Federico , Aguirre Jacobo 
Published: November 2019

AbstractA wide variety of social, biological or technological systems can be described as processes taking place on networked structures in continuous interaction with other networks. We propose here a new methodology to describe, anticipate and manage, in real time, the out-of-equilibrium dynamics of processes that evolve on interconnected networks. This goal is achieved through the full analytical treatment of the phenomenology and its reduction to a two-dimensional flux diagram, allowing us to predict at every time step the dynamical consequences of modifying the links between the different ensembles. Our results are consistent with real data and the methodology can be translated to clustered networks and/or interconnected networks of any size, topology or origin, from the struggle for knowledge on innovation structures to international economic relations or disease spreading on social groups.
Chiral donor–acceptor azetines as powerful reactants for synthesis of amino acid derivatives
Authors: Marichev Kostiantyn O. , Dong Kuiyong , Massey Lynée A. , Deng Yongming , De Angelis Luca , Wang Kan , Arman Hadi , Doyle Michael P. 
Published: November 2019

AbstractCoupling reactions of amines and alcohols are of central importance for applications in chemistry and biology. These transformations typically involve the use of a reagent, activated as an electrophile, onto which nucleophile coupling results in the formation of a carbon-nitrogen or a carbon–oxygen bond. Several promising reagents and procedures have been developed to achieve these bond forming processes in high yields with excellent stereocontrol, but few offer direct coupling without the intervention of a catalyst. Herein, we report the synthesis of chiral donor–acceptor azetines by highly enantioselective [3 + 1]-cycloaddition of enoldiazoacetates with aza-ylides and their selective coupling with nitrogen and oxygen nucleophiles via 3-azetidinones to form amino acid derivatives, including those of peptides and natural products. The overall process is general for a broad spectrum of nucleophiles, has a high degree of electronic and steric selectivity, and retains the enantiopurity of the original azetine.
Quantum Generative Adversarial Networks for learning and loading random distributions
Authors: Zoufal Christa , Lucchi Aurélien , Woerner Stefan 
Published: November 2019

AbstractQuantum algorithms have the potential to outperform their classical counterparts in a variety of tasks. The realization of the advantage often requires the ability to load classical data efficiently into quantum states. However, the best known methods require $${\mathcal{O}}\left({2}^{n}\right)$$O2n gates to load an exact representation of a generic data structure into an $$n$$n-qubit state. This scaling can easily predominate the complexity of a quantum algorithm and, thereby, impair potential quantum advantage. Our work presents a hybrid quantum-classical algorithm for efficient, approximate quantum state loading. More precisely, we use quantum Generative Adversarial Networks (qGANs) to facilitate efficient learning and loading of generic probability distributions - implicitly given by data samples - into quantum states. Through the interplay of a quantum channel, such as a variational quantum circuit, and a classical neural network, the qGAN can learn a representation of the probability distribution underlying the data samples and load it into a quantum state. The loading requires $${\mathcal{O}}\left(poly\left(n\right)\right)$$Opolyn gates and can thus enable the use of potentially advantageous quantum algorithms, such as Quantum Amplitude Estimation. We implement the qGAN distribution learning and loading method with Qiskit and test it using a quantum simulation as well as actual quantum processors provided by the IBM Q Experience. Furthermore, we employ quantum simulation to demonstrate the use of the trained quantum channel in a quantum finance application.
SeaFlow data v1, high-resolution abundance, size and biomass of small phytoplankton in the North Pacific
Authors: Ribalet François , Berthiaume Chris , Hynes Annette , Swalwell Jarred , Carlson Michael , Clayton Sophie , Hennon Gwenn , Poirier Camille , Shimabukuro Eric , White Angelicque , Armbrust E. Virginia 
Published: November 2019

AbstractSeaFlow is an underway flow cytometer that provides continuous shipboard observations of the abundance and optical properties of small phytoplankton (<5 μm in equivalent spherical diameter, ESD). Here we present data sets consisting of SeaFlow-based cell abundance, forward light scatter, and pigment fluorescence of individual cells, as well as derived estimates of ESD and cellular carbon content of picophytoplankton, which includes the cyanobacteria Prochlorococcus, Synechococcus and small-sized Crocosphaera (<5 μm ESD), and picophytoplankton and nanophytoplankton (2–5 μm ESD). Data were collected in surface waters (≈5 m depth) from 27 oceanographic cruises carried out in the Northeast Pacific Ocean between 2010 and 2018. Thirteen cruises provide high spatial resolution (≈1 km) measurements across 32,500 km of the Northeast Pacific Ocean and 14 near-monthly cruises beginning in 2015 provide seasonal distributions at the long-term sampling site (Station ALOHA) of the Hawaii Ocean Time-Series. These data sets expand our knowledge of the current spatial and temporal distributions of picophytoplankton in the surface ocean.
Arabidopsis proteome and the mass spectral assay library
Authors: Zhang Huoming , Liu Pei , Guo Tiannan , Zhao Huayan , Bensaddek Dalila , Aebersold Ruedi , Xiong Liming 
Published: November 2019

AbstractArabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.
Pathways of ocean heat towards Pine Island and Thwaites grounding lines
Authors: Nakayama Yoshihiro , Manucharyan Georgy , Zhang Hong , Dutrieux Pierre , Torres Hector S. , Klein Patrice , Seroussi Helene , Schodlok Michael , Rignot Eric , Menemenlis Dimitris 
Published: November 2019

AbstractIn the Amundsen Sea, modified Circumpolar Deep Water (mCDW) intrudes into ice shelf cavities, causing high ice shelf melting near the ice sheet grounding lines, accelerating ice flow, and controlling the pace of future Antarctic contributions to global sea level. The pathways of mCDW towards grounding lines are crucial as they directly control the heat reaching the ice. A realistic representation of mCDW circulation, however, remains challenging due to the sparsity of in-situ observations and the difficulty of ocean models to reproduce the available observations. In this study, we use an unprecedentedly high-resolution (200 m horizontal and 10 m vertical grid spacing) ocean model that resolves shelf-sea and sub-ice-shelf environments in qualitative agreement with existing observations during austral summer conditions. We demonstrate that the waters reaching the Pine Island and Thwaites grounding lines follow specific, topographically-constrained routes, all passing through a relatively small area located around 104°W and 74.3°S. The temporal and spatial variabilities of ice shelf melt rates are dominantly controlled by the sub-ice shelf ocean current. Our findings highlight the importance of accurate and high-resolution ocean bathymetry and subglacial topography for determining mCDW pathways and ice shelf melt rates.
Qualitative microbiome profiling along a wastewater system in Kampala, Uganda
Authors: Schneeberger Pierre H. H. , Fuhrimann Samuel , Becker Sören L. , Pothier Joël F. , Duffy Brion , Beuret Christian , Frey Jürg E. , Utzinger Jürg 
Published: November 2019

AbstractKampala, the capital city of Uganda, is rapidly expanding without adequate wastewater treatment facilities to accommodate the current estimated population of 1.68 million people. Hence, freshwater bodies and natural ecosystems around the city are heavily polluted with organic and inorganic contaminants. Yet, there is a paucity of data on pathogenic microorganisms, which potentially threatens health of local communities. We performed a qualitative microbial analysis using a whole metagenome sequencing approach encompassing over 150 gigabases of sequencing data to characterize the Nakivubo wastewater system, which includes a wastewater channel and surrounding wetlands. We found that microbial diversity is heterogeneous throughout the system and that three community state types could be differentiated. We showed the presence of various waterborne agents of gastrointestinal infections in humans, which were associated with leakage occurring around two locations along the wastewater channel. Our data indicate that the microbial decontamination capacity of the local wastewater treatment facility was insufficient at the time of sampling, and that several areas of the wetlands were contaminated with human pathogens, indicating that parts of the wetlands are potentially unsafe for urban agriculture.
Pleiotropic effects of alpha-SNAP M105I mutation on oocyte biology: ultrastructural and cellular changes that adversely affect female fertility in mice
Authors: de Paola Matilde , Miró María Paz , Ratto Marcelo , Bátiz Luis Federico , Michaut Marcela Alejandra 
Published: November 2019

AbstractAfter sperm-oocyte fusion, cortical granules (CGs) located in oocyte cortex undergo exocytosis and their content is released into the perivitelline space to avoid polyspermy. Thus, cortical granule exocytosis (CGE) is a key process for fertilization success. We have demonstrated that alpha-SNAP -and its functional partner NSF- mediate fusion of CGs with the plasma membrane in mouse oocytes. Here, we examined at cellular and ultrastructural level oocytes from hyh (hydrocephalus with hop gait) mice, which present a missense mutation in the Napa gene that results in the substitution of methionine for isoleucine at position 105 (M105I) of alpha-SNAP. Mutated alpha-SNAP was mislocalized in hyh oocytes while NSF expression increased during oocyte maturation. Staining of CGs showed that 9.8% of hyh oocytes had abnormal localization of CGs and oval shape. Functional tests showed that CGE was impaired in hyh oocytes. Interestingly, in vitro fertilization assays showed a decreased fertilization rate for hyh oocytes. Furthermore, fertilized hyh oocytes presented an increased polyspermy rate compared to wild type ones. At ultrastructural level, hyh oocytes showed small mitochondria and a striking accumulation and secretion of degradative structures. Our findings demonstrate the negative effects of alpha-SNAP M105 mutation on oocyte biology and further confirm the relevance of alpha-SNAP in female fertility.
Feasibility of a circulation model for the assessment of endovascular recanalization procedures and periprocedural thromboembolism in-vitro
Authors: Rusch René , Trentmann Jens , Hummitzsch Lars , Rusch Melanie , Aludin Schekeb , Haneya Assad , Albrecht Martin , Schäfer Jost Philipp , Puehler Thomas , Cremer Jochen , Berndt Rouven 
Published: November 2019

AbstractAim of this study was to establish a simple and highly reproducible physiological circulation model to investigate endovascular device performance. The developed circulation model included a pneumatically driven pulsatile pump to generate a flow rate of 2.7 L/min at 70 beats per minute. Sections from the superficial femoral arteries were used in order to simulate device/tissue interaction and a filter was integrated to analyze periinterventional thromboembolism of white, red and mixed thrombi. The working fluid (3 L) was a crystalloid solution constantly tempered at 36.5 °C. To evaluate the model, aspiration thrombectomy, stent-implantation and thrombectomy with the Fogarty catheter were performed. Usability of the model was measured by the System Usability Scale (SUS) – Score. Histological specimens were prepared and analyzed postinterventional to quantify tissue/device interaction. Moreover, micro- and macroembolism were evaluated for each thrombus entity and each device. Results were tested for normality using the D’Agostino-Pearson test. Statistical comparisons of two groups were performed using the Student’s t-test. All devices were able to remove the occlusions after a maximum of 2 attempts. First-pass-recanalization was not fully achieved for aspiration thrombectomy of mixed thrombi (90.6%), aspiration thrombectomy of red thrombi (84.4%) and stent-implantation in occlusions of red thrombi (92.2%). Most micro- and macroembolism were observed using the Fogarty catheter and after stent-implantation in occlusions of white thrombi. Histological examinations revealed a significant reduction of the vascular layers suggesting vascular damage after use of the Fogarty catheter (327.3 ± 3.5 μm vs. 440.6 ± 3.9 μm; p = 0.026). Analysis of SUS rendered a mean SUS-Score of 80.4 which corresponds to an excellent user acceptability of the model. In conclusion, we describe a stable, easy to handle and reproducible physiological circulation model for the simulation of endovascular thrombectomy including device performance and thromboembolism.
Follistatin impacts Tumor Angiogenesis and Outcome in Thymic Epithelial Tumors
Authors: Janik Stefan , Bekos Christine , Hacker Philipp , Raunegger Thomas , Schiefer Ana-Iris , Müllauer Leonhard , Veraar Cecilia , Dome Balazs , Klepetko Walter , Ankersmit Hendrik Jan , Moser Bernhard 
Published: November 2019

AbstractTumor angiogenesis is a key factor in the progression of thymic epithelial tumors (TETs). Activin A, a member of the TGFβ family, and its antagonist Follistatin are involved in several human malignancies and angiogenesis. We investigated Activin A and Follistatin in serum and tumor tissue of patients with TETs in relation to microvessel density (MVD), WHO histology classification, tumor stage and outcome. Membranous Activin A expression was detected in all tumor tissues of TETs, while Follistatin staining was found in tumor nuclei and cytoplasm. Patients with TETs presented with significantly higher Activin A and Follistatin serum concentrations compared to healthy volunteers, respectively. Follistatin serum concentrations correlated significantly with tumor stage and decreased to physiologic values after complete tumor resection. Follistatin serum concentrations correlated further with MVD and were associated with significantly worse freedom from recurrence (FFR). Low numbers of immature tumor vessels represented even an independent worse prognostic factor for FFR at multivariable analysis. To conclude, the Activin A - Follistatin axis is involved in the pathogenesis of TETs. Further study of Follistatin and Activin A in TETs is warranted as the molecules may serve as targets to inhibit tumor angiogenesis and tumor progression.
Diffusive Memristive Switching on the Nanoscale, from Individual Nanoparticles towards Scalable Nanocomposite Devices
Authors: Vahl Alexander , Carstens Niko , Strunskus Thomas , Faupel Franz , Hassanien Abdou 
Published: November 2019

AbstractNanoscale memristive phenomena are of great interest not only to miniaturize devices and improve their performance but also to understand the details of the underlying mechanism. Herein, we utilize conductive atomic force microscopy (C-AFM) as a non-invasive method to examine the nanoscale memristive properties of individual noble metal alloy nanoparticles that are sparsely encapsulated in a thin SiO2 dielectric matrix. The measurement of current-voltage hysteresis loops at the level of individual nanoparticles, enabled by the nanoscopic contact area of the C-AFM tip, indicates reliable memristive switching for several hours of continuous operations. Alongside the electrical characterization on the nanoscale, the method of C-AFM offers the potential for in situ monitoring of long term operation induced morphological alterations and device failure, which is demonstrated at the example of nanoparticle-based devices with additional Cr wetting layer. The application of alloy nanoparticles as reservoir for mobile silver species effectively limits the formation of stable metallic filaments and results in reproducible diffusive switching characteristics. Notably, similar behaviour is encountered on macroscopic nanocomposite devices, which incorporate multiple stacks of nanoparticles and offer a high design versatility to tune switching properties and engineer scalable memristive devices with diffusive switching characteristics. No additional forming step is required for the operation of the presented alloy nanoparticle based memristive devices, which renders them very attractive for applications.
Carbene-based Difluoromethylation of Bisphenols: Application to the Instantaneous Tagging of Bisphenol A in Spiked Soil for Its Detection and Identification by Electron Ionization Gas Chromatography-Mass Spectrometry
Authors: Valdez Carlos A. , Leif Roald N. , Hok Saphon 
Published: November 2019

AbstractThe rapid and efficient difluoromethylation of a panel of eleven bisphenols (BPs) for their enhanced detection and identification by Electron-Ionization Gas Chromatography-Mass Spectrometry (EI-GC-MS) is presented. The derivatization employs the inexpensive, environmentally benign agent diethyl (bromodifluoromethyl) phosphonate (DBDFP) as a difluorocarbene-generating species that converts the BPs into bis-difluoromethylated ethers that can be detected and identified by GC-MS means. Key attributes of the protocol include its extreme rapidity (30 seconds) at ambient temperature, high specificity for BPs amidst other alcohol-containing analytes, and its biphasic nature that allows for its convenient adaptation to the analysis of BPs in organic as well as aqueous matrices. The protocol furnishes stable, novel BP ethers armed with a total of four fluorine atoms for their subsequent analysis by EI-GC-MS. Furthermore, each derivatized bisphenol exhibits unique retention times vastly different from their native counterparts leading to their unequivocal identification. The effectiveness and robustness of the developed methodology was applied to the tagging of the most famous member of this family of compounds, bisphenol-A (BPA), when spiked (at 1 μg.g−1 concentration) in the physically and compositionally complex Nebraska EPA standard soil. The method detection limit (MDL) for the bis-difluoromethylated BPA was determined to be 0.01 μg.mL−1. The bis-difluoromethylated BPA was conveniently detected on the organic layers from the biphasic, derivatized mixtures, highlighting the protocol’s practicality and utility in the rapid, qualitative detection of this endocrine disruptor during environmental analysis.
Multiplex profiling identifies clinically relevant signalling proteins in an isogenic prostate cancer model of radioresistance
Authors: Inder S. , Bates M. , Ni Labhrai N. , McDermott N. , Schneider J. , Erdmann G. , Jamerson T. , Belle V. A. , Prina-Mello A. , Thirion P. , Manecksha P. R. , Cormican D. , Finn S. , Lynch T. , Marignol L. 
Published: November 2019

AbstractThe exact biological mechanism governing the radioresistant phenotype of prostate tumours at a high risk of recurrence despite the delivery of advanced radiotherapy protocols remains unclear. This study analysed the protein expression profiles of a previously generated isogenic 22Rv1 prostate cancer model of radioresistance using DigiWest multiplex protein profiling for a selection of 90 signalling proteins. Comparative analysis of the profiles identified a substantial change in the expression of 43 proteins. Differential PARP-1, AR, p53, Notch-3 and YB-1 protein levels were independently validated using Western Blotting. Pharmacological targeting of these proteins was associated with a mild but significant radiosensitisation effect at 4Gy. This study supports the clinical relevance of isogenic in vitro models of radioresistance and clarifies the molecular radiation response of prostate cancer cells.