bluuebunny/crossref_metadata_2025 huggingface dataset:
CONFLICTING EVIDENCE OF EXPLICIT AND IMPLICIT KNOWLEDGE FROM OBJECTIVE AND SUBJECTIVE MEASURES
Authors: Maie Ryo , DeKeyser Robert M.
Published: November 2019

This study is the first to compare objective and subjective measures of explicit and implicit knowledge under learning from incidental exposure. An experiment was conducted, during which L1 English speakers were trained on a semiartificial language, Japlish. A measure of explicit knowledge and a recently proposed measure of implicit knowledge (i.e., an untimed auditory grammaticality judgment and a word-monitoring task) were applied to gauge the two types of knowledge at two testing sessions, and their results were compared with those of subjective measures of awareness. Results revealed clear discrepancies between the two measurement approaches in terms of their sensitivity. In particular, while the subjective measures varied in identifying explicit and implicit knowledge of various Japlish constructions, the objective measures indicated that most of the knowledge was explicit, and development of implicit knowledge (measured by the word-monitoring task) was minimal, only manifested in detecting a case-missing violation at the delayed posttest. The results are discussed with reference to the current literature on explicit and implicit learning and knowledge, and it is concluded that the criterion of (un)awareness might not be by itself sufficient to provide a full account of L2 knowledge developed under incidental conditions.
Investigation of the Image Contrast in an Ultra-Low Voltage Scanning Electron Microscope Using an Auger Electron Spectrometer
Authors: Sakuda Yusuke , Asahina Shunsuke , Togashi Takanari , Terasaki Osamu , Kurihara Masato
Published: November 2019

Surface-sensitive information on a bulk sample can be obtained by using a low incident electron energy (low accelerating voltage/landing voltage) in a scanning electron microscope (SEM). However, topography and composition contrast obtained at low incident electron energies may not be intuitive and should be analyzed carefully. By combining an Auger electron spectrometer (AES) with a low incident electron energy SEM (LE-SEM), we investigated the SEM contrast carefully by separating the secondary electron (SE) and back-scattered electron (BSE) components with high accuracy. For this, we modified an AES to measure the electron energy in the range of 0–0.6 keV with a sample bias voltage of 0 to −0.3 keV. We could clearly observe reversed brightness of gold and carbon (graphite) in BSE images when the energy of the incident electrons was reduced to 0.2–0.3 keV. In addition, reflected electron energy spectroscopy (REELS) is known to be a tool for chemical state analysis of the sample. We demonstrated that it is possible to study the electron states of graphite, diamond, and graphene by acquiring low incident energy REELS spectra from their surfaces with the newly modified AES. This will be a new method for analyzing the electron states of local areas of a surface.
The Eocene Protohierodula crabbi Ross, 2019 cannot be reliably assigned to Manteidae (Insecta: Mantodea): A reply
Authors: ROSS Andrew J.
Published: November 2019

I accept Schubnel & Nel's (2019) opinion that Protohierodula belongs to the clade Artimantodea, that it cannot be reliably assigned to the family Manteidae and should be regarded as family incertae sedis.
Rapid Stage‐Discharge Rating Curve Assessment Using Hydraulic Modeling in an Uncertainty Framework
Authors: Mansanarez Valentin , Westerberg Ida K. , Lam Norris , Lyon Steve W.
Published: November 2019

Establishing reliable streamflow time series is essential for hydrological studies and water‐related decisions, but it can be both time‐consuming and costly since streamflow is typically calculated from water level using rating curves based on numerous calibration measurements (gaugings). It can take many years of gauging data collection to estimate reliable rating curves, and even then extreme‐flow estimates often still depend on rating curve extrapolation. Hydraulically modeled rating curves are a promising alternative to traditional methods as they can be rapidly derived with few concurrent stage‐discharge gaugings. We introduce a novel framework for Rating curve Uncertainty estimation using Hydraulic Modelling (RUHM), based on Bayesian inference and physically based hydraulic modeling for estimating stage‐discharge rating curves and their associated uncertainty. The framework incorporates information from the river shape, hydraulic configuration, and the control gaugings as well as uncertainties in the gaugings and model parameters. We explored the interaction of uncertainty sources within RUHM by (1) assessing its performance at two Swedish stations, (2) investigating the sensitivity of the results to the number and magnitude of the calibration gaugings, and (3) evaluating the importance of prior information on the model parameters. We found that rating curves with constrained uncertainty could be estimated using only three gaugings for either low or low and medium flows that have a high probability of occurrence, thereby enabling rapid rating curve estimation. Prior information about the water‐surface slope‐stage relation, obtainable from site surveys, was needed to adequately constrain uncertainty estimates.
A Subcritical Water Extractor Prototype for Potential Astrobiology Spaceflight Missions
Authors: Kehl F. , Kovarik N. A. , Creamer J. S. , da Costa E. T. , Willis P. A.
Published: November 2019

A top‐level NASA exploration goal is the search for signs of life beyond Earth. Molecular biosignatures can be sought via in situ organic chemical analyses of samples collected from planetary bodies. Current spaceflight‐ready technologies lack the required sensitivity to perform these analyses on key polar organic species primarily due to the low efficiency of transferring these molecules from natural samples into chemical instrumentation. One promising approach to improve the liberation of these molecules from sample matrices prior to analysis is through the use of liquid extraction, in which organic molecules are dissolved in heated, pressurized water. This process has never been performed on a spaceflight mission. As part of instrument maturation efforts, we describe the development of the first spaceflight prototype of a fully automated subcritical water extractor designed to provide this essential functionality on a potential future planetary mission. The prototype extractor was mounted on a Mars test rover platform and successfully operated remotely in the Atacama Desert, Chile. Samples acquired by the rover's drill and sample acquisition/delivery system were remotely transferred to the extractor inlet funnel, and all subsequent extractor operations were performed automatically. To validate the instrument and demonstrate its suitability as a front‐end unit for an organic analyzer, we tested low‐bioload Atacama Desert soil extracts for amino acid content using capillary electrophoresis coupled to laser‐induced fluorescence. We show that hot extraction under subcritical conditions is required to liberate amino acids from the sample, as no amino acids were found in the extract produced at room temperature.
Measuring the Elemental Composition of Phobos: The Mars‐moon Exploration with GAmma rays and NEutrons (MEGANE) Investigation for the Martian Moons eXploration (MMX) Mission
Authors: Lawrence David J. , Peplowski Patrick N. , Beck Andrew W. , Burks Morgan T. , Chabot Nancy L. , Cully Michael J. , Elphic Richard C. , Ernst Carolyn M. , Fix Samuel , Goldsten John O. , Hoffer Erin M. , Kusano Hiroki , Murchie Scott L. , Schratz Brian C. , Usui Tomohiro , Yokley Zachary W.
Published: November 2019

The Mars‐moon Exploration with GAmma rays and NEutrons (MEGANE) investigation will use gamma‐ray and neutron spectroscopy to measure the elemental composition of Mars' moon Phobos. MEGANE is part of the Japanese Martian Moons eXploration (MMX) mission that will make comprehensive remote sensing measurements of both of Mars' moons Phobos and Deimos. MMX will also return to Earth regolith samples of Phobos. The science goals of the MEGANE investigation mirror those of the MMX mission. MEGANE will use elemental composition measurements to determine if Phobos is a captured asteroid or the end result of a giant impact event on Mars, study Phobos surface processes, provide reconnaissance to support the sample site selection, and supply compositional context for the returned samples. To accomplish its measurements, MEGANE will use a high‐purity Ge gamma‐ray spectrometer (GRS), and a neutron spectrometer (NS) that consists of two3He gas proportional neutron sensors. The GRS derives heritage from similar instruments from NASA's MErcury Surface, Space ENvironment, GEochemistry, and Ranging mission and the Psyche mission that is currently in development; the NS is based on similar instruments used for NASA's Lunar Prospector and Psyche missions.
Deadly Collision Blows an Asteroid Apart
Authors: Redd Nola
Published: November 2019

Active asteroids lurk in the asteroid belt, unseen until they’re blown to smithereens.
Fugitive Gas Abetted by Barometric Pressure
Authors: Derouin Sarah
Published: November 2019

Barometric pressure, in addition to factors such as lithology and the depth of the water table, can influence patterns of natural gas that escapes to subsurface soils.
How Conflict Influenced Land Use in Colombia
Authors: Wheeling Kate
Published: November 2019

Researchers use new maps and statistical techniques to infer how armed conflict influenced land cover in the understudied Caribbean region of the country.
Impact of Special Collections in JGR Space Physics
Authors: Liemohn Michael W. , Wooden Paige R.
Published: November 2019

Journals occasionally solicit manuscripts for special collections, in which all papers are focused on a particular topic within the journal's scope. For the Journal of Geophysical Research: Space Physics, there have been 51 special collections from 2005 through 2018, with a total of 1,009 papers out of the 8,881 total papers in the journal over those years (11%). Taken together, the citations to special collection papers, as well as other metrics, are slightly higher than papers not in special collections. Several paper characteristics were examined to assess whether they could explain the higher citation and download values for special collection papers, but they cannot. In addition, indirect methods were conducted for assessing self‐citations as an explanation for the increased citations, but no evidence was found to support this hypothesis. It was found that some paper types, notably Commentaries and Technical Reports, have lower average citations but higher average downloads than Research Articles (the most common type of paper in this journal). This implies that such paper types have a different kind of impact than “regular” science‐result‐focused papers. In addition to having higher average citations and downloads, special collections focus community attention on that particular research topic, providing a deadline for manuscript submissions and a single webpage at which many related papers are listed. It is concluded that special collections are worth the extra community effort in organization, writing, and reviewing these papers.
Self‐Organizing Maps for Evaluation of Biogeochemical Processes and Temporal Variations in Water Quality of Subtropical Reservoirs
Authors: Melo Darllene S. , Gontijo Erik S. J. , Frascareli Daniele , Simonetti Vanessa C. , Machado Leila S. , Barth Johannes A. C. , Moschini‐Carlos Viviane , Pompêo Marcelo L. , Rosa André H. , Friese Kurt
Published: November 2019

Water quality in reservoirs is often compromised in many regions worldwide by nutrients and trace metals. This demands continuous monitoring; however, analyses of large data sets collected during regular monitoring remain a difficult task. Multivariate techniques offer a fast and robust approach for interpreting complex results. The objective of this study was to check the efficacy of self‐organizing maps (SOMs) as a tool to investigate biogeochemical processes. This tool can also help to illustrate influences of land use patterns on the water quality of reservoirs. Here we use the Itupararanga Reservoir in Brazil as a subtropical example. Vertical profiles were sampled from seven sites in the reservoir in a total of seven campaigns over 24 months. Next to physicochemical parameters in the water column (dissolved oxygen, Eh, pH, and temperature), levels of nutrients (NO3−, NH4+, and PO43−), transition and trace metals (Al, Ba, Ca, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, and Zn), and chlorophyll‐a (Chla) were measured. These variables were correlated with land use using SOM. With this technique samples were classified into 17 distinct groups that showed distinct influences of spatial heterogeneity and seasonality. The analyses helped to reveal a seasonal stratification period, where Fe, Mn, and P were released from sediments. Nutrients and some metal inputs (Al and Fe) were related to agricultural, urban, and grass/pasture areas around the reservoir. Our approach also helped to explain physical and biogeochemical seasonality in the reservoir.
Biochemical sensing in graphene-enhanced microfiber resonators with individual molecule sensitivity and selectivity
Authors: Cao Zhongxu , Yao Baicheng , Qin Chenye , Yang Run , Guo Yanhong , Zhang Yufeng , Wu Yu , Bi Lei , Chen Yuanfu , Xie Zhenda , Peng Gangding , Huang Shu-Wei , Wong Chee Wei , Rao Yunjiang
Published: November 2019

Photonic sensors that are able to detect and track biochemical molecules offer powerful tools for information acquisition in applications ranging from environmental analysis to medical diagnosis. The ultimate aim of biochemical sensing is to achieve both quantitative sensitivity and selectivity. As atomically thick films with remarkable optoelectronic tunability, graphene and its derived materials have shown unique potential as a chemically tunable platform for sensing, thus enabling significant performance enhancement, versatile functionalization and flexible device integration. Here, we demonstrate a partially reduced graphene oxide (prGO) inner-coated and fiber-calibrated Fabry-Perot dye resonator for biochemical detection. Versatile functionalization in the prGO film enables the intracavity fluorescent resonance energy transfer (FRET) to be chemically selective in the visible band. Moreover, by measuring the intermode interference via noise canceled beat notes and locked-in heterodyne detection with Hz-level precision, we achieved individual molecule sensitivity for dopamine, nicotine and single-strand DNA detection. This work combines atomic-layer nanoscience and high-resolution optoelectronics, providing a way toward high-performance biochemical sensors and systems.
A brainstem-central amygdala circuit underlies defensive responses to learned threats
Authors: Gu Yiran , Piper Walter T. , Branigan Lauren A. , Vazey Elena M. , Aston-Jones Gary , Lin Longnian , LeDoux Joseph E. , Sears Robert M.
Published: November 2019

Norepinephrine (NE) plays a central role in the acquisition of aversive learning via actions in the lateral nucleus of the amygdala (LA) [1, 2]. However, the function of NE in expression of aversively-conditioned responses has not been established. Given the role of the central nucleus of the amygdala (CeA) in the expression of such behaviors [3–5], and the presence of NE axons projections in this brain nucleus [6], we assessed the effects of NE activity in the CeA on behavioral expression using receptor-specific pharmacology and cell- and projection-specific chemogenetic manipulations. We found that inhibition and activation of locus coeruleus (LC) neurons decreases and increases freezing to aversively conditioned cues, respectively. We then show that locally inhibiting or activating LC terminals in CeA is sufficient to achieve this bidirectional modulation of defensive reactions. These findings support the hypothesis that LC projections to CeA are critical for the expression of defensive responses elicited by conditioned threats.
Clinical significance and biological role of L1 cell adhesion molecule in gastric cancer
Authors: Ichikawa Takashi , Okugawa Yoshinaga , Toiyama Yuji , Tanaka Koji , Yin Chengzeng , Kitajima Takahito , Kondo Satoru , Shimura Tadanobu , Ohi Masaki , Araki Toshimitsu , Kusunoki Masato
Published: November 2019

Background

L1 cell adhesion molecule (L1CAM) is highly expressed in malignant tumours and might play a pivotal role in tumour progression.

Methods

We analysed by immunohistochemistry L1CAM protein expression in formalin-fixed, paraffin-embedded specimens from 309 GC patients. We performed propensity score matching (PSM) analysis to clarify the prognostic impact of L1CAM in GC patients. We evaluated L1CAM gene expression in fresh frozen specimens from another group of 131 GC patients to establish its clinical relevance. The effects of changes in L1CAM were investigated in vitro and in vivo.

Results

L1CAM was mainly expressed in tumour cells of GC tissues. Elevated L1CAM expression was an independent prognostic factor for overall and disease-free survival, and an independent risk factor for distant metastasis in GC patients. PSM analysis showed that high L1CAM expression was significantly associated with poor prognosis. L1CAM gene expression using fresh frozen specimens successfully validated all of these findings in an independent cohort. Inhibition of L1CAM suppressed cell proliferation, cycle progress, invasion, migration and anoikis resistance in GC cells. Furthermore, L1CAM inhibition suppressed the growth of peritoneal metastasis.

Conclusion

L1CAM may serve as a feasible biomarker for identification of patients who have a high risk of recurrence of GC.
Evidence that cyanobacterial Sll1217 functions analogously to PGRL1 in enhancing PGR5-dependent cyclic electron flow
Authors: Dann Marcel , Leister Dario
Published: November 2019

In plants and cyanobacteria, the PGR5 protein contributes to cyclic electron flow around photosystem I. In plants, PGR5 interacts with PGRL1 during cyclic electron flow, but cyanobacteria appear to lack PGRL1 proteins. We have heterologously expressed the PGR5 and PGRL1 proteins from the plant Arabidopsis in various genetic backgrounds in the cyanobacterium Synechocystis. Our results show that plant PGR5 suffices to re-establish cyanobacterial cyclic electron flow (CEF), albeit less efficiently than the cyanobacterial PGR5 or the plant PGR5 and PGRL1 proteins together. A mutation that inactivates Arabidopsis PGR5 destabilises the protein in Synechocystis. Furthermore, the Synechocystis protein Sll1217, which exhibits weak sequence similarity with PGRL1, physically interacts with both plant and cyanobacterial PGR5 proteins, and stimulates CEF in Synechocystis. Therefore, Sll1217 partially acts as a PGRL1 analogue, the mode of action of PGR5 and PGRL1/Sll1217 proteins is similar in cyanobacteria and plants, and PGRL1 could have evolved from a cyanobacterial ancestor.
Structure of the native supercoiled flagellar hook as a universal joint
Authors: Kato Takayuki , Makino Fumiaki , Miyata Tomoko , Horváth Péter , Namba Keiichi
Published: November 2019

The Bacterial flagellar hook is a short supercoiled tubular structure made from a helical assembly of the hook protein FlgE. The hook acts as a universal joint that connects the flagellar basal body and filament, and smoothly transmits torque generated by the rotary motor to the helical filament propeller. In peritrichously flagellated bacteria, the hook allows the filaments to form a bundle behind the cell for swimming, and for the bundle to fall apart for tumbling. Here we report a native supercoiled hook structure at 3.6 Å resolution by cryoEM single particle image analysis of the polyhook. The atomic model built into the three-dimensional (3D) density map reveals the changes in subunit conformation and intersubunit interactions that occur upon compression and extension of the 11 protofilaments during their smoke ring-like rotation. These observations reveal how the hook functions as a dynamic molecular universal joint with high bending flexibility and twisting rigidity.
Synergy between Cyclase-associated protein and Cofilin accelerates actin filament depolymerization by two orders of magnitude
Authors: Shekhar Shashank , Chung Johnson , Kondev Jane , Gelles Jeff , Goode Bruce L.
Published: November 2019

Cellular actin networks can be rapidly disassembled and remodeled in a few seconds, yet in vitro actin filaments depolymerize slowly over minutes. The cellular mechanisms enabling actin to depolymerize this fast have so far remained obscure. Using microfluidics-assisted TIRF, we show that Cyclase-associated protein (CAP) and Cofilin synergize to processively depolymerize actin filament pointed ends at a rate 330-fold faster than spontaneous depolymerization. Single molecule imaging further reveals that hexameric CAP molecules interact with the pointed ends of Cofilin-decorated filaments for several seconds at a time, removing approximately 100 actin subunits per binding event. These findings establish a paradigm, in which a filament end-binding protein and a side-binding protein work in concert to control actin dynamics, and help explain how rapid actin network depolymerization is achieved in cells.
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

Multi-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

A 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

Coupling 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

Quantum 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

SeaFlow 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

Arabidopsis 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

In 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

Kampala, 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

After 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

Aim 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

Tumor 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

Nanoscale 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

The 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.
Author Correction: New Ca. Liberibacter psyllaurous haplotype resurrected from a 49-year-old specimen of Solanum umbelliferum: a native host of the psyllid vector
Authors: Mauck Kerry Elizabeth , Sun Penglin , Meduri Venkata RamaSravani , Hansen Allison K.
Published: November 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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

The 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.
Oral microbiome diversity in chimpanzees from Gombe National Park
Authors: Ozga Andrew T. , Gilby Ian , Nockerts Rebecca S. , Wilson Michael L. , Pusey Anne , Stone Anne C.
Published: November 2019

Historic calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies.
Spontaneous eye blink rate predicts individual differences in exploration and exploitation during reinforcement learning
Authors: Van Slooten Joanne C. , Jahfari Sara , Theeuwes Jan
Published: November 2019

Spontaneous eye blink rate (sEBR) has been linked to striatal dopamine function and to how individuals make value-based choices after a period of reinforcement learning (RL). While sEBR is thought to reflect how individuals learn from the negative outcomes of their choices, this idea has not been tested explicitly. This study assessed how individual differences in sEBR relate to learning by focusing on the cognitive processes that drive RL. Using Bayesian latent mixture modelling to quantify the mapping between RL behaviour and its underlying cognitive processes, we were able to differentiate low and high sEBR individuals at the level of these cognitive processes. Further inspection of these cognitive processes indicated that sEBR uniquely indexed explore-exploit tendencies during RL: lower sEBR predicted exploitative choices for high valued options, whereas higher sEBR predicted exploration of lower value options. This relationship was additionally supported by a network analysis where, notably, no link was observed between sEBR and how individuals learned from negative outcomes. Our findings challenge the notion that sEBR predicts learning from negative outcomes during RL, and suggest that sEBR predicts individual explore-exploit tendencies. These then influence value sensitivity during choices to support successful performance when facing uncertain reward.