bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface Currents and Significant Wave Height Gradients: Matching Numerical Models and High‐Resolution Altimeter Wave Heights in the Agulhas Current Region
Authors: Marechal Gwendal , Ardhuin Fabrice 
Published: February 2021

AbstractAdvances in the understanding and modeling of surface currents have revealed the importance of internal waves, mesoscale and submesoscale features. Indeed, all these features should have a large influence on wind waves and in particular on wave heights. Still, the quantitative impact of currents on waves is not well known due to the complexity of the random wavefields and currents that are found in the ocean and the lack of observations of both currents and waves at scales shorter than 150 km. Here, we compare novel satellite altimetry data and state of the art phase‐averaged numerical wave models forced both by wind and currents. Currents used are taken from the oceanic model Coastal and Regional Ocean COmmunity, run at high resolution. The influence of current field resolution is investigated by applying Gaussian filters of different width to that same high‐resolution current field. We find that a numerical wave model that uses currents with resolutions of ∼30 km or less and a directional resolution of 7.5° can provide accurate representations of the significant wave height gradients found in the Agulhas current. Using smoother current fields such as derived from altimeters measurements alone, coarse directional spectral resolution or larger directional spread of the wave model generally underestimates gradients and extreme wave heights. Hence, satellite altimetry provides high‐resolution wave height with a gradient magnitude that is highly sensitive to underlying surface current gradients, at resolutions that may not be resolved by today's altimeters measurements. This is demonstrated here for relatively steady currents averaged over 3 years.
A Comodulation Analysis of Atmospheric Energy Injection Into the Ground Motion at InSight, Mars
Authors: Charalambous C. , Stott A. E. , Pike W. T. , McClean J. B. , Warren T. , Spiga A. , Banfield D. , Garcia R. F. , Clinton J. , Stähler S. , Navarro S. , Lognonné P. , Scholz J.‐R. , Kawamura T. , van Driel M. , Böse M. , Ceylan S. , Khan A. , Horleston A. , Orhand‐Mainsant G. , Sotomayor L. M. , Murdoch N. , Giardini D. , Banerdt W. B. 
Published: February 2021

AbstractSeismic observations involve signals that can be easily masked by noise injection. For the NASA Mars lander InSight, the atmosphere is a significant noise contributor, impeding the identification of seismic events for two‐thirds of a Martian day. While the noise is below that seen at even the quietest sites on Earth, the amplitude of seismic signals on Mars is also considerably lower, requiring an understanding and quantification of environmental injection at unprecedented levels. Mars’ ground and atmosphere are a continuously coupled seismic system, and although atmospheric functions are of distinct origins, the superposition of these noise contributions is poorly understood, making separation a challenging task. We present a novel method for partitioning the observed signal into seismic and environmental contributions. Atmospheric pressure and wind fluctuations are shown to exhibit temporal cross‐frequency coupling across multiple bands, injecting noise that is neither random nor coherent. We investigate this through comodulation, quantifying the synchrony of the seismic motion, wind and pressure signals. By working in the time‐frequency domain, we discriminate between the different origins of underlying processes and determine the site's environmental sensitivity. Our method aims to create a virtual vault at InSight's landing site on Mars, shielding the seismometers with effective postprocessing in lieu of a physical vault. This allows us to describe the environmental and seismic signals over a sequence of sols, to quantify the wind and pressure injection and estimate the seismic content of possible marsquakes with a signal‐to‐noise ratio that can be quantified in terms of environmental independence. Finally, we exploit the relationship between the comodulated signals to identify their sources.
TGF-β1-mediated transition of resident fibroblasts to cancer-associated fibroblasts promotes cancer metastasis in gastrointestinal stromal tumor
Authors: Yoon Hyunho , Tang Chih-Min , Banerjee Sudeep , Delgado Antonio L. , Yebra Mayra , Davis Jacob , Sicklick Jason K. 
Published: February 2021

AbstractCancer-associated fibroblasts (CAFs) are the most abundant cells in the tumor microenvironment. Crosstalk between tumor cells and CAFs contributes to tumor survival in most epithelial cancers. Recently, utilizing gastrointestinal stromal tumor (GIST) as a model for sarcomas, we identified paracrine networks by which CAFs promote tumor progression and metastasis. However, the mechanisms by which CAFs arise in sarcomas remain unclear. Here, RNA sequencing analysis revealed that transforming growth factor-β1 (TGF-β1) is highly expressed in both tumor cells and CAFs. To determine the functional role of TGF-β1, we treated normal gastric fibroblasts (GFs) with recombinant TGF-β1, which caused the GFs to adopt a more stellate morphology, as well as increased the mRNA expression of CAF-mediated genes (CCL2, RAB3B, and TNC) and genes encoding fibroblast growth factors (FGFs). Moreover, while either GIST or CAF conditioned media enhanced the transition from GFs to CAFs, a TGF-β1-blocking antibody attenuated this effect. Transwell migration assays revealed that the TGF-β1-mediated transition from GFs to CAFs enhanced tumor cell migration. This migratory effect was abrogated by an anti-TGF-β1 antibody, suggesting that TGF-β1 secreted from GIST cells or CAFs is associated with GIST migration via GF-to-CAF transition. In addition, the murine spleen-to-liver metastasis model showed that GF pre-treated with TGF-β1 promoted GIST metastasis. Collectively, these findings reveal unappreciated crosstalk among tumor cells, CAFs, and normal resident fibroblasts in the stroma of sarcomas, which enhances a GF-to-CAF transition associated with tumor migration and metastasis.
Increasing flavonoid concentrations in root exudates enhance associations between arbuscular mycorrhizal fungi and an invasive plant
Authors: Tian Baoliang , Pei Yingchun , Huang Wei , Ding Jianqing , Siemann Evan 
Published: February 2021

Abstract
Many invasive plants have enhanced mutualistic arbuscular mycorrhizal (AM) fungal associations, however, mechanisms underlying differences in AM fungal associations between introduced and native populations of invasive plants have not been explored. Here we test the hypothesis that variation in root exudate chemicals in invasive populations affects AM fungal colonization and then impacts plant performance. We examined flavonoids (quercetin and quercitrin) in root exudates of native and introduced populations of the invasive plant Triadica sebifera and tested their effects on AM fungi and plant performance. We found that plants from introduced populations had higher concentrations of quercetin in root exudates, greater AM fungal colonization and higher biomass. Applying root exudates more strongly increased AM fungal colonization of target plants and AM fungal spore germination when exudate donors were from introduced populations. The role of root exudate chemicals was further confirmed by decreased AM fungal colonization when activated charcoal was added into soil. Moreover, addition of quercetin into soil increased AM fungal colonization, indicating quercetin might be a key chemical signal stimulating AM fungal associations. Together these results suggest genetic differences in root exudate flavonoids play an important role in enhancing AM fungal associations and invasive plants’ performance, thus considering root exudate chemicals is critical to unveiling mechanisms governing shifting plant-soil microbe interactions during plant invasions.
Seventy years of data from the world’s longest grazed and irrigated pasture trials
Authors: McDowell Rich. W. , Moss R. A. , Gray C. W. , Smith L. C. , Sneath G. 
Published: February 2021

AbstractPastures are the most widespread land use, globally. The Winchmore trials were established in 1948–1949 in Canterbury, New Zealand and examined either different rates of phosphorus (P) fertiliser on the same irrigation schedule (Fertiliser trial), or different irrigation scheduling at the same rate of P application (Irrigation trial). About 96,000 records of soil chemistry and physical data and pasture yield and botanical composition are available along with nearly 7000 soil samples. These data have been used in 475 publications that have explored topics as diverse as: improvements in sheep, dairy and deer production; the efficacy and scheduling of irrigation; improvements in pasture and crop production; agronomic and environmental soil and water research; and entomology. In addition to above topics, these data are invaluable for calibrating models to predict long-term issues like the accumulation of soil carbon or contaminants like cadmium and informing policy on climate change and agricultural practices. The data and soil samples are available for use and may yet yield discoveries, unforeseen 70 years ago.
Solanum linnaeanum and Solanum sisymbriifolium as a sustainable strategy for the management of Meloidogyne chitwoodi
Authors: Perpétuo Laura Soraia , da Cunha Maria J. M. , Batista Maria Teresa , Conceição Isabel Luci 
Published: February 2021

AbstractRoot-knot nematodes (RKN), Meloidogyne spp., are important crop pests that cause severe losses in crop production worldwide, reducing both productivity and crop quality. Meloidogyne chitwoodi Golden, O'Bannon, Santo & Finley, 1980 is considered a quarantine organism by the European and Mediterranean Plant Protection Organization (EPPO) causing damage in tomato and potato crops. The development of nonchemical and sustainable management strategies to reduce nematode damage is crucial. The resistance of Solanum linnaeanum Hepper & P.-M.L. Jaeger and S. sisymbriifolium Lamarck cv. Sis 6001 to M. chitwoodi was evaluated based on gall index (GI), the Bridge & Page (1980) rating chart and reproduction factor (RF). Both plant species were resistant to M. chitwoodi. Solanum linnaeanum had an average of 519 small root swellings/plant, with 45% adult nematodes inside the roots, all males. Solanum sisymbriifolium had GI ≤ 2 and RF ≤ 1 with a high percentage (69%) of nematodes inside the roots that did not develop beyond the sexually undifferentiated second-stage. The use of S. linnaeanum as a new source of resistance is a good alternative for the control of RKN in the quest to develop nonchemical and sustainable management strategies to protect crops.
Changes in parafoveal and peripapillary perfusion after decompression surgery in chiasmal compression due to pituitary tumors
Authors: Lee Ga-In , Park Kyung-Ah , Oh Sei Yeul , Kong Doo-Sik 
Published: February 2021

AbstractWe evaluated changes in parafoveal and peripapillary vessel density in chiasmal compression after decompression surgery using optical coherence tomography angiography (OCT-A). Sixty-two eyes with chiasmal compression for which preoperative and postoperative (4–6 months) OCT, OCT-A, visual field (VF), and comprehensive ophthalmic data were available, and 44 healthy eyes were evaluated. Vessel densities of the superficial retinal capillary plexus (SRCP), deep retinal capillary plexus (DRCP), and radial peripapillary capillary (RPC) segment were assessed using OCT-A. The postoperative measurements were compared with preoperative data. Preoperative peripapillary retinal nerve fiber layer, macular ganglion cell-inner plexiform layer thickness, and vessel densities of SRCP and RPC segments in patients’ eyes were significantly reduced compared to those of healthy controls (P < 0.0001, P < 0.0001, P = 0.0052, and P = 0.0085, respectively). Vessel densities were significantly decreased in the SRCP (P < 0.0001), DRCP (P = 0.0017), and RPC segments (P < 0.0001) after surgery compared to the preoperative values. Significant associations between the postoperative SRCP and DRCP vessel density changes and preoperative SRCP (r =  − 0.3195, P = 0.0114) and DRCP (r =  − 0.5165, P < 0.0001) vessel densities were found, respectively. There were also significant associations between postoperative SRCP vessel density changes and VF changes (r =  − 0.2586, P = 0.0424). These findings indicate that decreased perfusion around the optic nerve head and on the macula associated with chiasmal compression could further progress after decompression surgery. Further functional and longer-term clinical studies are needed to elucidate the clinical implications of these findings.
Protein complex formation in methionine chain-elongation and leucine biosynthesis
Authors: Chen Li-Qun , Chhajed Shweta , Zhang Tong , Collins Joseph M. , Pang Qiuying , Song Wenyuan , He Yan , Chen Sixue 
Published: February 2021

AbstractDuring the past two decades, glucosinolate (GLS) metabolic pathways have been under extensive studies because of the importance of the specialized metabolites in plant defense against herbivores and pathogens. The studies have led to a nearly complete characterization of biosynthetic genes in the reference plant Arabidopsis thaliana. Before methionine incorporation into the core structure of aliphatic GLS, it undergoes chain-elongation through an iterative three-step process recruited from leucine biosynthesis. Although enzymes catalyzing each step of the reaction have been characterized, the regulatory mode is largely unknown. In this study, using three independent approaches, yeast two-hybrid (Y2H), coimmunoprecipitation (Co-IP) and bimolecular fluorescence complementation (BiFC), we uncovered the presence of protein complexes consisting of isopropylmalate isomerase (IPMI) and isopropylmalate dehydrogenase (IPMDH). In addition, simultaneous decreases in both IPMI and IPMDH activities in a leuc:ipmdh1 double mutants resulted in aggregated changes of GLS profiles compared to either leuc or ipmdh1 single mutants. Although the biological importance of the formation of IPMI and IPMDH protein complexes has not been documented in any organisms, these complexes may represent a new regulatory mechanism of substrate channeling in GLS and/or leucine biosynthesis. Since genes encoding the two enzymes are widely distributed in eukaryotic and prokaryotic genomes, such complexes may have universal significance in the regulation of leucine biosynthesis.
Effects of hydrological regime and land use on in-stream Escherichia coli concentration in the Mekong basin, Lao PDR
Authors: Nakhle Paty , Ribolzi Olivier , Boithias Laurie , Rattanavong Sayaphet , Auda Yves , Sayavong Saysongkham , Zimmermann Rosalie , Soulileuth Bounsamay , Pando Anne , Thammahacksa Chanthamousone , Rochelle-Newall Emma J. , Santini William , Martinez Jean-Michel , Gratiot Nicolas , Pierret Alain 
Published: February 2021

AbstractIn the basin of Mekong, over 70 million people rely on unimproved surface water for their domestic requirements. Surface water is often contaminated with fecal matter and yet little information exists on the underlying mechanisms of fecal contamination in tropical conditions at large watershed scales. Our objectives were to (1) investigate the seasonality of fecal contamination usingEscherichia colias fecal indicator bacteria (FIB), and (2) establish links between the fecal contamination in stream water and its controlling factors (hydrology and land use). We present the results of (1) a sampling campaign at the outlet of 19 catchments across Lao PDR, in both the dry and the rainy seasons of 2016, and (2) a 10-day interval monitoring conducted in 2017 and 2018 at three point locations of three rivers (Nam Ou, Nam Suang, and Mekong) in northern Lao PDR. Our results show the presence of fecal contamination at most of the sampled sites, with a seasonality characterized by higher and extremeE. coliconcentrations occurring during the rainy season. The highestE. coliconcentrations, strongly correlated with total suspended sediment concentrations, were measured in catchments dominated by unstocked forest areas, especially in mountainous northern Lao PDR and in Vientiane province.
Brain-derived neurotrophic factor in cerebrospinal fluid and plasma is not a biomarker for Huntington’s disease
Authors: Ou Zhen-Yi Andy , Byrne Lauren M. , Rodrigues Filipe B. , Tortelli Rosanna , Johnson Eileanoir B. , Foiani Martha S. , Arridge Marzena , De Vita Enrico , Scahill Rachael I. , Heslegrave Amanda , Zetterberg Henrik , Wild Edward J. 
Published: February 2021

AbstractBrain-derived neurotrophic factor (BDNF) is implicated in the survival of striatal neurons. BDNF function is reduced in Huntington’s disease (HD), possibly because mutant huntingtin impairs its cortico-striatal transport, contributing to striatal neurodegeneration. The BDNF trophic pathway is a therapeutic target, and blood BDNF has been suggested as a potential biomarker for HD, but BDNF has not been quantified in cerebrospinal fluid (CSF) in HD. We quantified BDNF in CSF and plasma in the HD-CSF cohort (20 pre-manifest and 40 manifest HD mutation carriers and 20 age and gender-matched controls) using conventional ELISAs and an ultra-sensitive immunoassay. BDNF concentration was below the limit of detection of the conventional ELISAs, raising doubt about previous CSF reports in neurodegeneration. Using the ultra-sensitive method, BDNF concentration was quantifiable in all samples but did not differ between controls and HD mutation carriers in CSF or plasma, was not associated with clinical scores or MRI brain volumetric measures, and had poor ability to discriminate controls from HD mutation carriers, and premanifest from manifest HD. We conclude that BDNF in CSF and plasma is unlikely to be a biomarker of HD progression and urge caution in interpreting studies where conventional ELISA was used to quantify CSF BDNF.
A novel canine reference genome resolves genomic architecture and uncovers transcript complexity
Authors: Wang Chao , Wallerman Ola , Arendt Maja-Louise , Sundström Elisabeth , Karlsson Åsa , Nordin Jessika , Mäkeläinen Suvi , Pielberg Gerli Rosengren , Hanson Jeanette , Ohlsson Åsa , Saellström Sara , Rönnberg Henrik , Ljungvall Ingrid , Häggström Jens , Bergström Tomas F. , Hedhammar Åke , Meadows Jennifer R. S. , Lindblad-Toh Kerstin 
Published: February 2021

AbstractWe present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine “dark” regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.
CYK4 relaxes the bias in the off-axis motion by MKLP1 kinesin-6
Authors: Maruyama Yohei , Sugawa Mitsuhiro , Yamaguchi Shin , Davies Tim , Osaki Toshihisa , Kobayashi Takuya , Yamagishi Masahiko , Takeuchi Shoji , Mishima Masanori , Yajima Junichiro 
Published: February 2021

AbstractCentralspindlin, a complex of the MKLP1 kinesin-6 and CYK4 GAP subunits, plays key roles in metazoan cytokinesis. CYK4-binding to the long neck region of MKLP1 restricts the configuration of the two MKLP1 motor domains in the centralspindlin. However, it is unclear how the CYK4-binding modulates the interaction of MKLP1 with a microtubule. Here, we performed three-dimensional nanometry of a microbead coated with multiple MKLP1 molecules on a freely suspended microtubule. We found that beads driven by dimeric MKLP1 exhibited persistently left-handed helical trajectories around the microtubule axis, indicating torque generation. By contrast, centralspindlin, like monomeric MKLP1, showed similarly left-handed but less persistent helical movement with occasional rightward movements. Analysis of the fluctuating helical movement indicated that the MKLP1 stochastically makes off-axis motions biased towards the protofilament on the left. CYK4-binding to the neck domains in MKLP1 enables more flexible off-axis motion of centralspindlin, which would help to avoid obstacles along crowded spindle microtubules.
Inhibition of miR-96-5p in the mouse brain increases glutathione levels by altering NOVA1 expression
Authors: Kinoshita Chisato , Kikuchi-Utsumi Kazue , Aoyama Koji , Suzuki Ryo , Okamoto Yayoi , Matsumura Nobuko , Omata Daiki , Maruyama Kazuo , Nakaki Toshio 
Published: February 2021

AbstractGlutathione (GSH) is an important antioxidant that plays a critical role in neuroprotection. GSH depletion in neurons induces oxidative stress and thereby promotes neuronal damage, which in turn is regarded as a hallmark of the early stage of neurodegenerative diseases. The neuronal GSH level is mainly regulated by cysteine transporter EAAC1 and its inhibitor, GTRAP3-18. In this study, we found that the GTRAP3-18 level was increased by up-regulation of the microRNA miR-96-5p, which was found to decrease EAAC1 levels in our previous study. Since the 3’-UTR region of GTRAP3-18 lacks the consensus sequence for miR-96-5p, an unidentified protein should be responsible for the intermediate regulation of GTRAP3-18 expression by miR-96-5p. Here, we discovered that RNA-binding protein NOVA1 functions as an intermediate protein for GTRAP3-18 expression via miR-96-5p. Moreover, we show that intra-arterial injection of a miR-96-5p-inhibiting nucleic acid to living mice by a drug delivery system using microbubbles and ultrasound decreased the level of GTRAP3-18 via NOVA1 and increased the levels of EAAC1 and GSH in the dentate gyrus of the hippocampus. These findings suggest that the delivery of a miR-96-5p inhibitor to the brain would efficiently increase the neuroprotective activity by increasing GSH levels via EAAC1, GTRAP3-18 and NOVA1.