bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tunable rainbow light trapping in ultrathin resonator arrays
Authors: Dixon Katelyn , Montazeri Arthur O. , Shayegannia Moein , Barnard Edward S. , Cabrini Stefano , Matsuura Naomi , Holman Hoi-Ying , Kherani Nazir P. 
Published: November 2020

AbstractRainbow light trapping in plasmonic devices allows for field enhancement of multiple wavelengths within a single device. However, many of these devices lack precise control over spatial and spectral enhancement profiles and cannot provide extremely high localised field strengths. Here we present a versatile, analytical design paradigm for rainbow trapping in nanogroove arrays by utilising both the groove-width and groove-length as tuning parameters. We couple this design technique with fabrication through multilayer thin-film deposition and focused ion beam milling, which enables the realisation of unprecedented feature sizes down to 5 nm and corresponding extreme normalised local field enhancements up to 103. We demonstrate rainbow trapping within the devices through hyperspectral microscopy and show agreement between the experimental results and simulation. The combination of expeditious design and precise fabrication underpins the implementation of these nanogroove arrays for manifold applications in sensing and nanoscale optics.
LCVP, The Leipzig catalogue of vascular plants, a new taxonomic reference list for all known vascular plants
Authors: Freiberg Martin , Winter Marten , Gentile Alessandro , Zizka Alexander , Muellner-Riehl Alexandra Nora , Weigelt Alexandra , Wirth Christian 
Published: November 2020

AbstractThe lack of comprehensive and standardized taxonomic reference information is an impediment for robust plant research, e.g. in systematics, biogeography or macroecology. Here we provide an updated and much improved reference list of 1,315,562 scientific names for all described vascular plant species globally. The Leipzig Catalogue of Vascular Plants (LCVP; version 1.0.3) contains 351,180 accepted species names (plus 6,160 natural hybrids), within 13,460 genera, 564 families and 84 orders. The LCVP a) contains more information on the taxonomic status of global plant names than any other similar resource, and b) significantly improves the reliability of our knowledge by e.g. resolving the taxonomic status of ~181,000 names compared to The Plant List, the up to date most commonly used plant name resource. We used ~4,500 publications, existing relevant databases and available studies on molecular phylogenetics to construct a robust reference backbone. For easy access and integration into automated data processing pipelines, we provide an ‘R’-package (lcvplants) with the LCVP.
Impacts of sub-micrometer sediment particles on early-stage growth and survival of the kelp Ecklonia bicyclis
Authors: Matsumoto Akira , Sato Minami , Arakawa Hisayuki 
Published: November 2020

AbstractMarine forests have declined in many urbanized regions in recent years. One cause is the inflow of fine particles into coastal rocky shores. We examined the influence of sub-micrometre (sub-micro) particles on the early growth stages of the large brown macrophyte Ecklonia bicyclis. The percentage of substrate attachment of zoospores decreased with an increase in sub-micro sediments. As the size of the particles decreased, the negative effect became greater. There was an increase in poor levels of gametophyte survival and growth as more and smaller sediment was deposited. We consider that the causes of these phenomena owing to increasing amounts of sediment is a decrease in availability of substrate for zoospore attachment and that of area for substance exchange on the gametophytes. We also evaluated the effects in sea areas, based on the amount and size distribution of seabed sediment in the algal communities deforested by particles, and found that the inhibition of zoospore attachment and gametophyte growth by sub-micro particles was remarkably large. The sub-micro sediment on the substrate has seriously negative effects on the early stages of macrophytes. Inflow of very fine particles to natural marine forests may result in severe degradation of rocky reef ecosystems.
Cell geometry and the cytoskeleton impact the nucleo-cytoplasmic localisation of the SMYD3 methyltransferase
Authors: Pereira David , Richert Alain , Medjkane Souhila , Hénon Sylvie , Weitzman Jonathan B. 
Published: November 2020

AbstractMechanical cues from the cellular microenvironment are converted into biochemical signals controlling diverse cell behaviours, including growth and differentiation. But it is still unclear how mechanotransduction ultimately affects nuclear readouts, genome function and transcriptional programs. Key signaling pathways and transcription factors can be activated, and can relocalize to the nucleus, upon mechanosensing. Here, we tested the hypothesis that epigenetic regulators, such as methyltransferase enzymes, might also contribute to mechanotransduction. We found that the SMYD3 lysine methyltransferase is spatially redistributed dependent on cell geometry (cell shape and aspect ratio) in murine myoblasts. Specifically, elongated rectangles were less permissive than square shapes to SMYD3 nuclear accumulation, via reduced nuclear import. Notably, SMYD3 has both nuclear and cytoplasmic substrates. The distribution of SMYD3 in response to cell geometry correlated with cytoplasmic and nuclear lysine tri-methylation (Kme3) levels, but not Kme2. Moreover, drugs targeting cytoskeletal acto-myosin induced nuclear accumulation of Smyd3. We also observed that square vs rectangular geometry impacted the nuclear-cytoplasmic relocalisation of several mechano-sensitive proteins, notably YAP/TAZ proteins and the SETDB1 methyltransferase. Thus, mechanical cues from cellular geometric shapes are transduced by a combination of transcription factors and epigenetic regulators shuttling between the cell nucleus and cytoplasm. A mechanosensitive epigenetic machinery could potentially affect differentiation programs and cellular memory.
Plasma imatinib levels and ABCB1 polymorphism influences early molecular response and failure-free survival in newly diagnosed chronic phase CML patients
Authors: Rajamani Bharathi M. , Benjamin Esther Sathya Bama , Abraham Aby , Ganesan Sukanya , Lakshmi Kavitha M. , Anandan Senthamizhselvi , Karathedath Sreeja , Varatharajan Savitha , Mohanan Ezhilpavai , Janet Nancy Beryl , Srivastava Vivi M. , Ramachandran Velayudhan Shaji , Kulkarni Uday P. , Devasia Anup J. , Fouzia N. A. , Korula Anu , George Biju , Srivastava Alok , Mathews Vikram , Balasubramanian Poonkuzhali 
Published: November 2020

AbstractAchieving early molecular response (EMR) has been shown to be associated with better event free survival in patients with chronic phase chronic myeloid leukemia (CP-CML) on Imatinib therapy. We prospectively evaluated the factors influencing the 2-year failure free survival (FFS) and EMR to imatinib therapy in these patients including day29 plasma Imatinib levels, genetic variants and the gene expression of target genes in imatinib transport and biotransformation. Patients with low and intermediate Sokal score had better 2-year FFS compared to those with high Sokal Score (p = 0.02). Patients carrying ABCB1-C1236T variants had high day29 plasma imatinib levels (P = 0.005), increased EMR at 3 months (P = 0.044) and a better 2 year FFS (P = 0.003) when compared to those with wild type genotype. This translates to patients with lower ABCB1 mRNA expression having a significantly higher intracellular imatinib levels (P = 0.029). Higher day29 plasma imatinib levels was found to be strongly associated with patients achieving EMR at 3 months (P = 0.022), MMR at 12 months (P = 0.041) which essentially resulted in better 2-year FFS (p = 0.05). Also, patients who achieved EMR at 3 months, 6 months and MMR at 12 months had better FFS when compared to those who did not. This study suggests the incorporation of these variables in to the imatinib dosing algorithm as predictive biomarkers of response to Imatinib therapy.
Overexpression of corticotropin-releasing factor in intestinal mucosal eosinophils is associated with clinical severity in Diarrhea-Predominant Irritable Bowel Syndrome
Authors: Salvo-Romero Eloísa , Martínez Cristina , Lobo Beatriz , Rodiño-Janeiro Bruno K. , Pigrau Marc , Sánchez-Chardi Alejandro D. , González-Castro Ana M. , Fortea Marina , Pardo-Camacho Cristina , Nieto Adoración , Expósito Elba , Guagnozzi Danila , Rodríguez-Urrutia Amanda , de Torres Inés , Farré Ricard , Azpiroz Fernando , Alonso-Cotoner Carmen , Santos Javier , Vicario María 
Published: November 2020

AbstractCorticotropin-releasing factor (CRF) has been identified in intestinal mucosal eosinophils and associated with psychological stress and gut dysfunction. Irritable bowel syndrome (IBS) is commonly characterized by altered intestinal motility, immune activation, and increased gut barrier permeability along with heightened susceptibility to psychosocial stress. Despite intensive research, the role of mucosal eosinophils in stress-associated gut dysfunction remains uncertain. In this study, we evaluated eosinophil activation profile and CRF content in the jejunal mucosa of diarrhea-predominant IBS (IBS-D) and healthy controls (HC) by gene/protein expression and transmission electron microscopy. We also explored the association between intestinal eosinophil CRF and chronic stress, and the potential mechanisms underlying the stress response by assessing eosinophil response to neuropeptides. We found that mucosal eosinophils displayed higher degranulation profile in IBS-D as compared to HC, with increased content of CRF in the cytoplasmic granules, which significantly correlated with IBS clinical severity, life stress background and depression. Eosinophils responded to substance P and carbachol by increasing secretory activity and CRF synthesis and release, without promoting pro-inflammatory activity, a profile similar to that found in mucosal eosinophils from IBS-D. Collectively, our results suggest that intestinal mucosal eosinophils are potential contributors to stress-mediated gut dysfunction through CRF production and release.
Overdrive pacing of spiral waves in a model of human ventricular tissue
Authors: Pravdin Sergei F. , Epanchintsev Timofei I. , Panfilov Alexander V. 
Published: November 2020

AbstractHigh-voltage electrical defibrillation remains the only reliable method of quickly controlling life-threatening cardiac arrhythmias. This paper is devoted to studying an alternative approach, low-voltage cardioversion (LVC), which is based on ideas from non-linear dynamics and aims to remove sources of cardiac arrhythmias by applying high-frequency stimulation to cardiac tissue. We perform a detailed in-silico study of the elimination of arrhythmias caused by rotating spiral waves in a TP06 model of human cardiac tissue. We consider three parameter sets with slopes of the APD restitution curve of 0.7, 1.1 and 1.4, and we study LVC at the baseline and under the blocking of INa and ICaL and under the application of the drugs verapamil and amiodarone. We show that pacing can remove spiral waves; however, its efficiency can be substantially reduced by dynamic instabilities. We classify these instabilities and show that the blocking of INa and the application of amiodarone increase the efficiency of the method, while the blocking of ICaL and the application of verapamil decrease the efficiency. We discuss the mechanisms and the possible clinical applications resulting from our study.
Integron gene cassettes harboring novel variants of d-alanine-d-alanine ligase confer high-level resistance to d-cycloserine
Authors: Rahman Md. Ajijur , Kaiser Frank , Jamshidi Shirin , Freitas Monteiro Marta , Rahman Khondaker Miraz , Mullany Peter , Roberts Adam P. 
Published: November 2020

AbstractAntibiotic resistance poses an increasing threat to global health. To tackle this problem, the identification of principal reservoirs of antibiotic resistance genes (ARGs) plus an understanding of drivers for their evolutionary selection are important. During a PCR-based screen of ARGs associated with integrons in saliva-derived metagenomic DNA of healthy human volunteers, two novel variants of genes encoding a d-alanine-d-alanine ligase (ddl6 and ddl7) located within gene cassettes in the first position of a reverse integron were identified. Treponema denticola was identified as the likely host of the ddl cassettes. Both ddl6 and ddl7 conferred high level resistance to d-cycloserine when expressed in Escherichia coli with ddl7 conferring four-fold higher resistance to D-cycloserine compared to ddl6. A SNP was found to be responsible for this difference in resistance phenotype between the two ddl variants. Molecular dynamics simulations were used to explain the mechanism of this phenotypic change at the atomic scale. A hypothesis for the evolutionary selection of ddl containing integron gene cassettes is proposed, based on molecular docking of plant metabolites within the ATP and d-cycloserine binding pockets of Ddl.
Identification of a novel enzyme from E. pacifica that acts as an eicosapentaenoic 8R-LOX and docosahexaenoic 10R-LOX
Authors: Yuki Sayaka , Uemura Aiko , Hakozaki Mayuka , Yano Akira , Abe Masato , Misawa Yoshihisa , Baba Naomichi , Yamada Hidetoshi 
Published: November 2020

AbstractNorth Pacific krill (Euphausia pacifica) contain 8R-hydroxy-eicosapentaenoic acid (8R-HEPE), 8R-hydroxy-eicosatetraenoic acid (8R-HETE) and 10R-hydroxy-docosahexaenoic acid (10R-HDHA). These findings indicate that E. pacifica must possess an R type lipoxygenase, although no such enzyme has been identified in krill. We analyzed E. pacifica cDNA sequence using next generation sequencing and identified two lipoxygenase genes (PK-LOX1 and 2). PK-LOX1 and PK-LOX2 encode proteins of 691 and 686 amino acids, respectively. Recombinant PK-LOX1 was generated in Sf9 cells using a baculovirus expression system. PK-LOX1 metabolizes eicosapentaenoic acid (EPA) to 8R-HEPE, arachidonic acid (ARA) to 8R-HETE and docosahexaenoic acid (DHA) to 10R-HDHA. Moreover, PK-LOX1 had higher activity for EPA than ARA and DHA. In addition, PK-LOX1 also metabolizes 17S-HDHA to 10R,17S-dihydroxy-docosahexaenoic acid (10R,17S-DiHDHA). PK-LOX1 is a novel lipoxygenase that acts as an 8R-lipoxygenase for EPA and 10R-lipoxygenase for DHA and 17S-HDHA. Our findings show PK-LOX1 facilitates the enzymatic production of hydroxy fatty acids, which are of value to the healthcare sector.
Mycosporine-like amino acid and aromatic amino acid transcriptome response to UV and far-red light in the cyanobacterium Chlorogloeopsis fritschii PCC 6912
Authors: Llewellyn Carole A. , Greig Carolyn , Silkina Alla , Kultschar Bethan , Hitchings Matthew D. , Farnham Garry 
Published: November 2020

AbstractThe “UV sunscreen” compounds, the mycosporine-like amino acids (MAAs) are widely reported in cyanobacteria and are known to be induced under ultra-violet (UV) light. However, the impact of far red (FR) light on MAA biosynthesis has not been studied. We report results from two experiments measuring transcriptional regulation of MAA and aromatic amino acid pathways in the filamentous cyanobacteriumChlorogloeopsis fritschiiPCC 6912. The first experiment, comparing UV with white light, shows the expected upregulation of the characteristic MAAmys gene cluster. The second experiment, comparing FR with white light, shows that three genes of the fourmysgene cluster encoding up to mycosporine-glycine are also upregulated under FR light. This is a new discovery. We observed corresponding increases in MAAs under FR light using HPLC analysis. The tryptophan pathway was upregulated under UV, with no change under FR. The tyrosine and phenylalanine pathways were unaltered under both conditions. However, nitrate ABC transporter genes were upregulated under UV and FR light indicating increased nitrogen requirement under both light conditions. The discovery that MAAs are upregulated under FR light supports MAAs playing a role in photon dissipation and thermoregulation with a possible role in contributing to Earth surface temperature regulation.
Strategies for the efficient use of diagnostic resource under constraints: a model-based study on overflow of patients and insufficient diagnostic kits
Authors: Tsuchida Naoshi , Nakamura Fumihiko , Matsuda Kazunori , Saikawa Takafumi , Okumura Takashi 
Published: November 2020

AbstractThis article addresses an optimisation problem of distributing rapid diagnostic kits among patients when the demands far surpass the supplies. This problem has not been given much attention in the field, and therefore, this article aims to provide a preliminary result in this problem domain. First, we describe the problem and define the goal of the optimisation by introducing an evaluation metric that measures the efficiency of the distribution strategies. Then, we propose two simple strategies, and a strategy that incorporates a prediction of patients’ visits utilising a standard epidemic model. The strategies were evaluated using the metric, with past statistics in Kitami City, Hokkaido, Japan, and the prediction-based strategy outperformed the other distribution strategies. We discuss the properties of the strategies and the limitations of the proposed approach. Although the problem must be generalised before the actual deployment of the suggested strategy, the preliminary result is promising in its ability to address the shortage of diagnostic capacity currently observed worldwide because of the ongoing coronavirus disease pandemic.
Antifungal activity of Xenorhabdus spp. and Photorhabdus spp. against the soybean pathogenic Sclerotinia sclerotiorum
Authors: Chacón-Orozco Julie G. , Bueno César , Shapiro-Ilan David I. , Hazir Selcuk , Leite Luís G. , Harakava Ricardo 
Published: November 2020

AbstractThe fungus, Sclerotinia sclerotiorum, causes white mold disease and infects a broad spectrum of host plants (> 500), including soybean with yield losses of up to 70%. Biological control is a potential alternative for management of this severe plant pathogen, and relative to chemical fungicides, provides broad benefits to the environment, farmers and consumers. The symbiotic bacteria of entomopathogenic nematodes, Xenorhabdus spp. and Photorhabdus spp., are characterized by the production of antimicrobial compounds, which could serve as potential sources for new bio-fungicides. The objectives of this study were to assess cell-free supernatants (CFS) of 16 strains of these bacteria cultures on S. sclerotiorum mycelium growth; assess the volatiles of X. szentirmaii cultures on the fungus mycelium and sclerotium inhibition; and evaluate the X. szentirmaii cultures as well as their CFS on the protection of soybean seeds against the white mold disease. Among the 16 strains, the CFS of X. szentirmaii showed the highest fungicidal effect on growth of S. sclerotiorum. The CFS of X. szentirmaii inhibited > 98% of fungus growth from mycelium and sclerotia, whereas the volatiles generated by the bacterium culture inhibited to 100% of fungus growth and 100% of sclerotia production. The bacterial culture diluted to 33% in water and coated on soybean seeds inhibited S. sclerotiorum and protected soybean plants, allowing 78.3% of seed germination and 56.6% of plant development. Our findings indicate potential for a safe and novel control method for S. sclerotiorum in soybean. Moreover, this is the first study to indicate that volatile organic compounds from Xenorhabdus spp. can be used in plant disease suppression.
Pregnant alpha-1-microglobulin (A1M) knockout mice exhibit features of kidney and placental damage, hemodynamic changes and intrauterine growth restriction
Authors: Aleksenko Larysa , Åkerström Bo , Hansson Eva , Erlandsson Lena , Hansson Stefan R. 
Published: November 2020

AbstractAlpha-1-microglobulin (A1M) is an antioxidant previously shown to be elevated in maternal blood during pregnancies complicated by preeclampsia and suggested to be important in the endogenous defense against oxidative stress. A knockout mouse model of A1M (A1Mko) was used in the present study to assess the importance of A1M during pregnancy in relation to the kidney, heart and placenta function. Systolic blood pressure (SBP) and heart rate (HR) were determined before and throughout gestation. The morphology of the organs was assessed by both light and electron microscopy. Gene expression profiles relating to vascular tone and oxidative stress were analyzed using RT-qPCR with validation of selected gene expression relating to vascular tone and oxidative stress response. Pregnant age-matched wild type mice were used as controls. In the A1Mko mice there was a significantly higher SBP before pregnancy that during pregnancy was significantly reduced compared to the control. In addition, the HR was higher both before and during pregnancy compared to the controls. Renal morphological abnormalities were more frequent in the A1Mko mice, and the gene expression profiles in the kidney and the heart showed downregulation of transcripts associated with vasodilation. Simultaneously, an upregulation of vasoconstrictors, blood pressure regulators, and genes for osmotic stress response, ion transport and reactive oxygen species (ROS) metabolism occurred. Fetal weight was lower in the A1Mko mice at E17.5. The vessels in the labyrinth zone of the placentas and the endoplasmic reticulum in the spongiotrophoblasts were collapsed. The gene profiles in the placenta showed downregulation of antioxidants, ROS metabolism and oxidative stress response genes. In conclusion, intact A1M expression is necessary for the maintenance of normal kidney, heart as well as placental structure and function for a normal pregnancy adaptation.
Retroreflection and diffraction of a Bose–Einstein condensate by evanescent standing wave potential
Authors: Akram Javed , Qasim Khan , Wei Lei 
Published: November 2020

AbstractThe characteristic of the angular distributions of accelerated Bose–Einstein condensate (BEC) atoms incidence on the surface is designed using the mathematical modeling method. Here, we proposed the idea to study retroreflection and diffraction of a BEC from an evanescent standing wave potential (ESWP). The ESWP is formed by multiple reflections of the laser beam from the surface of the prism under the influence of gravity. After BEC’s reflection and diffraction, the so-called BEC’s density rainbow patterns develop due to the interference which depends on the surface structure which we model with the periodic decaying evanescent field. The interaction of accelerated bosonic atoms with a surface can help to demonstrate surface structures or to determine surface roughness, or to build future high spatial resolution and high sensitivity magnetic-field sensors in two-dimensional systems.