bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strong North Pacific Subtropical Mode Water Volume and Density Decrease in Year 1999
Authors: Cerovečki I. , Hendershott M. C. , Yulaeva E. 
Published: July 2019

AbstractA strong decrease of volume and density of North Pacific Subtropical Mode Water (NPSTMW) in 1999 was analyzed in a regional high‐resolution (0.1°) numerical ocean circulation model simulation. Both shoaling of the bottom and deepening of the top of the NPSTMW layer contributed equally to volume decrease. They were locally governed by different physical processes, but both seem to be associated with basin‐wide changes in wind. A westward propagating negative thermocline depth anomaly that developed in the Central Pacific when the Pacific Decadal Oscillation index changed from a positive to a negative phase in 1998 caused shoaling of the bottom of the NPSTMW layer. Deepening of the top of the NPSTMW layer was due to an increase in the near surface stratification, caused by an increase in wind‐driven lateral heat transport convergence by the Kuroshio Extension jet starting in 1997. Both processes increased the potential vorticity in the NPSTMW region, decreasing the volume of water in the NPSTMW density range that satisfied the low potential vorticity constraint that is part of the definition of “mode water.” The strong near‐surface density decrease provided preconditioning for preferential surface formation of a lighter variety of NPSTMW, further decreasing its density. It also resulted in decrease of the outcrop window in the NPSTMW density range, strongly reducing its formation rate in 1998 and 1999 despite strong surface heat loss.
Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria
Authors: Geddes Barney A. , Paramasivan Ponraj , Joffrin Amelie , Thompson Amber L. , Christensen Kirsten , Jorrin Beatriz , Brett Paul , Conway Stuart J. , Oldroyd Giles E. D. , Poole Philip S. 
Published: July 2019

AbstractThe root microbiota is critical for agricultural yield, with growth-promoting bacteria able to solubilise phosphate, produce plant growth hormones, antagonise pathogens and fix N2. Plants control the microorganisms in their immediate environment and this is at least in part through direct selection, the immune system, and interactions with other microorganisms. Considering the importance of the root microbiota for crop yields it is attractive to artificially regulate this environment to optimise agricultural productivity. Towards this aim we express a synthetic pathway for the production of the rhizopine scyllo-inosamine in plants. We demonstrate the production of this bacterial derived signal in both Medicago truncatula and barley and show its perception by rhizosphere bacteria, containing bioluminescent and fluorescent biosensors. This study lays the groundwork for synthetic signalling networks between plants and bacteria, allowing the targeted regulation of bacterial gene expression in the rhizosphere for delivery of useful functions to plants.
Designing development programs for non-traditional antibacterial agents
Authors: Rex John H. , Fernandez Lynch Holly , Cohen I. Glenn , Darrow Jonathan J. , Outterson Kevin 
Published: July 2019

AbstractIn the face of rising rates of antibacterial resistance, many responses are being pursued in parallel, including ‘non-traditional’ antibacterial agents (agents that are not small-molecule drugs and/or do not act by directly targeting bacterial components necessary for bacterial growth). In this Perspective, we argue that the distinction between traditional and non-traditional agents has only limited relevance for regulatory purposes. Rather, most agents in both categories can and should be developed using standard measures of clinical efficacy demonstrated with non-inferiority or superiority trial designs according to existing regulatory frameworks. There may, however, be products with non-traditional goals focused on population-level benefits that would benefit from extension of current paradigms. Discussion of such potential paradigms should be undertaken by the development community.
Transposition favors the generation of large effect mutations that may facilitate rapid adaption
Authors: Quadrana Leandro , Etcheverry Mathilde , Gilly Arthur , Caillieux Erwann , Madoui Mohammed-Amin , Guy Julie , Bortolini Silveira Amanda , Engelen Stefan , Baillet Victoire , Wincker Patrick , Aury Jean-Marc , Colot Vincent 
Published: July 2019

AbstractTransposable elements (TEs) are mobile parasitic sequences that have been repeatedly coopted during evolution to generate new functions and rewire gene regulatory networks. Yet, the contribution of active TEs to the creation of heritable mutations remains unknown. Using TE accumulation lines in Arabidopsis thaliana we show that once initiated, transposition produces an exponential spread of TE copies, which rapidly leads to high mutation rates. Most insertions occur near or within genes and targets differ between TE families. Furthermore, we uncover an essential role of the histone variant H2A.Z in the preferential integration of Ty1/copia retrotransposons within environmentally responsive genes and away from essential genes. We also show that epigenetic silencing of new Ty1/copia copies can affect their impact on major fitness-related traits, including flowering time. Our findings demonstrate that TEs are potent episodic (epi)mutagens that, thanks to marked chromatin tropisms, limit the mutation load and increase the potential for rapid adaptation.
Mapping brain function during naturalistic viewing using high-density diffuse optical tomography
Authors: Fishell Andrew K. , Burns-Yocum Tracy M. , Bergonzi Karla M. , Eggebrecht Adam T. , Culver Joseph P. 
Published: July 2019

AbstractNaturalistic stimuli, such as movies, more closely recapitulate “real life” sensory processing and behavioral demands relative to paradigms that rely on highly distilled and repetitive stimulus presentations. The rich complexity inherent in naturalistic stimuli demands an imaging system capable of measuring spatially distributed brain responses, and analysis tools optimized for unmixing responses to concurrently presented features. In this work, the combination of passive movie viewing with high-density diffuse optical tomography (HD-DOT) is developed as a platform for naturalistic brain mapping. We imaged healthy young adults during free viewing of a feature film using HD-DOT and observed reproducible, synchronized cortical responses across a majority of the field-of-view, most prominently in hierarchical cortical areas related to visual and auditory processing, both within and between individuals. In order to more precisely interpret broad patterns of cortical synchronization, we extracted visual and auditory features from the movie stimulus and mapped the cortical responses to the features. The results demonstrate the sensitivity of HD-DOT to evoked responses during naturalistic viewing, and that feature-based decomposition strategies enable functional mapping of naturalistic stimulus processing, including human-generated speech.
Fabrication of spent FCC catalyst composites by loaded V2O5 and TiO2 and their comparative photocatalytic activities
Authors: Xu Jiasheng , Zhang Te 
Published: July 2019

AbstractThe spent fluid catalytic cracking catalyst (FCC) has been loaded with different content of V2O5 and TiO2 through a modified-impregnation method. X-ray Diffraction (XRD), ultraviolet-visible spectrophotometry (UV-Vis), Scanning Electron Microscope (SEM), and Fourier Transform Infrared spectroscopy (FT-IR) are used to characterize the structure and morphology of these samples. Their photocatalytic activity was evaluated by degradation of methylene blue (MB) solution under 300 W Xenon lamp irradiation. The interplanar spacing of the zeolite Y (111) plane is affected by the amount of the loaded V2O5 on spent FCC catalyst. The (111) plane of spent FCC catalyst loaded with V2O5 and TiO2 sample is 1.404 nm, which is higher than that of the zeolite Y (1.395 nm). The amount of adsorption of MB and the photocatalytic activity for the degradation increased with increasing the interplanar spacing of the (111) plane of sample. We fabricated of spent FCC catalyst composites by loaded V2O5 and TiO2, which effectively solved the spent FCC catalyst disposal problem. The efficiency of the developed sample provides a potentially economical way of degrading MB.
Tunable large free spectral range microring resonators in lithium niobate on insulator
Authors: Krasnokutska Inna , Tambasco Jean-Luc J. , Peruzzo Alberto 
Published: July 2019

AbstractMicroring resonators are critical photonic components used in filtering, sensing and nonlinear applications. To date, the development of high performance microring resonators in LNOI has been limited by the sidewall angle, roughness and etch depth of fabricated rib waveguides. We present large free spectral range microring resonators patterned via electron beam lithography in high-index contrast Z-cut LNOI. Our microring resonators achieve an FSR greater than 5 nm for ring radius of 30 μm and a large 3 dB resonance bandwidth. We demonstrate 3 pm/V electro-optic tuning of a 70 μm-radius ring. This work will enable efficient on-chip filtering in LNOI and precede future, more complex, microring resonator networks and nonlinear field enhancement applications.
Comparative Study of Subcutaneous and Orthotopic Mouse Models of Prostate Cancer: Vascular Perfusion, Vasculature Density, Hypoxic Burden and BB2r-Targeting Efficacy
Authors: Zhang Wenting , Fan Wei , Rachagani Satyanarayana , Zhou Zhengyuan , Lele Subodh M. , Batra Surinder K. , Garrison Jered C. 
Published: July 2019

AbstractThe gastrin-releasing peptide receptor (BB2r) is overexpressed in a variety of cancers including prostate cancer. As a consequence, the development of BB2r-targeted diagnostic/therapeutic radiopharmaceuticals has been widely explored. Both subcutaneous and orthotopic mouse models have been extensively used in BB2r-targeted agent development, but side-by-side studies examining how biological parameters (tumor perfusion efficacy, hypoxic burden and microvasculature density) impact BB2r-targeted agent delivery has not been reported. Herein, we examine these biological parameters using subcutaneous and orthotopic PC-3 xenografts. Using a dual isotope biodistribution study, tumor perfusion was accessed using [99mTc]NaTcO4 and BB2r-targeted uptake evaluated by utilization of a novel 177Lu-labeled conjugate ([177Lu]Lu-DOTA-SP714). Immunofluorescence, immunohistochemistry and autoradiography were utilized to examine the tumor vascular density, hypoxic burden and microdistribution of the BB2r-targeted agent. Our studies demonstrated that compared to the subcutaneous model the PC-3 orthotopic tumors had significantly higher levels of perfusion that led to higher BB2r-targeted uptake and lower levels of hypoxia burden. It is anticipated that our results will allow researchers to better understand the biological variables affecting drug delivery and assist them in more clearly interpreting their results in this common prostate cancer mouse model.
Laser-driven vacuum breakdown waves
Authors: Samsonov A. S. , Nerush E. N. , Kostyukov I. Yu. 
Published: July 2019

AbstractIt is demonstrated by three-dimensional quantum electrodynamics — particle-in-cell (QED-PIC) simulations that vacuum breakdown wave in the form of QED cascade front can propagate in an extremely intense plane electromagnetic wave. The result disproves the statement that the self-sustained cascading is not possible in a plane wave configuration. In the simulations the cascade is initiated during laser-foil interaction in the light sail regime. As a result, a constantly growing electron-positron plasma cushion is formed between the foil and laser radiation. The cushion plasma efficiently absorbs the laser energy and decouples the radiation from the moving foil thereby interrupting the ion acceleration. The models describing propagation of the cascade front and electrodynamics of the cushion plasma are presented and their predictions are in a qualitative agreement with the results of numerical simulations.
A Novel Framework for Early Detection of Hypertension using Magnetic Resonance Angiography
Authors: Kandil Heba , Soliman Ahmed , Ghazal Mohammed , Mahmoud Ali , Shalaby Ahmed , Keynton Robert , Elmaghraby Adel , Giridharan Guruprasad , El-Baz Ayman 
Published: July 2019

AbstractHypertension is a leading mortality cause of 410,000 patients in USA. Cerebrovascular structural changes that occur as a result of chronically elevated cerebral perfusion pressure are hypothesized to precede the onset of systemic hypertension. A novel framework is presented in this manuscript to detect and quantify cerebrovascular changes (i.e. blood vessel diameters and tortuosity changes) using magnetic resonance angiography (MRA) data. The proposed framework consists of: 1) A novel adaptive segmentation algorithm to delineate large as well as small blood vessels locally using 3-D spatial information and appearance features of the cerebrovascular system; 2) Estimating the cumulative distribution function (CDF) of the 3-D distance map of the cerebrovascular system to quantify alterations in cerebral blood vessels’ diameters; 3) Calculation of mean and Gaussian curvatures to quantify cerebrovascular tortuosity; and 4) Statistical and correlation analyses to identify the relationship between mean arterial pressure (MAP) and cerebral blood vessels’ diameters and tortuosity alterations. The proposed framework was validated using MAP and MRA data collected from 15 patients over a 700-days period. The novel adaptive segmentation algorithm recorded a 92.23% Dice similarity coefficient (DSC), a 94.82% sensitivity, a 99.00% specificity, and a 10.00% absolute vessels volume difference (AVVD) in delineating cerebral blood vessels from surrounding tissues compared to the ground truth. Experiments demonstrated that MAP is inversely related to cerebral blood vessel diameters (p-value < 0.05) globally (over the whole brain) and locally (at circle of Willis and below). A statistically significant direct correlation (p-value < 0.05) was found between MAP and tortuosity (medians of Gaussian and mean curvatures, and average of mean curvature) globally and locally (at circle of Willis and below). Quantification of the cerebrovascular diameter and tortuosity changes may enable clinicians to predict elevated blood pressure before its onset and optimize medical treatment plans of pre-hypertension and hypertension.
Detection of dynamic protein complexes through Markov Clustering based on Elephant Herd Optimization Approach
Authors: Rani R. Ranjani , Ramyachitra D. , Brindhadevi A. 
Published: July 2019

AbstractThe accessibility of a huge amount of protein-protein interaction (PPI) data has allowed to do research on biological networks that reveal the structure of a protein complex, pathways and its cellular organization. A key demand in computational biology is to recognize the modular structure of such biological networks. The detection of protein complexes from the PPI network, is one of the most challenging and significant problems in the post-genomic era. In Bioinformatics, the frequently employed approach for clustering the networks is Markov Clustering (MCL). Many of the researches for protein complex detection were done on the static PPI network, which suffers from a few drawbacks. To resolve this problem, this paper proposes an approach to detect the dynamic protein complexes through Markov Clustering based on Elephant Herd Optimization Approach (DMCL-EHO). Initially, the proposed method divides the PPI network into a set of dynamic subnetworks under various time points by combining the gene expression data and secondly, it employs the clustering analysis on every subnetwork using the MCL along with Elephant Herd Optimization approach. The experimental analysis was employed on different PPI network datasets and the proposed method surpasses various existing approaches in terms of accuracy measures. This paper identifies the common protein complexes that are expressively enriched in gold-standard datasets and also the pathway annotations of the detected protein complexes using the KEGG database.
A potential role for rare species in ecosystem dynamics
Authors: Säterberg Torbjörn , Jonsson Tomas , Yearsley Jon , Berg Sofia , Ebenman Bo 
Published: July 2019

AbstractThe ecological importance of common species for many ecosystem processes and functions is unquestionably due to their high abundance. Yet, the importance of rare species is much less understood. Here we take a theoretical approach, exposing dynamical models of ecological networks to small perturbations, to explore the dynamical importance of rare and common species. We find that both species types contribute to the recovery of communities following generic perturbations (i.e. perturbations affecting all species). Yet, when perturbations are selective (i.e. affects only one species), perturbations to rare species have the most pronounced effect on community stability. We show that this is due to the strong indirect effects induced by perturbations to rare species. Because indirect effects typically set in at longer timescales, our results indicate that the importance of rare species may be easily overlooked and thus underrated. Hence, our study provides a potential ecological motive for the management and protection of rare species.
Artificial intelligence for morphology-based function prediction in neovascular age-related macular degeneration
Authors: von der Emde Leon , Pfau Maximilian , Dysli Chantal , Thiele Sarah , Möller Philipp T. , Lindner Moritz , Schmid Matthias , Fleckenstein Monika , Holz Frank G. , Schmitz-Valckenberg Steffen 
Published: July 2019

AbstractSpatially-resolved mapping of rod- and cone-function may facilitate monitoring of macular diseases and serve as a functional outcome parameter. However, mesopic and dark-adapted two-color fundus-controlled perimetry (FCP, also called “microperimetry”) constitute laborious examinations. We have devised a machine-learning-based approach to predict mesopic and dark-adapted (DA) retinal sensitivity in eyes with neovascular age-related macular degeneration (nAMD). Extensive psychophysical testing and volumetric multimodal retinal imaging data were acquired including mesopic, DA red and DA cyan FCP, spectral-domain optical coherence tomography and confocal scanning laser ophthalmoscopy infrared reflectance and fundus autofluorescence imaging. With patient-wise leave-one-out cross-validation, we have been able to achieve prediction accuracies of (mean absolute error, MAE [95% CI]) 3.94 dB [3.38, 4.5] for mesopic, 4.93 dB [4.59, 5.27] for DA cyan and 4.02 dB [3.63, 4.42] for DA red testing. Partial addition of patient-specific sensitivity data decreased the cross-validated MAE to 2.8 dB [2.51, 3.09], 3.71 dB [3.46, 3.96], and 2.85 dB [2.62, 3.08]. The most important predictive feature was outer nuclear layer thickness. This artificial intelligence-based analysis strategy, termed “inferred sensitivity”, herein, enables to estimate differential effects of retinal structural abnormalities on cone- and rod-function in nAMD, and may be used as quasi-functional surrogate endpoint in future clinical trials.
Knockout of Acinar Enriched microRNAs in Mice Promote Duct Formation But Not Pancreatic Cancer
Authors: Sutaria Dhruvitkumar S. , Jiang Jinmai , Azevedo-Pouly Ana Clara , Wright Lais , Bray Julie A. , Fredenburg Kristianna , Liu Xiuli , Lu Jun , Torres Carolina , Mancinelli Georgina , Grippo Paul J. , Coppola Vincenzo , Schmittgen Thomas D. 
Published: July 2019

AbstractThe pancreatic acinar-enriched miR-216a, miR-216b and miR-217 are encoded within the miR217HG. These miRNAs have been purported to play a tumor suppressive role as their expression is reduced in both human and mouse pancreatic ductal adenocarcinoma (PDAC). To examine this possibility, we generated individual, germline knockout (KO) mice of miR-216a, miR-216b or miR-217. Unlike our previous study showing germline deletion of the miR217HG was embryonic lethal, CRISPR-Cas9 deleted portions of the 5’ seed region of the miRNAs produced live births. To investigate possible phenotypes during pancreatic acinar ductal metaplasia (ADM), pancreatic acini from wild type and KO mice were plated on collagen and allowed to transdifferentiate over 4 days. Acini from each of the three miRNA KO mice produced greater numbers of ducts compared to controls. Evaluation of the gene expression during in vitro ADM demonstrated an increase in Krt19 and a reduction in acinar genes (Carboxypeptidase A1, Amylase2a) on day 4 of the transdifferentiation. Recovery was delayed for the miR-216a and miR-216b KOs following caerulein-induced acute pancreatitis. Also predominate in the caerulein treated miR-216a and miR-216b KO mice was the presence of pancreatic duct glands (PDGs). To further establish a phenotype, miRNA KO mice were crossed with EL-KRASG12D (EK) mice and followed up to 13 months of age. While all mice developed severe dysplasia and cystic papillary neoplasms, there existed no apparent phenotypic difference in the miRNA KO/EK mice compared to EK mice. Our data does not support a tumor suppressor role for miR-216a, miR-216b or miR-217 in PDAC and emphasizes the need for phenotypic evaluation of miRNAs in complex in vivo models beyond that performed using cell culture.
Miltefosine increases macrophage cholesterol release and inhibits NLRP3-inflammasome assembly and IL-1β release
Authors: Iacano Amanda J. , Lewis Harvey , Hazen Jennie E. , Andro Heather , Smith Jonathan D. , Gulshan Kailash 
Published: July 2019

AbstractMiltefosine is an FDA approved oral drug for treating cutaneous and visceral leishmaniasis. Leishmania is a flagellated protozoa, which infects and differentiates in macrophages. Here, we studied the effects of Miltefosine on macrophage’s lipid homeostasis, autophagy, and NLRP3 inflammasome assembly/activity. Miltefosine treatment conferred multiple effects on macrophage lipid homeostasis leading to increased cholesterol release from cells, increased lipid-raft disruption, decreased phosphatidylserine (PS) flip from the cell-surface, and redistribution of phosphatidylinositol 4,5-bisphosphate (PIP2) from the plasma membrane to actin rich regions in the cells. Enhanced basal autophagy, lipophagy and mitophagy was observed in cells treated with Miltefosine vs. control. Miltefosine treated cells showed marked increased in phosphorylation of kinases involved in autophagy induction such as; Adenosine monophosphate-activated protein kinase (AMPK) and Unc-51 like autophagy activating kinase (ULK1). The Toll like receptor (TLR) signaling pathway was blunted by Miltefosine treatment, resulting in decreased TLR4 recruitment to cell-surface and ~75% reduction in LPS induced pro-IL-1β mRNA levels. Miltefosine reduced endotoxin-mediated mitochondrial reactive oxygen species and protected the mitochondrial membrane potential. Miltefosine treatment induced mitophagy and dampened NLRP3 inflammasome assembly. Collectively, our data shows that Miltefosine induced ABCA1 mediated cholesterol release, induced AMPK phosphorylation and mitophagy, while dampening NLRP3 inflammasome assembly and IL-1β release.