bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioprospecting desert plant Bacillus endophytic strains for their potential to enhance plant stress tolerance
Authors: Bokhari Ameerah , Essack Magbubah , Lafi Feras F. , Andres-Barrao Cristina , Jalal Rewaa , Alamoudi Soha , Razali Rozaimi , Alzubaidy Hanin , Shah Kausar H. , Siddique Shahid , Bajic Vladimir B. , Hirt Heribert , Saad Maged M. 
Published: December 2019

AbstractPlant growth-promoting bacteria (PGPB) are known to increase plant tolerance to several abiotic stresses, specifically those from dry and salty environments. In this study, we examined the endophyte bacterial community of five plant species growing in the Thar desert of Pakistan. Among a total of 368 culturable isolates, 58 Bacillus strains were identified from which the 16 most divergent strains were characterized for salt and heat stress resilience as well as antimicrobial and plant growth-promoting (PGP) activities. When the 16 Bacillus strains were tested on the non-host plant Arabidopsis thaliana, B. cereus PK6-15, B. subtilis PK5-26 and B. circulans PK3-109 significantly enhanced plant growth under salt stress conditions, doubling fresh weight levels when compared to uninoculated plants. B. circulans PK3-15 and PK3-109 did not promote plant growth under normal conditions, but increased plant fresh weight by more than 50% when compared to uninoculated plants under salt stress conditions, suggesting that these salt tolerant Bacillus strains exhibit PGP traits only in the presence of salt. Our data indicate that the collection of 58 plant endophytic Bacillus strains represents an important genomic resource to decipher plant growth promotion at the molecular level.
Neurite regrowth stimulation by a red-light spot focused on the neuronal cell soma following blue light-induced retraction
Authors: Kao Yu-Chiu , Liao Yu-Cing , Cheng Pei-Lin , Lee Chau-Hwang 
Published: December 2019

AbstractThe interaction of light with biological tissues has been considered for various therapeutic applications. Light-induced neurite growth has the potential to be a clinically useful technique for neuron repair. However, most previous studies used either a large illumination area to accelerate overall neurite growth or employed a light spot to guide a growing neurite. It is not clear if optical stimulation can induce the regrowth of a retracted neurite. In the present work, we used blue light (wavelength: 473 nm) to cause neurite retraction, and we proved that using a red-light (wavelength: 650 nm) spot to illuminate the soma near the junction of the retracted neurite could induce neurite regrowth. As a comparison, we found that green light (wavelength 550 nm) had a 62% probability of inducing neurite regrowth, while red light had a 75% probability of inducing neurite regrowth at the same power level. Furthermore, the neurite regrowth length induced by red light was increased by the pre-treatment with inhibitors of myosin functions. We also observed actin propagation from the soma to the tip of the re-growing neurite following red-light stimulation of the soma. The red light-induced extension and regrowth were abrogated in the calcium-free medium. These results suggest that illumination with a red-light spot on the soma may trigger the regrowth of a neurite after the retraction caused by blue-light illumination.
Application of fluorescence spectroscopy using classical right angle technique in white wines classification
Authors: Suciu Ramona-Crina , Zarbo Liviu , Guyon Francois , Magdas Dana Alina 
Published: December 2019

AbstractThe potential of excitation - emission matrices (EEM) measurements using classical right angle technique, in conjunction with chemometrics, was prospected for white wine classification with respect to their cultivar and geographical origin. For this purpose, wines belonging to four cultivars (Chardonnay, Pinot Gris, Riesling and Sauvignon) from two different countries (Romania and France) were investigated. The excitation – emission matrices were statistically processed using parallel factor analysis (PARAFAC). According to Soft Independent Modeling Classification Analogy (SIMCA) model, for cultivar differentiation, only 3 out of 107 wine samples (1 Pinot Gris (Romania); 1 Riesling (Romania) and 1 Sauvignon (France)) were misclassified while for geographical origin assessment, only 2 wines (1 Romania and 1 France) were misclassified. This study demonstrates the potential of excitation – emission fluorescence matrices spectroscopy using the classical right angle technique in wine authentication, without sample dilution.
Microplastics ingestion and heterotrophy in thermally stressed corals
Authors: Axworthy Jeremy B. , Padilla-Gamiño Jacqueline L. 
Published: December 2019

AbstractRising sea temperatures and increasing pollution threaten the fate of coral reefs and millions of people who depend on them. Some reef-building corals respond to thermal stress and subsequent bleaching with increases in heterotrophy, which may increase the risk of ingesting microplastics. Whether this heterotrophic plasticity affects microplastics ingestion or whether ingesting microplastics affects heterotrophic feeding in corals is unknown. To determine this, two coral species, Montipora capitata and Pocillopora damicornis, were exposed to ambient (~27 °C) and increased (~30 °C) temperature and then fed microplastics, Artemia nauplii, or both. Following thermal stress, both species significantly reduced feeding on Artemia but no significant decrease in microplastics ingestion was observed. Interestingly, P. damicornis only ingested microplastics when Artemia were also present, providing evidence that microplastics are not selectively ingested by this species and are only incidentally ingested when food is available. As the first study to examine microplastics ingestion following thermal stress in corals, our results highlight the variability in the risk of microplastics ingestion among species and the importance of considering multiple drivers to project how corals will be affected by global change.
Preferential flow pathways in a deforming granular material: self-organization into functional groups for optimized global transport
Authors: van der Linden Joost H. , Tordesillas Antoinette , Narsilio Guillermo A. 
Published: December 2019

AbstractExisting definitions of where and why preferential flow in porous media occurs, or will occur, assume a priori knowledge of the fluid flow and do not fully account for the connectivity of available flow paths in the system. Here we propose a method for identifying preferential pathways through a flow network, given its topology and finite link capacities. Using data from a deforming granular medium, we show that the preferential pathways form a set of percolating pathways that is optimized for global transport of interstitial pore fluid in alignment with the applied pressure gradient. Two functional subgroups emerge. The primary subgroup comprises the main arterial paths that transmit the greatest flow through shortest possible routes. The secondary subgroup comprises inter- and intra-connecting bridges that connect the primary paths, provide alternative flow routes, and distribute flow through the system to maximize throughput. We examine the multiscale relationship between functionality and subgroup structure as the sample dilates in the lead up to the failure regime where the global volume then remains constant. Preferential flow pathways chain together large, well-connected pores, reminiscent of force chain structures that transmit the majority of the load in the solid grain phase.
Marked TGF-β-regulated miRNA expression changes in both COPD and control lung fibroblasts
Authors: Ong J. , Faiz A. , Timens W. , van den Berge M. , Terpstra M. M. , Kok K. , van den Berg A. , Kluiver J. , Brandsma C. A. 
Published: December 2019

AbstractCOPD is associated with disturbed tissue repair, possibly due to TGF-β-regulated miRNA changes in fibroblasts. Our aim was to identify TGF-β-regulated miRNAs and their differential regulation and expression in COPD compared to control fibroblasts. Small RNA sequencing was performed on TGF-β-stimulated and unstimulated lung fibroblasts from 15 COPD patients and 15 controls. Linear regression was used to identify TGF-β-regulated and COPD-associated miRNAs. Interaction analysis was performed to compare miRNAs that responded differently to TGF-β in COPD and control. Re-analysis of previously generated Ago2-IP data and Enrichr were used to identify presence and function of potential target genes in the miRNA-targetome of lung fibroblasts. In total, 46 TGF-β-regulated miRNAs were identified in COPD and 86 in control fibroblasts (FDR < 0.05). MiR-27a-5p was the most significantly upregulated miRNA. MiR-148b-3p, miR-589-5p and miR-376b-3p responded differently to TGF-β in COPD compared to control (FDR < 0.25). MiR-660-5p was significantly upregulated in COPD compared to control (FDR < 0.05). Several predicted targets of miR-27a-5p, miR-148b-3p and miR-660-5p were present in the miRNA-targetome, and were mainly involved in the regulation of gene transcription. In conclusion, altered TGF-β-induced miRNA regulation and differential expression of miR-660-5p in COPD fibroblasts, may represent one of the mechanisms underlying aberrant tissue repair and remodelling in COPD.
Targeting ARID1A-mutant colorectal cancer: depletion of ARID1B increases radiosensitivity and modulates DNA damage response
Authors: Niedermaier B. , Sak A. , Zernickel E. , Xu Shan , Groneberg M. , Stuschke M. 
Published: December 2019

AbstractThe SWI/SNF chromatin remodeling complex has been found mutated in a wide range of human cancers, causing alterations in gene expression patterns, proliferation and DNA damage response that have been linked to poor clinical prognosis. Here, we investigated weather knockdown of ARID1B, one of two mutually exclusive subunits within the SWI/SNF complex, can sensitize colorectal cancer cell lines mutated in the other subunit, ARID1A, to ionizing radiation (IR). ARID1A-mutated colorectal cancer (CRC) cell lines are selectively sensitized to IR after siRNA mediated ARID1B depletion, as measured by clonogenic survival. This is characterized by a decrease in the surviving cell fraction to 87.3% ± 2.1%, 86.0% ± 1.1% and 77.2% ± 1.5% per 1 Gy compared with control siRNA exposed cells in the dose range of 0–6 Gy for the LS180, RKO and SW48 lines, respectively (p < 0.0001, F-test). The magnitude of this dose modifying effect was significantly larger in ARID1A mutated than in non-mutated cell lines (Spearman rank correlation rs = 0.88, p = 0.02). Furthermore, initial formation of RAD51 foci at 4 h after IR, as a measure for homologous recombination repair, was significantly reduced in ARID1A-mutant CRC cell lines but not in the majority of wildtype lines nor in fibroblasts. These findings open up perspectives for targeting ARID1B in combination with radiotherapy to improve outcomes of patients with ARID1A-mutant CRC.
Machine Learning based Analytical Framework for Automatic Hyperspectral Raman Analysis of Lithium-ion Battery Electrodes
Authors: Baliyan Ankur , Imai Hideto 
Published: December 2019

AbstractThe intelligence to synchronously identify multiple spectral signatures in a lithium-ion battery electrode (LIB) would facilitate the usage of analytical technique for inline quality control and product development. Here, we present an analytical framework (AF) to automatically identify the existing spectral signatures in the hyperspectral Raman dataset of LIB electrodes. The AF is entirely automated and requires fewer or almost no human assistance. The end-to-end pipeline of AF own the following features; (i) intelligently pre-processing the hyperspectral Raman dataset to eliminate the cosmic noise and baseline, (ii) extract all the reliable spectral signatures from the hyperspectral dataset and assign the class labels, (iii) training a neural network (NN) on to the precisely “labelled” spectral signature, and finally, examined the interoperability/reusability of already trained NN on to the newly measured dataset taken from the same LIB specimen or completely different LIB specimen for inline real-time analytics. Furthermore, we demonstrate that it is possible to quantitatively assess the capacity degradation of LIB via a capacity retention coefficient that can be calculated by comparing the LMO signatures extracted by the analytical framework (AF). The present approach is suited for real-time vibrational spectroscopy based industrial applications; multicomponent chemical reactions, chromatographic, spectroscopic mixtures, and environmental monitoring.
Somatic mutation signatures in primary liver tumors of workers exposed to ionizing radiation
Authors: Goerlitz David S. , Blancato Jan , Ramesh Archana , Islam Md. , Graham Garrett T. , Revina Valentina , Kallakury Bhaskar , Zeck Jay , Kirillova Evgeniya , Loffredo Christopher A. 
Published: December 2019

AbstractLiver cancer is associated with genetic mutations caused by environmental exposures, including occupational exposure to alpha radiation emitted by plutonium. We used whole exome sequencing (WES) to characterize somatic mutations in 3 histologically distinct primary liver tumors (angiosarcoma of the liver (ASL), cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC)) from Mayak worker subjects occupationally exposed to ionizing radiation (IR) to investigate the contribution of IR to the mutational landscape of liver cancer. DNA sequence analysis revealed these tumors harbor an excess of deletions, with a deletions:substitutions ratio similar to that previously reported in radiation-associated tumors. These tumors were also enriched for clustered mutations, a signature of radiation exposure. Multiple tumors displayed similarities in abrogated gene pathways including actin cytoskeletal signaling and DNA double-strand break (DSB) repair. WES identified novel candidate driver genes in ASL involved in angiogenesis and PIK3CA/AKT/mTOR signaling. We confirmed known driver genes of CCA, and identified candidate driver genes involved in chromatin remodeling. In HCC tumors we validated known driver genes, and identified novel putative driver genes involved in Wnt/β-catenin signaling, chromatin remodeling, PIK3CA/AKT/mTOR signaling, and angiogenesis. This pilot study identifies several novel candidate driver mutations that are likely to be caused by IR exposure, and provides the first data on the mutational landscape of liver cancer after IR exposure.
Identifying Ear Abnormality from 2D Photographs Using Convolutional Neural Networks
Authors: Hallac Rami R. , Lee Jeon , Pressler Mark , Seaward James R. , Kane Alex A. 
Published: December 2019

AbstractQuantifying ear deformity using linear measurements and mathematical modeling is difficult due to the ear’s complex shape. Machine learning techniques, such as convolutional neural networks (CNNs), are well-suited for this role. CNNs are deep learning methods capable of finding complex patterns from medical images, automatically building solution models capable of machine diagnosis. In this study, we applied CNN to automatically identify ear deformity from 2D photographs. Institutional review board (IRB) approval was obtained for this retrospective study to train and test the CNNs. Photographs of patients with and without ear deformity were obtained as standard of care in our photography studio. Profile photographs were obtained for one or both ears. A total of 671 profile pictures were used in this study including: 457 photographs of patients with ear deformity and 214 photographs of patients with normal ears. Photographs were cropped to the ear boundary and randomly divided into training (60%), validation (20%), and testing (20%) datasets. We modified the softmax classifier in the last layer in GoogLeNet, a deep CNN, to generate an ear deformity detection model in Matlab. All images were deemed of high quality and usable for training and testing. It took about 2 hours to train the system and the training accuracy reached almost 100%. The test accuracy was about 94.1%. We demonstrate that deep learning has a great potential in identifying ear deformity. These machine learning techniques hold the promise in being used in the future to evaluate treatment outcomes.
Population pharmacokinetics of afatinib and exposure-safety relationships in Japanese patients with EGFR mutation-positive non-small cell lung cancer
Authors: Nakao Keiko , Kobuchi Shinji , Marutani Shuhei , Iwazaki Ayano , Tamiya Akihiro , Isa Shunichi , Okishio Kyoichi , Kanazu Masaki , Tamiya Motohiro , Hirashima Tomonori , Imai Kimie , Sakaeda Toshiyuki , Atagi Shinji 
Published: December 2019

AbstractTo investigate the exposure–safety relationships of afatinib in Japanese population, we performed population pharmacokinetics (PK) analysis of afatinib in Japanese advanced non-small cell lung cancer patients harboring epidermal growth factor receptor mutation. Plasma samples were collected at 0.5–1, 2–3, 8–12, and 24 h after oral afatinib (40 mg) administration on day 1 and day 8. Plasma afatinib concentrations were determined using high-performance liquid chromatography. Data was analyzed following the population approach and using the software Phoenix® NLMETM Version 7.0 software (Certara USA, Inc., Princeton, NJ, USA). From 34 patients, a total of 354 afatinib plasma concentration values were available for the population PK analysis. Significant covariates in the population PK model included aspartate aminotransferase and creatinine clearance on CL/F, and age and body mass index on V/F. Results of simulation based on final PK model indicated that hepatic impairment had a significant effect on afatinib levels in plasma after multiple dosing. Afatinib trough plasma concentrations on day 8 were higher in patients with adverse events of grade 3 or higher. The population PK analysis showed that hepatic impairment affected afatinib PK parameters and contributed to the high inter-patient variability and high plasma concentrations of afatinib following multiple treatments.
Frequentist and Bayesian approaches for food allergen risk assessment: risk outcome and uncertainty comparisons
Authors: Birot Sophie , Crépet Amélie , Remington Benjamin C. , Madsen Charlotte B. , Kruizinga Astrid G. , Baumert Joseph L. , Brockhoff Per B. 
Published: December 2019

AbstractPeer-reviewed probabilistic methods already predict the probability of an allergic reaction resulting from an accidental exposure to food allergens, however, the methods calculate it in different ways. The available methods utilize the same three major input parameters in the risk model: the risk is estimated from the amount of food consumed, the concentration of allergen in the contaminated product and the distribution of thresholds among allergic persons. However, consensus is lacking about the optimal method to estimate the risk of allergic reaction and the associated uncertainty. This study aims to compare estimation of the risk of allergic reaction and associated uncertainty using different methods and suggest improvements. Four cases were developed based on the previous publications and the risk estimations were compared. The risk estimation was found to agree within 0.5% with the different simulation cases. Finally, an uncertainty analysis method is also presented in order to evaluate the uncertainty propagation from the input parameters to the risk.
Transcriptome-wide Profiling of Cerebral Cavernous Malformations Patients Reveal Important Long noncoding RNA molecular signatures
Authors: Subhash Santhilal , Kalmbach Norman , Wegner Florian , Petri Susanne , Glomb Torsten , Dittrich-Breiholz Oliver , Huang Caiquan , Bali Kiran Kumar , Kunz Wolfram S. , Samii Amir , Bertalanffy Helmut , Kanduri Chandrasekhar , Kar Souvik 
Published: December 2019

AbstractCerebral cavernous malformations (CCMs) are low-flow vascular malformations in the brain associated with recurrent hemorrhage and seizures. The current treatment of CCMs relies solely on surgical intervention. Henceforth, alternative non-invasive therapies are urgently needed to help prevent subsequent hemorrhagic episodes. Long non-coding RNAs (lncRNAs) belong to the class of non-coding RNAs and are known to regulate gene transcription and involved in chromatin remodeling via various mechanism. Despite accumulating evidence demonstrating the role of lncRNAs in cerebrovascular disorders, their identification in CCMs pathology remains unknown. The objective of the current study was to identify lncRNAs associated with CCMs pathogenesis using patient cohorts having 10 CCM patients and 4 controls from brain. Executing next generation sequencing, we performed whole transcriptome sequencing (RNA-seq) analysis and identified 1,967 lncRNAs and 4,928 protein coding genes (PCGs) to be differentially expressed in CCMs patients. Among these, we selected top 6 differentially expressed lncRNAs each having significant correlative expression with more than 100 differentially expressed PCGs. The differential expression status of the top lncRNAs, SMIM25 and LBX2-AS1 in CCMs was further confirmed by qRT-PCR analysis. Additionally, gene set enrichment analysis of correlated PCGs revealed critical pathways related to vascular signaling and important biological processes relevant to CCMs pathophysiology. Here, by transcriptome-wide approach we demonstrate that lncRNAs are prevalent in CCMs disease and are likely to play critical roles in regulating important signaling pathways involved in the disease progression. We believe, that detailed future investigations on this set of identified lncRNAs can provide useful insights into the biology and, ultimately, contribute in preventing this debilitating disease.
Upgraded antennas for pulsar observations in the Argentine Institute of Radio astronomy
Authors: Gancio G. , Lousto C. O. , Combi L. , del Palacio S. , López Armengol F. G. , Combi J. A. , García F. , Kornecki P. , Müller A. L. , Gutiérrez E. , Hauscarriaga F. , Mancuso G. C. 
Published: December 2019

Context. The Argentine Institute of Radio astronomy (IAR) is equipped with two single-dish 30 m radio antennas capable of performing daily observations of pulsars and radio transients in the southern hemisphere at 1.4 GHz.
Aims. We aim to introduce to the international community the upgrades performed and to show that the IAR observatory has become suitable for investigations in numerous areas of pulsar radio astronomy, such as pulsar timing arrays, targeted searches of continuous gravitational waves sources, monitoring of magnetars and glitching pulsars, and studies of a short time scale interstellar scintillation.
Methods. We refurbished the two antennas at IAR to achieve high-quality timing observations. We gathered more than 1000 h of observations with both antennas in order to study the timing precision and sensitivity they can achieve.
Results. We introduce the new developments for both radio telescopes at IAR. We present daily observations of the millisecond pulsar J0437−4715 with timing precision better than 1 μs. We also present a follow-up of the reactivation of the magnetar XTE J1810–197 and the measurement and monitoring of the latest (Feb. 1, 2019) glitch of the Vela pulsar (J0835–4510).
Conclusions. We show that IAR is capable of performing pulsar monitoring in the 1.4 GHz radio band for long periods of time with a daily cadence. This opens up the possibility of pursuing several goals in pulsar science, including coordinated multi-wavelength observations with other observatories. In particular, daily observations of the millisecond pulsar J0437−4715 would increase the sensitivity of pulsar timing arrays. We also show IAR’s great potential for studying targets of opportunity and transient phenomena, such as magnetars, glitches, and fast-radio-burst sources.