bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time of flight dual photon emission computed tomography
Authors: Chiang Chih-Chieh , Chuang Chun-Chao , Ni Yu-Ching , Jan Meei-Ling , Chuang Keh-Shih , Lin Hsin-Hon 
Published: November 2020

AbstractTime-of-flight dual photon emission computed tomography (TOF-DuPECT) is an imaging system that can obtain radionuclide distributions using time information recorded from two cascade-decay photons. The potential decay locations in the image space, a hyperbolic response curve, can be determined via time-difference-of-arrival (TDOA) estimations from two instantaneous coincidence photons. In this feasibility study, Monte Carlo simulations were performed to generate list-mode coincidence data. A full-ring positron emission tomography-like detection system geometry was built in the simulation environment. A contrast phantom and a Jaszczak-like phantom filled with Selenium-75 (Se-75) were used to evaluate the image quality. A TOF-DuPECT system with varying coincidence time resolution (CTR) was then evaluated. We used the stochastic origin ensemble (SOE) algorithm to reconstruct images from the recorded list-mode data. The results indicate that the SOE method can be successfully employed for the TOF-DuPECT system and can achieve acceptable image quality when the CTR is less than 100 ps. Therefore, the TOF-DuPECT imaging system is feasible. With the improvement of the detector with time, future implementations and applications of TOF-DuPECT are promising. Further quantitative imaging techniques such as attenuation and scatter corrections for the TOF-DuPECT system will be developed in future.
COVID-Net: a tailored deep convolutional neural network design for detection of COVID-19 cases from chest X-ray images
Authors: Wang Linda , Lin Zhong Qiu , Wong Alexander 
Published: November 2020

AbstractThe Coronavirus Disease 2019 (COVID-19) pandemic continues to have a devastating effect on the health and well-being of the global population. A critical step in the fight against COVID-19 is effective screening of infected patients, with one of the key screening approaches being radiology examination using chest radiography. It was found in early studies that patients present abnormalities in chest radiography images that are characteristic of those infected with COVID-19. Motivated by this and inspired by the open source efforts of the research community, in this study we introduce COVID-Net, a deep convolutional neural network design tailored for the detection of COVID-19 cases from chest X-ray (CXR) images that is open source and available to the general public. To the best of the authors’ knowledge, COVID-Net is one of the first open source network designs for COVID-19 detection from CXR images at the time of initial release. We also introduce COVIDx, an open access benchmark dataset that we generated comprising of 13,975 CXR images across 13,870 patient patient cases, with the largest number of publicly available COVID-19 positive cases to the best of the authors’ knowledge. Furthermore, we investigate how COVID-Net makes predictions using an explainability method in an attempt to not only gain deeper insights into critical factors associated with COVID cases, which can aid clinicians in improved screening, but also audit COVID-Net in a responsible and transparent manner to validate that it is making decisions based on relevant information from the CXR images. By no means a production-ready solution, the hope is that the open access COVID-Net, along with the description on constructing the open source COVIDx dataset, will be leveraged and build upon by both researchers and citizen data scientists alike to accelerate the development of highly accurate yet practical deep learning solutions for detecting COVID-19 cases and accelerate treatment of those who need it the most.
The role of soluble mediators in the clinical course of EBV infection and B cell homeostasis after kidney transplantation
Authors: Bajda Sharon , Blazquez-Navarro Arturo , Samans Björn , Wehler Patrizia , Kaliszczyk Sviatlana , Amini Leila , Schmueck-Henneresse Michael , Witzke Oliver , Dittmer Ulf , Westhoff Timm H. , Viebahn Richard , Reinke Petra , Thomusch Oliver , Hugo Christian , Olek Sven , Roch Toralf , Babel Nina 
Published: November 2020

AbstractEpstein-Barr virus (EBV) reactivation can lead to serious complications in kidney transplant patients, including post-transplant lymphoproliferative disorder (PTLD). Here, we have assessed the impact of EBV on B cell homeostasis at cellular and humoral level. In a multicenter study monitoring 540 kidney transplant patients during the first post-transplant year, EBV reactivation was detected in 109 patients. Thirteen soluble factors and B cell counts were analyzed in an EBV+sub-cohort (N = 54) before, at peak and after EBV clearance and compared to a control group (N = 50). The B cell activating factor (BAFF) was significantly elevated among EBV+patients. No additional soluble factors were associated with EBV. Importantly, in vitro experiments confirmed the proliferative effect of BAFF on EBV-infected B cells, simultaneously promoting EBV production. In contrast, elevated levels of BAFF in EBV+patients did not lead to B cell expansion in vivo. Moreover, diminished positive inter-correlations of soluble factors and alterations of the bi-directional interplay between B cell and soluble factors were observed in EBV+patients at peak and after clearance. Our data suggest that such alterations may counteract the proliferative effect of BAFF, preventing B cell expansion. The role of these alterations in lymphoma development should be analyzed in future studies.
Sampling technique biases in the analysis of fruit fly volatiles: a case study of Queensland fruit fly
Authors: Noushini Saeedeh , Park Soo Jean , Jamie Ian , Jamie Joanne , Taylor Phillip 
Published: November 2020

AbstractDiverse methods have been used to sample insect semiochemicals. Sampling methods can differ in efficiency and affinity and this can introduce significant biases when interpreting biological patterns. We compare common methods used to sample tephritid fruit fly rectal gland volatiles (‘pheromones’), focusing on Queensland fruit fly, Bactrocera tryoni. Solvents of different polarity, n-hexane, dichloromethane and ethanol, were compared using intact and crushed glands. Polydimethylsiloxane, polydimethylsiloxane/divinylbenzene and polyacrylate were compared as adsorbents for solid phase microextraction. Tenax-GR and Porapak Q were compared as adsorbents for dynamic headspace sampling. Along with compounds previously reported for B. tryoni, we detected five previously unreported compounds in males, and three in females. Dichloromethane extracted more amides while there was no significant difference between the three solvents in extraction of spiroacetals except for (E,E)-2,8-dimethyl-1,7-dioxaspiro[5.5]undecane for which n-hexane extracted higher amount than both dichloromethane and ethanol. Ethanol failed to contain many of the more volatile compounds. Crushed rectal gland samples provided higher concentrations of extracted compounds than intact rectal gland samples, but no compounds were missed in intact samples. Of solid phase microextraction fibers, polyacrylate had low affinity for spiroacetals, ethyl isobutyrate and ethyl-2-methylbutanoate. Polydimethylsiloxane was more efficient for spiroacetals while type of fiber did not affect the amounts of amides and esters. In dynamic headspace sampling, Porapak was more efficient for ethyl isobutyrate and spiroacetals, while Tenax was more efficient for other esters and amides, and sampling time was a critical factor. Biases that can be introduced by sampling methods are important considerations when collecting and interpreting insect semiochemical profiles.
Assessment of post-harvest losses and carbon footprint in intensive lowland rice production in Myanmar
Authors: Gummert Martin , Nguyen-Van-Hung  , Cabardo Christopher , Quilloy Reianne , Aung Yan Lin , Thant Aung Myo , Kyaw Myo Aung , Labios Romeo , Htwe Nyo Me , Singleton Grant R. 
Published: November 2020

AbstractThis paper examines how a move from traditional post-harvest operations of smallholder rice farms in the Ayeyarwaddy delta, Myanmar, to improved post-harvest operations affected income, energy efficiency and greenhouse gas emissions (GHGE). Harvest and post-harvest losses were investigated in a field experiment with 5 replications per scenario. A comparative analysis on energy efficiency and cost-benefits was conducted for different practices of rice production from cultivation to milling. GHGE of different practices were also considered using a life-cycle assessment approach. The study demonstrates that the mechanized practices increased the net income by 30–50% compared with traditional practices. Despite using additional energy for machine manufacturing and fuel consumption, the mechanized practices significantly reduced postharvest losses and did not increase the total life-cycle enegy and GHGE. Combine harvesting helped to significantly reduce harvesting loss in a range of 3 to 7% (by weight of the rice product). Improved post-harvest management practices with a flatbed dryer and hermetic storage reduced the discoloration of rice grains by 3 to 4% and increased head-rice recovery by 20 to 30% (by weight of rice product). The research findings provide empirical evidence that improved post-harvest management of rice in the Ayeyarwaddy delta, compared to traditional post-harvest operations by smallholder farmers, reduce post-harvest losses and improve the quality of rice. The findings provide valuable information for policy makers involved in formulating evidence-based mechanization policies in South and Southeast Asia.
Ready-to-use nanopore platform for the detection of any DNA/RNA oligo at attomole range using an Osmium tagged complementary probe
Authors: Kang Albert S. W. , Bernasconi Janette G. , Jack William , Kanavarioti Anastassia 
Published: November 2020

AbstractNanopores can serve as single molecule sensors. We exploited the MinION, a portable nanopore device from Oxford Nanopore Technologies, and repurposed it to detect any DNA/RNA oligo (target) in a complex mixture by conducting voltage-driven ion-channel measurements. The detection and quantitation of the target is enabled by the use of a unique complementary probe. Using a validated labeling technology, probes are tagged with a bulky Osmium tag (Osmium tetroxide 2,2′-bipyridine), in a way that preserves strong hybridization between probe and target. Intact oligos traverse the MinION’s nanopore relatively quickly compared to the device’s acquisition rate, and exhibit count of events comparable to the baseline. Counts are reported by a publicly available software, OsBp_detect. Due to the presence of the bulky Osmium tag, probes traverse more slowly, produce multiple counts over the baseline, and are even detected at single digit attomole (amole) range. In the presence of the target the probe is “silenced”. Silencing is attributed to a 1:1 double stranded (ds) complex that does not fit and cannot traverse this nanopore. This ready-to-use platform can be tailored as a diagnostic test to meet the requirements for point-of-care cell-free tumor DNA (ctDNA) and microRNA (miRNA) detection and quantitation in body fluids.
EEG distinguishes heroic narratives in ISIS online video propaganda
Authors: Yoder Keith J. , Ruby Keven , Pape Robert , Decety Jean 
Published: November 2020

AbstractThe Islamic State (ISIS) was uniquely effective among extremist groups in the Middle East at recruiting Westerners. A major way ISIS accomplished this was by adopting Hollywood-style narrative structures for their propaganda videos. In particular, ISIS utilized a heroic martyr narrative, which focuses on an individual’s personal glory and empowerment, in addition to traditional social martyr narratives, which emphasize duty to kindred and religion. The current work presented adult participants (n = 238) video clips from ISIS propaganda which utilized either heroic or social martyr narratives and collected behavioral measures of appeal, narrative transportation, and psychological dispositions (egoism and empathy) associated with attraction to terrorism. Narrative transportation and the interaction between egoism and empathy predicted video recruitment appeal. A subset of adults (n = 80) underwent electroencephalographic (EEG) measurements while watching a subset of the video-clips. Complementary univariate and multivariate techniques characterized spectral power density differences when perceiving the different types of narratives. Heroic videos show increased beta power over frontal sites, and globally increased alpha. In contrast, social narratives showed greater frontal theta, an index of negative feedback and emotion regulation. The results provide strong evidence that ISIS heroic narratives are specifically processed, and appeal to psychological predispositions distinctly from other recruitment narratives.
EZH2 inhibition reduces cartilage loss and functional impairment related to osteoarthritis
Authors: Allas Lyess , Brochard Sybille , Rochoux Quitterie , Ribet Jules , Dujarrier Cleo , Veyssiere Alexis , Aury-Landas Juliette , Grard Ophélie , Leclercq Sylvain , Vivien Denis , Ea Hang-Korng , Maubert Eric , Cohen-Solal Martine , Boumediene Karim , Agin Véronique , Baugé Catherine 
Published: November 2020

AbstractHistone methyltransferase EZH2 is upregulated during osteoarthritis (OA), which is the most widespread rheumatic disease worldwide, and a leading cause of disability. This study aimed to assess the impact of EZH2 inhibition on cartilage degradation, inflammation and functional disability. In vitro, gain and loss of EZH2 function were performed in human articular OA chondrocytes stimulated with IL-1β. In vivo, the effects of EZH2 inhibition were investigated on medial meniscectomy (MMX) OA mouse model. The tissue alterations were assayed by histology and the functional disabilities of the mice by actimetry and running wheel. In vitro, EZH2 overexpression exacerbated the action of IL-1β in chondrocytes increasing the expression of genes involved in inflammation, pain (NO, PGE2, IL6, NGF) and catabolism (MMPs), whereas EZH2 inhibition by a pharmacological inhibitor, EPZ-6438, reduced IL-1β effects. Ex vivo, EZH2 inhibition decreased IL-1β-induced degradation of cartilage. In vivo, intra-articular injections of the EZH2 inhibitor reduced cartilage degradation and improved motor functions of OA mice. This study demonstrates that the pharmacological inhibition of the histone methyl-transferase EZH2 slows the progression of osteoarthritis and improves motor functions in an experimental OA model, suggesting that EZH2 could be an effective target for the treatment of OA by reducing catabolism, inflammation and pain.
Influence of red mud and waste glass on the microstructure, strength, and leaching behavior of bottom ash-based geopolymer composites
Authors: Bobirică Constantin , Orbeci Cristina , Bobirică Liliana , Palade Petru , Deleanu Călin , Pantilimon Cristian Mircea , Pîrvu Cristian , Radu Ionuţ Cristian 
Published: November 2020

AbstractThe influence of waste glass and red mud addition as alternative source of aluminosilicate precursors on the microstructural, mechanical, and leaching properties of bottom ash-based geopolymer was studied in this work through mineralogical, morphological, and spectroscopic analysis, as well as by conducting compressive strength and leaching tests. The bottom ash-based geopolymer composites were synthesized by adding a constant amount of waste glass (10% by weight) and increasing amounts of red mud (up to 30% by weight). The results derived from FTIR, 29Si and 27Al MAS NMR, and SEM–EDX revealed that adding up to 10% (by weight) red mud to the synthesis mixes leads to an increase in the degree of geopolymerization of the activated mixes. The compressive strength followed the same trend. An increase of more than 10% (by weight) red mud added to the synthesis mixes results in a significant decrease of compressive strength of the geopolymer composites. A low leachability of geopolymer composites in regard with their contaminants was revealed especially for those with good compressive strength.
The effect of rapid adjustments to halocarbons and N2O on radiative forcing
Authors: Hodnebrog Øivind , Myhre Gunnar , Kramer Ryan J. , Shine Keith P. , Andrews Timothy , Faluvegi Gregory , Kasoar Matthew , Kirkevåg Alf , Lamarque Jean-François , Mülmenstädt Johannes , Olivié Dirk , Samset Bjørn H. , Shindell Drew , Smith Christopher J. , Takemura Toshihiko , Voulgarakis Apostolos 
Published: November 2020

AbstractRapid adjustments occur after initial perturbation of an external climate driver (e.g., CO2) and involve changes in, e.g. atmospheric temperature, water vapour and clouds, independent of sea surface temperature changes. Knowledge of such adjustments is necessary to estimate effective radiative forcing (ERF), a useful indicator of surface temperature change, and to understand global precipitation changes due to different drivers. Yet, rapid adjustments have not previously been analysed in any detail for certain compounds, including halocarbons and N2O. Here we use several global climate models combined with radiative kernel calculations to show that individual rapid adjustment terms due to CFC-11, CFC-12 and N2O are substantial, but that the resulting flux changes approximately cancel at the top-of-atmosphere due to compensating effects. Our results further indicate that radiative forcing (which includes stratospheric temperature adjustment) is a reasonable approximation for ERF. These CFCs lead to a larger increase in precipitation per kelvin surface temperature change (2.2 ± 0.3% K−1) compared to other well-mixed greenhouse gases (1.4 ± 0.3% K−1 for CO2). This is largely due to rapid upper tropospheric warming and cloud adjustments, which lead to enhanced atmospheric radiative cooling (and hence a precipitation increase) and partly compensate increased atmospheric radiative heating (i.e. which is associated with a precipitation decrease) from the instantaneous perturbation.
A GDSL lipase-like from Ipomoea batatas catalyzes efficient production of 3,5-diCQA when expressed in Pichia pastoris
Authors: Miguel Sissi , Legrand Guillaume , Duriot Léonor , Delporte Marianne , Menin Barbara , Michel Cindy , Olry Alexandre , Chataigné Gabrielle , Salwinski Aleksander , Bygdell Joakim , Vercaigne Dominique , Wingsle Gunnar , Hilbert Jean Louis , Bourgaud Frédéric , Hehn Alain , Gagneul David 
Published: November 2020

AbstractThe synthesis of 3,5-dicaffeoylquinic acid (3,5-DiCQA) has attracted the interest of many researchers for more than 30 years. Recently, enzymes belonging to the BAHD acyltransferase family were shown to mediate its synthesis, albeit with notably low efficiency. In this study, a new enzyme belonging to the GDSL lipase-like family was identified and proven to be able to transform chlorogenic acid (5-O-caffeoylquinic acid, 5-CQA, CGA) in 3,5-DiCQA with a conversion rate of more than 60%. The enzyme has been produced in different expression systems but has only been shown to be active when transiently synthesized in Nicotiana benthamiana or stably expressed in Pichia pastoris. The synthesis of the molecule could be performed in vitro but also by a bioconversion approach beginning from pure 5-CQA or from green coffee bean extract, thereby paving the road for producing it on an industrial scale.
Altered transcriptional and chromatin responses to rhinovirus in bronchial epithelial cells from adults with asthma
Authors: Helling Britney A. , Sobreira Débora R. , Hansen Grace T. , Sakabe Noboru J. , Luo Kaixuan , Billstrand Christine , Laxman Bharathi , Nicolae Raluca I. , Nicolae Dan L. , Bochkov Yury A. , Gern James E. , Nobrega Marcelo A. , White Steven R. , Ober Carole 
Published: November 2020

AbstractThere is a life-long relationship between rhinovirus (RV) infection and the development and clinical manifestations of asthma. In this study we demonstrate that cultured primary bronchial epithelial cells from adults with asthma (n = 9) show different transcriptional and chromatin responses to RV infection compared to those without asthma (n = 9). Both the number and magnitude of transcriptional and chromatin responses to RV were muted in cells from asthma cases compared to controls. Pathway analysis of the transcriptionally responsive genes revealed enrichments of apoptotic pathways in controls but inflammatory pathways in asthma cases. Using promoter capture Hi-C we tethered regions of RV-responsive chromatin to RV-responsive genes and showed enrichment of these regions and genes at asthma GWAS loci. Taken together, our studies indicate a delayed or prolonged inflammatory state in cells from asthma cases and highlight genes that may contribute to genetic risk for asthma.
Non-aqueous, zwitterionic solvent as an alternative for dimethyl sulfoxide in the life sciences
Authors: Kuroda Kosuke , Komori Tetsuo , Ishibashi Kojiro , Uto Takuya , Kobayashi Isao , Kadokawa Riki , Kato Yui , Ninomiya Kazuaki , Takahashi Kenji , Hirata Eishu 
Published: November 2020

AbstractDimethyl sulfoxide (DMSO) is widely used as a solvent in the life sciences, however, it is somewhat toxic and affects cell behaviours in a range of ways. Here, we propose a zwitterionic liquid (ZIL), a zwitterion-type ionic liquid containing histidine-like module, as a new alternative to DMSO. ZIL is not cell permeable, less toxic to cells and tissues, and has great potential as a vehicle for various hydrophobic drugs. Notably, ZIL can serve as a solvent for stock solutions of platinating agents, whose anticancer effects are completely abolished by dissolution in DMSO. Furthermore, ZIL possesses suitable affinity to the plasma membrane and acts as a cryoprotectant. Our results suggest that ZIL is a potent, multifunctional and biocompatible solvent that compensates for many shortcomings of DMSO.
Single electron transfer-based peptide/protein bioconjugations driven by biocompatible energy input
Authors: Weng Yue , Song Chunlan , Chiang Chien-Wei , Lei Aiwen 
Published: November 2020

AbstractBioconjugation reactions play a central facilitating role in engendering modified peptides and proteins. Early progress in this area was inhibited by challenges such as the limited range of substrates and the relatively poor biocompatibility of bioconjugation reagents. However, the recent developments in visible-light induced photoredox catalysis and electrochemical catalysis reactions have permitted significant novel reactivities to be developed in the field of synthetic and bioconjugation chemistry. This perspective describes recent advances in the use of biocompatible energy input for the modification of peptides and proteins mainly, via the single electron transfer (SET) process, as well as key future developments in this area.