bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered non-coding RNA expression profile in F1 progeny 1 year after parental irradiation is linked to adverse effects in zebrafish
Authors: Martín Leonardo , Kamstra Jorke H. , Hurem Selma , Lindeman Leif C. , Brede Dag A. , Aanes Håvard , Babiak Igor , Arenal Amilcar , Oughton Deborah , Salbu Brit , Lyche Jan Ludvig , Aleström Peter 
Published: February 2021

AbstractGamma radiation produces DNA instability and impaired phenotype. Previously, we observed negative effects on phenotype, DNA methylation, and gene expression profiles, in offspring of zebrafish exposed to gamma radiation during gametogenesis. We hypothesize that previously observed effects are accompanied with changes in the expression profile of non-coding RNAs, inherited by next generations. Non-coding RNA expression profile was analysed in F1 offspring (5.5 h post-fertilization) by high-throughput sequencing 1 year after parental irradiation (8.7 mGy/h, 5.2 Gy total dose). Using our previous F1-γ genome-wide gene expression data (GSE98539), hundreds of mRNAs were predicted as targets of differentially expressed (DE) miRNAs, involved in pathways such as insulin receptor, NFkB and PTEN signalling, linking to apoptosis and cancer. snRNAs belonging to the five major spliceosomal snRNAs were down-regulated in the F1-γ group, Indicating transcriptional and post-transcriptional alterations. In addition, DEpiRNA clusters were associated to 9 transposable elements (TEs) (LTR, LINE, and TIR) (p = 0.0024), probable as a response to the activation of these TEs. Moreover, the expression of the lincRNAs malat-1, and several others was altered in the offspring F1, in concordance with previously observed phenotypical alterations. In conclusion, our results demonstrate diverse gamma radiation-induced alterations in the ncRNA profiles of F1 offspring observable 1 year after parental irradiation.
Theory and experimental verification of configurable computing with stochastic memristors
Authors: Naous Rawan , Siemon Anne , Schulten Michael , Alahmadi Hamzah , Kindsmüller Andreas , Lübben Michael , Heittmann Arne , Waser Rainer , Salama Khaled Nabil , Menzel Stephan 
Published: February 2021

AbstractThe inevitable variability within electronic devices causes strict constraints on operation, reliability and scalability of the circuit design. However, when a compromise arises among the different performance metrics, area, time and energy, variability then loosens the tight requirements and allows for further savings in an alternative design scope. To that end, unconventional computing approaches are revived in the form of approximate computing, particularly tuned for resource-constrained mobile computing. In this paper, a proof-of-concept of the approximate computing paradigm using memristors is demonstrated. Stochastic memristors are used as the main building block of probabilistic logic gates. As will be shown in this paper, the stochasticity of memristors’ switching characteristics is tightly bound to the supply voltage and hence to power consumption. By scaling of the supply voltage to appropriate levels stochasticity gets increased. In order to guide the design process of approximate circuits based on memristors a realistic device model needs to be elaborated with explicit emphasis of the probabilistic switching behavior. Theoretical formulation, probabilistic analysis, and simulation of the underlying logic circuits and operations are introduced. Moreover, the expected output behavior is verified with the experimental measurements of valence change memory cells. Hence, it is shown how the precision of the output is varied for the sake of the attainable gains at different levels of available design metrics. This approach represents the first proposition along with physical verification and mapping to real devices that combines stochastic memristors into unconventional computing approaches.
Bioabsorbable nerve conduits three-dimensionally coated with human induced pluripotent stem cell-derived neural stem/progenitor cells promote peripheral nerve regeneration in rats
Authors: Onode Ema , Uemura Takuya , Takamatsu Kiyohito , Yokoi Takuya , Shintani Kosuke , Hama Shunpei , Miyashima Yusuke , Okada Mitsuhiro , Nakamura Hiroaki 
Published: February 2021

AbstractPeripheral nerve regeneration using nerve conduits has been less effective than autogenous nerve grafts. To overcome this hurdle, we developed a tissue-engineered nerve conduit coated with mouse induced pluripotent stem cell (iPSC)-derived neurospheres, for the first time, which accelerated nerve regeneration in mice. We previously demonstrated the long-term efficacy and safety outcomes of this hybrid nerve conduit for mouse peripheral nerve regeneration. In this study, we investigated the therapeutic potential of nerve conduits coated with human iPSC (hiPSC)-derived neurospheres in rat sciatic nerve defects, as a translational preclinical study. The hiPSC-derived quaternary neurospheres containing neural stem/progenitor cells were three-dimensionally cultured within the nerve conduit (poly l-lactide and polycaprolactone copolymer) for 14 days. Complete 5-mm defects were created as a small size peripheral nerve defect in sciatic nerves of athymic nude rats and reconstructed with nerve conduit alone (control group), nerve conduits coated with hiPSC-derived neurospheres (iPS group), and autogenous nerve grafts (autograft group) (n = 8 per group). The survival of the iPSC-derived neurospheres was continuously tracked using in vivo imaging. At 12 weeks postoperatively, motor and sensory function and histological nerve regeneration were evaluated. Before implantation, the hiPSC-derived quaternary neurospheres that three-dimensional coated the nerve conduit were differentiated into Schwann-like cells. The transplanted hiPSC-derived neurospheres survived for at least 56 days after implantation. The iPS group showed non-significance higher sensory regeneration than the autograft group. Although there was no actual motor functional nerve regeneration in the three groups: control, iPS, and autograft groups, the motor function in the iPS group recovered significantly better than that in the control group, but it did not recover to the same level as that in the autograft group. Histologically, the iPS group demonstrated significantly higher axon numbers and areas, and lower G-ratio values than the control group, whereas the autograft group demonstrated the highest axon numbers and areas and the lowest G-ratio values. Nerve conduit three-dimensionally coated with hiPSC-derived neurospheres promoted axonal regeneration and functional recovery in repairing rat sciatic nerve small size defects. Transplantation of hiPSC-derived neurospheres with nerve conduits is a promising clinical iPSC-based cell therapy for the treatment of peripheral nerve defects.
Associations between fecal short-chain fatty acids and sleep continuity in older adults with insomnia symptoms
Authors: Magzal Faiga , Even Carmel , Haimov Iris , Agmon Maayan , Asraf Kfir , Shochat Tamar , Tamir Snait 
Published: February 2021

AbstractInsomnia is a disorder characterized by difficulty falling asleep and poor sleep continuity and is associated with increased risks for physical and cognitive decline. Insomnia with short sleep duration is considered the most biologically severe phenotype of the disorder. Evidence suggests that short-chain fatty acids (SCFAs), the main byproducts of fiber fermentation in the gut, may affect sleep via gut–brain communications. This study explores associations between SCFAs and sleep continuity and compares SCFA concentrations in short vs. normal sleep insomnia phenotypes in older adults. Fifty-nine participants with insomnia symptoms (≥ 65 years), completed 2 weeks of objective sleep monitoring (actigraphy), and were divided into short and normal sleep duration phenotypes via cluster analysis. Sleep measures included total sleep time (TST), sleep onset latency (SOL), sleep efficiency (SE), and wake after sleep onset (WASO). Stool samples were collected and fecal SCFA concentrations were determined by gas-chromatography-mass-spectrometry (GCMS). Higher concentrations of acetate, butyrate, and propionate, and total SCFAs, were associated with lower SE and longer SOL after controlling for Body Mass Index (BMI). Concentrations were higher in the short sleep duration phenotype. Age, BMI, TST, and SOL explained 40.7% of the variance in total SCFAs. Findings contribute to understanding pathways along the gut–brain axis and may lead to the use of SCFAs as biomarkers of insomnia phenotypes.
Assisting scalable diagnosis automatically via CT images in the combat against COVID-19
Authors: Liu Bohan , Liu Pan , Dai Lutao , Yang Yanlin , Xie Peng , Tan Yiqing , Du Jicheng , Shan Wei , Zhao Chenghui , Zhong Qin , Lin Xixiang , Guan Xizhou , Xing Ning , Sun Yuhui , Wang Wenjun , Zhang Zhibing , Fu Xia , Fan Yanqing , Li Meifang , Zhang Na , Li Lin , Liu Yaou , Xu Lin , Du Jingbo , Zhao Zhenhua , Hu Xuelong , Fan Weipeng , Wang Rongpin , Wu Chongchong , Nie Yongkang , Cheng Liuquan , Ma Lin , Li Zongren , Jia Qian , Liu Minchao , Guo Huayuan , Huang Gao , Shen Haipeng , Zhang Liang , Zhang Peifang , Guo Gang , Li Hao , An Weimin , Zhou Jianxin , He Kunlun 
Published: February 2021

AbstractThe pandemic of Coronavirus Disease 2019 (COVID-19) is causing enormous loss of life globally. Prompt case identification is critical. The reference method is the real-time reverse transcription PCR (RT-PCR) assay, whose limitations may curb its prompt large-scale application. COVID-19 manifests with chest computed tomography (CT) abnormalities, some even before the onset of symptoms. We tested the hypothesis that the application of deep learning (DL) to 3D CT images could help identify COVID-19 infections. Using data from 920 COVID-19 and 1,073 non-COVID-19 pneumonia patients, we developed a modified DenseNet-264 model, COVIDNet, to classify CT images to either class. When tested on an independent set of 233 COVID-19 and 289 non-COVID-19 pneumonia patients, COVIDNet achieved an accuracy rate of 94.3% and an area under the curve of 0.98. As of March 23, 2020, the COVIDNet system had been used 11,966 times with a sensitivity of 91.12% and a specificity of 88.50% in six hospitals with PCR confirmation. Application of DL to CT images may improve both efficiency and capacity of case detection and long-term surveillance.
Trans-ethnic meta-analysis identifies new loci associated with longitudinal blood pressure traits
Authors: Gouveia Mateus H. , Bentley Amy R. , Leonard Hampton , Meeks Karlijn A. C. , Ekoru Kenneth , Chen Guanjie , Nalls Michael A. , Simonsick Eleanor M. , Tarazona-Santos Eduardo , Lima-Costa Maria Fernanda , Adeyemo Adebowale , Shriner Daniel , Rotimi Charles N. 
Published: February 2021

AbstractGenome-wide association studies (GWAS) have identified thousands of genetic loci associated with cross-sectional blood pressure (BP) traits; however, GWAS based on longitudinal BP have been underexplored. We performed ethnic-specific and trans-ethnic GWAS meta-analysis using longitudinal and cross-sectional BP data of 33,720 individuals from five cohorts in the US and one in Brazil. In addition to identifying several known loci, we identified thirteen novel loci with nine based on longitudinal and four on cross-sectional BP traits. Most of the novel loci were ethnic- or study-specific, with the majority identified in African Americans (AA). Four of these discoveries showed additional evidence of association in independent datasets, including an intergenic variant (rs4060030, p = 7.3 × 10–9) with reported regulatory function. We observed a high correlation between the meta-analysis results for baseline and longitudinal average BP (rho = 0.48). BP trajectory results were more correlated with those of average BP (rho = 0.35) than baseline BP(rho = 0.18). Heritability estimates trended higher for longitudinal traits than for cross-sectional traits, providing evidence for different genetic architectures. Furthermore, the longitudinal data identified up to 20% more BP known associations than did cross-sectional data. Our analyses of longitudinal BP data in diverse ethnic groups identified novel BP loci associated with BP trajectory, indicating a need for further longitudinal GWAS on BP and other age-related traits.
Pentaradial eukaryote suggests expansion of suspension feeding in White Sea-aged Ediacaran communities
Authors: Cracknell Kelsie , García-Bellido Diego C. , Gehling James G. , Ankor Martin J. , Darroch Simon A. F. , Rahman Imran A. 
Published: February 2021

AbstractSuspension feeding is a key ecological strategy in modern oceans that provides a link between pelagic and benthic systems. Establishing when suspension feeding first became widespread is thus a crucial research area in ecology and evolution, with implications for understanding the origins of the modern marine biosphere. Here, we use three-dimensional modelling and computational fluid dynamics to establish the feeding mode of the enigmatic Ediacaran pentaradial eukaryote Arkarua. Through comparisons with two Cambrian echinoderms, Cambraster and Stromatocystites, we show that flow patterns around Arkarua strongly support its interpretation as a passive suspension feeder. Arkarua is added to the growing number of Ediacaran benthic suspension feeders, suggesting that the energy link between pelagic and benthic ecosystems was likely expanding in the White Sea assemblage (~ 558–550 Ma). The advent of widespread suspension feeding could therefore have played an important role in the subsequent waves of ecological innovation and escalation that culminated with the Cambrian explosion.
Extracts of select endemic plants from the Republic of Mauritius exhibiting anti-cancer and immunomodulatory properties
Authors: Kauroo Shahin , Govinden-Soulange Joyce , Ranghoo-Sanmukhiya V. Mala , Miranda Kathryn , Cotham William E. , Walla Michael D. , Nagarkatti Mitzi , Nagarkatti Prakash 
Published: February 2021

AbstractMauritius Island possesses unique plant biodiversity with a potential reservoir of biologically active compounds of pharmacological interest. In the current study, we investigated Mauritius endemic plant families Asteraceae, Ebenaceae, Sapotaceae, and Erythroxylaceae, for anti-cancer properties on T cell lymphoma and B16F10 Melanoma cells and immunomodulatory properties on primary T and B cells. The cytotoxicity of methanolic plant extracts at 1, 10, 25 µg/ml was determined. The most active plant species were evaluated for their apoptosis-inducing effects. The immunomodulatory properties of the plants were also studied, and preliminary phytochemical screening of selected plants was done by LC–MS analysis. Psiadia lithospermifolia (Lam.) Cordem (Asteraceae) at 25 µg/ml was the most cytotoxic on both EL4 and B16 cells and triggered apoptosis by the death receptor pathway, and at least in part, by the mitochondrial pathway. Most plant species from Asteraceae, Ebenaceae, Erythroxylaceae, and Sapotaceae inhibited the proliferation of activated T and B cells, although some promoted T cell proliferation. LC–MS profile of Asteraceae plants showed the presence of terpenes, terpenoids, fatty acids, and phenolic. Flavonoids and phenolic acid were also detected from Ebenaceae and Sapotaceae plants. Together, our study demonstrated that Mauritius endemic flora exhibit potential anti-cancer and anti-inflammatory properties worthy of further in-depth studies.
Stabilization and electronic topological transition of hydrogen-rich metal Li5MoH11 under high pressures from first-principles predictions
Authors: Tsuppayakorn-aek Prutthipong , Sukmas Wiwittawin , Ahuja Rajeev , Luo Wei , Bovornratanaraks Thiti 
Published: February 2021

AbstractRegarded as doped binary hydrides, ternary hydrides have recently become the subject of investigation since they are deemed to be metallic under pressure and possibly potentially high-temperature superconductors. Herein, the candidate structure of Li5MoH11 is predicted by exploiting the evolutionary searching. Its high-pressure phase adopts a hexagonal structure with P63/mcm space group. We used first-principles calculations including the zero-point energy to investigate the structures up to 200 GPa and found that the P63cm structure transforms into the P63/mcm structure at 48 GPa. Phonon calculations confirm that the P63/mcm structure is dynamically stable. Its stability is mainly attributed to the isostructural second-order phase transition. Our calculations reveal the electronic topological transition displaying an isostructural second-order phase transition at 160 GPa as well as the topology of its Fermi surfaces. We used the projected crystal orbital Hamilton population (pCOHP) to examine the nature of the chemical bonding and demonstrated that the results obtained from the pCOHP calculation are associated with the electronic band structure and electronic localized function.
Neural mechanisms of credit card spending
Authors: Banker Sachin , Dunfield Derek , Huang Alex , Prelec Drazen 
Published: February 2021

AbstractCredit cards have often been blamed for consumer overspending and for the growth in household debt. Indeed, laboratory studies of purchase behavior have shown that credit cards can facilitate spending in ways that are difficult to justify on purely financial grounds. However, the psychological mechanisms behind this spending facilitation effect remain conjectural. A leading hypothesis is that credit cards reduce the pain of payment and so ‘release the brakes’ that hold expenditures in check. Alternatively, credit cards could provide a ‘step on the gas,’ increasing motivation to spend. Here we present the first evidence of differences in brain activation in the presence of real credit and cash purchase opportunities. In an fMRI shopping task, participants purchased items tailored to their interests, either by using a personal credit card or their own cash. Credit card purchases were associated with strong activation in the striatum, which coincided with onset of the credit card cue and was not related to product price. In contrast, reward network activation weakly predicted cash purchases, and only among relatively cheaper items. The presence of reward network activation differences highlights the potential neural impact of novel payment instruments in stimulating spending—these fundamental reward mechanisms could be exploited by new payment methods as we transition to a purely cashless society.
Accurate prediction of terahertz spectra of molecular crystals of fentanyl and its analogs
Authors: Wang Chun-Hung , Terracciano Anthony C. , Masunov Artёm E. , Xu Mengyu , Vasu Subith S. 
Published: February 2021

AbstractFentanyl is a potent synthetic opioid pain reliever with a high bioavailability that can be used as prescription anesthetic. Rapid identification via non-contact methods of both known and emerging opioid substances in the fentanyl family help identify the substances and enable rapid medical attention. We apply PBEh-3c method to identify vibrational normal modes from 0.01 to 3 THz in solid fentanyl and its selected analogs. The molecular structure of each fentanyl analog and unique arrangement of H-bonds and dispersion interactions significantly change crystal packing and is subsequently reflected in the THz spectrum. Further, the study of THz spectra of a series of stereoisomers shows that small changes in molecular structure results in distinct crystal packing and significantly alters THz spectra as well. We discuss spectral features of synthetic opioids with higher potency than conventional fentanyl such as ohmefentanyl and sufentanil and discover the pattern of THz spectra of fentanyl analogs.
Novel methods to establish whole-body primary cell cultures for the cnidarians Nematostella vectensis and Pocillopora damicornis
Authors: Nowotny James D. , Connelly Michael T. , Traylor-Knowles Nikki 
Published: February 2021

AbstractCnidarians are emerging model organisms for cell and molecular biology research. However, successful cell culture development has been challenging due to incomplete tissue dissociation and contamination. In this report, we developed and tested several different methodologies to culture primary cells from all tissues of two species of Cnidaria:Nematostella vectensisandPocillopora damicornis. In over 170 replicated cell cultures, we demonstrate that physical dissociation was the most successful method for viable and diverseN. vectensiscells while antibiotic-assisted dissociation was most successful for viable and diverseP. damicorniscells. We also demonstrate that a rigorous antibiotic pretreatment results in less initial contamination in cell cultures. Primary cultures of both species averaged 12–13 days of viability, showed proliferation, and maintained high cell diversity including cnidocytes, nematosomes, putative gastrodermal, and epidermal cells. Overall, this work will contribute a needed tool for furthering functional cell biology experiments in Cnidaria.
Affinity-based proteomics reveals novel binding partners for Rab46 in endothelial cells
Authors: Pedicini Lucia , Wiktor Sabina D. , Simmons Katie J. , Money Ashley , McKeown Lynn 
Published: February 2021

AbstractRab46 is a novel Ca2+-sensing Rab GTPase shown to have important functions in endothelial and immune cells. The presence of functional Ca2+-binding, coiled-coil and Rab domains suggest that Rab46 will be important for coupling rapid responses to signalling in many cell types. The molecular mechanisms underlying Rab46 function are currently unknown. Here we provide the first resource for studying Rab46 interacting proteins. Using liquid chromatography tandem mass spectrometry (LC–MS/MS) to identify affinity purified proteins that bind to constitutively active GFP-Rab46 or inactive GFP-Rab46 expressed in endothelial cells, we have revealed 922 peptides that interact with either the GTP-bound Rab46 or GDP-bound Rab46. To identify proteins that could be potential Rab46 effectors we performed further comparative analyses between nucleotide-locked Rab46 proteins and identified 29 candidate effector proteins. Importantly, through biochemical and imaging approaches we have validated two potential effector proteins; dynein and the Na2+/ K+ ATPase subunit alpha 1 (ATP1α1). Hence, our use of affinity purification and LC–MS/MS to identify Rab46 neighbouring proteins provides a valuable resource for detecting Rab46 effector proteins and analysing Rab46 functions.
Information diversity in individual auditory cortical neurons is associated with functionally distinct coordinated neuronal ensembles
Authors: See Jermyn Z. , Homma Natsumi Y. , Atencio Craig A. , Sohal Vikaas S. , Schreiner Christoph E. 
Published: February 2021

AbstractNeuronal activity in auditory cortex is often highly synchronous between neighboring neurons. Such coordinated activity is thought to be crucial for information processing. We determined the functional properties of coordinated neuronal ensembles (cNEs) within primary auditory cortical (AI) columns relative to the contributing neurons. Nearly half of AI cNEs showed robust spectro-temporal receptive fields whereas the remaining cNEs showed little or no acoustic feature selectivity. cNEs can therefore capture either specific, time-locked information of spectro-temporal stimulus features or reflect stimulus-unspecific, less-time specific processing aspects. By contrast, we show that individual neurons can represent both of those aspects through membership in multiple cNEs with either high or absent feature selectivity. These associations produce functionally heterogeneous spikes identifiable by instantaneous association with different cNEs. This demonstrates that single neuron spike trains can sequentially convey multiple aspects that contribute to cortical processing, including stimulus-specific and unspecific information.