bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microfluidic-based processors and circuits design
Authors: Azizbeigi Kasra , Zamani Pedram Maysam , Sanati-Nezhad Amir 
Published: May 2021

AbstractDroplets produced within microfluidics have not only attracted the attention of researchers to develop complex biological, industrial and clinical testing systems but also played a role as a bit of data. The flow of droplets within a network of microfluidic channels by stimulation of their movements, trajectories, and interaction timing, can provide an opportunity for preparation of complex and logical microfluidic circuits. Such mechanical-based circuits open up avenues to mimic the logic of electrical circuits within microfluidics. Recently, simple microfluidic-based logical elements such as AND, OR, and NOT gates have been experimentally developed and tested to model basic logic conditions in laboratory settings. In this work, we develop new microfluidic networks, control the shape of channels and speed of droplet movement, and regulate the size of bubbles in order to extend the logical elements to six new logic gates, including AND/OR type 1, AND/OR type 2, NOT type 1, NOT type 2, Flip-Flop, Synchronizer, and a parametric model of T-junction as a bubble generator. We further designed and simulated a novel microfluidic Decoder 1 to 2, a Decoder 2 to 4, and a microfluidic circuit that combines several individual logic gates into one complex circuit. Further fabrication and experimental testing of these newly introduced logic gates within microfluidics enable implementing complex circuits in high-throughput microfluidic platforms for tissue engineering, drug testing and development, and chemical synthesis and process design.
High expression of PARD3 predicts poor prognosis in hepatocellular carcinoma
Authors: Li Songwei , Huang Jian , Yang Fan , Zeng Haiping , Tong Yuyun , Li Kejia 
Published: May 2021

AbstractHepatocellular carcinoma (HCC) is one of the most commonly cancers with poor prognosis and drug response. Identifying accurate therapeutic targets would facilitate precision treatment and prolong survival for HCC. In this study, we analyzed liver hepatocellular carcinoma (LIHC) RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA), and identified PARD3 as one of the most significantly differentially expressed genes (DEGs). Then, we investigated the relationship between PARD3 and outcomes of HCC, and assessed predictive capacity. Moreover, we performed functional enrichment and immune infiltration analysis to evaluate functional networks related to PARD3 in HCC and explore its role in tumor immunity. PARD3 expression levels in 371 HCC tissues were dramatically higher than those in 50 paired adjacent liver tissues (p < 0.001). High PARD3 expression was associated with poor clinicopathologic feathers, such as advanced pathologic stage (p = 0.002), vascular invasion (p = 0.012) and TP53 mutation (p = 0.009). Elevated PARD3 expression also correlated with lower overall survival (OS, HR = 2.08, 95% CI = 1.45–2.98, p < 0.001) and disease-specific survival (DSS, HR = 2.00, 95% CI = 1.27–3.16, p = 0.003). 242 up-regulated and 71 down-regulated genes showed significant association with PARD3 expression, which were involved in genomic instability, response to metal ions, and metabolisms. PARD3 is involved in diverse immune infiltration levels in HCC, especially negatively related to dendritic cells (DCs), cytotoxic cells, and plasmacytoid dendritic cells (pDCs). Altogether, PARD3 could be a potential prognostic biomarker and therapeutic target of HCC.
MeCP2 deficiency exacerbates the neuroinflammatory setting and autoreactive response during an autoimmune challenge
Authors: Zalosnik M. I. , Fabio M. C. , Bertoldi M. L. , Castañares C. N. , Degano A. L. 
Published: May 2021

AbstractRett syndrome is a severe and progressive neurological disorder linked to mutations in the MeCP2 gene. It has been suggested that immune alterations may play an active role in the generation and/or maintenance of RTT phenotypes. However, there is no clear consensus about which pathways are regulated in vivo by MeCP2 in the context of immune activation. In the present work we set to characterize the role of MeCP2 during the progression of Experimental Autoimmune Encephalomyelitis (EAE) using the MeCP2308/y mouse model (MUT), which represents a condition of “MeCP2 function deficiency”. Our results showed that MeCP2 deficiency increased the susceptibility to develop EAE, along with a defective induction of anti-inflammatory responses and an exacerbated MOG-specific IFNγ expression in immune sites. In MUT-EAE spinal cord, we found a chronic increase in pro-inflammatory cytokines gene expression (IFNγ, TNFα and IL-1β) and downregulation of genes involved in immune regulation (IL-10, FoxP3 and CX3CR1). Moreover, our results indicate that MeCP2 acts intrinsically upon immune activation, affecting neuroimmune homeostasis by regulating the pro-inflammatory/anti-inflammatory balance in vivo. These results are relevant to identify the potential consequences of MeCP2 mutations on immune homeostasis and to explore novel therapeutic strategies for MeCP2-related disorders.
HDAC6 inhibitors sensitize non-mesenchymal triple-negative breast cancer cells to cysteine deprivation
Authors: Alothaim Tahiyat , Charbonneau Morgan , Tang Xiaohu 
Published: May 2021

AbstractTriple-negative breast cancer (TNBC) is a highly malignant type of breast cancer and lacks effective therapy. Targeting cysteine-dependence is an emerging strategy to treat the mesenchymal TNBC. However, many TNBC cells are non-mesenchymal and unresponsive to cysteine deprivation. To overcome such resistance, three selective HDAC6 inhibitors (Tubacin, CAY10603, and Tubastatin A), identified by epigenetic compound library screening, can synergize with cysteine deprivation to induce cell death in the non-mesenchymal TNBC. Despite the efficacy of HDAC6 inhibitor, knockout of HDAC6 did not mimic the synthetic lethality induced by its inhibitors, indicating that HDAC6 is not the actual target of HDAC6 inhibitor in this context. Instead, transcriptomic profiling showed that tubacin triggers an extensive gene transcriptional program in combination with erastin, a cysteine transport blocker. Notably, the zinc-related gene response along with an increase of labile zinc was induced in cells by the combination treatment. The disturbance of zinc homeostasis was driven by PKCγ activation, which revealed that the PKCγ signaling pathway is required for HDAC6 inhibitor-mediated synthetic lethality. Overall, our study identifies a novel function of HDAC6 inhibitors that function as potent sensitizers of cysteine deprivation and are capable of abolishing cysteine-independence in non-mesenchymal TNBC.
Impact of US vaccination strategy on COVID-19 wave dynamics
Authors: Cot Corentin , Cacciapaglia Giacomo , Islind Anna Sigridur , Óskarsdóttir María , Sannino Francesco 
Published: May 2021

AbstractWe employ the epidemic Renormalization Group (eRG) framework to understand, reproduce and predict the COVID-19 pandemic diffusion across the US. The human mobility across different geographical US divisions is modelled via open source flight data alongside the impact of social distancing for each such division. We analyse the impact of the vaccination strategy on the current pandemic wave dynamics in the US. We observe that the ongoing vaccination campaign will not impact the current pandemic wave and therefore strict social distancing measures must still be enacted. To curb the current and the next waves our results indisputably show that vaccinations alone are not enough and strict social distancing measures are required until sufficient immunity is achieved. Our results are essential for a successful vaccination strategy in the US.
Seagrass blue carbon stocks and sequestration rates in the Colombian Caribbean
Authors: Serrano Oscar , Gómez-López Diana Isabel , Sánchez-Valencia Laura , Acosta-Chaparro Andres , Navas-Camacho Raul , González-Corredor Juan , Salinas Cristian , Masque Pere , Bernal Cesar A. , Marbà Núria 
Published: May 2021

AbstractSeagrass ecosystems rank amongst the most efficient natural carbon sinks on earth, sequestering CO2through photosynthesis and storing organic carbon (Corg) underneath their soils for millennia and thereby, mitigating climate change. However, estimates of Corgstocks and accumulation rates in seagrass meadows (blue carbon) are restricted to few regions, and further information on spatial variability is required to derive robust global estimates. Here we studied soil Corgstocks and accumulation rates in seagrass meadows across the Colombian Caribbean. We estimated thatThalassia testudinummeadows store 241 ± 118 Mg Corgha−1(mean ± SD) in the top 1 m-thick soils, accumulated at rates of 122 ± 62 and 15 ± 7 g Corgm−2 year−1over the last ~ 70 years and up to 2000 years, respectively. The tropical climate of the Caribbean Sea and associated sediment run-off, together with the relatively high primary production ofT. testudinum, influencing biotic and abiotic drivers of Corgstorage linked to seagrass and soil respiration rates, explains their relatively high Corgstocks and accumulation rates when compared to other meadows globally. Differences in soil Corgstorage among Colombian Caribbean regions are largely linked to differences in the relative contribution of Corgsources to the soil Corgpool (seagrass, algaeHalimeda tuna, mangrove and seston) and the content of soil particles < 0.016 mm binding Corgand enhancing its preservation. Despite the moderate areal extent ofT. testudinumin the Colombian Caribbean (661 km2), it sequesters around 0.3 Tg CO2year−1, which is equivalent to ~ 0.4% of CO2emissions from fossil fuels in Colombia. This study adds data from a new region to a growing dataset on seagrass blue carbon and further explores differences in meadow Corgstorage based on biotic and abiotic environmental factors, while providing the basis for the implementation of seagrass blue carbon strategies in Colombia.
Comprehensive profiling analysis of the N6-methyladenosine-modified circular RNA transcriptome in cultured cells infected with Marek’s disease virus
Authors: Sun Aijun , Wang Rui , Yang Shuaikang , Zhu Xiaojing , Liu Ying , Teng Man , Zheng Luping , Luo Jun , Zhang Gaiping , Zhuang Guoqing 
Published: May 2021

AbstractMarek’s disease virus (MDV) induces severe immunosuppression and lymphomagenesis in the chicken, its natural host, and results in a condition that investigated the pathogenesis of MDV and have begun to focus on the expression profiling of circular RNAs (circRNAs). However, little is known about how the expression of circRNAs is referred to as Marek’s disease. Previous reports have is regulated during MDV replication. Here, we carried out a comprehensive profiling analysis of N6-methyladenosine (m6A) modification on the circRNA transcriptome in infected and uninfected chicken embryonic fibroblast (CEF) cells. Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) revealed that m6A modification was highly conserved in circRNAs. Comparing to the uninfected group, the number of peaks and conserved motifs were not significantly different in cells that were infected with MDV, although reduced abundance of circRNA m6A modifications. However, gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses revealed that the insulin signaling pathway was associated with the regulation of m6A modified circRNAs in MDV infection. This is the first report to describe alterations in the transcriptome-wide profiling of m6A modified circRNAs in MDV-infected CEF cells.
In situ photografting during direct laser writing in thermoplastic microchannels
Authors: Han Jung Y. , Warshawsky Sarah , DeVoe Don L. 
Published: May 2021

AbstractA method for in situ photografting during direct laser writing by two-photon polymerization is presented. The technique serves as a powerful approach to the formation of covalent bonds between 3D photoresist structures and thermoplastic surfaces. By leveraging the same laser for both pattern generation and localized surface reactions, crosslinking between the bulk photoresist and thermoplastic surface is achieved during polymerization. When applied to in-channel direct laser writing for microfluidic device fabrication, the process yields exceptionally strong adhesion and robust bond interfaces that can withstand pressure gradients as high as 7 MPa through proper channel design, photoinitiator selection, and processing conditions.
Thermally tolerant intertidal triplefin fish (Tripterygiidae) sustain ATP dynamics better than subtidal species under acute heat stress
Authors: Willis Jaime R. , Hickey Anthony J. R. , Devaux Jules B. L. 
Published: May 2021

AbstractTemperature is a key factor that affects all levels of organization. Minute shifts away from thermal optima result in detrimental effects that impact growth, reproduction and survival. Metabolic rates of ectotherms are especially sensitive to temperature and for organisms exposed to high acute temperature changes, in particular intertidal species, energetic processes are often negatively impacted. Previous investigations exploring acute heat stress have implicated cardiac mitochondrial function in determining thermal tolerance. The brain, however, is by weight, one of the most metabolically active and arguably the most temperature sensitive organ. It is essentially aerobic and entirely reliant on oxidative phosphorylation to meet energetic demands, and as temperatures rise, mitochondria become less efficient at synthesising the amount of ATP required to meet the increasing demands. This leads to an energetic crisis. Here we used brain homogenate of three closely related triplefin fish species (Bellapiscis medius, Forsterygion lapillum,andForsterygion varium) and measured respiration and ATP dynamics at three temperatures (15, 25 and 30 °C). We found that the intertidalB. mediusandF. lapillumwere able to maintain rates of ATP production above rates of ATP hydrolysis at high temperatures, compared to the subtidalF. varium, which showed no difference in rates at 30 °C. These results showed that brain mitochondria became less efficient at temperatures below their respective species thermal limits, and that energetic surplus of ATP synthesis over hydrolysis narrows. In subtidal species synthesis matches hydrolysis, leaving no scope to elevate ATP supply.
Comprehensive analysis of competitive endogenous RNA associated with immune infiltration in lung adenocarcinoma
Authors: Chen Wenjie , Li Wen , Liu Zhenkun , Ma Guangzhi , Deng Yunfu , Li Xiaogang , Wang Zhu , zhou Qinghua 
Published: May 2021

AbstractTo identify the prognostic biomarker of the competitive endogenous RNA (ceRNA) and explore the tumor infiltrating immune cells (TIICs) which might be the potential prognostic factors in lung adenocarcinoma. In addition, we also try to explain the crosstalk between the ceRNA and TIICs to explore the molecular mechanisms involved in lung adenocarcinoma. The transcriptome data of lung adenocarcinoma were obtained from The Cancer Genome Atlas (TCGA) database, and the hypergeometric correlation of the differently expressed miRNA-lncRNA and miRNA-mRNA were analyzed based on the starBase. In addition, the Kaplan–Meier survival and Cox regression model analysis were used to identify the prognostic ceRNA network and TIICs. Correlation analysis was performed to analysis the correlation between the ceRNA network and TIICs. In the differently expressed RNAs between tumor and normal tissue, a total of 190 miRNAs, 224 lncRNAs and 3024 mRNAs were detected, and the constructed ceRNA network contained 5 lncRNAs, 92 mRNAs and 10 miRNAs. Then, six prognostic RNAs (FKBP3, GPI, LOXL2, IL22RA1, GPR37, andhas-miR-148a-3p) were viewed as the key members for constructing the prognostic prediction model in the ceRNA network, and three kinds of TIICs (Monocytes, Macrophages M1, activated mast cells) were identified to be significantly related with the prognosis in lung adenocarcinoma. Correlation analysis suggested that theFKBP3was associated with Monocytes and Macrophages M1, and theGPIwas obviously related with Monocytes and Macrophages M1. Besides, theLOXL2was associated with Monocytes and Activated mast cells, and theIL22RA1was significantly associated with Monocytes and Macrophages M1, while theGPR37and Macrophages M1 was closely related. The constructed ceRNA network and identified Monocytes, Macrophages M1 and activated Mast cells are all prognostic factors for lung adenocarcinoma. Moreover, the crosstalk between the ceRNA network and TIICs might be a potential molecular mechanism involved.
Sustainable laser-based technology for insect pest control
Authors: Gaetani R. , Lacotte V. , Dufour V. , Clavel A. , Duport G. , Gaget K. , Calevro F. , Da Silva P. , Heddi A. , Vincent D. , Masenelli B. 
Published: May 2021

AbstractAphids damage directly or indirectly cultures by feeding and spreading diseases, leading to huge economical losses. So far, only the use of pesticides can mitigate their impact, causing severe health and environmental issues. Hence, innovative eco-friendly and low-cost solutions must be promoted apart from chemical control. Here, we have investigated the use of laser radiation as a reliable solution. We have analyzed the lethal dose required to kill 90% of a population for two major pest aphid species (Acyrthosiphon pisum and Rhopalosiphum padi). We showed that irradiating insects at an early stage (one-day old nymph) is crucial to lower the lethal dose without affecting plant growth and health. The laser is mostly lethal, but it can also cause insect stunting and a reduction of survivors’ fecundity. Nevertheless, we did not notice any significant visible effect on the offspring of the surviving irradiated generation. The estimated energy cost and the harmless effect of laser radiation on host plants show that this physics-based strategy can be a promising alternative to chemical pesticides.
Variation on a Zernike wavefront sensor theme: Optimal use of photons
Authors: Chambouleyron V. , Fauvarque O. , Sauvage J-F. , Dohlen K. , Levraud N. , Vigan A. , N’Diaye M. , Neichel B. , Fusco T. 
Published: May 2021

Aims. The Zernike wavefront sensor (ZWFS) is a concept belonging to the wide class of Fourier-filtering wavefront sensors (FFWFSs). The ZWFS is known for its extremely high sensitivity and low dynamic range, which makes it a unique sensor for second stage adaptive optics systems or quasi-static aberration calibration sensors. This sensor is composed of a focal plane mask made of a phase shifting dot that is fully described by two parameters: its diameter and depth. We aim to improve the performance of this sensor by changing the diameter of its phase shifting dot.
Methods. We begin with a general theoretical framework, providing an analytical description of the FFWFS properties. We then predict the expected ZWFS sensitivity for different configurations of dot diameters and depths. The analytical predictions are then validated with end-to-end simulations. From this, we propose a variation of the classical ZWFS shape that exhibits extremely appealing properties.
Results. We show that the ZWFS sensitivity can be optimized by modifying the dot diameter and it can even reach the optimal theoretical limit, though with the trade-off of low spatial frequency sensitivity. As an example, we show that a ZWFS with a 2 λ/D dot diameter (where λ is the sensing wavelength and D the telescope diameter), hereafter called a Z2WFS, exhibits a sensitivity twice higher than the classical 1.06 λ/D ZWFS for all the phase spatial components except for tip-tilt modes. Furthermore, this gain in sensitivity does not impact the dynamic range of the sensor, and the Z2WFS exhibits a similar dynamical range as the classical 1.06 λ/D ZWFS. This study opens the path to the conception of a diameter-optimized ZWFS.
Geolectric field measurement, modelling and validation during geomagnetic storms in the UK
Authors: Beggan Ciarán D. , Richardson Gemma S. , Baillie Orsi , Hübert Juliane , Thomson Alan W. P. 
Published: May 2021

Significant geoelectric fields are produced by the interaction of rapidly varying magnetic fields with the conductive Earth, particularly during intense geomagnetic activity. Though usually harmless, large or sustained geoelectric fields can damage grounded infrastructure such as high-voltage transformers and pipelines via geomagnetically induced currents (GICs). A key aspect of understanding the effects of space weather on grounded infrastructure is through the spatial and temporal variation of the geoelectric field. Globally, there are few long-term monitoring sites of the geoelectric field, so in 2012 measurements of the horizontal surface field were started at Lerwick, Eskdalemuir and Hartland observatories in the UK. Between 2012 and 2020, the maximum value of the geoelectric field observed was around 1 V/km in Lerwick, 0.5 V/km in Eskdalemuir and 0.1 V/km in Hartland during the March 2015 storm. These long-term observations also allow comparisons with models of the geoelectric field to be made. We use the measurements to compute magnetotelluric impedance transfer functions at each observatory for periods from 20 to 30,000 s. These are then used to predict the geoelectric field at the observatory sites during selected storm times that match the recorded fields very well (correlation around 0.9). We also compute geoelectric field values from a thin-sheet model of Britain, accounting for the diverse geological and bathymetric island setting. We find the thin-sheet model captures the peak and phase of the band-passed geoelectric field reasonably well, with linear correlation of around 0.4 in general. From these two modelling approaches, we generate geoelectric field values for historic storms (March 1989 and October 2003) and find the estimates of past peak geoelectric fields of up to 1.75 V/km in Eskdalemuir. However, evidence from high voltage transformer GIC measurements during these storms suggests these estimates are likely to represent an underestimate of the true value.
Performance of digital servos in an optical frequency transfer network
Authors: Hu Liang , Xue Ruimin , Wu Guiling , Chen Jianping 
Published: May 2021

We demonstrate the use of three kinds of flexible digital servos for the stabilization of the optical fiber link, the interferometer temperature, and the polarization of the transmitted light at the remote site, respectively. The main fiber noise cancellation digital servo provides a large phase detection range (∼210π radians), automatic relock function, and low cycle-slip rate over a 62 km field-deployed fiber link achieved by utilizing a feedback optical actuator of an acousto-optic modulator fed by a voltage-controlled oscillator. The temperature control and polarization control digital servos enable that the temperature of the interferometer can be stabilized at a stability of 0.01 K and the data uptime is enhanced from 85.5% to 99.9% by implementing the polarization controller. The results demonstrate that the performance of the three digital servos is sufficient for high-precision optical frequency transfer applications and indicates comparable performance to existing analog optical frequency control systems. The full digital controlled optical frequency transfer method demonstrated here provides guidance for the development of a low-cost, low-complexity, and high-reliability optical frequency transfer system.