bluuebunny/crossref_metadata_2025 huggingface dataset:
2.5 Hz sample rate time-domain near-infrared optical tomography based on SPAD-camera image tissue hemodynamics
Authors: Jiang Jingjing , Costanzo Mata Aldo Di , Lindner Scott , Charbon Edoardo , Wolf Martin , Kalyanov Alexander
Published: November 2021

Time-domain near-infrared optical tomography (TD NIROT) techniques based on diffuse light were gaining performance over the last years. They are capable of imaging tissue at several centimeters depth and reveal clinically relevant information, such as tissue oxygen saturation. In this work, we present the very first in vivo results of our SPAD camera-based TD NIROT reflectance system with a temporal resolution of ∼116 ps. It provides 2800 time of flight source-detector pairs in a compact probe of only 6 cm in diameter. Additionally, we describe a 3-step reconstruction procedure that enables accurate recovery of structural information and of the optical properties. We demonstrate the system’s performance firstly in reconstructing the 3D-structure of a heterogeneous tissue phantom with tissue-like scattering and absorption properties within a volume of 9 cm diameter and 5 cm thickness. Furthermore, we performed in vivo tomography of an index finger located within a homogeneous scattering medium. We employed a fast sampling rate of 2.5 Hz to detect changes in tissue oxygenation. Tomographic reconstructions were performed in true 3D, and without prior structural information, demonstrating the powerful capabilities of the system. This shows its potential for clinical applications.
Shot-noise limited tunable dual-vibrational frequency stimulated Raman scattering microscopy
Authors: Heuke Sandro , Rimke Ingo , Sarri Barbara , Gasecka Paulina , Appay Romain , Legoff Loic , Volz Peter , Büttner Edlef , Rigneault Hervé
Published: November 2021

We present a shot-noise limited SRS implementation providing a >200 mW per excitation wavelength that is optimized for addressing two molecular vibrations simultaneously. As the key to producing a 3 ps laser of different colors out of a single fs-laser (15 nm FWHM), we use ultra-steep angle-tunable optical filters to extract 2 narrow-band Stokes laser beams (1–2 nm & 1–2 ps), which are separated by 100 cm−1. The center part of the fs-laser is frequency doubled to pump an optical parametric oscillator (OPO). The temporal width of the OPO’s output (1 ps) is matched to the Stokes beams and can be tuned from 650–980 nm to address simultaneously two Raman shifts separated by 100 cm−1 that are located between 500 cm−1 and 5000 cm−1. We demonstrate background-free SRS imaging of C-D labeled biological samples (bacteria and Drosophila). Furthermore, high quality virtual stimulated Raman histology imaging of a brain adenocarcinoma is shown for pixel dwell times of 16 µs.
Development of a Doppler-broadened NICE-OHMS system for trace gas detection based on a single sideband phase modulator
Authors: Liu Jianxin , Zhao Gang , Ma Weiguang , Axner Ove
Published: November 2021

To expand the applicability of noise-immune cavity-enhanced optical heterodyne molecular spectrometer (NICE-OHMS), a universal system incorporating a fiber-coupled single-sideband modulator (f-SSM) for control of the laser frequency has been developed. A homemade PID servo mainly composed of two integrators has been designed, resulting in a locking bandwidth of 170 kHz and a continuous tuning range of 2.2 GHz. The system exhibits a noise-equivalent Doppler-broadened absorption limit of 8.0×10−14 cm−1 for an integration time of 64 s. Since the f-SSM is the sole external frequency actuator, this opens up for NICE-OHMS based on a multitude of laser systems.
Delafossite AgAlO2 modified long-period grating for highly-sensitive ammonia sensor
Authors: Rong Dandan , Meng Gang , Fang Xiaodong , You Libing , Deng Zanhong
Published: November 2021

Owing to the unique merits of high sensitivity and large range detection, long-period grating (LPG) optical fiber sensor modified with functional coatings has attracted significant attention recently. As a refractive index sensor, the appropriate choice of the coating properties is critical for exploring the high-performance LPG sensor. In this study, p-type delafossite AgAlO2 (AAO) nanoparticles were proposed as a novel sensitive coating material for the cladding modification of LPG develop a high-sensitivity fiber-optic ammonia sensor. As the resistance/dielectric constant of AAO cladding layer is sensitive to concentration variation of ammonia vapor even at room temperature. Sensing performances of the LPG optical fiber sensor could be substantially enhanced with the presence of AAO cladding layer. A linear sensitivity of 2.07 pm/ppm to ammonia from 25 ppm to 400 ppm was achieved at room temperature. Moreover, the LPG sensor exhibits short response (38 s) and recovery time (50 s), and high selectivity to ammonia compared to several possible interfering vapors.
Surface temperature determination using long range thermal emission spectroscopy based on a first order scanning Fabry-Pérot interferometer
Authors: Jørgensen Anders Løchte , Larsen Mads Nibe , Petrunin Victor , Kjelstrup-Hansen Jakob , Jørgensen Bjarke
Published: November 2021

Determination of the surface temperature of different materials based on thermographic imaging is a difficult task as the thermal emission spectrum is both temperature and emissivity dependent. Without prior knowledge of the emissivity of the object under investigation, it makes up a temperature-emissivity underdetermined system. This work demonstrates the possibility of recognizing specific materials from hyperspectral thermal images (HSTI) in the wavelength range from 8–14 µm. The hyperspectral images were acquired using a microbolometer sensor array in combination with a scanning 1st order Fabry-Pérot interferometer acting as a bandpass filter. A logistic regression model was used to successfully differentiate between polyimide tape, sapphire, borosilicate glass, fused silica, and alumina ceramic at temperatures as low as 34.0 ± 0.05 °C. Each material was recognized with true positive rates above 94% calculated from individual pixel spectra. The surface temperature of the samples was subsequently predicted using pre-fitted partial least squares (PLS) models, which predicted all surface temperature values with a common root mean square error (RMSE) of 1.10 °C and thereby outperforming conventional thermography. This approach paves the way for a practical solution to the underdetermined temperature-emissivity system.
Object-independent tilt detection for optical sparse aperture system with large-scale piston error via deep convolution neural network
Authors: Tang Ju , Ren Zhenbo , Wu Xiaoyan , Di Jianglei , Liu Guodong , Zhao Jianlin
Published: November 2021

The optical sparse aperture technique can improve the imaging resolution significantly under the ideal co-phase condition. However, the position deviation between different sub-apertures leads to notorious co-phase errors, seriously impacting the image quality. While the position deviation arises in practical applications, it is difficult to detect the errors in real-time for traditional iterative algorithms because of their narrow detection range and long-time iteration process. The deep neural network has shown its potential in optical information process, and it has some attempts in the detection of piston error. However, all existing deep learning-based methods just focus on the detection of piston error with the weak or corrected tilt error, which is not in line with reality. Here we implement the deep convolutional neural network to detect tilt error with large-scale piston error, and compare the detection performance of two kinds of network, one takes the point spread function as input while the other takes the phase diversity features as the input. The detection ability and generalization capability of network are verified under single wavelength, broadband light and turbulence aberration in simulation. The object-independent of tilt error detection ability is offered because the phase diversity features and point spread function are all unrelated to the object. In addition, the cyclic correction strategy is carried out to improve the generalization performance facing the larger errors. As a result, the deep learning-based method can detect the tilt error accurately with fast calculation, and the trained network is hopeful for the real-time correction with cyclic correction strategy.
High-quality dense 3D point clouds with active stereo and a miniaturizable interferometric pattern projector
Authors: Thorstensen Jostein , Thielemann Jens T. , Risholm Petter , Gjessing Jo , Dahl-Hansen Runar , Tschudi Jon
Published: November 2021

We have built and characterized a compact, simple and flexible 3D camera based on interferometric fringe projection and stereo reconstruction. The camera uses multi-frame active stereo as basis for 3D reconstruction, providing full-field 3D images with 3D measurement standard deviation of 0.09 mm, 12.5 Hz 3D image capture rate and 3D image resolution of 500 × 500 pixels. Interferometric projection enables a compact, low-power projector that consumes < 1 W of electrical power. The key component in the projector, a movable micromirror, has undergone initial vibration, thermal vacuum cycling (TVAC) and radiation testing, with no observed component degradation. The system's low power, small size and component longevity makes it well suitable for space applications.
Third-order nonlinear properties and reverse absorption behavior in layered Ti3C2 MXene in the near infrared region
Authors: Zhang Tong , Chu Hongwei , Li Ying , Zhao Shengzhi , Li Dechun
Published: November 2021

Two-dimensional transition metal carbides/nitrides (MXenes) have attracted a lot of attention as optical materials owing to their unique electronic and optical features. In this paper, we demonstrated the nonlinear optical response of Ti3C2 MXene in the near infrared (NIR) regime at 1 and 1.3 µm. The nonlinear optical absorption behavior was systematically studied by the open/closed aperture (OA/CA) Z-scan techniques. Under a low excitation intensity, the saturable absorption dominated the optical nonlinear process, and the maximum effective nonlinear absorption coefficients βeff were −0.59 cm/MW and −0.68 cm/MW at 1 and 1.3 µm, respectively. The nonlinear refractive index n2 and the third-order susceptibility of Ti3C2 Mxene at 1 µm were −2.18 ×10−2 cm2/GW and 3.65×10−3 esu, respectively. While with the excitation laser at 1.3 µm, the nonlinear refractive index n2 was −1.64×10−2 cm2/GW and the third-order susceptibility was 2.75×10−3 esu. With the increase of incident optical intensity, the two-photon absorption (TPA) process was observed, leading to the reverse absorption phenomenon. Our results confirmed that Ti3C2 MXene possessed intensity-depended nonlinear optical properties, which could be applied in various nonlinear optical devices.
Multiparticle resonant optical sorting using a topological photonic structure
Authors: Shi Bojian , Cao Yongyin , Zhu Tongtong , Li Hang , Zhang Yanxia , Feng Rui , Sun Fangkui , Ding Weiqiang
Published: November 2021

Resonance between light and object is highly desired in optical manipulation because the optical forces reach maximum values in this case. However, in traditional waveguide structures, the resonant interaction also greatly perturbs the incident field and weakens or completely destroys the manipulation on the subsequent particles. In order to avoid this dilemma, we propose to perform optical manipulation in a topological photonic structure. Owing to the topological protection, the light mode can almost keep its original form when an object is being manipulated. Therefore, resonant optical sorting can be achieved in a multiple and high throughput manner. The mechanism and results presented here pave the way for efficient on-chip optical sorting for biophysical and biochemical analysis.
Ultra-sensitive Dirac-point-based biosensing on terahertz metasurfaces comprising patterned graphene and perovskites
Authors: Yan Xin , Li Tengteng , Ma Guohong , Gao Ju , Wang Tongling , Yao Haiyun , Yang Maosheng , Liang Lanju , Li Jing , Li Jie , Wei Dequan , Wang Meng , Ye Yunxia , Song Xiaoxian , Zhang Haiting , Ma Chao , Ren Yunpeng , Ren Xudong , Yao Jianquan
Published: November 2021

Biosensors are a focus of research on terahertz metasurfaces. However, reports of ultra-sensitive biosensors based on Dirac points are rare. Here, a new terahertz metasurface is proposed that consists of patterned graphene and perovskites. This serves as an ultra-sensitive Dirac-point-based biosensor for qualitative detection of sericin. Theoretically, sericin may make graphene n-doped and drive the Fermi level to shift from the valence band to the Dirac point, causing a dramatic decrease in conductivity. Correspondingly, the dielectric environment on the metasurface undergoes significant change, which is suited for ultra-sensitive biosensing. In addition, metal halide perovskites, which are up-to-date optoelectronic materials, have a positive effect on the phase during terahertz wave transmission. Thus, this sensor was used to successfully detect sericin with a detection limit of 780 pg/mL, achieved by changing the amplitude and phase. The detection limit of this sensor is as much as one order of magnitude lower than that of sensors in published works. These results show that the Dirac-point-based biosensor is a promising platform for a wide range of ultra-sensitive and qualitative detection in biosensing and biological sciences.
Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data
Authors: Kos Pavel I. , Galitsyna Aleksandra A. , Ulianov Sergey V. , Gelfand Mikhail S. , Razin Sergey V. , Chertovich Alexander V.
Published: November 2021

Construction of chromosomes 3D models based on single cell Hi-C data constitute an important challenge. We present a reconstruction approach, DPDchrom, that incorporates basic knowledge whether the reconstructed conformation should be coil-like or globular and spring relaxation at contact sites. In contrast to previously published protocols, DPDchrom can naturally form globular conformation due to the presence of explicit solvent. Benchmarking of this and several other methods on artificial polymer models reveals similar reconstruction accuracy at high contact density and DPDchrom advantage at low contact density. To compare 3D structures insensitively to spatial orientation and scale, we propose the Modified Jaccard Index. We analyzed two sources of the contact dropout: contact radius change and random contact sampling. We found that the reconstruction accuracy exponentially depends on the number of contacts per genomic bin allowing to estimate the reconstruction accuracy in advance. We applied DPDchrom to model chromosome configurations based on single-cell Hi-C data of mouse oocytes and found that these configurations differ significantly from a random one, that is consistent with other studies.
Inferred expression regulator activities suggest genes mediating cardiometabolic genetic signals
Authors: Hoskins Jason W. , Chung Charles C. , O’Brien Aidan , Zhong Jun , Connelly Katelyn , Collins Irene , Shi Jianxin , Amundadottir Laufey T.
Published: November 2021

Expression QTL (eQTL) analyses have suggested many genes mediating genome-wide association study (GWAS) signals but most GWAS signals still lack compelling explanatory genes. We have leveraged an adipose-specific gene regulatory network to infer expression regulator activities and phenotypic master regulators (MRs), which were used to detect activity QTLs (aQTLs) at cardiometabolic trait GWAS loci. Regulator activities were inferred with the VIPER algorithm that integrates enrichment of expected expression changes among a regulator’s target genes with confidence in their regulator-target network interactions and target overlap between different regulators (i.e., pleiotropy). Phenotypic MRs were identified as those regulators whose activities were most important in predicting their respective phenotypes using random forest modeling. While eQTLs were typically more significant than aQTLs in cis, the opposite was true among candidate MRs in trans. Several GWAS loci colocalized with MR trans-eQTLs/aQTLs in the absence of colocalized cis-QTLs. Intriguingly, at the 1p36.1 BMI GWAS locus the EPHB2 cis-aQTL was stronger than its cis-eQTL and colocalized with the GWAS signal and 35 BMI MR trans-aQTLs, suggesting the GWAS signal may be mediated by effects on EPHB2 activity and its downstream effects on a network of BMI MRs. These MR and aQTL analyses represent systems genetic methods that may be broadly applied to supplement standard eQTL analyses for suggesting molecular effects mediating GWAS signals.
A first assessment of the distribution and abundance of large pelagic species at Cocos Ridge seamounts (Eastern Tropical Pacific) using drifting pelagic baited remote cameras
Authors: Cambra Marta , Lara-Lizardi Frida , Peñaherrera-Palma César , Hearn Alex , Ketchum James T. , Zarate Patricia , Chacón Carlos , Suárez-Moncada Jenifer , Herrera Esteban , Espinoza Mario
Published: November 2021

Understanding the link between seamounts and large pelagic species (LPS) may provide important insights for the conservation of these species in open water ecosystems. The seamounts along the Cocos Ridge in the Eastern Tropical Pacific (ETP) ocean are thought to be ecologically important aggregation sites for LPS when moving between Cocos Island (Costa Rica) and Galapagos Islands (Ecuador). However, to date, research efforts to quantify the abundance and distribution patterns of LPS beyond the borders of these two oceanic Marine Protected Areas (MPAs) have been limited. This study used drifting-pelagic baited remote underwater video stations (BRUVS) to investigate the distribution and relative abundance of LPS at Cocos Ridge seamounts. Our drifting-pelagic BRUVS recorded a total of 21 species including elasmobranchs, small and large teleosts, dolphins and one sea turtle; of which four species are currently threatened. Depth of seamount summit was the most significant driver for LPS richness and abundance which were significantly higher at shallow seamounts (< 400 m) compared to deeper ones (> 400m). Distance to nearest MPA was also a significant predictor for LPS abundance, which increased at increasing distances from the nearest MPA. Our results suggest that the Cocos Ridge seamounts, specifically Paramount and West Cocos which had the highest LPS richness and abundance, are important aggregation sites for LPS in the ETP. However, further research is still needed to demonstrate a positive association between LPS and Cocos Ridge seamounts. Our findings showed that drifting pelagic BRUVS are an effective tool to survey LPS in fully pelagic ecosystems of the ETP. This study represents the first step towards the standardization of this technique throughout the region.
Evaluation of NPP using three models compared with MODIS-NPP data over China
Authors: Sun Jinke , Yue Ying , Niu Haipeng
Published: November 2021

Estimating net primary productivity (NPP) is significant in global climate change research and carbon cycle. However, there are many uncertainties in different NPP modeling results and the process of NPP is challenging to model on the absence of data. In this study, we used meteorological data as input to simulate vegetation NPP through climate-based model, synthetic model and CASA model. Then, the results from three models were compared with MODIS NPP and observed data over China from 2000 to 2015. The statistics evaluation metrics (Relative Bias (RB), Pearson linear Correlation Coefficient (CC), Root Mean Square Error (RMSE), and Nash-Sutcliffe efficiency coefficient (NSE)) between simulated NPP and MODIS NPP were calculated. The results implied that the CASA-model performed better than the other two models in terms of RB, RMSE, NSE and CC whether on the national or the regional scale. It has a higher CC with 0.51 and a smaller RMSE with 111.96 g C·m-2·yr-1 in the whole country. The synthetic model and CASA-model has the same advantages at some regions, and there are lower RMSE in Southern China (86.35 g C·m-2·yr-1), Xinjiang (85.53 g C·m-2·yr-1) and Qinghai-Tibet Plateau (93.22 g C·m-2·yr-1). The climate-based model has widespread overestimation and large systematic errors, along with worse performances (NSEmax = 0.45) and other metric indexes unsatisfactory, especially Qinghai-Tibet Plateau with relatively lower accuracy because of the unavailable observation data. Overall, the CASA-model is much more ideal for estimating NPP all over China in the absence of data. This study provides a comprehensive intercomparison of different NPP-simulated models and can provide powerful help for researchers to select the appropriate NPP evaluation model.
Defining dual-axis landscape gradients of human influence for studying ecological processes
Authors: Padilla Benjamin Juan , Sutherland Chris
Published: November 2021

Ecological processes are strongly shaped by human landscape modification, and understanding the reciprocal relationship between ecosystems and modified landscapes is critical for informed conservation. Single axis measures of spatial heterogeneity proliferate in the contemporary gradient ecology literature, though they are unlikely to capture the complexity of ecological responses. Here, we develop a standardized approach for defining multi-dimensional gradients of human influence in heterogeneous landscapes and demonstrate this approach to analyze landscape characteristics of ten ecologically distinct US cities. Using occupancy data of a common human-adaptive songbird collected in each of the cities, we then use our dual-axis gradients to evaluate the utility of our approach. Spatial analysis of landscapes surrounding ten US cities revealed two important axes of variation that are intuitively consistent with the characteristics of multi-use landscapes, but are often confounded in single axis gradients. These were, a hard-to-soft gradient, representing transition from developed areas to non-structural soft areas; and brown-to-green, differentiating between two dominant types of soft landscapes: agriculture (brown) and natural areas (green). Analysis of American robin occurrence data demonstrated that occupancy responds to both hard-to-soft (decreasing with development intensity) and brown-to-green gradient (increasing with more natural area). Overall, our results reveal striking consistency in the dominant sources of variation across ten geographically distinct cities and suggests that our approach advances how we relate variation in ecological responses to human influence. Our case study demonstrates this: robins show a remarkably consistent response to a gradient differentiating agricultural and natural areas, but city-specific responses to the more traditional gradient of development intensity, which would be overlooked with a single gradient approach. Managing ecological communities in human dominated landscapes is extremely challenging due to a lack of standardized approaches and a general understanding of how socio-ecological systems function, and our approach offers promising solutions.
Association between early gestation passive smoke exposure and neonatal size among self-reported non-smoking women by race/ethnicity: A cohort study
Authors: Amyx Melissa M. , Sundaram Rajeshwari , Buck Louis Germaine M. , Gerlanc Nicole M. , Bever Alaina M. , Kannan Kurunthachalam , Robinson Morgan , Smarr Melissa M. , He Dian , Tekola-Ayele Fasil , Zhang Cuilin , Grantz Katherine L.
Published: November 2021

Understanding implications of passive smoke exposure during pregnancy is an important public health issue under the Developmental Origins of Health and Disease paradigm. In a prospective cohort of low-risk non-smoking pregnant women (NICHD Fetal Growth Studies—Singletons, 2009–2013, N = 2055), the association between first trimester passive smoke exposure and neonatal size was assessed by race/ethnicity. Plasma biomarker concentrations (cotinine, nicotine) assessed passive smoke exposure. Neonatal anthropometric measures included weight, 8 non-skeletal, and 2 skeletal measures. Linear regression evaluated associations between continuous biomarker concentrations and neonatal anthropometric measures by race/ethnicity. Cotinine concentrations were low and the percent above limit of quantification varied by maternal race/ethnicity (10% Whites; 14% Asians; 15% Hispanics; 49% Blacks). The association between cotinine concentration and infant weight differed by race/ethnicity (Pinteraction = 0.034); compared to women of the same race/ethnicity, per 1 log-unit increase in cotinine, weight increased 48g (95%CI -44, 139) in White and 51g (95%CI -81, 183) in Hispanic women, but decreased -90g (95%CI -490, 309) in Asian and -93g (95%CI -151, -35) in Black women. Consistent racial/ethnic differences and patterns were found for associations between biomarker concentrations and multiple non-skeletal measures for White and Black women (Pinteraction<0.1). Among Black women, an inverse association between cotinine concentration and head circumference was observed (−0.20g; 95%CI −0.38, −0.02). Associations between plasma cotinine concentration and neonatal size differed by maternal race/ethnicity, with increasing concentrations associated with decreasing infant size among Black women, who had the greatest biomarker concentrations. Public health campaigns should advocate for reducing pregnancy exposure, particularly for vulnerable populations.
Environmental sustainability assessment of biodiesel production from Jatropha curcas L. seeds oil in Pakistan
Authors: Khanam Taslima , Khalid Faisal , Manzoor Wajiha , Rashedi Ahmad , Hadi Rana , Ullah Faizan , Rehman Fariha , Akhtar Andleeb , Babu N. B. Karthik , Hussain Majid
Published: November 2021

According to IPCC Annual Report (AR-5), environmental impact assessment of any product prototype is recommended before its large-scale commercialization; however, no environmental profile analysis of any biodiesel prototype has been conducted in Pakistan. Therefore, objective of this study was to conduct a comprehensive life cycle assessment (LCA), water footprint and cumulative energy demand (CED) of biodiesel production fromJatropha curcas L. (JC) seeds oil in Pakistan. A cradle-to-gate LCA approach was applied for 400 liter (L)JCbiodiesel produced in Pakistan.JCbiodiesel production chain was divided into three stages i.e., 1). cultivation ofJCcrop 2). crude oil extraction fromJCseeds and 3). crude oil conversion to biodiesel. Primary data for all the stages were acquired through questionnaire surveys, field visits and measurements in the field. Potential environmental impacts were calculated in SimaPro v.9.2 software using Eco-indicator 99 methodology. Results showed that crude oil extraction stage accounted for highest emissions (77%) to the overall environmental impact categories evaluated, followed by oil conversion stage (21%) andJCcultivation stage (02%), respectively. The three stages ofJCbiodiesel production chain are major contributor to ecotoxicity with a contribution of 57% to this impact category. Higher contribution to ecotoxicity was due to agrochemicals used in theJCcultivation. Similarly, fossil fuels impact category was responsible for 38% of overall environmental impacts. In addition, water footprint ofJCbiodiesel production chain was 2632.54 m3/reference unit. Cumulative energy required for 400LJCbiodiesel production chain was 46745.70 MJ in Pakistan. Fossil diesel consumption, synthetic fertilizers use and purchased electricity were major hotspot sources to environmental burdens caused byJCbiodiesel production in Pakistan. By performing sensitivity analysis at 20% reduction of the baseline values of fossil diesel used, synthetic fertilizers and purchased electricity, a marked decrease in environmental footprint was observed. It is highly recommended that use of renewable energy instead of fossil energy would provide environmental benefits such as lower greenhouse gases and other toxic emissions as compared to conventional petroleum fuels. It is also recommended thatJCas a biofuel plant, has been reported to have many desired characteristics such as quick growth, easy cultivation, drought resistance, pest and insect resistance, and mainly great oil content in JC seeds (27–40%). Therefore,JCplant is highly recommended to Billion Tree Afforestation Project (BTAP) for plantation on wasteland because it has multipurpose benefits.
Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples
Authors: Gauthier Nick P. G. , Nelson Cassidy , Bonsall Michael B. , Locher Kerstin , Charles Marthe , MacDonald Clayton , Krajden Mel , Chorlton Samuel D. , Manges Amee R.
Published: November 2021

Objectives

The COVID-19 pandemic has underscored the need for rapid novel diagnostic strategies. Metagenomic Next-Generation Sequencing (mNGS) may allow for the detection of pathogens that can be missed in targeted assays. The goal of this study was to assess the performance of nanopore-based Sequence-Independent Single Primer Amplification (SISPA) for the detection and characterization of SARS-CoV-2.

Methods

We performed mNGS on clinical samples and designed a diagnostic classifier that corrects for barcode crosstalk between specimens. Phylogenetic analysis was performed on genome assemblies.

Results

Our assay yielded 100% specificity overall and 95.2% sensitivity for specimens with a RT-PCR cycle threshold value less than 30. We assembled 10 complete, and one near-complete genomes from 20 specimens that were classified as positive by mNGS. Phylogenetic analysis revealed that 10/11 specimens from British Columbia had a closest relative to another British Columbian specimen. We found 100% concordance between phylogenetic lineage assignment and Variant of Concern (VOC) PCR results. Our assay was able to distinguish between the Alpha and Gamma variants, which was not possible with the current standard VOC PCR being used in British Columbia.

Conclusions

This study supports future work examining the broader feasibility of nanopore mNGS as a diagnostic strategy for the detection and characterization of viral pathogens.
Down-regulation of cyclin D2 in amyloid β toxicity, inflammation, and Alzheimer’s disease
Authors: Czapski Grzegorz A. , Cieślik Magdalena , Białopiotrowicz Emilia , Lukiw Walter J. , Strosznajder Joanna B.
Published: November 2021

In the current study, we analyzed the effects of the systemic inflammatory response (SIR) and amyloid β (Aβ) peptide on the expression of genes encoding cyclins and cyclin-dependent kinase (Cdk) in:(i)PC12 cells overexpressing human beta amyloid precursor protein (βAPP), wild-type (APPwt-PC12), or carrying the Swedish mutantion (APPsw-PC12);(ii)the murine hippocampus during SIR; and(iii)Alzheimer’s disease (AD) brain. In APPwt-PC12 expression of cyclin D2 (cD2) was exclusively reduced, and in APPsw-PC12 cyclins cD2 and also cA1 were down-regulated, but cA2, cB1, cB2, and cE1 were up-regulated. In the SIR cD2, cB2, cE1 were found to be significantly down-regulated and cD3, Cdk5, and Cdk7 were significantly up-regulated. Cyclin cD2 was also found to be down-regulated in AD neocortex and hippocampus. Our novel data indicate that Aβ peptide and inflammation both significantly decreased the expression of cD2, suggesting that Aβ peptides may also contribute to downregulation of cD2 in AD brain.
Empirical validation of the psychological concept of a perceived feeling of ‘energy’: Advancement into the study of positive psychology
Authors: Phan Huy P. , Ngu Bing H. , Chen Si-Chi , Lin Ruey-Yih , Wang Hui-Wen , Shih Jen-Hwa , Shi Sheng-Ying
Published: November 2021

Theparadigm of positive psychology, significant in nature, helps to explain the proactivity and motivation of human agency, such as a secondary school student’s state of autonomy, confidence, and personal resolve to strive for optimal learning and/or non-learning experiences. Our recent research development, in tandem with other scholars’ inquiries, has focused on one aspect of positive psychology–namely, a person’s achievement of ‘optimal best’, which reflects the maximization of his/her state of functioning (e.g., cognitive functioning). Capitalizing on our previous research, we develop a psychological concept that we term as a ‘perceived feeling of energy’. A perceived feeling of energy (e.g., a perceived feeling of liveliness) is proposed to act as a ‘motivational engine’, or as a central driver, which then could predict and enhance a person’s achievement of optimal best. Six hundred and twenty-seven university students (N = 438 women, 189 men) responded to a suite of self-report questionnaires. Structural equation modelling (SEM) techniques were used to test a conceptual model, where we focused on theantecedent(i.e., the direct impact ofself-efficacyon a perceived feeling of energy) andconsequenceof a perceived feeling energy (i.e., the impact of a perceived feeling of energy onpersonal resolve, and thesustainingof optimal best). Analysis of results showed support for our original hypothesized model–for example: self-efficacy as an antecedent of energy and the central role of the energy as a predictor and potential mediator of future outcomes.
Transcriptomic survey reveals multiple adaptation mechanisms in response to nitrogen deprivation in marine Porphyridium cruentum
Authors: Wei Li , You Wuxin , Xu Zhengru , Zhang Wenfei
Published: November 2021

Single-cell red microalga Porphyridium cruentum is potentially considered to be the bioresource for biofuel and pharmaceutical production. Nitrogen is a kind of nutrient component for photosynthetic P. cruentum. Meanwhile, nitrogen stress could induce to accumulate some substances such as lipid and phycoerythrin and affect its growth and physiology. However, how marine microalga Porphyridium cruentum respond and adapt to nitrogen starvation remains elusive. Here, acclimation of the metabolic reprogramming to changes in the nutrient environment was studied by high-throughput mRNA sequencing in the unicellular red alga P. cruentum. Firstly, to reveal transcriptional regulation, de novo transcriptome was assembled and 8,244 unigenes were annotated based on different database. Secondly, under nitrogen deprivation, 2100 unigenes displayed differential expression (1134 upregulation and 966 downregulation, respectively) and some pathways including carbon/nitrogen metabolism, photosynthesis, and lipid metabolism would be reprogrammed in P. cruentum. The result demonstrated that nitrate assimilation (with related unigenes of 8–493 fold upregulation) would be strengthen and photosynthesis (with related unigenes of 6–35 fold downregulation) be impaired under nitrogen deprivation. Importantly, compared to other green algae, red microalga P. cruentum presented a different expression pattern of lipid metabolism in response to nitrogen stress. These observations will also provide novel insight for understanding adaption mechanisms and potential targets for metabolic engineering and synthetic biology in P. cruentum.
Inactive status is an independent predictor of liver transplant waitlist mortality and is associated with a transplant centers median meld at transplant
Authors: Merola Jonathan , Gan Geliang , Stewart Darren , Noreen Samantha , Mulligan David , Batra Ramesh , Haakinson Danielle , Deng Yanhong , Kulkarni Sanjay
Published: November 2021

Background

Approximately 30% of patients on the liver transplant waitlist experience at least one inactive status change which makes them temporarily ineligible to receive a deceased donor transplant. We hypothesized that inactive status would be associated with higher mortality which may differ on a transplant centers’ or donor service areas’ (DSA) Median MELD at Transplant (MMaT).

Methods

Multi-state models were constructed (OPTN database;06/18/2013-06/08/2018) using DSA-level and transplant center-level data where MMaT were numerically ranked and categorized into tertiles. Hazards ratios were calculated between DSA and transplant center tertiles, stratified by MELD score, to determine differences in inactive to active transition probabilities.

Results

7,625 (30.2% of sample registrants;25,216 total) experienced at least one inactive status change in the DSA-level cohort and 7,623 experienced at least one inactive status change in the transplant-center level cohort (30.2% of sample registrants;25,211 total). Inactive patients with MELD≤34 had a higher probability of becoming re-activated if they were waitlisted in a low or medium MMaT transplant center or DSA. Transplant rates were higher and lower re-activation probability was associated with higher mortality for the MELD 26–34 group in the high MMaT tertile. There were no significant differences in re-activation, transplant probability, or waitlist mortality for inactivated patients with MELD≥35 regardless of a DSA’s or center’s MMaT.

Conclusion

This study shows that an inactive status change is independently associated with waitlist mortality. This association differs by a centers’ and a DSAs’ MMaT. Prioritization through care coordination to resolve issues of inactivity is fundamental to improving access.
Toponym-assisted map georeferencing: Evaluating the use of toponyms for the digitization of map collections
Authors: Bahgat Karim , Runfola Dan
Published: November 2021

A great deal of information is contained within archival maps—ranging from historic political boundaries, to mineral resources, to the locations of cultural landmarks. There are many ongoing efforts to preserve and digitize historic maps so that the information contained within them can be stored and analyzed efficiently. A major barrier to such map digitizing efforts is that the geographic location of each map is typically unknown and must be determined through an often slow and manual process known as georeferencing. To mitigate the time costs associated with the georeferencing process, this paper introduces a fully automated method based on map toponym (place name) labels. It is the first study to demonstrate these methods across a wide range of both simulated and real-world maps. We find that toponym-based georeferencing is sufficiently accurate to be used for data extraction purposes in nearly half of all cases. We make our implementation available to the wider research community through fully open-source replication code, as well as an online georeferencing tool, and highlight areas of improvement for future research. It is hoped that the practical implications of this research will allow for larger and more efficient processing and digitizing of map information for researchers, institutions, and the general public.
A computational in silico approach to predict high-risk coding and non-coding SNPs of human PLCG1 gene
Authors: Khan Safayat Mahmud , Faisal Ar-Rafi Md. , Nila Tasnin Akter , Binti Nabila Nawar , Hosen Md. Ismail , Shekhar Hossain Uddin
Published: November 2021

PLCG1gene is responsible for many T-cell lymphoma subtypes, including peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL), cutaneous T-cell lymphoma (CTCL), adult T-cell leukemia/lymphoma along with other diseases. Missense mutations of this gene have already been found in patients of CTCL and AITL. The non-synonymous single nucleotide polymorphisms (nsSNPs) can alter the protein structure as well as its functions. In this study, probable deleterious and disease-related nsSNPs inPLCG1were identified using SIFT, PROVEAN, PolyPhen-2, PhD-SNP, Pmut, and SNPS&GO tools. Further, their effect on protein stability was checked along with conservation and solvent accessibility analysis by I-mutant 2.0, MUpro, Consurf, and Netsurf 2.0 server. Some SNPs were finalized for structural analysis with PyMol and BIOVIA discovery studio visualizer. Out of the 16 nsSNPs which were found to be deleterious, ten nsSNPs had an effect on protein stability, and six mutations (L411P, R355C, G493D, R1158H, A401V and L455F) were predicted to be highly conserved. Among the six highly conserved mutations, four nsSNPs (R355C, A401V, L411P and L455F) were part of the catalytic domain. L411P, L455F and G493D made significant structural change in the protein structure. Two mutations-Y210C and R1158H had post-translational modification. In the 5’ and 3’ untranslated region, three SNPs, rs139043247, rs543804707, and rs62621919 showed possible miRNA target sites and DNA binding sites. Thisin silicoanalysis has provided a structured dataset ofPLCG1gene for furtherin vivoresearches. With the limitation of computational study, it can still prove to be an asset for the identification and treatment of multiple diseases associated with the target gene.
MicroRNA-5195-3p alleviates high glucose‑induced injury in human ARPE-19 cells by targeting GMFB
Authors: Liu Jingjing , Hou Yongsheng , Lin Lili , Yu Nannan , Zhang Yanyan
Published: November 2021

Hyperglycemia is generally considered to be an important cause of diabetic retinopathy (DR). The aim of the present study was to investigate the role of miR-5195-3p in high glucose (HG)-induced human retinal pigment epithelial ARPE-19 cell injury. Here, we first found that the expression level of miR-5195-3p was significantly downregulated in HG-stimulated ARPE-19 cells using reverse transcription quantitative PCR. Overexpression of miR-5195-3p attenuated the impaired cell viability, increased apoptosis and pro-inflammatory cytokines secretion in ARPE-19 cells under HG condition using CCK-8 assay, flow cytometry and ELISA assay, respectively. Luciferase reporter assay showed that miR-5195-3p could specifically bind to the 3’UTR of glia maturation factor-β (GMFB). GMFB overexpression reversed, while knockdown enhanced the protective effects of miR-5195-3p overexpression against HG-induced ARPE-19 cell injury. In summary, miR-5195-3p targeting GMFB might be a potential therapeutic target for DR.
Comparison of VividTrac, King Vision and Macintosh laryngoscopes in normal and difficult airways during simulated cardiopulmonary resuscitation among novices
Authors: Keresztes Dóra , Mérei Ákos , Rozanovic Martin , Nagy Edina , Kovács-Ábrahám Zoltán , Oláh János , Maróti Péter , Rendeki Szilárd , Nagy Bálint , Woth Gábor
Published: November 2021

Introduction

Early endotracheal intubation improves neurological outcomes in cardiopulmonary resuscitation, although cardiopulmonary resuscitation is initially carried out by personnel with limited experience in a significant proportion of cases. Videolaryngoscopes might decrease the number of attempts and time needed, especially among novices. We sought to compare videolaryngoscopes with direct laryngoscopes in simulated cardiopulmonary resuscitation scenarios.

Materials and methods

Forty-four medical students were recruited to serve as novice users. Following brief, standardized training, students executed endotracheal intubation with the King Vision®, Macintosh and VividTrac® laryngoscopes, on a cardiopulmonary resuscitation trainer in normal and difficult airway scenarios. We evaluated the time to and proportion of successful intubation, the best view of the glottis, esophageal intubation, dental trauma and user satisfaction.

Results

In the normal airway scenario, significantly shorter intubation times were achieved using the King Vision® than the Macintosh laryngoscope. In the difficult airway scenario, we found that the VividTrac® was superior to the King Vision® and Macintosh laryngoscopes in the laryngoscopy time. In both scenarios, we noted no difference in the first-attempt success rate, but the best view of the glottis and dental trauma, esophageal intubation and bougie use were more frequent with the Macintosh laryngoscope than with the videolaryngoscopes. The shortest tube insertion times were achieved using the King Vision® in both scenarios.

Conclusion

All providers achieved successful intubation within three attempts, but we found no device superior in any of our scenarios regarding the first-attempt success rate. The King Vision® was superior to the Macintosh laryngoscope in the intubation time in the normal airway scenario and noninferior in the difficult airway scenario for novice users. We noted significantly less esophageal intubation using the videolaryngoscopes than using the Macintosh laryngoscope in both scenarios. Based on our results, the KingVision® might be recommended over the VividTrac® and Macintosh laryngoscopes for further evaluation.
Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada
Authors: Vogt Nadine A. , Hetman Benjamin M. , Pearl David L. , Vogt Adam A. , Reid-Smith Richard J. , Parmley E. Jane , Janecko Nicol , Bharat Amrita , Mulvey Michael R. , Ricker Nicole , Bondo Kristin J. , Allen Samantha E. , Jardine Claire M.
Published: November 2021

To better understand the contribution of wildlife to the dissemination ofSalmonellaand antimicrobial resistance inSalmonellaandEscherichia coli, we examined whole-genome sequence data fromSalmonellaandE.coliisolates collected from raccoons(Procyon lotor) and environmental sources on farms in southern Ontario. AllSalmonellaand phenotypically resistantE.colicollected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159Salmonellaand 96 resistantE.coliisolates were included. A diversity ofSalmonellaserovars and sequence types were identified, and, in some cases, we found similar or identicalSalmonellaisolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission ofSalmonellaand AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.