bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq
Authors: Hahaut Vincent , Pavlinic Dinko , Carbone Walter , Schuierer Sven , Balmer Pierre , Quinodoz Mathieu , Renner Magdalena , Roma Guglielmo , Cowan Cameron S. , Picelli Simone 
Published: May 2022

AbstractWe present FLASH-seq (FS), a full-length single-cell RNA sequencing (scRNA-seq) method with increased sensitivity and reduced hands-on time compared to Smart-seq3. The entire FS protocol can be performed in ~4.5 hours, is simple to automate and can be easily miniaturized to decrease resource consumption. The FS protocol can also use unique molecular identifiers (UMIs) for molecule counting while displaying reduced strand-invasion artifacts. FS will be especially useful for characterizing gene expression at high resolution across multiple samples.
In utero origin of myelofibrosis presenting in adult monozygotic twins
Authors: Sousos Nikolaos , Ní Leathlobhair Máire , Simoglou Karali Christina , Louka Eleni , Bienz Nicola , Royston Daniel , Clark Sally-Ann , Hamblin Angela , Howard Kieran , Mathews Vikram , George Biju , Roy Anindita , Psaila Bethan , Wedge David C. , Mead Adam J. 
Published: May 2022

AbstractThe latency between acquisition of an initiating somatic driver mutation by a single-cell and clinical presentation with cancer is largely unknown. We describe a remarkable case of monozygotic twins presenting with CALR mutation-positive myeloproliferative neoplasms (MPNs) (aged 37 and 38 years), with a clinical phenotype of primary myelofibrosis. The CALR mutation was absent in T cells and dermal fibroblasts, confirming somatic acquisition. Whole-genome sequencing lineage tracing revealed a common clonal origin of the CALR-mutant MPN clone, which occurred in utero followed by twin-to-twin transplacental transmission and subsequent similar disease latency. Index sorting and single-colony genotyping revealed phenotypic hematopoietic stem cells (HSCs) as the likely MPN-propagating cell. Furthermore, neonatal blood spot analysis confirmed in utero origin of the JAK2V617F mutation in a patient presenting with polycythemia vera (aged 34 years). These findings provide a unique window into the prolonged evolutionary dynamics of MPNs and fitness advantage exerted by MPN-associated driver mutations in HSCs.
Using generative adversarial networks for genome variant calling from low depth ONT sequencing data
Authors: Yang Han , Gu Fei , Zhang Lei , Hua Xian-Sheng 
Published: May 2022

AbstractGenome variant calling is a challenging yet critical task for subsequent studies. Existing methods almost rely on high depth DNA sequencing data. Performance on low depth data drops a lot. Using public Oxford Nanopore (ONT) data of human being from the Genome in a Bottle (GIAB) Consortium, we trained a generative adversarial network for low depth variant calling. Our method, noted as LDV-Caller, can project high depth sequencing information from low depth data. It achieves 94.25% F1 score on low depth data, while the F1 score of the state-of-the-art method on two times higher depth data is 94.49%. By doing so, the price of genome-wide sequencing examination can reduce deeply. In addition, we validated the trained LDV-Caller model on 157 public Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples. The mean sequencing depth of these samples is 2982. The LDV-Caller yields 92.77% F1 score using only 22x sequencing depth, which demonstrates our method has potential to analyze different species with only low depth sequencing data.
Group VR experiences can produce ego attenuation and connectedness comparable to psychedelics
Authors: Glowacki David R. , Williams Rhoslyn Roebuck , Wonnacott Mark D. , Maynard Olivia M. , Freire Rachel , Pike James E. , Chatziapostolou Mike 
Published: May 2022

AbstractWith a growing body of research highlighting the therapeutic potential of experiential phenomenology which diminishes egoic identity and increases one’s sense of connectedness, there is significant interest in how to elicit such ‘self-transcendent experiences’ (STEs) in laboratory contexts. Psychedelic drugs (YDs) have proven particularly effective in this respect, producing subjective phenomenology which reliably elicits intense STEs. With virtual reality (VR) emerging as a powerful tool for constructing new perceptual environments, we describe a VR framework called ‘Isness-distributed’ (Isness-D) which harnesses the unique affordances of distributed multi-person VR to blur conventional self-other boundaries. Within Isness-D, groups of participants co-habit a shared virtual space, collectively experiencing their bodies as luminous energetic essences with diffuse spatial boundaries. It enables moments of ‘energetic coalescence’, a new class of embodied intersubjective experience where bodies can fluidly merge, enabling participants to include multiple others within their self-representation. To evaluate Isness-D, we adopted a citizen science approach, coordinating an international network of Isness-D 'nodes'. We analyzed the results (N = 58) using 4 different self-report scales previously applied to analyze subjective YD phenomenology (the inclusion of community in self scale, ego-dissolution inventory, communitas scale, and the MEQ30 mystical experience questionnaire). Despite the complexities associated with a distributed experiment like this, the Isness-D scores on all 4 scales were statistically indistinguishable from recently published YD studies, demonstrating that distributed VR can be used to design intersubjective STEs where people dissolve their sense of self in the connection to others.
Competition between Pseudomonas aeruginosa and Staphylococcus aureus is dependent on intercellular signaling and regulated by the NtrBC two-component system
Authors: Alford Morgan A. , Mann Simranpreet , Akhoundsadegh Noushin , Hancock Robert E. W. 
Published: May 2022

AbstractPseudomonas aeruginosa and Staphylococcus aureus are often comorbid human pathogens, isolated from expectorated sputum of cystic fibrosis patients and chronically infected wounds. Prior studies revealed a competitive advantage of P. aeruginosa over S. aureus in vitro that was slightly muted in vivo. Here, we demonstrated that the two-component regulatory system NtrBC influences the competitive advantage of P. aeruginosa over S. aureus in skin organoid and mouse models of co-infection. Expression of ntrBC was induced during co-culture of the two species and could be recapitulated in monoculture by the addition of the metabolite N-acetylglucosamine that is released from S. aureus following lysis. P. aeruginosa LESB58 WT, but not mutant (ΔntrC and ΔntrBC) strains, induced lysis of S. aureus USA300 LAC during planktonic growth and outcompeted S. aureus USA300 LAC during biofilm formation in vitro. We confirmed these findings in a murine abscess model of high-density infection. Accordingly, the secretory profile of P. aeruginosa LESB58 mutants revealed reduced production of anti-staphylococcal virulence factors including pyoverdine, pyocyanin and elastase. These phenotypes of LESB58 ΔntrBC could be at least partly complemented by overexpression of quorum sensing molecules including homoserine lactones or alkylquinolone signaling molecules. These data implicate the NtrBC two-component system in the complex regulatory cascade triggered by interspecies signaling that gives P. aeruginosa LESB58 a competitive edge over S. aureus USA300 LAC.
Metabolic responses of plankton to warming during different productive seasons in coastal Mediterranean waters revealed by in situ mesocosm experiments
Authors: Soulié Tanguy , Vidussi Francesca , Courboulès Justine , Mas Sébastien , Mostajir Behzad 
Published: May 2022

AbstractThe response of coastal lagoon plankton communities to warming was studied during two in situ mesocosm experiments in spring and fall of 2018 in the Mediterranean. Phytoplankton biomass, gross primary production (GPP), community respiration (R), phytoplankton growth (µ), and loss (l) rates were estimated using high-frequency chlorophyll-a fluorescence and dissolved oxygen sensors, and daily sampling was used to evaluate the nutrient status and phytoplankton pigment functional groups. Warming strongly depressed the dominant phytoplankton functional groups, mainly the prymnesiophytes, diatoms (spring), and green flagellates (fall). It favored minor groups such as the dinoflagellates (spring) and diatoms (fall). In spring, warming depressed GPP and R by half; however, µ (+ 18%) and l (+ 37%) were enhanced. In contrast, both GPP and µ were enhanced by 21% and 28%, respectively, in fall, and no effects were observed for R and l. Warming strongly decreased phytoplankton biomass and oxygen production in spring, and enhanced them, to a lesser extent, in fall. This led to an overall loss of production over both seasons. This study improves understanding of the contrasting effects of warming during two productive seasons, which depend on plankton community composition and interactions between components and environmental conditions.
Online education and the mental health of faculty during the COVID-19 pandemic in Japan
Authors: Kita Yosuke , Yasuda Shoko , Gherghel Claudia 
Published: May 2022

AbstractWhile the negative impact of the pandemic on students’ mental health has been studied around the world, very little is known about the mental health of faculty and staff. This research aims to examine mental health among Japanese faculty members who taught online courses during the COVID-19 pandemic. We recruited 537 university faculty members and assessed their mental health using the World Health Organization-Five Well-Being Index (WHO-5), both retrospectively (during the academic year before the onset of the pandemic) and during the pandemic. We also evaluated workload (number of online lectures taught and preparation time per class), difficulty in using information technology (IT) for online classes, and satisfaction with the university support service for online education. As a result, the WHO-5 score during the COVID-19 pandemic was significantly lower than before, and 33.5% of the faculty members were recognized as being at risk for mental illness during the COVID-19 pandemic. A binomial logistic regression analysis revealed two significant risk factors for mental illness—faculty members were more at risk for mental illness when they experienced difficulty in using IT for online classes, and were unsatisfied with the administrative support for online education. The deterioration of mental health during the COVID-19 was not predicted by workload, such as the number of online lectures and preparation time. These results suggest the importance of improving workplace support services, especially IT support, to prevent mental health deterioration among faculty teaching online.
Improved in-vivo airway gene transfer via magnetic-guidance, with protocol development informed by synchrotron imaging
Authors: Donnelley Martin , Cmielewski Patricia , Morgan Kaye , Delhove Juliette , Reyne Nicole , McCarron Alexandra , Rout-Pitt Nathan , Drysdale Victoria , Carpentieri Chantelle , Spiers Kathryn , Takeuchi Akihisa , Uesugi Kentaro , Yagi Naoto , Parsons David 
Published: May 2022

AbstractGene vectors to treat cystic fibrosis lung disease should be targeted to the conducting airways, as peripheral lung transduction does not offer therapeutic benefit. Viral transduction efficiency is directly related to the vector residence time. However, delivered fluids such as gene vectors naturally spread to the alveoli during inspiration, and therapeutic particles of any form are rapidly cleared via mucociliary transit. Extending gene vector residence time within the conducting airways is important, but hard to achieve. Gene vector conjugated magnetic particles that can be guided to the conducting airway surfaces could improve regional targeting. Due to the challenges of in-vivo visualisation, the behaviour of such small magnetic particles on the airway surface in the presence of an applied magnetic field is poorly understood. The aim of this study was to use synchrotron imaging to visualise the in-vivo motion of a range of magnetic particles in the trachea of anaesthetised rats to examine the dynamics and patterns of individual and bulk particle behaviour in-vivo. We also then assessed whether lentiviral-magnetic particle delivery in the presence of a magnetic field increases transduction efficiency in the rat trachea. Synchrotron X-ray imaging revealed the behaviour of magnetic particles in stationary and moving magnetic fields, both in-vitro and in-vivo. Particles could not easily be dragged along the live airway surface with the magnet, but during delivery deposition was focussed within the field of view where the magnetic field was the strongest. Transduction efficiency was also improved six-fold when the lentiviral-magnetic particles were delivered in the presence of a magnetic field. Together these results show that lentiviral-magnetic particles and magnetic fields may be a valuable approach for improving gene vector targeting and increasing transduction levels in the conducting airways in-vivo.
SARS-CoV-2 RNA in exhaled air of hospitalized COVID-19 patients
Authors: Kurver Lisa , van den Kieboom Corné H. , Lanke Kjerstin , Diavatopoulos Dimitri A. , Overheul Gijs J. , Netea Mihai G. , ten Oever Jaap , van Crevel Reinout , Mulders-Manders Karin , van de Veerdonk Frank L. , Wertheim Heiman , Schouten Jeroen , Rahamat-Langendoen Janette , van Rij Ronald P. , Bousema Teun , van Laarhoven Arjan , de Jonge Marien I. 
Published: May 2022

AbstractKnowledge about contagiousness is key to accurate management of hospitalized COVID-19 patients. Epidemiological studies suggest that in addition to transmission through droplets, aerogenic SARS-CoV-2 transmission contributes to the spread of infection. However, the presence of virus in exhaled air has not yet been sufficiently demonstrated. In pandemic situations low tech disposable and user-friendly bedside devices are required, while commercially available samplers are unsuitable for application in patients with respiratory distress. We included 49 hospitalized COVID-19 patients and used a disposable modular breath sampler to measure SARS-CoV-2 RNA load in exhaled air samples and compared these to SARS-CoV-2 RNA load of combined nasopharyngeal throat swabs and saliva. Exhaled air sampling using the modular breath sampler has proven feasible in a clinical COVID-19 setting and demonstrated viral detection in 25% of the patients.
The melanopsin-mediated pupil response is reduced in idiopathic hypersomnia with long sleep time
Authors: Rach Héloïse , Kilic-Huck Ulker , Reynaud Eve , Hugueny Laurence , Peiffer Emilie , Roy de Belleplaine Virginie , Fuchs Fanny , Bourgin Patrice , Geoffroy Pierre A. 
Published: May 2022

AbstractIdiopathic hypersomnia (IH), characterized by an excessive day-time sleepiness, a prolonged total sleep time on 24 h and/or a reduced sleep latency, affects 1 in 2000 individuals from the general population. However, IH remains underdiagnosed and inaccurately treated despite colossal social, professional and personal impacts. The pathogenesis of IH is poorly known, but recent works have suggested possible alterations of phototransduction. In this context, to identify biomarkers of IH, we studied the Post-Illumination Pupil Response (PIPR) using a specific pupillometry protocol reflecting the melanopsin-mediated pupil response in IH patients with prolonged total sleep time (TST > 660 min) and in healthy subjects. Twenty-eight patients with IH (women 86%, 25.4 year-old ± 4.9) and 29 controls (women 52%, 27.1 year-old ± 3.9) were included. After correction on baseline pupil diameter, the PIPR was compared between groups and correlated to sociodemographic and sleep parameters. We found that patients with IH had a lower relative PIPR compared to controls (32.6 ± 9.9% vs 38.5 ± 10.2%, p = 0.037) suggesting a reduced melanopsin response. In addition, the PIPR was not correlated to age, chronotype, TST, nor depressive symptoms. The melanopsin-specific PIPR may be an innovative trait marker of IH and the pupillometry might be a promising tool to better characterize hypersomnia.
Changes in plant biodiversity facets of rocky outcrops and their surrounding rangelands across precipitation and soil gradients
Authors: Rafiee Fahime , Ejtehadi Hamid , Farzam Mohammad , Zare Habib , Bashirzadeh Maral 
Published: May 2022

AbstractClimate and soil factors induce substantial controls over plant biodiversity in stressful ecosystems. Despite of some studies on plant biodiversity in extreme ecosystems including rocky outcrops, simultaneous effects of climate and soil factors have rarely been studied on different facets of biodiversity including taxonomic and functional diversity in these ecosystems. In addition, we know little about plant biodiversity variations in such extreme ecosystems compared to natural environments. It seems that environmental factors acting in different spatial scales specifically influence some facets of plant biodiversity. Therefore, we studied changes in taxonomic and functional diversity along precipitation and soil gradients in both landscapes (i) rocky outcrops and (ii) their nearby rangeland sites in northeast of Iran. In this regard, we considered six sites across precipitation and soil gradients in each landscape, and established 90 1m2 quadrates in them (i.e. 15 quadrats in each site; 15 × 6 = 90 in each landscape). Then, taxonomic and functional diversity were measured using RaoQ index, FDis and CWM indices. Finally, we assessed impacts of precipitation and soil factors on biodiversity indices in both landscapes by performing regression models and variation partitioning procedure. The patterns of taxonomic diversity similarly showed nonlinear changes along the precipitation and soil factors in both landscapes (i.e. outcrop and rangeland). However, we found a more negative and significant trends of variation in functional diversity indices (except for CWMSLA) across precipitation and soil factors in outcrops than their surrounding rangelands. Variations of plant biodiversity were more explained by precipitation factors in surrounding rangelands, whereas soil factors including organic carbon had more consistent and significant effects on plant biodiversity in outcrops. Therefore, our results represent important impacts of soil factors in structuring plant biodiversity facets in stressful ecosystems. While, environmental factors acting in regional and broad scales such as precipitation generally shape vegetation and plant biodiversity patterns in natural ecosystems. We can conclude that rocky outcrops provide suitable microenvironments to present plant species with similar yields that are less able to be present in rangeland ecosystems.
Visible-NIR hyperspectral classification of grass based on multivariate smooth mapping and extreme active learning approach
Authors: Zhao Xuanhe , Pan Xin , Yan Weihong , Zhang Shengwei 
Published: May 2022

AbstractGrass community classification is the basis for the development of animal husbandry and dynamic monitoring of environment, which has become a critical problem to further strengthen the intelligent management of grassland. Compared with grass survey based on satellite remote sensing, the visible near infrared (NIR) hyperspectral not only monitor dynamically in a short distance, but also have high dimensions and detailed spectral information in each pixel. However, the hyperspectral labeled sample for classification is expensive and manual selection is more subjective. In order to solve above limitations, we proposed a visible-NIR hyperspectral classification model for grass based on multivariate smooth mapping and extreme active learning (MSM–EAL). Firstly, MSM is used to preprocess and reconstruct the spectrum. Secondly, by jointing XGBoost and active learning (AL), the advanced samples with the largest amount of information are actively selected to improve the performance of target classification. Innovation lies in: (1) MSM global enhanced preprocessing spectral reconstruction algorithm is proposed, in which isometric feature mapping is effectively applied to the grass hyperspectral for the first time. (2) EAL framework is constructed to solve the issue of high cost and small number for hyperspectral labeled samples, at the same time, enhance the physical essence behind spectral classification more intuitively. A field hyperspectral collection platform is assembled to establish nm resolution visible-NIR hyperspectral dataset of grass, Grass1, containing 750 samples, which to verify the effectiveness of the model. Experiments on the Grass1 dataset confirmed that compared with the full spectrum, the time consumption of MSM was reduced by 9.471 s with guaranteed overall accuracy (OA). Comparing EAL with AL, and other classification algorithms, EAL improves OA 22.2% over AL, and XAL has the best performance value on Kappa, Macro, Recall and F1-score, respectively. Altogether, the lightweight MSM–EAL model realizes intelligent and real-time classification, providing a new method for obtaining high-precision inter group classification of grass.
Analysis of multiple databases identifies crucial genes correlated with prognosis of hepatocellular carcinoma
Authors: Lin Zhifeng , Huang Xuqiong , Ji Xiaohui , Tian Nana , Gan Yu , Ke Li 
Published: May 2022

AbstractDespite advancements made in the therapeutic strategies on hepatocellular carcinoma (HCC), the survival rate of HCC patient is not satisfactory enough. Therefore, there is an urgent need for the valuable prognostic biomarkers in HCC therapy. In this study, we aimed to screen hub genes correlated with prognosis of HCC via multiple databases. 117 HCC-related genes were obtained from the intersection of the four databases. We subsequently identify 10 hub genes (JUN, IL10, CD34, MTOR, PTGS2, PTPRC, SELE, CSF1, APOB, MUC1) from PPI network by Cytoscape software analysis. Significant differential expression of hub genes between HCC tissues and adjacent tissues were observed in UALCAN, HCCDB and HPA databases. These hub genes were significantly associated with immune cell infiltrations and immune checkpoints. The hub genes were correlated with clinical parameters and survival probability of HCC patients. 147 potential targeted therapeutic drugs for HCC were identified through the DGIdb database. These hub genes could be used as novel prognostic biomarkers for HCC therapy.