bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel box for aerosol and droplet guarding and evacuation in respiratory infection (BADGER) for COVID-19 and future outbreaks
Authors: Le Hau D. , Novak Gordon A. , Janek Kevin C. , Wang Jesse , Huynh Khang N. , Myer Chris , Weinstein Adam , Oberstar Erick L. , Rasmussen Jim , Bertram Timothy H. 
Published: February 2021

AbstractThe coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected millions and killed more than 1.7 million people worldwide as of December 2020. Healthcare providers are at increased risk of infection when caring for patients with COVID-19. The mechanism of transmission of SARS-CoV-2 is beginning to emerge as airborne spread in addition to direct droplet and indirect contact as main routes of transmission. Here, we report on the design, construction, and testing of the BADGER (Box for Aerosol and Droplet Guarding and Evacuation in Respiratory Infection), an affordable, scalable device that contains droplets and aerosol particles, thus minimizing the risk of infection to healthcare providers. A semi-sealed environment is created inside the BADGER, which is placed over the head of the patient and maintains at least 12-air changes per hour using in-wall vacuum suction. Multiple hand-ports enable healthcare providers to perform essential tasks on a patient’s airway and head. Overall, the BADGER has the potential to contain large droplets and small airborne particles as demonstrated by simulated qualitative and quantitative assessments to provide an additional layer of protection for healthcare providers treating COVID-19 and future respiratory contagions.
Vertical distribution of soil available phosphorus and soil available potassium in the critical zone on the Loess Plateau, China
Authors: Tian Hanyang , Qiao Jiangbo , Zhu Yuanjun , Jia Xiaoxu , Shao Ming’an 
Published: February 2021

AbstractSoil available phosphorus (SAP) and soil available potassium (SAK) are important elements in the growth of plants. However, limited data are available regarding the vertical distribution of SAP and SAK in deep soil profiles. In this study, we investigated the vertical variations in SAP and SAK in the critical zone on the Loess Plateau (50–200 m), China, by using classical statistical and geostatistical methods. The soil samples were collected from the top of the soil profile down to the bedrock by soil core drilling at five typical sites. SAP decreased throughout the profile. Whereas the SAK exhibited an increasing trend at all sites. The mean SAP concentration ranged from 0.94 to 32.56 mg kg–1 at the sampling sites and the SAK concentration ranged from 44.51 to 229.31 mg kg–1. At all of the sampling sites, SAK was significantly positively correlated with the depth and clay content, but there was a significantly negative correlation between the SAK and the sand content. The exponential model could fit most variograms of SAP and SAK at all sampling sites. The results obtained in this study to improve our comprehension of the SAP or SAK distribution conditions on the Loess Plateau, which is important for reasonable fertilizer application and vegetation planting practices.
Pseudomonas eucalypticola sp. nov., a producer of antifungal agents isolated from Eucalyptus dunnii leaves
Authors: Liu Yujing , Song Zhang , Zeng Hualong , Lu Meng , Zhu Weiyao , Wang Xiaoting , Lian Xinkun , Zhang Qinghua 
Published: February 2021

AbstractPseudomonas are ubiquitously occurring microorganisms and are known for their ability to produce antimicrobials. An endophytic bacterial strain NP-1 T, isolated from Eucalyptus dunnii leaves, exhibits antifungal properties against five tested phytopathogenic fungi. The strain is a Gram-negative rod-shaped bacterium containing a single polar flagellum. It is strictly aerobic, grows at 4–37 °C, 2–5% NaCl, and pH 3–7. The 16S rRNA sequence analysis showed that NP-1 T belongs to the Pseudomonas genus. Phylogenetic analysis based on four concatenated partial genes (16S rDNA, gyrB, rpoB and rpoD) and the phylogenomic tree indicated that NP-1 T belongs to Pseudomonas fluorescens lineage but is distinct from any known Pseudomonas species. The G + C mol % of NP-1 T genome is 63.96, and the differences between NP-1 T and related species are larger than 1. The digital DNA-DNA hybridization and tetranucleotide signatures are 23.8 and 0.97, which clearly separates strain NP-1 T from its closest neighbours, Pseudomonas coleopterorum and Pseudomonas rhizosphaerae. Its phenotypic and chemotaxonomic features confirmed its differentiation from related taxa. The results from this polyphasic approach support the classification of NP-1 T as a novel species of Pseudomonas, and the name of Pseudomonas eucalypticola is thus proposed for this strain, whose type is NP-1 T (= CCTCC M2018494T = JCM 33572 T).
Long-term efficacy of triple semicircular canal plugging in the treatment of patients with ipsilateral delayed endolymphatic hydrops
Authors: Zhang Daogong , Lv Yafeng , Li Xiaofei , Li Yawei , Song Yongdong , Fan Zhaomin , Wang Haibo 
Published: February 2021

AbstractThis study aims to explore the long-term efficacy of triple semicircular canal plugging (TSCP) in the treatment of intractable ipsilateral delayed endolymphatic hydrops (DEH), so as to provide an alternative therapy for this disease. Forty-eight patients diagnosed with ipsilateral DEH referred to vertigo clinic of our hospital between Dec. 2010 and Dec. 2017, were included in this study for retrospective analysis. All patients were followed up for 2 years. Vertigo control and auditory functions were measured and analyzed. Pure tone audiometry, caloric test, and vestibular evoked myogenic potential (VEMP) were performed in two-year follow-up. Forty-five patients who accepted intratympanic gentamicin (26.7 mg/mL) twice given one week apart were selected as a control group. The total control rate of vertigo in TSCP group was 97.9% (47/48) in the two-year follow-up, with complete control rate of 83.3% (40/48) and substantial control rate of 14.6% (7/48). The rate of hearing loss was 22.9% (11/48). The total control rate of vertigo in intratympanic gentamicin group was 80.0% (36/45), with complete control rate of 57.8% (26/45) and substantial control rate of 22.2% (10/45), and the rate of hearing loss was 20.0% (9/45). The vertigo control rate of TSCP was significantly higher than that of intratympanic gentamicin (χ2 = 6.01, p < 0.05). There was no significant difference of hearing loss rate between two groups. (χ2 = 0.12, p > 0.05). TSCP, which can reduce vertiginous symptoms in patients with intractable ipsilateral DEH, represents an effective therapy for this disorder.
No evidence that monkeys attribute mental states to animated shapes in the Heider–Simmel videos
Authors: Schafroth Jamie L. , Basile Benjamin M. , Martin Alex , Murray Elisabeth A. 
Published: February 2021

AbstractHuman Theory of Mind (ToM) is so automatic and pervasive that we spontaneously attribute mental states to animated abstract shapes, as evidenced by the classic Heider–Simmel findings. The extent to which this represents a fundamental characteristic of primate social cognition is debated. Prior research suggests that monkeys spontaneously predict behavior and attribute basic goals to conspecifics, but it remains unclear whether, like humans, they spontaneously ascribe mental states to animated shapes. Here, we address this question by analyzing rhesus monkeys’ viewing patterns of the classic Heider–Simmel animations. We hypothesized that if rhesus monkeys also spontaneously attribute mental states to animated shapes, then, like humans, they would have the longest fixation durations for theory of mind animations, medium duration fixation for goal-directed animations, and shortest fixations for animations with random motion. In contrast, if attributing mental states to animations is specific to humans and perhaps other apes, then we predict no differences in looking time across animation categories. Unlike humans, monkeys did not fixate longer on ToM videos. Critically, monkeys’ viewing patterns did not correlate with humans’ viewing patterns or intentionality ratings from previously published research. The only major difference in viewing patterns between animation categories tracked differences in low-level visual motion. Thus, monkeys do not view the classic Heider–Simmel animations like humans do and we found no evidence that they spontaneously attribute mental states to animated shapes.
Correlative atom probe tomography and scanning transmission electron microscopy reveal growth sequence of LPSO phase in Mg alloy containing Al and Gd
Authors: Inoue Koji , Yoshida Kenta , Nagai Yasuyoshi , Kishida Kyosuke , Inui Haruyuki 
Published: February 2021

AbstractAtom probe tomography (APT) and transmission electron microscopy (TEM)/scanning transmission electron microscopy (STEM) have been used correlatively to explore atomic-scale local structure and chemistry of the exactly same area in the vicinity of growth front of a long-period stacking ordered (LPSO) phase in a ternary Mg–Al–Gd alloy. It is proved for the first time that enrichment of Gd atoms in four consecutive (0001) atomic layers precedes enrichment of Al atoms so that the formation of Al6Gd8 clusters occurs only after sufficient Al atoms to form Al6Gd8 clusters diffuse into the relevant portions. Lateral growth of the LPSO phase is found to occur by ‘ledge’ mechanism with the growth habit plane either {1$$\overline{1}$$

1
¯

00} or {11$$\overline{2}$$

2
¯

0} planes. The motion of ledges that give rise to lateral growth of the LPSO phase is considered to be controlled by diffusion of Al atoms.
Ensemble bias correction of climate simulations: preserving internal variability
Authors: Vaittinada Ayar Pradeebane , Vrac Mathieu , Mailhot Alain 
Published: February 2021

AbstractClimate simulations often need to be adjusted (i.e., corrected) before any climate change impacts studies. However usual bias correction approaches do not differentiate the bias from the different uncertainties of the climate simulations: scenario uncertainty, model uncertainty and internal variability. In particular, in the case of a multi-run ensemble of simulations (i.e., multiple runs of one model), correcting, as usual, each member separately, would mix up the model biases with its internal variability. In this study, two ensemble bias correction approaches preserving the internal variability of the initial ensemble are proposed. These “Ensemble bias correction” (EnsBC) approaches are assessed and compared to the approach where each ensemble member is corrected separately, using precipitation and temperature series at two locations in North America from a multi-member regional climate ensemble. The preservation of the internal variability is assessed in terms of monthly mean and hourly quantiles. Besides, the preservation of the internal variability in a changing climate is evaluated. Results show that, contrary to the usual approach, the proposed ensemble bias correction approaches adequately preserve the internal variability even in changing climate. Moreover, the climate change signal given by the original ensemble is also conserved by both approaches.
Addressing limited weight resolution in a fully optical neuromorphic reservoir computing readout
Authors: Ma Chonghuai , Laporte Floris , Dambre Joni , Bienstman Peter 
Published: February 2021

AbstractUsing optical hardware for neuromorphic computing has become more and more popular recently, due to its efficient high-speed data processing capabilities and low power consumption. However, there are still some remaining obstacles to realizing the vision of a completely optical neuromorphic computer. One of them is that, depending on the technology used, optical weighting elements may not share the same resolution as in the electrical domain. Moreover, noise of the weighting elements are important considerations as well. In this article, we investigate a new method for improving the performance of optical weighting components, even in the presence of noise and in the case of very low resolution. Our method utilizes an iterative training procedure and is able to select weight connections that are more robust to quantization and noise. As a result, even with only 8 to 32 levels of resolution, in noisy weighting environments, the method can outperform both nearest rounding low-resolution weighting and random rounding weighting by up to several orders of magnitude in terms of bit error rate and can deliver performance very close to full-resolution weighting elements.
Newborn screening of duchenne muscular dystrophy specifically targeting deletions amenable to exon-skipping therapy
Authors: Beckers Pablo , Caberg Jean-Hubert , Dideberg Vinciane , Dangouloff Tamara , den Dunnen Johan T. , Bours Vincent , Servais Laurent , Boemer François 
Published: February 2021

AbstractDuchenne Muscular Dystrophy (DMD) is a lethal progressive muscle-wasting disease. New treatment strategies relying on DMD gene exon-skipping therapy have recently been approved and about 30% of patients could be amenable to exon 51, 53 or 45 skipping. We evaluated the spectrum of deletions reported in DMD registries, and designed a method to screen newborns and identify DMD deletions amenable to exon 51, 53 and 45 skipping. We developed a multiplex qPCR assay identifying hemi(homo)-zygotic deletions of the flanking exons of these therapeutic targets in DMD exons (i.e. exons 44, 46, 50, 52 and 54). We conducted an evaluation of our new method in 51 male patients with a DMD phenotype, 50 female carriers of a DMD deletion and 19 controls. Studies were performed on dried blood spots with patient’s consent. We analyzed qPCR amplification curves of controls, carriers, and DMD patients to discern the presence or the absence of the target exons. Analysis of the exons flanking the exon-skipping targets permitted the identification of patients that could benefit from exon-skipping. All samples were correctly genotyped, with either presence or absence of amplification of the target exon. This proof-of-concept study demonstrates that this new assay is a highly sensitive method to identify DMD patients carrying deletions that are rescuable by exon-skipping treatment. The method is easily scalable to population-based screening. This targeted screening approach could address the new management paradigm in DMD, and could help to optimize the beneficial therapeutic effect of DMD therapies by permitting pre-symptomatic care.
microRNA let-7i-5p mediates the relationship between muscle fat infiltration and neck pain disability following motor vehicle collision: a preliminary study
Authors: Elliott James M. , Rueckeis Cathleen A. , Pan Yue , Parrish Todd B. , Walton David M. , Linnstaedt Sarah D. 
Published: February 2021

AbstractPersistent neck-pain disability (PNPD) is common following traumatic stress exposures such as motor vehicle collision (MVC). Substantial literature indicates that fat infiltration into neck muscle (MFI) is associated with post-MVC PNPD. However, little is known about the molecular mediators underlying this association. In the current study, we assessed whether microRNA expression signatures predict PNPD and whether microRNA mediate the relationship between neck MFI and PNPD. A nested cohort of 43 individuals from a longitudinal study of MVC survivors, who provided blood (PAXgene RNA) and underwent magnetic resonance imaging (MRI), were included in the current study. Peritraumatic microRNA expression levels were quantified via small RNA sequencing, neck MFI via MRI, and PNPD via the Neck Disability Index two-weeks, three-months, and twelve-months following MVC. Repeated measures regression models were used to assess the relationship between microRNA and PNPD and to perform mediation analyses. Seventeen microRNA predicted PNPD following MVC. One microRNA, let-7i-5p, mediated the relationship between neck MFI and PNPD. Peritraumatic blood-based microRNA expression levels predict PNPD following MVC and let-7i-5p might contribute to the underlying effects of neck MFI on persistent disability. In conclusion, additional studies are needed to validate this finding.
The enhancer activity of long interspersed nuclear element derived microRNA 625 induced by NF-κB
Authors: Lee Hee-Eun , Park Sang-Je , Huh Jae-Won , Imai Hiroo , Kim Heui-Soo 
Published: February 2021

AbstractTransposable elements (TEs) are DNA sequences that cut or introduced into the genome, and they represent a massive portion of the human genome. TEs generate a considerable number of microRNAs (miRNAs) are derived from TEs (MDTEs). Numerous miRNAs are related to cancer, and hsa-miRNA-625 is a well-known oncomiR derived from long interspersed nuclear elements (LINEs). The relative expression of hsa-miRNA-625-5p differs in humans, chimpanzees, crab-eating monkeys, and mice, and four primers were designed against the 3′UTR of GATAD2B to analyze the different quantities of canonical binding sites and the location of miRNA binding sites. Luciferase assay was performed to score for the interaction between hsa-miRNA-625 and the 3′UTR of GATAD2B, while blocking NF-κB. In summary, the different numbers of canonical binding sites and the locations of miRNA binding sites affect gene expression, and NF-κB induces the enhancer activity of hsa-miRNA-625-5p by sharing the binding sites.
Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA
Authors: Dunwell Thomas L. , Dailey Simon C. , Ottestad Anine L. , Yu Jihang , Becker Philipp W. , Scaife Sarah , Richman Susan D. , Wood Henry M. , Slaney Hayley , Bottomley Daniel , Yang Xiangsheng , Xiao Hui , Wahl Sissel G. F. , Grønberg Bjørn H. , Dai Hongyan , Fu Guoliang 
Published: February 2021

AbstractLiquid biopsy testing utilising Next Generation Sequencing (NGS) is rapidly moving towards clinical adoption for personalised oncology. However, before NGS can fulfil its potential any novel testing approach must identify ways of reducing errors, allowing separation of true low-frequency mutations from procedural artefacts, and be designed to improve upon current technologies. Popular NGS technologies typically utilise two DNA capture approaches; PCR and ligation, which have known limitations and seem to have reached a development plateau with only small, stepwise improvements being made. To maximise the ultimate utility of liquid biopsy testing we have developed a highly versatile approach to NGS: Adaptor Template Oligo Mediated Sequencing (ATOM-Seq). ATOM-Seq's strengths and versatility avoid the major limitations of both PCR- and ligation-based approaches. This technology is ligation free, simple, efficient, flexible, and streamlined, and it offers novel advantages that make it perfectly suited for use on highly challenging clinical material. Using reference and clinical materials, we demonstrate detection of known SNVs down to allele frequencies of 0.1% using as little as 20–25 ng of cfDNA, as well as the ability to detect fusions from RNA. We illustrate ATOM-Seq’s suitability for clinical testing by showing high concordance rates between paired cfDNA and FFPE clinical samples.
A simplified combined index of structure and function for detecting and staging glaucomatous damage
Authors: Wu Zhichao , Medeiros Felipe A. 
Published: February 2021

AbstractGlaucomatous damage results in characteristics structural and functional changes on optical coherence tomography (OCT) imaging and standard automated perimetry (SAP) testing. The clinical utility of these measures differs based on disease severity, as they are evaluated along different measurement scales. This study therefore sought to examine if a simplified combined structure–function index (sCSFI) could improve the detection and staging of glaucomatous damage, compared to the use of average retinal nerve fiber layer thickness (RNFL) measurements from OCT and mean deviation (MD) values from SAP alone, and also an estimated retinal ganglion cell counts (eRGC) measure derived using empirical formulas described previously. Examining 577 eyes from 354 participants with perimetric glaucoma and 241 normal eyes from 138 healthy participants, we found that the sCSFI performed significantly better than average RNFL, MD and eRGC count for discriminating between glaucoma and healthy eyes (P ≤ 0.008 for all). The sCSFI also performed significantly better than RNFL and eRGC count at discriminating between different levels of visual field damage in glaucoma eyes (P < 0.001 for both). These findings highlight the clinical utility of combining structural and functional information for detecting and staging glaucomatous damage using the simplified index developed in this study.
The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions
Authors: Lazcano Cristina , Boyd Eric , Holmes Gerald , Hewavitharana Shashika , Pasulka Alexis , Ivors Kelly 
Published: February 2021

AbstractMicrobial-root associations are important to help plants cope with abiotic and biotic stressors. Managing these interactions offers an opportunity for improving the efficiency and sustainability of agricultural production. By characterizing the bacterial and archaeal community (via 16S rRNA sequencing) associated with bulk and rhizosphere soil of sixteen strawberry cultivars in two controlled field studies, we explored the relationships between the soil microbiome and plant resistance to two soil-borne fungal pathogens (Verticillium dahliae and Macrophomina phaseolina). Overall, the plants had a distinctive and genotype-dependent rhizosphere microbiome with higher abundances of known beneficial bacteria such as Pseudomonads and Rhizobium. The rhizosphere microbiome played a significant role in the resistance to the two soil-borne pathogens as shown by the differences in microbiome between high and low resistance cultivars. Resistant cultivars were characterized by higher abundances of known biocontrol microorganisms including actinobacteria (Arthrobacter, Nocardioides and Gaiella) and unclassified acidobacteria (Gp6, Gp16 and Gp4), in both pathogen trials. Additionally, cultivars that were resistant to V. dahliae had higher rhizosphere abundances of Burkholderia and cultivars resistant to M. phaseolina had higher abundances of Pseudomonas. The mechanisms involved in these beneficial plant-microbial interactions and their plasticity in different environments should be studied further for the design of low-input disease management strategies.