bluuebunny/crossref_metadata_2025 huggingface dataset:
Immunomodulatory lipid mediator profiling of cerebrospinal fluid following surgery in older adults
Authors: Terrando Niccolò , Park John J. , Devinney Michael , Chan Cliburn , Cooter Mary , Avasarala Pallavi , Mathew Joseph P. , Quinones Quintin J. , Maddipati Krishna Rao , Berger Miles ,   for the MADCO-PC Study Team, Brigman Brian , Browndyke Jeffrey , Bullock William M. , Carter Jessica , Chapman Joseph , Colin Brian , D’Amico Thomas A. , DeOrio James K. , Esclamado Ramon M. , Ferrandino Michael N. , Gadsden Jeffrey , Garrigues Grant E. , Guercio Jason , Habib Ashraf , Harpole David H. , Hartwig Mathew G. , Iboaya Ehimemen , Inman Brant A. , Khan Anver , Lagoo-Deenadayalan Sandhya , Lee Paula S. , Lee Walter T. , Lemm John , Levinson Howard , Mantyh Christopher , McDonagh David L. , Migaly John , Mithani Suhail K. , Moretti Eugene , Moul Judd W. , Newman Mark F. , Ohlendorf Brian , Perez Alexander , Peterson Andrew C. , Preminger Glenn M. , Robertson Cary N. , Roman Sanziana A. , Runyon Scott , Sandler Aaron , Sbahi Faris M. , Scheri Randall P. , Smith S. Kendall , Talbot Leonard , Thacker Julie K. M. , Thomas Jake , Tong Betty C. , Vaslef Steven N. , Waldron Nathan , Wang Xueyuan , Young Christopher
Published: February 2021

Arachidonic acid (AA), docosahexaenoic acid (DHA), and eicosapentaenoic acid (EPA) derived lipids play key roles in initiating and resolving inflammation. Neuro-inflammation is thought to play a causal role in perioperative neurocognitive disorders, yet the role of these lipids in the human central nervous system in such disorders is unclear. Here we used liquid chromatography–mass spectrometry to quantify AA, DHA, and EPA derived lipid levels in non-centrifuged cerebrospinal fluid (CSF), centrifuged CSF pellets, and centrifuged CSF supernatants of older adults obtained before, 24 h and 6 weeks after surgery. GAGE analysis was used to determine AA, DHA and EPA metabolite pathway changes over time. Lipid mediators derived from AA, DHA and EPA were detected in all sample types. Postoperative lipid mediator changes were not significant in non-centrifuged CSF (p > 0.05 for all three pathways). The AA metabolite pathway showed significant changes in centrifuged CSF pellets and supernatants from before to 24 h after surgery (p = 0.0000247, p = 0.0155 respectively), from before to 6 weeks after surgery (p = 0.0000497, p = 0.0155, respectively), and from 24 h to 6 weeks after surgery (p = 0.0000499, p = 0.00363, respectively). These findings indicate that AA, DHA, and EPA derived lipids are detectable in human CSF, and the AA metabolite pathway shows postoperative changes in centrifuged CSF pellets and supernatants.
Metabolic profiling of historical and modern wheat cultivars using proton nuclear magnetic resonance spectroscopy
Authors: Poudel Rachana , Bhinderwala Fatema , Morton Martha , Powers Robert , Rose Devin J.
Published: February 2021

To determine changes in the grain components between historical and modern wheat (Triticum aestivumL.) cultivars, wholemeal flours from 19 wheat cultivars and 2 landraces released or introduced between 1870 and 2013 and grown over two crop years were extracted using hydroalcoholic solution and analyzed using one dimensional1H NMR spectral profiling. Grain yield, grain volume weight (GVW), and grain protein concentration were also measured. Grain yield increased while protein concentration decreased by release year (p < 0.001). Increasing trends (p < 0.01) were observed for tryptophan, sum of the measured amino acids, chlorogenic acid, ferulic acid, vanillic acid, and sum of the measured phenolic acids. Grain yield, phenolic acids, and tryptophan were mainly associated with modern cultivars, whereas grain protein concentration and GVW were associated with historical cultivars. The findings from this study showed changes in concentration of grain components over a century of breeding that may have implications for grain quality and human health.
Western listeners detect boundary hierarchy in Indian music: a segmentation study
Authors: Popescu Tudor , Widdess Richard , Rohrmeier Martin
Published: February 2021

How are listeners able to follow and enjoy complex pieces of music? Several theoretical frameworks suggest links between the process of listening and the formal structure of music, involving a division of the musical surface into structural units at multiple hierarchical levels. Whether boundaries between structural units are perceivable to listeners unfamiliar with the style, and are identified congruently between naïve listeners and experts, remains unclear. Here, we focused on the case of Indian music, and asked 65 Western listeners (of mixed levels of musical training; most unfamiliar with Indian music) to intuitively segment into phrases a recording of sitar ālāp of two different rāga-modes. Each recording was also segmented by two experts, who identified boundary regions at section and phrase levels. Participant- and region-wise scores were computed on the basis of "clicks" inside or outside boundary regions (hits/false alarms), inserted earlier or later within those regions (high/low "promptness"). We found substantial agreement—expressed as hit rates and click densities—among participants, and between participants' and experts' segmentations. The agreement and promptness scores differed between participants, levels, and recordings. We found no effect of musical training, but detected real-time awareness of grouping completion and boundary hierarchy. The findings may potentially be explained by underlying general bottom-up processes, implicit learning of structural relationships, cross-cultural musical similarities, or universal cognitive capacities.
Association between low potassium intake and the number of teeth in Korean adults: based on the national data (2013–2015)
Authors: Kim Eun-Jeong , Lee Hye-Ju
Published: February 2021

General health and oral health are very closely related. This study aimed to analyze the nutritional factors associated with the number of present teeth in Korean elderly adults. A total of 6,356 individuals were surveyed from the sixth Korean National Health and Nutrition Examination Survey conducted from 2013–2015. The number of existing teeth was divided into three categories: 0–10, 11–20, and over 21, and the nutrition survey covers eating habits, food frequency and food intake using face-to-face interviews. Multiple logistic regression analysis was performed to evaluate the association between nutrient intake and the number of existing teeth after adjusting for socio-demographic factors and general and oral health behaviors and status. As age increases, the number of teeth decreases. Individuals with more teeth had a significantly higher mean daily intake of protein, calcium, phosphorus, potassium and riboflavin (p < 0.05). After adjusting for sociodemographic factors in model 1 and the lower number of teeth in model 2, the strength of the association between the number of teeth and daily calcium intake remained significant. Statistically significant associations were present for dietary potassium intake in models 1 and 2 and in the 11–20 teeth group in model 3 (p < 0.05). We demonstrated a significant association between calcium and potassium intake and the number of teeth.
The G127V variant of the prion protein interferes with dimer formation in vitro but not in cellulo
Authors: Sangeetham Sudheer Babu , Engelke Anna Dorothee , Fodor Elfrieda , Krausz Sarah Laura , Tatzelt Jörg , Welker Ervin
Published: February 2021

Scrapie prion, PrPSc, formation is the central event of all types of transmissible spongiform encephalopathies (TSEs), while the pathway with possible intermediates and their mechanism of formation from the normal isoform of prion (PrP), remains not fully understood. Recently, the G127V variant of the human PrP is reported to render the protein refractory to transmission of TSEs, via a yet unknown mechanism. Molecular dynamics studies suggested that this mutation interferes with the formation of PrP dimers. Here we analyze the dimerization of 127G and 127VPrP, in both in vitro and a mammalian cell culture system. Our results show that while molecular dynamics may capture the features affecting dimerization in vitro, G127V inhibiting dimer formation of PrP, these are not evidenced in a more complex cellular system.
Accurate spectra for high energy ions by advanced time-of-flight diamond-detector schemes in experiments with high energy and intensity lasers
Authors: Salvadori Martina , Consoli F. , Verona C. , Cipriani M. , Anania M. P. , Andreoli P. L. , Antici P. , Bisesto F. , Costa G. , Cristofari G. , De Angelis R. , Di Giorgio G. , Ferrario M. , Galletti M. , Giulietti D. , Migliorati M. , Pompili R. , Zigler A.
Published: February 2021

Time-Of-Flight (TOF) methods are very effective to detect particles accelerated in laser-plasma interactions, but they show significant limitations when used in experiments with high energy and intensity lasers, where both high-energy ions and remarkable levels of ElectroMagnetic Pulses (EMPs) in the radiofrequency-microwave range are generated. Here we describe a novel advanced diagnostic method for the characterization of protons accelerated by intense matter interactions with high-energy and high-intensity ultra-short laser pulses up to the femtosecond and even future attosecond range. The method employs a stacked diamond detector structure and the TOF technique, featuring high sensitivity, high resolution, high radiation hardness and high signal-to-noise ratio in environments heavily affected by remarkable EMP fields. A detailed study on the use, the optimization and the properties of a single module of the stack is here described for an experiment where a fast diamond detector is employed in an highly EMP-polluted environment. Accurate calibrated spectra of accelerated protons are presented from an experiment with the femtosecond Flame laser (beyond 100 TW power and ~ 1019 W/cm2intensity) interacting with thin foil targets. The results can be readily applied to the case of complex stack configurations and to more general experimental conditions.
Temperature and species-dependent regulation of browning in retrobulbar fat
Authors: Rajaii Fatemeh , Kim Dong Won , Pan Jianbo , Mahoney Nicholas R. , Eberhart Charles G. , Qian Jiang , Blackshaw Seth
Published: February 2021

Retrobulbar fat deposits surround the posterior retina and optic nerve head, but their function and origin are obscure. We report that mouse retrobulbar fat is a neural crest-derived tissue histologically and transcriptionally resembles interscapular brown fat. In contrast, human retrobulbar fat closely resembles white adipose tissue. Retrobulbar fat is also brown in other rodents, which are typically housed at temperatures below thermoneutrality, but is white in larger animals. We show that retrobulbar fat in mice housed at thermoneutral temperature show reduced expression of the brown fat marker Ucp1, and histological properties intermediate between white and brown fat. We conclude that retrobulbar fat can potentially serve as a site of active thermogenesis, that this capability is both temperature and species-dependent, and that this may facilitate regulation of intraocular temperature.
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

The 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

Soil 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

Pseudomonas 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

This 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

Human 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

Atom 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

Climate 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

Using 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

Duchenne 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

Persistent 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

Transposable 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

Liquid 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

Glaucomatous 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

Microbial-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.
The mitotic checkpoint is a targetable vulnerability of carboplatin-resistant triple negative breast cancers
Authors: Moens Stijn , Zhao Peihua , Baietti Maria Francesca , Marinelli Oliviero , Van Haver Delphi , Impens Francis , Floris Giuseppe , Marangoni Elisabetta , Neven Patrick , Annibali Daniela , Sablina Anna A. , Amant Frédéric
Published: February 2021

Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype, lacking effective therapy. Many TNBCs show remarkable response to carboplatin-based chemotherapy, but often develop resistance over time. With increasing use of carboplatin in the clinic, there is a pressing need to identify vulnerabilities of carboplatin-resistant tumors. In this study, we generated carboplatin-resistant TNBC MDA-MB-468 cell line and patient derived TNBC xenograft models. Mass spectrometry-based proteome profiling demonstrated that carboplatin resistance in TNBC is linked to drastic metabolism rewiring and upregulation of anti-oxidative response that supports cell replication by maintaining low levels of DNA damage in the presence of carboplatin. Carboplatin-resistant cells also exhibited dysregulation of the mitotic checkpoint. A kinome shRNA screen revealed that carboplatin-resistant cells are vulnerable to the depletion of the mitotic checkpoint regulators, whereas the checkpoint kinases CHEK1 and WEE1 are indispensable for the survival of carboplatin-resistant cells in the presence of carboplatin. We confirmed that pharmacological inhibition of CHEK1 by prexasertib in the presence of carboplatin is well tolerated by mice and suppresses the growth of carboplatin-resistant TNBC xenografts. Thus, abrogation of the mitotic checkpoint by CHEK1 inhibition re-sensitizes carboplatin-resistant TNBCs to carboplatin and represents a potential strategy for the treatment of carboplatin-resistant TNBCs.
Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19 infection
Authors: Teo Alvin Kuo Jing , Choudhury Yukti , Tan Iain Beehuat , Cher Chae Yin , Chew Shi Hao , Wan Zi Yi , Cheng Lionel Tim Ee , Oon Lynette Lin Ean , Tan Min Han , Chan Kian Sing , Hsu Li Yang
Published: February 2021

We aimed to test the sensitivity of naso-oropharyngeal saliva and self-administered nasal (SN) swab compared to nasopharyngeal (NP) swab for COVID-19 testing in a large cohort of migrant workers in Singapore. We also tested the utility of next-generation sequencing (NGS) for diagnosis of COVID-19. Saliva, NP and SN swabs were collected from subjects who presented with acute respiratory infection, their asymptomatic roommates, and prior confirmed cases who were undergoing isolation at a community care facility in June 2020. All samples were tested using RT-PCR. SARS-CoV-2 amplicon-based NGS with phylogenetic analysis was done for 30 samples. We recruited 200 subjects, of which 91 and 46 were tested twice and thrice respectively. In total, 62.0%, 44.5%, and 37.7% of saliva, NP and SN samples were positive. Cycle threshold (Ct) values were lower during the earlier period of infection across all sample types. The percentage of test-positive saliva was higher than NP and SN swabs. We found a strong correlation between viral genome coverage by NGS and Ct values for SARS-CoV-2. Phylogenetic analyses revealed Clade O and lineage B.6 known to be circulating in Singapore. We found saliva to be a sensitive and viable sample for COVID-19 diagnosis.
Auditory beat perception is related to speech output fluency in post-stroke aphasia
Authors: Stefaniak James D. , Lambon Ralph Matthew A. , De Dios Perez Blanca , Griffiths Timothy D. , Grube Manon
Published: February 2021

Aphasia affects at least one third of stroke survivors, and there is increasing awareness that more fundamental deficits in auditory processing might contribute to impaired language performance in such individuals. We performed a comprehensive battery of psychoacoustic tasks assessing the perception of tone pairs and sequences across the domains of pitch, rhythm and timbre in 17 individuals with post-stroke aphasia and 17 controls. At the level of individual differences we demonstrated a correlation between metrical pattern (beat) perception and speech output fluency with strong effect (Spearman’s rho = 0.72). This dissociated from more basic auditory timing perception, which did not correlate with output fluency. This was also specific in terms of the language and cognitive measures, amongst which phonological, semantic and executive function did not correlate with beat detection. We interpret the data in terms of a requirement for the analysis of the metrical structure of sound to construct fluent output, with both being a function of higher-order “temporal scaffolding”. The beat perception task herein allows measurement of timing analysis without any need to account for motor output deficit, and could be a potential clinical tool to examine this. This work suggests strategies to improve fluency after stroke by training in metrical pattern perception.
Particle size and cholesterol content of circulating HDL correlate with cardiovascular death in chronic heart failure
Authors: Teis Albert , Cediel G. , Amigó N. , Julve J. , Aranyó J. , Andrés-Cordón J. , Puig-Jové C. , Castelblanco E. , Gual-Capllonch F. , Ferrer-Sistach E. , Vallejo N. , Juncà G. , López-Ayerbe J. , De Antonio M. , Domingo M. , Santiago-Vacas E. , Codina P. , Mauricio D. , Lupón J. , Alonso Nuria , Bayes-Genis A.
Published: February 2021

Evidence regarding any association of HDL-particle (HDL-P) derangements and HDL-cholesterol content with cardiovascular (CV) death in chronic heart failure (HF) is lacking. To investigate the prognostic value of HDL-P size (HDL-Sz) and the number of cholesterol molecules per HDL-P for CV death in HF patients. Outpatient chronic HF patients were enrolled. Baseline HDL-P number, subfractions and HDL-Sz were measured using 1H-NMR spectroscopy. The HDL-C/P ratio was calculated as HDL-cholesterol over HDL-P. Endpoint was CV death, with non-CV death as the competing event. 422 patients were included and followed-up during a median of 4.1 (0–8) years. CV death occurred in 120 (30.5%) patients. Mean HDL-Sz was higher in CV dead as compared with survivors (8.39 nm vs. 8.31 nm, p < 0.001). This change in size was due to a reduction in the percentage of small HDL-P (54.6% vs. 60% for CV-death vs. alive; p < 0.001). HDL-C/P ratio was higher in the CV-death group (51.0 vs. 48.3, p < 0.001). HDL-Sz and HDL-C/P ratio were significantly associated with CV death after multivariable regression analysis (HR 1.22 [95% CI 1.01–1.47], p = 0.041 and HR 1.04 [95% CI 1.01–1.07], p = 0.008 respectively). HDL-Sz and HDL-C/P ratio are independent predictors of CV death in chronic HF patients.
Identifications of immune-responsive genes for adaptative traits by comparative transcriptome analysis of spleen tissue from Kazakh and Suffolk sheep
Authors: Yang Hua , Yang Yong-Lin , Li Guo-Qing , Yu Qian , Yang Jinzeng
Published: February 2021

Aridity and heat are significant environmental stressors that affect sheep adaptation and adaptability, thus influencing immunity, growth, reproduction, production performance, and profitability. The aim of this study was to profile mRNA expression levels in the spleen of indigenous Kazakh sheep breed for comparative analysis with the exotic Suffolk breed. Spleen histomorphology was observed in indigenous Kazakh sheep and exotic Suffolk sheep raised in Xinjiang China. Transcriptome sequencing of spleen tissue from the two breeds were performed via Illumina high-throughput sequencing technology and validated by RT-qPCR. Blood cytokine and IgG levels differed between the two breeds and IgG and IL-1β were significantly higher in Kazakh sheep than in Suffolk sheep (p < 0.05), though spleen tissue morphology was the same. A total of 52.04 Gb clean reads were obtained and the clean reads were assembled into 67,271 unigenes using bioinformatics analysis. Profiling analysis of differential gene expression showed that 1158 differentially expressed genes were found when comparing Suffolk with Kazakh sheep, including 246 up-regulated genes and 912 down-regulated genes. Utilizing gene ontology annotation and pathway analysis, 21 immune- responsive genes were identified as spleen-specific genes associated with adaptive traits and were significantly enriched in hematopoietic cell lineage, natural killer cell-mediated cytotoxicity, complement and coagulation cascades, and in the intestinal immune network for IgA production. Four pathways and up-regulated genes associated with immune responses in indigenous sheep played indispensable and promoting roles in arid and hot environments. Overall, this study provides valuable transcriptome data on the immunological mechanisms related to adaptive traits in indigenous and exotic sheep and offers a foundation for research into adaptive evolution.
Transverse susceptibility of nickel thin films with uniaxial anisotropy
Authors: Mathews Scott A. , Musi Christopher , Charipar Nicholas
Published: February 2021

A finite temperature Stoner–Wohlfarth model has been used to calculate the transverse susceptibility of an ensemble of ferromagnetic particles with distributed anisotropy. The simulated transverse susceptibility is in excellent agreement with data acquired from thin film samples of elemental nickel, deposited on 128° Y-cut LiNb03. A strong, well-defined, uniaxial anisotropy is induced in the nickel film by low temperature annealing. Three peaks in the transverse susceptibility are observed in both the measured and simulated data when the applied field is misaligned with the hard axis by a few degrees. Two broad, reversible peaks occur when the applied field is equal to the anisotropy field. A single, sharp irreversible peak occurs when the absolute value of the applied field is less than the anisotropy field, and is associated with a metastable magnetic state. The irreversible peak disappears when the applied field is well aligned with the hard axis. The observed transverse susceptibility is consistent with the theoretical predictions of Aharoni et al.and is therefore consistent with the Stoner–Wohlfarth model.
Mutated clones driving leukemic transformation are already detectable at the single-cell level in CD34-positive cells in the chronic phase of primary myelofibrosis
Authors: Parenti Sandra , Rontauroli Sebastiano , Carretta Chiara , Mallia Selene , Genovese Elena , Chiereghin Chiara , Peano Clelia , Tavernari Lara , Bianchi Elisa , Fantini Sebastian , Sartini Stefano , Romano Oriana , Bicciato Silvio , Tagliafico Enrico , Della Porta Matteo , Manfredini Rossella
Published: February 2021

Disease progression of myeloproliferative neoplasms is the result of increased genomic complexity. Since the ability to predict disease evolution is crucial for clinical decisions, we studied single-cell genomics and transcriptomics of CD34-positive cells from a primary myelofibrosis (PMF) patient who progressed to acute myeloid leukemia (AML) while receiving Ruxolitinib. Single-cell genomics allowed the reconstruction of clonal hierarchy and demonstrated that TET2 was the first mutated gene while FLT3 was the last one. Disease evolution was accompanied by increased clonal heterogeneity and mutational rate, but clones carrying TP53 and FLT3 mutations were already present in the chronic phase. Single-cell transcriptomics unraveled repression of interferon signaling suggesting an immunosuppressive effect exerted by Ruxolitinib. Moreover, AML transformation was associated with a differentiative block and immune escape. These results suggest that single-cell analysis can unmask tumor heterogeneity and provide meaningful insights about PMF progression that might guide personalized therapy.
Simultaneous sensing of cysteine/homocysteine and glutathione with a fluorescent probe based on a single atom replacement strategy
Authors: Yao Jingfeng , Yin Guoxing , Yu Ting , Li Haitao , Yin Peng
Published: February 2021

Novel and simple fluorescent probes are utilized for the simultaneous monitor of Cys/Hcy and GSH.
Identifying a Li-rich superionic conductor from charge–discharge structural evolution study: Li2MnO3
Authors: Zhang Xiaofeng , Zheng Feng , Wu Shunqing , Zhu Zizhong
Published: February 2021

As Li2MnO3 transforms from monoclinic phase to trigonal phase, the diffusion rate of Li ions has been significantly improved.
Improvement of NOx uptake/release over Pd/Beta by propylene: shielding effect of intermediates on adsorbed NOx species
Authors: Liu Chao , Wang Jun , Chen Zexiang , Wang Jianqiang , Shen Meiqing
Published: February 2021

A novel chemistry about NOx adsorption and desorption in the presence of C3H6 was proposed, where the intermediate Pd–NC3H6O played an important role.
Study of the removal of ciprofloxacin by Zn–GO@SA aerogel microspheres
Authors: Li Kaijia , Ou Hongxiang , Zhou Dongsheng , Gong Chenxia , Xue Honglai , Li Yuyan
Published: February 2021

Zn–GO@SA aerogel microspheres were prepared via a simple ionic–gel method, showing excellent adsorption performance toward ciprofloxacin and easy separation from solution.
Alcohol-soluble fluorene derivate functionalized with pyridyl groups as a high-performance cathode interfacial material in organic solar cells
Authors: Lin Lin , Huang Zeping , Luo Yuanqi , Peng Tingen , He Baitian , Chen Guiting , Hao Hongqing , Li Xin , Cai Ping , Yang Wei
Published: February 2021

The synthesis and application as a cathode interlayer in organic photovoltaics of a fluorene derivative with pyridyl functional chains are presented.
Magnetic field effect on the photocatalytic degradation of methyl orange by commercial TiO2 powder
Authors: Bian Yuecheng , Zheng Ganhong , Ding Wei , Hu Lin , Sheng Zhigao
Published: February 2021

In this work, by taking commercial P25 hydrophilic titanium dioxide (TiO2) as a photocatalyst, the magnetic field effect (MFE) on the photodegradation rate of methyl orange is studied.
Simple, green, ultrasound-assisted preparation of novel core–shell microcapsules from octyl methoxycinnamate and oligomeric proanthocyanidins for UV-stable sunscreen
Authors: Song Jie , Chen Siqi , Zhao Xu , Cheng Junbo , Ma Yanli , Ren Shixue , Li Shujun
Published: February 2021

With oligomeric proanthocyanidins (OPCs) as the outer shell and ultraviolet absorbers (OMC) as the inner core, OMC/OPCs composite microcapsules were prepared and characterized, and their UV resistance was studied.