bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling aquifer storage and recovery in the eastern district of the United Arab Emirates using MODFLOW
Authors: Khalil Karim , Khan Qasim , Mohamed Mohamed
Published: October 2022

The Emirate of Abu Dhabi has relied on groundwater as a source of fresh water for several decades, which has resulted in the deterioration of non-renewable groundwater aquifers. This has led to the installation of desalination plants for fresh water supply. This research aims to increase strategic water reserves in the eastern district of Abu Dhabi by analyzing the best locations for aquifer storage and recovery (ASR). The ASR technology offers an opportunity to store large volumes of water for later beneficial use. This study explores an option of using excess desalination water for ASR recharge in the eastern district Al Ain region of Abu Dhabi. A limiting factor in the application of the ASR technology is the lack of suitable sites. Detailed hydrogeological and operational knowledge of the studied areas helped in identifying potential sites for ASR based on a scoring system. Determining best locations for managed aquifer recharge is a crucial design step. Five scenarios were studied at Al-Khrair and Al-Shuwaib sites in Al Ain region. Results show that a wider distribution of injection wells with intervals more than 1200 m is more suitable to overcome the excessive head buildup. Based on the adopted criteria, Al-Khrair was the best site for recharge followed by Al-Shuwaib. Al-Khrair site can be recharged at 64,000 m3 d−1 for seven years, while Al-Shuwaib site can be recharged at 64,000 m3 d−1 for only two years.
Chemical forms of cadmium in soil and its distribution in French marigold sub-cells in response to chelator GLDA
Authors: Li Hongchuan , Kong Deming , Zhang Borui , Kalkhajeh Yusef Kianpoor , Zhao Yingying , Huang Jieying , Hu Hongxiang
Published: October 2022

The use of degradable chelating agents to facilitate phytoextraction is a promising low-cost method for the remediation of heavy metal-contaminated soils. However, there are few studies on how plants and soils respond to the chelating agents. In this study, the responses of French marigold (Tagetes patula L.) and soil cadmium (Cd) to the chelator tetrasodium glutamate (GLDA) was investigated in a 180 d field trial. Five GLDA treatments (0, 292.5, 585, 1170, and 2340 kg hm−2) were carried out in a Cd-contaminated soil (0.47 mg kg−1) under French marigold plantation. The results showed that the application of GLDA promoted the transformation of other forms of Cd in soil to exchangeable state, and the exchangeable Cd and Fe–Mn oxide bound state increased by 42.13% and 32.97% (p < 0.05), respectively. The cell wall Cd accumulations significantly increased 9.39% (p < 0.05) and the percentages of soluble fractions increased by 460.33% (p < 0.05). Furthermore, increases occurred in soil pH, as well as DOC and DTPA-Cd contents with increasing the total amount of GLDA. The composite application of GLDA (2340 kg hm−2) with French marigold reduced the total soil Cd content by 7.59% compared with the soil background. Altogether, results of this study suggested that the application of GLDA can effectively activate soil Cd and enhance the capability of French marigold for the remediation of Cd-contaminated soils.
Extended visuomotor experience with inverted movements can overcome the inversion effect in biological motion perception
Authors: Wang Xiaoye Michael , Wilson Margaret A. , Song Yu , Ma Gulandanmu , Dong Mingkai , Zhu Qin
Published: October 2022

Studies have demonstrated that perceiving human and animal movements as point-light displays is effortless. However, simply inverting the display can significantly impair this ability. Compared to non-dancers and typical dancers, vertical dancers have the unique experience of observing and performing movements upside down as being suspended in the air. We studied whether this unique visuomotor experience makes them better at perceiving the inverted movements. We presented ten pairs of dance movements as point-light displays. Each pair included a version performed on the ground whereas the other was in the air. We inverted the display in half of the trials and asked vertical dancers, typical dancers, and non-dancers about whether the display was inverted. We found that only vertical dancers, who have extended visual and motor experience with the configural and dynamic information of the movements, could identify the inversion of movements performed in the air. Neither typical dancers nor non-dancers, who have no motor experience with performing the inverted movements, could detect the inversion. Our findings suggest that motor experience plays a more critical role in enabling the observers to use dynamic information for identifying artificial inversion in biological motion.
The genomic response of human granulosa cells (KGN) to melatonin and specific agonists/antagonists to the melatonin receptors
Authors: Arjoune Asma , Sirard Marc-André
Published: October 2022

Melatonin is a known modulator of follicle development; it acts through several molecular cascades via binding to its two specific receptors MT1 and MT2. Even though it is believed that melatonin can modulate granulosa cell (GC) functions, there is still limited knowledge of how it can act in human GC through MT1 and MT2 and which one is more implicated in the effects of melatonin on the metabolic processes in the dominant follicle. To better characterize the roles of these receptors on the effects of melatonin on follicular development, human granulosa-like tumor cells (KGN) were treated with specific melatonin receptor agonists and antagonists, and gene expression was analyzed with RNA-seq technology. Following appropriate normalization and the application of a fold change cut-off of 1.5 (FC 1.5, p ≤ 0.05) for each treatment, lists of the principal differentially expressed genes (DEGs) are generated. Analysis of major upstream regulators suggested that the MT1 receptor may be involved in the melatonin antiproliferative effect by reprogramming the metabolism of human GC by activating the PKB signaling pathway. Our data suggest that melatonin may act complementary through both MT1 and MT2 receptors to modulate human GC steroidogenesis, proliferation, and differentiation. However, MT2 receptors may be the ones implicated in transducing the effects of melatonin on the prevention of GC luteinization and follicle atresia at the antral follicular stage through stimulating the PKA pathway.
Epigenetic impact of a 1-week intensive multimodal group program for adolescents with multiple adverse childhood experiences
Authors: Kaliman Perla , Cosín-Tomás Marta , Madrid Andy , Roque López Susana , Llanez-Anaya Elkin , Papale Ligia A. , Alisch Reid S. , Davidson Richard J.
Published: October 2022

Adverse childhood experiences (ACEs, i.e., abuse, neglect, household dysfunction) represent a potential risk factor for a wide range of long-lasting diseases and shorter life expectancy. We recently described a 1-week residential group program, based on mindfulness training, artistic expression and EMDR group therapy, that significantly reduced PTSD-related symptoms and increased attention/awareness-related outcomes in adolescent girls with multiple ACEs in a randomized controlled study. Since epigenetic mechanisms (i.e., DNA methylation) have been associated with the long-lasting effects of ACEs, the present report extends these prior findings by exploring genome-wide DNA methylation changes following the program. Saliva samples from all participants (n = 44) were collected and genomic DNA was extracted prior (T1) and following (T2) the intervention. Genome-wide DNA methylation analysis using the MethylationEPIC beadchip array (Illumina) revealed 49 differentially methylated loci (DML; p value < 0.001; methylation change > 10%) that were annotated to genes with roles in biological processes linked to early childhood adversity (i.e., neural, immune, and endocrine pathways, cancer and cardiovascular disease). DNA sequences flanking these DML showed significant enrichment of transcription factor binding sites involved in inflammation, cancer, cardiovascular disease, and brain development. Methylation changes in SIRT5 and TRAPPC2L genes showed associations with changes in trauma-related psychological measures. Results presented here suggest that this multimodal group program for adolescents with multiple victimization modulates the DNA methylome at sites of potential relevance for health and behavioral disorders associated with ACEs.
Quantitatively evaluate the impact of domestic aviation control measures on the spread of COVID-19 in China
Authors: Wang Yu , Li Ke , Yuan Ting , Liu Yi
Published: October 2022

To quantitatively evaluate the impact of domestic aviation control measures on the spread of COVID-19 in China. The number of international flights from March to September 2019 simulated the number of flights from March to September 2020 without implementing aviation control measures. In addition, the proportion of asymptomatic persons and the delay in case reporting were adjusted to estimate the prevalence of each country during the same period and calculate the estimated imported cases. The estimated imported cases were assigned each day with weight, and the estimated daily reported cases were obtained based on the actual daily number of domestic cases in China. Effective Reproduction Number ($$R_t$$Rt) was calculated based on delayed distribution, Basic Reproductive Number ($$R_0$$R0) distribution, and generation time distribution were reported in previous studies. Gaussian Process was used to estimate the effect of time-varying on$$R_t$$Rt, and the estimated$$R_t$$Rtwas compared with the actual$$R_t$$Rt. The estimated imported cases increased significantly compared with the actual number of imported cases. The estimated imported cases were mainly concentrated in North America and Europe from March to April and gradually increased in many East Asian countries from May to September. The difference between predicted$$R_t$$Rtand actual$$R_t$$Rtwas statistically significant. The estimated imported cases and the estimated$$R_t$$Rthave increased compared to the actual situation. This paper quantitatively proves that Chinese aviation control measures significantly suppress the COVID-19 epidemic, which is conducive to promoting and applying this measure.
Counts of hyaluronic acid-containing extracellular vesicles decrease in naturally occurring equine osteoarthritis
Authors: Mustonen Anne-Mari , Lehmonen Nina , Oikari Sanna , Capra Janne , Raekallio Marja , Mykkänen Anna , Paakkonen Tommi , Rilla Kirsi , Niemelä Tytti , Nieminen Petteri
Published: October 2022

Osteoarthritis (OA) is a degenerative joint disease with inadequately understood pathogenesis leading to pain and functional limitations. Extracellular vesicles (EVs) released by synovial joint cells can induce both pro- and anti-OA effects. Hyaluronic acid (HA) lubricates the surfaces of articular cartilage and is one of the bioactive molecules transported by EVs. In humans, altered EV counts and composition can be observed in OA synovial fluid (SF), while EV research is in early stages in the horse—a well-recognized OA model. The aim was to characterize SF EVs and their HA cargo in 19 horses. SF was collected after euthanasia from control, OA, and contralateral metacarpophalangeal joints. The SF HA concentrations and size distribution were determined with a sandwich-type enzyme-linked sorbent assay and size-exclusion chromatography. Ultracentrifugation followed by nanoparticle tracking analysis (NTA) were utilized to quantify small EVs, while confocal laser scanning microscopy (CLSM) and image analysis characterized larger EVs. The number and size distribution of small EVs measured by NTA were unaffected by OA, but these results may be limited by the lack of hyaluronidase pre-treatment of the samples. When visualized by CLSM, the number and proportion of larger HA-containing EVs (HA–EVs) decreased in OA SF (generalized linear model, count:p = 0.024, %:p = 0.028). There was an inverse association between the OA grade and total EV count, HA–EV count, and HA–EV % (rs = – 0.264 to – 0.327,p = 0.012–0.045). The total HA concentrations were also lower in OA (generalized linear model,p = 0.002). To conclude, the present study discovered a potential SF biomarker (HA–EVs) for naturally occurring equine OA. The roles of HA–EVs in the pathogenesis of OA and their potential as a joint disease biomarker and therapeutic target warrant future studies.
Individual-based modeling reveals that the COVID-19 isolation period can be shortened by community vaccination
Authors: Sararat Chayanin , Wangkanai Jidchanok , Wilasang Chaiwat , Chantanasaro Tanakorn , Modchang Charin
Published: October 2022

The isolation of infected individuals and quarantine of their contacts are usually employed to mitigate the transmission of SARS-CoV-2. Although 14-day isolation of infected individuals could effectively reduce the risk of subsequent transmission, it also substantially impacts the patient's psychological and emotional well-being. It is, therefore, vital to investigate how the isolation duration could be shortened when effective vaccines are available. Here, an individual-based modeling approach was employed to estimate the likelihood of secondary infections and the likelihood of an outbreak following the isolation of a primary case for a range of isolation periods. Our individual-based model integrated the viral loads and infectiousness profiles of vaccinated and unvaccinated infected individuals. The effects of waning vaccine-induced immunity against infection were also considered. By simulating the transmission of the SARS-CoV-2 Delta (B.1.617.2) variant in a community, we found that in the baseline scenario in which all individuals were unvaccinated and nonpharmaceutical interventions were not used, there was an approximately 3% chance that an unvaccinated individual would lead to at least one secondary infection after being isolated for 14 days, and a sustained chain of transmission could occur with a less than 1% chance. With the outbreak risk equivalent to that of the 14-day isolation in the baseline scenario, we found that the isolation duration could be shortened to 7.33 days (95% CI 6.68–7.98) if 75% of people in the community were fully vaccinated with the BNT162b2 vaccine within the last three months. In the best-case scenario in which all individuals in the community are fully vaccinated, isolation of Delta variant-infected individuals may no longer be necessary. However, to keep the outbreak risk lower than 1%, a booster vaccination may be necessary three months after full vaccination.
High throughput screening of mesenchymal stem cell lines using deep learning
Authors: Kim Gyuwon , Jeon Jung Ho , Park Keonhyeok , Kim Sung Won , Kim Do Hyun , Lee Seungchul
Published: October 2022

Mesenchymal stem cells (MSCs) are increasingly used as regenerative therapies for patients in the preclinical and clinical phases of various diseases. However, the main limitations of such therapies include functional heterogeneity and the lack of appropriate quality control (QC) methods for functional screening of MSC lines; thus, clinical outcomes are inconsistent. Recently, machine learning (ML)-based methods, in conjunction with single-cell morphological profiling, have been proposed as alternatives to conventional in vitro/vivo assays that evaluate MSC functions. Such methods perform in silico analyses of MSC functions by training ML algorithms to find highly nonlinear connections between MSC functions and morphology. Although such approaches are promising, they are limited in that extensive, high-content single-cell imaging is required; moreover, manually identified morphological features cannot be generalized to other experimental settings. To address these limitations, we propose an end-to-end deep learning (DL) framework for functional screening of MSC lines using live-cell microscopic images of MSC populations. We quantitatively evaluate various convolutional neural network (CNN) models and demonstrate that our method accurately classifies in vitro MSC lines to high/low multilineage differentiating stress-enduring (MUSE) cells markers from multiple donors. A total of 6,120 cell images were obtained from 8 MSC lines, and they were classified into two groups according to MUSE cell markers analyzed by immunofluorescence staining and FACS. The optimized DenseNet121 model showed area under the curve (AUC) 0.975, accuracy 0.922, F1 0.922, sensitivity 0.905, specificity 0.942, positive predictive value 0.940, and negative predictive value 0.908. Therefore, our DL-based framework is a convenient high-throughput method that could serve as an effective QC strategy in future clinical biomanufacturing processes.
De novo transcriptome assembly of Conium maculatum L. to identify candidate genes for coniine biosynthesis
Authors: Peddinti Gopal , Hotti Hannu , Teeri Teemu H. , Rischer Heiko
Published: October 2022

Poison hemlock (Conium maculatum L.) is a notorious weed containing the potent alkaloid coniine. Only some of the enzymes in the coniine biosynthesis have so far been characterized. Here, we utilize the next-generation RNA sequencing approach to report the first-ever transcriptome sequencing of five organs of poison hemlock: developing fruit, flower, root, leaf, and stem. Using a de novo assembly approach, we derived a transcriptome assembly containing 123,240 transcripts. The assembly is deemed high quality, representing over 88% of the near-universal ortholog genes of the Eudicots clade. Nearly 80% of the transcripts were functionally annotated using a combination of three approaches. The current study focuses on describing the coniine pathway by identifying in silico transcript candidates for polyketide reductase, l-alanine:5-keto-octanal aminotransferase, γ-coniceine reductase, and S-adenosyl-l-methionine:coniine methyltransferase. In vitro testing will be needed to confirm the assigned functions of the selected candidates.
Comparison of fractal and grid electrodes for studying the effects of spatial confinement on dissociated retinal neuronal and glial behavior
Authors: Moslehi Saba , Rowland Conor , Smith Julian H. , Griffiths Willem , Watterson William J. , Niell Cristopher M. , Alemán Benjamín J. , Perez Maria-Thereza , Taylor Richard P.
Published: October 2022

Understanding the impact of the geometry and material composition of electrodes on the survival and behavior of retinal cells is of importance for both fundamental cell studies and neuromodulation applications. We investigate how dissociated retinal cells from C57BL/6J mice interact with electrodes made of vertically-aligned carbon nanotubes grown on silicon dioxide substrates. We compare electrodes with different degrees of spatial confinement, specifically fractal and grid electrodes featuring connected and disconnected gaps between the electrodes, respectively. For both electrodes, we find that neuron processes predominantly accumulate on the electrode rather than the gap surfaces and that this behavior is strongest for the grid electrodes. However, the ‘closed’ character of the grid electrode gaps inhibits glia from covering the gap surfaces. This lack of glial coverage for the grids is expected to have long-term detrimental effects on neuronal survival and electrical activity. In contrast, the interconnected gaps within the fractal electrodes promote glial coverage. We describe the differing cell responses to the two electrodes and hypothesize that there is an optimal geometry that maximizes the positive response of both neurons and glia when interacting with electrodes.
Modelling of the dilated sagittal sinuses found in multiple sclerosis suggests increased wall stiffness may be a contributing factor
Authors: Bateman Grant Alexander , Lechner-Scott Jeannette , Bateman Alexander Robert
Published: October 2022

The cross-sectional area of the superior sagittal sinus (SSS) is larger in multiple sclerosis than normal and correlates with disease severity and progression. The sinus could be enlarged due to a decrease in the pressure difference between the lumen and the subarachnoid space, an increase in wall thickness or increased wall stiffness. The cross-sectional area of the SSS and straight sinus (ST) were measured in 103 patients with multiple sclerosis and compared to 50 controls. The cross-sectional area of the SSS and ST were increased by 20% and 13% compared to the controls (p = 0.005 and 0.02 respectively). The deflection of the wall of the sinus was estimated. The change in pressure gradient, wall thickness or elastic modulus between groups was calculated by modelling the walls as simply supported beams. To account for these findings, the modelling suggests either a 70% reduction in transmural venous pressure or a 2.4 fold increase in SSS wall stiffness plus an 11% increase in wall thickness or a combination of changes. An increase in sinus pressure, although the most straight forward possibility to account for the change in sinus size may exist in only a minority of patients. An increase in sinus wall stiffness and thickness may need further investigation.
Developmental changes in action-outcome regularity perceptual sensitivity and its relationship to hand motor function in 5–16-year-old children
Authors: Nobusako Satoshi , Wen Wen , Nagakura Yusuke , Tatsumi Mitsuyo , Kataoka Shin , Tsujimoto Taeko , Sakai Ayami , Yokomoto Teruyuki , Takata Emiko , Furukawa Emi , Asano Daiki , Osumi Michihiro , Nakai Akio , Morioka Shu
Published: October 2022

Along with the comparator model, the perception of action-outcome regularity is involved in the generation of sense of agency. In addition, the perception of action-outcome regularity is related to motor performance. However, no studies have examined the developmental changes in the perception of action-outcome regularity. The current study measured perceptual sensitivity to action-outcome regularity and manual dexterity in 200 children aged between 5 and 16 years. The results showed that perceptual sensitivity to action-outcome regularity was significantly lower in 5–6-year-old children than in 9–16-year-old children, and that it was significantly lower in children with low manual dexterity than in children with medium to high manual dexterity. Correlation analyses revealed significant correlations of age and perceptual sensitivity to action-outcome regularity, but no significant correlation of manual dexterity and perceptual sensitivity to action-outcome regularity, either overall or in any age band. The present study suggests that perceptual sensitivity to action-outcome regularity is immature at 5–6 years of age and that it may be impaired in 5–16-year-old children with poor manual dexterity.
Influencing factors of coking coal dust explosion pressure and flame and effect of inert dust on its explosion suppression
Authors: Liu Tianqi , Zhao Xuan , Tian Weiye , Jia Ruiheng , Wang Ning , Cai Zhixin
Published: October 2022

Coking coal is a precious resource in the world and an important raw material for the production of steel, but it is easy to cause explosion accidents in the process of coking coal mining, which is very detrimental to safe production. In order to reveal the influencing factors of coking coal dust explosion intensity and the suppression effect of inert dust on coking coal dust explosion, an experimental study was carried out in this paper. The results show that the particle size and the mass concentration of coal dust have a great influence on the explosion pressure and flame. By analyzing the suppression effects of NaCl, KCl, and NH4H2PO4 on coking coal dust explosion, it is got that NH4H2PO4 has the best explosion suppression effect. When the mass percentage of NH4H2PO4 mixed into coking coal dust increases to 60%, the maximum explosion pressure decreases by 0.47 MPa, and the maximum flame length decreases by 0.50 m. As the particle size of NH4H2PO4 decreases, the explosion intensity continue to decrease. When the particle size of NH4H2PO4 is 0 ~ 25 μm, and the mass percentage of NH4H2PO4 mixed into coking coal dust is 50%, the explosion doesn’t occur anymore.
Sarcopenia and mortality risk in community-dwelling Brazilian older adults
Authors: Pereira Cristina Camargo , Pagotto Valéria , de Oliveira Cesar , Silveira Erika Aparecida
Published: October 2022

We estimated the impact of sarcopenia parameters on mortality risk and assessed its prevalence and associated factors in the older adults according to the European Working Group on Sarcopenia in Older People’s 2010 (EWGSOP1) and 2018 (EWGSOP2) criteria. This was a 10-year follow-up cohort study. Low muscle mass (MM) was defined as low skeletal muscle mass index (SMI) using dual-energy X-ray absorptiometry (DXA), and low calf circumference (CC). Cox regression and the Kaplan–Meier method were performed. The prevalence of sarcopenia and associated factors were influenced by the MM measurement method and diagnostic criteria used [6.8% (SMI and EWGSOP2), 12.8% (CC and EWGSOP2; and SMI and EWGSOP1) and 17.4% (CC and EWGSOP1)]. While a low BMI was associated with sarcopenia regardless of the sarcopenia definitions, diabetes, and high TGs were associated with sarcopenia only when using the EWGSOP1 criteria. Low SMI increased mortality risk (EWGSOP1: HR = 2.01, 95% CI 1.03–3.92; EWGSOP2: HR = 2.07, 95% CI 1.05–4.06). The prevalence of sarcopenia was higher according to EWGSOP1 than EWGSOP2. A low BMI, diabetes, and high TGs were associated with sarcopenia. A low SMI doubled the risk of mortality in community-dwelling older adults.
Sociodemographic characteristics and health-related quality of life of individuals undergoing antidepressant therapy
Authors: Alfaifi Abdullah A. , Althemery Abdullah U.
Published: October 2022

An important factor for averting depression and creating awareness about clinical treatment is patient preference. Therefore, investigating health-related quality of life associated with different antidepressants is necessary. A retrospective cohort study was performed using the 2018 Medical Expenditure Panel Survey. The MEPS is a nationally representative database of the civilian and noninstitutionalized population spanning different ages, both sexes, and a wide range of sociodemographic and economic backgrounds. Differences in clinical and sociodemographic characteristics among patients using different antidepressant classes were explored. The differences in Veterans RAND 12-Item Health Survey (VR-12) results among groups were examined. The VR-12 metric was used since it measures a patient’s overall perspective of their health. Approximately 34.6 million of the patients reported using at least one antidepressant during 2018. Most patients receiving tricyclic therapy reported substantially better mental HRQoL than patients receiving selective serotonin reuptake inhibitors (SSRIs), serotonin-norepinephrine reuptake inhibitors (SNRIs), or combination therapy. Patients receiving atypical antidepressants reported substantially better mental HRQoL than those receiving other types of antidepressants. Most patients reported a substantial decline in HRQoL after SNRIs or combination therapy. This study found that HRQoL varied across antidepressant users. Thus, health care providers could benefit from taking into consideration quality of life when prescribing antidepressant agents. Moreover, further research is needed to explore other factors that could contribute to the quality of care for patients with depression.
Recapitulation of the embryonic transcriptional program in holometabolous insect pupae
Authors: Ozerova Alexandra M. , Gelfand Mikhail S.
Published: October 2022

Holometabolous insects are predominantly motionless during metamorphosis, when no active feeding is observed and the body is enclosed in a hardened cuticle. These physiological properties as well as undergoing processes resemble embryogenesis, since at the pupal stage organs and systems of the imago are formed. Therefore, recapitulation of the embryonic expression program during metamorphosis could be hypothesized. To assess this hypothesis at the transcriptome level, we have performed a comprehensive analysis of the developmental datasets available in the public domain. Indeed, for most datasets, the pupal gene expression resembles the embryonic rather than the larval pattern, interrupting gradual changes in the transcriptome. Moreover, changes in the transcriptome profile during the pupa-to-imago transition are positively correlated with those at the embryo-to-larvae transition, suggesting that similar expression programs are activated. Gene sets that change their expression level during the larval stage and revert it to the embryonic-like state during the metamorphosis are enriched with genes associated with metabolism and development.
A comprehensive evaluation of polygenic score and genotype imputation performances of human SNP arrays in diverse populations
Authors: Nguyen Dat Thanh , Tran Trang T. H. , Tran Mai Hoang , Tran Khai , Pham Duy , Duong Nguyen Thuy , Nguyen Quan , Vo Nam S.
Published: October 2022

Regardless of the overwhelming use of next-generation sequencing technologies, microarray-based genotyping combined with the imputation of untyped variants remains a cost-effective means to interrogate genetic variations across the human genome. This technology is widely used in genome-wide association studies (GWAS) at bio-bank scales, and more recently, in polygenic score (PGS) analysis to predict and stratify disease risk. Over the last decade, human genotyping arrays have undergone a tremendous growth in both number and content making a comprehensive evaluation of their performances became more important. Here, we performed a comprehensive performance assessment for 23 available human genotyping arrays in 6 ancestry groups using diverse public and in-house datasets. The analyses focus on performance estimation of derived imputation (in terms of accuracy and coverage) and PGS (in terms of concordance to PGS estimated from whole-genome sequencing data) in three different traits and diseases. We found that the arrays with a higher number of SNPs are not necessarily the ones with higher imputation performance, but the arrays that are well-optimized for the targeted population could provide very good imputation performance. In addition, PGS estimated by imputed SNP array data is highly correlated to PGS estimated by whole-genome sequencing data in most cases. When optimal arrays are used, the correlations of PGS between two types of data are higher than 0.97, but interestingly, arrays with high density can result in lower PGS performance. Our results suggest the importance of properly selecting a suitable genotyping array for PGS applications. Finally, we developed a web tool that provides interactive analyses of tag SNP contents and imputation performance based on population and genomic regions of interest. This study would act as a practical guide for researchers to design their genotyping arrays-based studies. The tool is available at:https://genome.vinbigdata.org/tools/saa/.
Sugar-terminated carbon-nanodots stimulate osmolyte accumulation and ROS detoxification for the alleviation of salinity stress in Vigna radiata
Authors: Sarkar Mahima Misti , Pradhan Nibedita , Subba Rewaj , Saha Puja , Roy Swarnendu
Published: October 2022

In recent times, nanotechnology has emerged as an efficient tool to manage the adverse effect of environmental stresses on plants. In this connection, carbon-nanodots (CNDs) have been reported to ameliorate the negative impacts of salinity stress. Further, surface modification of CNDs is believed to augment their stress-alleviating potential, however, very little has been known about the potential of surface-functionalized CNDs. In this purview, two sugar (trehalose and glucose) terminated CNDs (CNPT and CNPG) have been synthesized and assessed for their stress-alleviating effects onVigna radiata(a salt-sensitive legume) seedlings subjected to different concentrations of NaCl (0, 50, and 100 mM). The synthesized CNDs (CNPT and CNPG) exhibited a hydrodynamic size of 20–40 nm and zeta potential of up to − 22 mV with a 5–10 nm core. These water-soluble nanomaterials exhibited characteristic fluorescence emission properties viz.orange and greenish-yellow for CNPT and CNPG respectively. The successful functionalization of the sugar molecules on the CND cores was further confirmed using FTIR, XRD, and AFM. The results indicated that the application of both the CNDs improved seed germination, growth, pigment content, ionic and osmotic balance, and most importantly, the antioxidant defense which decreased ROS accumulation. At the same time, CNPT and CNPG exhibited no toxicity in theAllium ceparoot tip bioassay. Therefore, it can be concluded that sugar-terminated CNDs improved the plant responses to salinity stress by facilitating sugar uptake to the aerial part of the seedlings.
Attention neuroenhancement through tDCS or neurofeedback: a randomized, single-blind, controlled trial
Authors: Rêgo Gabriel Gaudencio , Gonçalves Óscar F. , Boggio Paulo Sérgio
Published: October 2022

Neurofeedback and transcranial Direct Current Stimulation (tDCS) are promising techniques for neuroenhancement of attentional performance. As far as we know no study compared both techniques on attentional performance in healthy participants. We compared tDCS and neurofeedback in a randomized, single-blind, controlled experiment assessing both behavioral (accuracy and time reaction) and electrophysiological (N1, P1, and P3 components) data of participants responding to the Attention Network Task (ANT). Eighty volunteers volunteered for this study. We adopted standard protocols for both techniques, i.e., a Sensorimotor Rhythm (SMR) protocol for neurofeedback and the right DLPFC anodal stimulation for tDCS, applied over nine sessions (two weeks). We did not find significant differences between treatment groups on ANT, neither at the behavioral nor at the electrophysiological levels. However, we found that participants from both neuromodulation groups, irrespective of if active or sham, reported attentional improvements in response to the treatment on a subjective scale. Our study adds another null result to the neuromodulation literature, showing that neurofeedback and tDCS effects are more complex than previously suggested and associated with placebo effect. More studies in neuroenhancement literature are necessary to fully comprehend neuromodulation mechanisms.
A critical path to producing high quality, reproducible data from quantitative western blot experiments
Authors: Taylor Sean C. , Rosselli-Murai Luciana K. , Crobeddu Bélinda , Plante Isabelle
Published: October 2022

Western blotting experiments were initially performed to detect a target protein in a complex biological sample and more recently, to measure relative protein abundance. Chemiluminescence coupled with film-based detection was traditionally the gold standard for western blotting but accurate and reproducible quantification has been a major challenge from this methodology. The development of sensitive, camera-based detection technologies coupled with an updated technical approach permits the production of reproducible, quantitative data. Fluorescence reagent and detection solutions are the latest innovation in western blotting but there remains questions and debate concerning their relative sensitivity and dynamic range versus chemiluminescence. A methodology to optimize and produce excellent, quantitative western blot results with rigorous data analysis from membranes probed with both fluorescent and chemiluminescent antibodies is described. The data reveal when and how to apply these detection methods to achieve reproducible data with a stepwise approach to data processing for quantitative analysis.
Multiomics analysis reveals that hepatocyte nuclear factor 1β regulates axon guidance genes in the developing mouse kidney
Authors: Shao Annie , Gearhart Micah D. , Chan Siu Chiu , Miao Zhen , Susztak Katalin , Igarashi Peter
Published: October 2022

The transcription factor hepatocyte nuclear factor 1β (HNF-1β) is essential for normal development of the kidney and other epithelial organs. In the developing mouse kidney, HNF-1β is required for the differentiation and patterning of immature nephrons and branching morphogenesis of the ureteric bud (UB). Here, we used ChIP-sequencing (ChIP-seq) and RNA sequencing (RNA-seq) to identify genes that are regulated by HNF-1β in embryonic mouse kidneys. ChIP-seq revealed that HNF-1β binds to 8284 sites in chromatin from E14.5 mouse kidneys. Comparison with previous ATAC-seq and histone modification studies showed that HNF-1β binding peaks colocalized with open chromatin and epigenetic marks of transcriptional activation (H3K27 acetylation, H3K4 trimethylation, H3K4 monomethylation), indicating that the binding sites were functional. To investigate the relationship between HNF-1β binding and HNF-1β-dependent gene regulation, RNA-seq was performed on UB cells purified from wild-type and HNF-1β mutant embryonic kidneys. A total of 1632 genes showed reduced expression in HNF-1β-deficient UB cells, and 485 genes contained nearby HNF-1β binding sites indicating that they were directly activated by HNF-1β. Conversely, HNF-1β directly repressed the expression of 526 genes in the UB. Comparison with snATAC-seq analysis of UB-derived cells showed that both HNF-1β-dependent activation and repression correlated with chromatin accessibility. Pathway analysis revealed that HNF-1β binds near 68 axon guidance genes in the developing kidney. RNA-seq analysis showed thatNrp1,Sema3c,Sema3d,Sema6a, andSlit2were activated by HNF-1β, whereasEfna1,Epha3,Epha4,Epha7,Ntn4,Plxna2,Sema3a,Sema4b,Slit3,Srgap1,Unc5candUnc5dwere repressed by HNF-1β. RNAscope in situ hybridization showed thatNrp1,Sema3c,Sema3d,Sema6a, andSlit2were expressed in wild-type UB and were dysregulated in HNF-1β mutant UB. These studies show that HNF-1β directly regulates the expression of multiple axon guidance genes in the developing mouse kidney. Dysregulation of axon guidance genes may underlie kidney defects in HNF-1β mutant mice.
Spontaneous instrumental avoidance learning in social contexts
Authors: Mennella Rocco , Bavard Sophie , Mentec Inès , Grèzes Julie
Published: October 2022

Adaptation to our social environment requires learning how to avoid potentially harmful situations, such as encounters with aggressive individuals. Threatening facial expressions can evoke automatic stimulus-driven reactions, but whether their aversive motivational value suffices to drive instrumental active avoidance remains unclear. When asked to freely choose between different action alternatives, participants spontaneously—without instruction or monetary reward—developed a preference for choices that maximized the probability of avoiding angry individuals (sitting away from them in a waiting room). Most participants showed clear behavioral signs of instrumental learning, even in the absence of an explicit avoidance strategy. Inter-individual variability in learning depended on participants’ subjective evaluations and sensitivity to threat approach feedback. Counterfactual learning best accounted for avoidance behaviors, especially in participants who developed an explicit avoidance strategy. Our results demonstrate that implicit defensive behaviors in social contexts are likely the product of several learning processes, including instrumental learning.
Fully controllable multichannel waveguides induced by counterpropagating Bessel beams
Authors: Chai Yue , Marsal Nicolas , Wolfersberger Delphine
Published: October 2022

We theoretically analyze the waveguiding structures photo-induced by two incoherent counter-propagating Bessel beams (BBs) in a biased photorefractive crystal. We demonstrate that the cross-coupling of two BBs enables adressable channels and tunability of the forming guiding structures. The truncation parameter of the BBs, their Bessel orders and the misalignment between the two beams are all key parameters for tailoring the characteristics of the photo-induced waveguides such as the number of outputs, the output intensity levels and the distance between each output channel. Accordingly, we optimized the different parameters for designing not only a fully tunable Y-coupler but also optical splitters with up to five outputs and even more complex star couplers for all-optical interconnect applications. Finally, we report on the stability behavior of the photo-induced platform. The stability threshold depends on the nonlinearity parameter beyond which the beams display time-periodic, quasi-periodic and turbulent dynamics where spatially localized instabilities can be observed. All these results suggest more opportunities for fully controllable complex waveguiding structures and new all-optical solutions for active components in optical telecommunication and innovative ways of performing optical computing based on spatiotemporal chaos.
Diversity of myxozoans parasitizing the catfish Rhamdia quelen (Siluriformes: Heptapteridae), in southeastern Brazil, based on morphological and molecular evidence
Authors: Mirandola Dias Vieira Diego Henrique , Bravin Narciso Rodrigo , da Silva Reinaldo José
Published: October 2022

Rhamdia quelen is a commercially important fish in South America. During the survey of myxozoan infections in fishes from Pardo River, Paranapanema River basin, São Paulo State, Brazil, we describe three new species of Henneguya found parasitizing gills of R. quelen: Henneguya bagre n. sp., Henneguya breviscauda n. sp and Henneguya novaerae n. sp. The descriptions were based on myxospores morphology and small subunit ribosomal DNA partial sequences. Phylogenetic analysis showed a clade formed by species that parasitize Siluriformes, with Henneguya jundiai as a sister species of Henneguya bagre n. sp., Henneguya breviscauda n. sp and Henneguya novaerae n. sp. Our study indicates that the parasites infecting R. quelen belong to a lineage of myxozoans infecting Heptapteridae fishes. Using molecular and morphological characterization, the species were identified as new species for the genus Henneguya. Based on our analysis we recommend monitoring the presence of these parasites in farmed fishes, to analyze possible pathologies caused by them.
Hyperspectral imaging for chemicals identification: a human-inspired machine learning approach
Authors: Kendler Shai , Mano Ziv , Aharoni Ran , Raich Raviv , Fishbain Barak
Published: October 2022

Data analysis has increasingly relied on machine learning in recent years. Since machines implement mathematical algorithms without knowing the physical nature of the problem, they may be accurate but lack the flexibility to move across different domains. This manuscript presents a machine-educating approach where a machine is equipped with a physical model, universal building blocks, and an unlabeled dataset from which it derives its decision criteria. Here, the concept of machine education is deployed to identify thin layers of organic materials using hyperspectral imaging (HSI). The measured spectra formed a nonlinear mixture of the unknown background materials and the target material spectra. The machine was educated to resolve this nonlinear mixing and identify the spectral signature of the target materials. The inputs for educating and testing the machine were a nonlinear mixing model, the spectra of the pure target materials (which are problem invariant), and the unlabeled HSI data. The educated machine is accurate, and its generalization capabilities outperform classical machines. When using the educated machine, the number of falsely identified samples is ~ 100 times lower than the classical machine. The probability for detection with the educated machine is 96% compared to 90% with the classical machine.
Do open data impact citizens’ behavior? Assessing face mask panic buying behaviors during the Covid-19 pandemic
Authors: Shibuya Yuya , Lai Chun-Ming , Hamm Andrea , Takagi Soichiro , Sekimoto Yoshihide
Published: October 2022

Data are essential for digital solutions and supporting citizens’ everyday behavior. Open data initiatives have expanded worldwide in the last decades, yet investigating the actual usage of open data and evaluating their impacts are insufficient. Thus, in this paper, we examine an exemplary use case of open data during the early stage of the Covid-19 pandemic and assess its impacts on citizens. Based on quasi-experimental methods, the study found that publishing local stores’ real-time face mask stock levels as open data may have influenced people’s purchase behaviors. Results indicate a reduced panic buying behavior as a consequence of the openly accessible information in the form of an online mask map. Furthermore, the results also suggested that such open-data-based countermeasures did not equally impact every citizen and rather varied among socioeconomic conditions, in particular the education level.
Dynamic changes in genomic 5-hydroxymethyluracil and N6-methyladenine levels in the Drosophila melanogaster life cycle and in response to different temperature conditions
Authors: Starczak Marta , Gawronski Maciej , Wasilow Aleksandra , Mijewski Pawel , Olinski Ryszard , Gackowski Daniel
Published: October 2022

In this study, the level of DNA modifications was investigated in three developmental stages of Drosophila melanogaster (larvae, pupae, imago) and in an in vitro model (Schneider 2 cells). Analysis was carried out using two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry. Our method made it possible, for the first time, to analyze a broad spectrum of DNA modifications in the three stages of Drosophila. Each stage was characterized by a specific modification pattern, and the levels of these compounds fluctuated throughout the D. melanogaster life cycle. The level of DNA modification was also compared between insects bred at 25 °C (optimal temperature) and at 18 °C, and the groups differed significantly. The profound changes in N6-methyladenine and 5-hydroxymethyluracil levels during the Drosophila life cycle and as a result of breeding temperature changes indicate that these DNA modifications can play important regulatory roles in response to environmental changes and/or biological conditions. Moreover, the supplementation of Schneider 2 cells with 1 mM L-ascorbic acid caused a time-dependent increase in the level of 5-(hydroxymethyl)-2′-deoxyuridine. These data suggest that a certain pool of this compound may arise from the enzymatic activity of the dTET protein.
An analysis of intestinal morphology and incretin-producing cells using tissue optical clearing and 3-D imaging
Authors: Hatoko Tomonobu , Harada Norio , Tokumoto Shinsuke , Yamane Shunsuke , Ikeguchi-Ogura Eri , Kato Tomoko , Yasuda Takuma , Tatsuoka Hisato , Shimazu-Kuwahara Satoko , Yabe Daisuke , Hayashi Yoshitaka , Inagaki Nobuya
Published: October 2022

Tissue optical clearing permits detailed evaluation of organ three-dimensional (3-D) structure as well as that of individual cells by tissue staining and autofluorescence. In this study, we evaluated intestinal morphology, intestinal epithelial cells (IECs), and enteroendocrine cells, such as incretin-producing cells, in reporter mice by intestinal 3-D imaging. 3-D intestinal imaging of reporter mice using optical tissue clearing enabled us to evaluate both detailed intestinal morphologies and cell numbers, villus length and crypt depth in the same samples. In disease mouse model of lipopolysaccharide (LPS)-injected mice, the results of 3-D imaging using tissue optical clearing in this study was consistent with those of 2-D imaging in previous reports and could added the new data of intestinal morphology. In analysis of incretin-producing cells of reporter mice, we could elucidate the number, the percentage, and the localization of incretin-producing cells in intestine and the difference of those between L cells and K cells. Thus, we established a novel method of intestinal analysis using tissue optical clearing and 3-D imaging. 3-D evaluation of intestine enabled us to clarify not only detailed intestinal morphology but also the precise number and localization of IECs and incretin-producing cells in the same samples.