bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations
Authors: Adhikari Laxman , Shrestha Sandesh , Wu Shuangye , Crain Jared , Gao Liangliang , Evers Byron , Wilson Duane , Ju Yoonha , Koo Dal-Hoe , Hucl Pierre , Pozniak Curtis , Walkowiak Sean , Wang Xiaoyun , Wu Jing , Glaubitz Jeffrey C. , DeHaan Lee , Friebe Bernd , Poland Jesse 
Published: October 2022

AbstractThe development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on the amount of data required, and could be extended to 3,072 samples or more. Panels of doubled haploid wheat lines (Triticum aestivum, CDC Stanley x CDC Landmark), wheat-barley (T. aestivum x Hordeum vulgare) and wheat-wheatgrass (Triticum durum x Thinopyrum intermedium) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1 × down to 0.01 × per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.
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

AbstractThe 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

AbstractThe 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

AbstractStudies 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

AbstractMelatonin 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

AbstractAdverse 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

AbstractTo 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

AbstractOsteoarthritis (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

AbstractThe 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

AbstractMesenchymal 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

AbstractPoison 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

AbstractUnderstanding 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

AbstractThe 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.