bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic reconstruction of cellular trajectories across mouse embryogenesis
Authors: Qiu Chengxiang , Cao Junyue , Martin Beth K. , Li Tony , Welsh Ian C. , Srivatsan Sanjay , Huang Xingfan , Calderon Diego , Noble William Stafford , Disteche Christine M. , Murray Stephen A. , Spielmann Malte , Moens Cecilia B. , Trapnell Cole , Shendure Jay 
Published: March 2022

AbstractMammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single-cell zygote gives rise to millions of cells expressing a panoply of molecular programs. Although intensively studied, a comprehensive delineation of the major cellular trajectories that comprise mammalian development in vivo remains elusive. Here, we set out to integrate several single-cell RNA-sequencing (scRNA-seq) datasets that collectively span mouse gastrulation and organogenesis, supplemented with new profiling of ~150,000 nuclei from approximately embryonic day 8.5 (E8.5) embryos staged in one-somite increments. Overall, we define cell states at each of 19 successive stages spanning E3.5 to E13.5 and heuristically connect them to their pseudoancestors and pseudodescendants. Although constructed through automated procedures, the resulting directed acyclic graph (TOME (trajectories of mammalian embryogenesis)) is largely consistent with our contemporary understanding of mammalian development. We leverage TOME to systematically nominate transcription factors (TFs) as candidate regulators of each cell type’s specification, as well as ‘cell-type homologs’ across vertebrate evolution.
Comprehensive RNA dataset of tissue and plasma from patients with esophageal cancer or precursor lesions
Authors: Schoofs Kathleen , Philippron Annouck , Avila Cobos Francisco , Koster Jan , Lefever Steve , Anckaert Jasper , De Looze Danny , Vandesompele Jo , Pattyn Piet , De Preter Katleen 
Published: March 2022

AbstractIn the past decades, the incidence of esophageal adenocarcinoma has increased dramatically in Western populations. Better understanding of disease etiology along with the identification of novel prognostic and predictive biomarkers are urgently needed to improve the dismal survival probabilities. Here, we performed comprehensive RNA (coding and non-coding) profiling in various samples from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy and disease esophageal tissue sample were included. In total, this comprehensive dataset consists of 102 sequenced libraries from 51 samples. Based on this data, 119 expression profiles are available for three biotypes, including miRNA (51), mRNA (51) and circRNA (17). This unique resource allows for discovery of novel biomarkers and disease mechanisms, comparison of tissue and liquid biopsy profiles, integration of coding and non-coding RNA patterns, and can serve as a validation dataset in other RNA landscaping studies. Moreover, structural RNA differences can be identified in this dataset, including protein coding mutations, fusion genes, and circular RNAs.
MIR17HG polymorphisms contribute to high-altitude pulmonary edema susceptibility in the Chinese population
Authors: Si Lining , Wang Haiyang , Jiang Yahui , Yi Yun , Wang Rong , Long Qifu , Zhao Yanli 
Published: March 2022

AbstractHigh-altitude pulmonary edema (HAPE) is a common acute altitude sickness. This study was designed to investigate the effect of MIR17HG polymorphisms on HAPE risk in the Chinese population. The Agena MassARRAY platform was used to genotype six single-nucleotide polymorphisms (SNPs) in the MIR17HG gene in 244 HAPE patients and 243 non-HAPE controls. The odds ratio (OR) and 95% confidence interval were used to evaluate the association between each MIR17HG polymorphisms and the risk of HAPE under a polygenetic model. Statistical analysis was performed using the χ2 test. Multifactor dimensionality reduction (MDR) analysis was used to analyze the impacts of SNP–SNP interactions on the risk of HAPE. According to the allele model, the HAPE risk of people with the rs7318578 A allele of MIR17HG was lower than that of people with the C allele (OR 0.74, p = 0.036).Logistic regression analysis of four models for all selected MIR17HG SNPs showed significant differences in the frequencies of rs7318578 (OR 0.74, p = 0.037) and rs17735387 (OR 1.51, p = 0.036) between cases and controls. The results of the sex stratification analysis showed that among males, rs17735387 in the MIR17HG gene is associated with an increased risk of HAPE. MDR analysis showed that the best combination model was a three-locus model incorporating rs72640334, rs7318578, and rs7336610. This study revealed the correlations between rs7318578 and rs17735387 on the MIR17HG gene and the risk of HAPE in the Chinese population, providing a theoretical basis for the early screening, prevention, and diagnosis of HAPE in high-risk populations.
Fabrication, characterization and antifungal evaluation of polyphenolic extract activated keratin starch coating on infected tomato fruits
Authors: Oluba Olarewaju M. , Obokare Onome , Bayo-Olorunmeke Opeyemi A. , Ojeaburu Samuel I. , Ogunlowo Olayemi M. , Irokanulo Emenike O. , Akpor Oghenerobor B. 
Published: March 2022

AbstractIn recent times, the application of protein-based bio-composite edible films in postharvest preservation of food and agricultural products is attracting increased attention due to their biodegradability, eco-friendliness and sustainability. In this study, an avocado pear peel polyphenolic extract enriched keratin-starch composite film was fabricated, characterized and evaluated for antimicrobial activity against fungal infected tomato fruits after 6 days of storage at room (25 ± 2 °C) temperature. The SEM/EDX and FTIR results revealed the successful film formation with high degree of compatibility and homogeneity. Following a 6-day post-coating loss in weight of the coated tomato fruits decreased significantly (p < 0.05) with increasing extract concentration while titratable acidity showed a significant (p < 0.05) increase with increasing extract load. Ascorbic acid and lycopene contents were significantly (p < 0.05) higher in the avocado pear peel polyphenolic extract-loaded films. No significant effect was observed in catechol oxidase activity of the tomato extract across the different treatment groups. In addition, fungal growth inhibition showed a dose dependent increase consistent with avocado pear peel polyphenolic load in coated tomato fruits compared to control. Results obtained in this study showed that polyphenolic activated keratin-starch coating was able to reduce spoilage-induce weight loss as well as conserve the overall quality (including titratable acid levels, lycopene and ascorbic acid contents) of fungal-infected tomato fruit and reduce microbial growth. Therefore polyphenolic activated keratin-starch coating could serve as a sustainable and ecofriendly postharvest preservation method to prolong the shelf life of tomato fruits.
The effects of socioeconomic and geographic factors on chronic phase long-term survival after stroke in South Korea
Authors: Park Dougho , Lee Su Yun , Jeong Eunhwan , Hong Daeyoung , Kim Mun-Chul , Choi Jun Hwa , Shin Eun Kyong , Son Kang Ju , Kim Hyoung Seop 
Published: March 2022

AbstractThe stroke incidence has increased rapidly in South Korea, calling for a national-wide system for long-term stroke management. We investigated the effects of socioeconomic status (SES) and geographic factors on chronic phase survival after stroke. We retrospectively enrolled 6994 patients who experienced a stroke event in 2009 from the Korean National Health Insurance database. We followed them up from 24 to 120 months after stroke onset. The endpoint was all-cause mortality. We defined SES using a medical-aid group and four groups divided by health insurance premium quartiles. Geographic factors were defined using Model 1 (capital, metropolitan, city, and county) and Model 2 (with or without university hospitals). The higher the insurance premium, the higher the survival rate tended to be (P < 0.001). The patient survival rate was highest in the capital city and lowest at the county level (P < 0.001). Regions with a university hospital(s) showed a higher survival rate (P = 0.006). Cox regression revealed that the medical-aid group was identified as an independent risk factor for chronic phase mortality. Further, NHIP level had a more significant effect than geographic factors on chronic stroke mortality. From these results, long-term nationwide efforts to reduce inter-regional as well as SES discrepancies affecting stroke management are needed.
Proteomic analysis of heat-stable proteins revealed an increased proportion of proteins with compositionally biased regions
Authors: Park Hongsun , Yamanaka Tomoyuki , Nukina Nobuyuki 
Published: March 2022

AbstractIntrinsically disordered proteins (IDPs) have been in the spotlight for their unique properties, such as their lack of secondary structures and low sequence complexity. Alpha-synuclein and tau are representative disease-related IDPs with low complexity regions in their sequences, accumulating in the brains of patients with Parkinson disease and Alzheimer disease, respectively. Their heat resistance in particular was what attracted our attention. We assumed that there exist many other unidentified proteins that are resistant to heat-treatment, referred to as heat-stable proteins, which would also have low sequence complexity. In this study, we performed proteomic analysis of heat-stable proteins of mouse brains and found that proteins with compositionally biased regions are abundant in the heat-stable proteins. The proteins related to neurodegeneration are known to undergo different types of post-translational modifications (PTMs) such as phosphorylation and ubiquitination. We then investigated the heat-stability and aggregation properties of phosphorylated synuclein and tau with different phosphorylation sites. We suggest that PTMs can be important factors that determine the heat-stability and aggregation properties of a protein. IDPs identified in the heat-stable proteins of mouse brains would be candidates for the pathogenic proteins for neurodegeneration.
Visual consciousness dynamics in adults with and without autism
Authors: Skerswetat Jan , Bex Peter J. , Baron-Cohen Simon 
Published: March 2022

AbstractSensory differences between autism and neuro-typical populations are well-documented and have often been explained by either weak-central-coherence or excitation/inhibition-imbalance cortical theories. We tested these theories with perceptual multi-stability paradigms in which dissimilar images presented to each eye generate dynamic cyclopean percepts based on ongoing cortical grouping and suppression processes. We studied perceptual multi-stability with Interocular Grouping (IOG), which requires the simultaneous integration and suppression of image fragments from both eyes, and Conventional Binocular Rivalry (CBR), which only requires global suppression of either eye, in 17 autistic adults and 18 neurotypical participants. We used a Hidden-Markov-Model as tool to analyze the multistable dynamics of these processes. Overall, the dynamics of multi-stable perception were slower (i.e. there were longer durations and fewer transitions among perceptual states) in the autistic group compared to the neurotypical group for both IOG and CBR. The weighted Markovian transition distributions revealed key differences between both groups and paradigms. The results indicate overall lower levels of suppression and decreased levels of grouping in autistic than neurotypical participants, consistent with elements of excitation/inhibition imbalance and weak-central-coherence theories.
Automated computation of nerve fibre inclinations from 3D polarised light imaging measurements of brain tissue
Authors: Menzel Miriam , Reuter Jan A. , Gräßel David , Costantini Irene , Amunts Katrin , Axer Markus 
Published: March 2022

AbstractThe method 3D polarised light imaging (3D-PLI) measures the birefringence of histological brain sections to determine the spatial course of nerve fibres (myelinated axons). While the in-plane fibre directions can be determined with high accuracy, the computation of the out-of-plane fibre inclinations is more challenging because they are derived from the amplitude of the birefringence signals, which depends e.g. on the amount of nerve fibres. One possibility to improve the accuracy is to consider the average transmitted light intensity (transmittance weighting). The current procedure requires effortful manual adjustment of parameters and anatomical knowledge. Here, we introduce an automated, optimised computation of the fibre inclinations, allowing for a much faster, reproducible determination of fibre orientations in 3D-PLI. Depending on the degree of myelination, the algorithm uses different models (transmittance-weighted, unweighted, or a linear combination), allowing to account for regionally specific behaviour. As the algorithm is parallelised and GPU optimised, it can be applied to large data sets. Moreover, it only uses images from standard 3D-PLI measurements without tilting, and can therefore be applied to existing data sets from previous measurements. The functionality is demonstrated on unstained coronal and sagittal histological sections of vervet monkey and rat brains.
Congenitally blind adults can learn to identify face-shapes via auditory sensory substitution and successfully generalize some of the learned features
Authors: Arbel Roni , Heimler Benedetta , Amedi Amir 
Published: March 2022

AbstractUnlike sighted individuals, congenitally blind individuals have little to no experience with face shapes. Instead, they rely on non-shape cues, such as voices, to perform character identification. The extent to which face-shape perception can be learned in adulthood via a different sensory modality (i.e., not vision) remains poorly explored. We used a visual-to-auditory Sensory Substitution Device (SSD) that enables conversion of visual images to the auditory modality while preserving their visual characteristics. Expert SSD users were systematically taught to identify cartoon faces via audition. Following a tailored training program lasting ~ 12 h, congenitally blind participants successfully identified six trained faces with high accuracy. Furthermore, they effectively generalized their identification to the untrained, inverted orientation of the learned faces. Finally, after completing the extensive 12-h training program, participants learned six new faces within 2 additional hours of training, suggesting internalization of face-identification processes. Our results document for the first time that facial features can be processed through audition, even in the absence of visual experience across the lifespan. Overall, these findings have important implications for both non-visual object recognition and visual rehabilitation practices and prompt the study of the neural processes underlying auditory face perception in the absence of vision.
A data driven approach to identify trajectories of prenatal alcohol consumption in an Australian population-based cohort of pregnant women
Authors: Muggli Evelyne , Hearps Stephen , Halliday Jane , Elliott Elizabeth J. , Penington Anthony , Thompson Deanne K. , Spittle Alicia , Forster Della A. , Lewis Sharon , Anderson Peter J. 
Published: March 2022

AbstractAccurate information on dose, frequency and timing of maternal alcohol consumption is critically important when investigating fetal risks from prenatal alcohol exposure. Identification of distinct alcohol use behaviours can also assist in developing directed public health messages about possible adverse child outcomes, including Fetal Alcohol Spectrum Disorder. We aimed to determine group-based trajectories of time-specific, unit-level, alcohol consumption using data from 1458 pregnant women in the Asking Questions about Alcohol in Pregnancy (AQUA) longitudinal study in Melbourne, Australia. Six alcohol consumption trajectories were identified incorporating four timepoints across gestation. Labels were assigned based on consumption in trimester one and whether alcohol use was continued throughout pregnancy: abstained (33.8%); low discontinued (trimester one) (14.4%); moderate discontinued (11.7%); low sustained (13.0%); moderate sustained (23.5%); and high sustained (3.6%). Median weekly consumption in trimester one ranged from 3 g (low discontinued) to 184 g of absolute alcohol (high sustained). Alcohol use after pregnancy recognition decreased dramatically for all sustained drinking trajectories, indicating some awareness of risk to the unborn child. Further, specific maternal characteristics were associated with different trajectories, which may inform targeted health promotion aimed at reducing alcohol use in pregnancy.
Characterization of the Portuguese population diagnosed with retinoblastoma
Authors: Castela Guilherme , Providência Joana , Monteiro Madalena , Silva Sonia , Brito Manuel , Sá Joaquim , Oliveiros Barbara , Murta Joaquim Neto , Correa Zelia , Branco Miguel Castelo 
Published: March 2022

AbstractThe purpose of this study is to characterize demographically and genetically the Portuguese population with retinoblastoma; to report the clinical stage at presentation and its impact on survival and ocular preservation rate and, finally, to assess the incidence of retinoblastoma in Portugal. Retrospective observational study including children consecutively diagnosed with retinoblastoma at the Portuguese National Referral Center of Intraocular Tumors, between October 2015 and October 2020. Twenty-eight children were diagnosed with retinoblastoma at our center, 15 hereditary from which 12 presented with bilateral retinoblastoma and 3 were unilateral. The overall mean age at diagnosis was 13.6 ± 11.1 months with hereditary retinoblastomas diagnosed slightly earlier at 9.6 ± 6.3 months. A familial history of retinoblastoma was found in only 4 (14.3%) of the cases. A pathogenic mutation in the RB1 gene was found in 13 (46.4%) of the children. The most frequent sign at referral was leukocoria in 71.4% of patients. Considering the ICRB classification of the tumors, 84.6% of non-hereditable hereditary retinoblastomas were referred to our center in advanced stages. In the group of hereditable retinoblastomas 86.7% presented with one of the eyes with advanced intraocular retinoblastoma. Fourteen children had one eye enucleated due to retinoblastoma. No deaths were registered during the study period. Considering the incidence analysis, we registered a year-of-birth controlled incidence analysis of 4.04 per 100.000 living births (IC 95% 1.59–6.49). This is the first characterization of the Portuguese Population diagnosed with Retinoblastoma in the National Reference Center.
Variation in the dynamic of absorption and efficiency of phosphorus use in tomato
Authors: Marques Douglas José , da Silva Ernani Clarete , Siqueira José Andrés Carreño , Abedi Elham , Veloso Fernanda Rosa , Maciel Gabriel Mascarenhas , Maluf Wilson Roberto 
Published: March 2022

AbstractChanges in root growth and metabolism of P in tomato cultivars are necessary in acidic soils in tropical and subtropical regions in response to P deficiency. This increase in the efficiency of phosphorus absorption by tomatoes can significantly reduce the doses of phosphate fertilizers used, as well as, possibly, the more immediate use of P fixed in the soil matrix, with favorable effects on agricultural sustainability, promoting the use of marginal areas in terms of soil fertility, and the national fertilizer economy. The tested hypothesis was that there would be no difference in the uptake and utilization of P by tomato cultivars; therefore, this study investigated the variation in the dynamics of absorption and efficiency of P-use through changes in the root, stem, leaf, gas exchange, and P-use efficiency in tomato cultivars contrasting P-absorption. The experimental design comprised a factorial scheme consisting of two cultivars that were tolerant and sensitive to P deficiency and three P concentrations (control, moderate deficiency, and severe deficiency). P limitation in the tolerant cultivar promoted high dry matter concentration (root, stem, and leaf), leaf area, root volume, nutrient translocation, rate of leaf gas exchange, and efficiency under P-deficiency stress. It was concluded from the research that the variation in the dynamics of absorption and efficiency of P use of the tolerant cultivar increased the production of roots, leaves, and leaf gas exchange under P stress conditions.
Slaked lime improves growth, antioxidant capacity and reduces Cd accumulation of peanut (Arachis hypogaea L.) under Cd stress
Authors: Zhang Liqing , Zou Dongsheng , Zeng Ningbo , Li Lin , Xiao Zhihua 
Published: March 2022

AbstractSlaked lime has been used to remediate contaminated agricultural soils as an in situ chemical immobilization amendment for a long time. However, the effects of slaked lime on peanut and soil cadmium (Cd) levels remain poorly understood with respect to remediating Cd-contaminated soil. In this study, six rates of slaked lime (e.g., 0, 300, 600, 900, 1200 and 1500 kg ha−1) were applied to evaluate the effects of slaked lime treatments on soil pH and the growth, Cd accumulation and physiology characteristics of peanut, which were in Cd-contaminated soil, and 0 kg ha−1 was taken as the control. The results indicated that slaked lime application significantly increased soil pH and reduced total Cd contents in peanut tissues at all growth stages. As the rates of slaked lime were increased, kernel biomass increased in the maturity stage, which increased peanut yields. The irregular variations in catalase, peroxidase, and superoxide dismutase activities and chlorophyll and malondialdehyde contents that were observed at all growth stages may be due to the interactions among soil pH, Ca nutrients and Cd, etc. In summary, slaked lime is suitable as an in situ chemical immobilization amendment to increase Cd immobilization and peanut yields in Cd-contaminated soil.
Tuning wettability and electrical conductivity of single-walled carbon nanotubes by the modified Hummers method
Authors: Stando Grzegorz , Han Sujie , Kumanek Bogumiła , Łukowiec Dariusz , Janas Dawid 
Published: March 2022

AbstractPartial oxidation of nanocarbon materials is one of the most straightforward methods to improve their compatibility with other materials, which widens its application potential. This work studied how the microstructure and properties of high crystallinity single-walled carbon nanotubes (SWCNTs) can be tailored by applying the modified Hummers method. The influence of temperature (0, 18, 40 °C), reaction time (0 min to 7 h), and the amount of KMnO4 oxidant was monitored. The results showed that depending on the oxidation conditions, the electronic characteristics of the material could be adjusted. After optimizing the parameters, the SWCNTs were much more conductive (1369 ± 84 S/cm with respect to 283 ± 32 S/cm for the untreated material). At the same time, the films made from them exhibited hydrophilic character of the surface (water contact angle changed from 71° to 27°).