bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of H19, Mest, Meg3, and Peg3 genes affecting growth and metabolism in umbilical cord blood cells of infants born to mothers with gestational diabetes and healthy mothers in Rafsanjan City, Iran
Authors: Abad Fatemeh Rahimi Mehdi , Hajizadeh Mohammad Reza , Mahmoodi Mehdi , Jalali Zahra , Kazeruni Fatemeh Nazem , Swann Jennifer , Hosseiniara Reza , Karimabad Mojgan Noroozi 
Published: July 2022

AbstractHyperglycemia during the first trimester leads to an increased risk of innate malformations as well as death at times close to delivery dates. The methylated genes include those from paternal H19 and PEG3 and those from maternal MEST and MEG3 that are necessary for the growth and regulation of the human fetus and its placenta. The aim of this study was to evaluate and compare the expression of these genes in the cord blood of healthy infants born to mothers with gestational diabetes mellitus (GDM) and healthy mothers.This case-control study was conducted on the cord blood of 40 infants born to mothers with GDM and 35 infants born to healthy mothers. Mothers were identified by measuring oral glucose tolerance in the 24th–26th week of pregnancy. Cord blood was obtained post-delivery, and cord blood mononuclear cells were immediately extracted, using Ficoll solution. Then, RNA extraction and cDNA synthesis were performed, and gene expression of MEG3, PEG3, H19, and MEST was assessed through quantitative real-time PCR.Findings show that the expression levels of MEG3, PEG3, H19, and MEST genes were significantly decreased in mononuclear cord blood cells of infants born to mothers with GDM when compared to those of the healthy control group.These findings reveal that the reduction of imprinted genes in mothers with GDM is most likely due to changes in their methylation by an epigenetic process. Considering the importance of GDM due to its high prevalence and its side effects both for mother and fetus, recognizing their exact mechanisms is of high importance. This has to be studied more widely.
Progress on deuterated potassium dihydrogen phosphate (DKDP) crystals for high power laser system application
Authors: Xu Mingxia , Liu Baoan , Zhang Lisong , Ren Hongkai , Gu Qingtian , Sun Xun , Wang Shenglai , Xu Xinguang 
Published: July 2022

AbstractIn this review, we introduce the progress in the growth of large-aperture DKDP crystals and some aspects of crystal quality including determination of deuterium content, homogeneity of deuterium distribution, residual strains, nonlinear absorption, and laser-induced damage resistance for its application in high power laser system. Large-aperture high-quality DKDP crystal with deuteration level of 70% has been successfully grown by the traditional method, which can fabricate the large single-crystal optics with the size exceeding 400 mm. Neutron diffraction technique is an efficient method to research the deuterium content and 3D residual strains in single crystals. More efforts have been paid in the processes of purity of raw materials, continuous filtration technology, thermal annealing and laser conditioning for increasing the laser-induced damage threshold (LIDT) and these processes enable the currently grown crystals to meet the specifications of the laser system for inertial confinement fusion (ICF), although the laser damage mechanism and laser conditioning mechanism are still not well understood. The advancements on growth of large-aperture high-quality DKDP crystal would support the development of ICF in China.
Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges
Authors: Sugden Scott , Holert Johannes , Cardenas Erick , Mohn William W , Stein Lisa Y 
Published: July 2022

Abstract
Sponges are known for hosting diverse communities of microbial symbionts, but despite persistent interest in the sponge microbiome, most research has targeted marine sponges; freshwater sponges have been the focus of less than a dozen studies. Here, we used 16 S rRNA gene amplicon sequencing and shotgun metagenomics to characterize the microbiome of the freshwater sponge Ephydatia muelleri and identify potential indicators of sponge-microbe mutualism. Using samples collected from the Sooke, Nanaimo, and Cowichan Rivers on Vancouver Island, British Columbia, we show that the E. muelleri microbiome is distinct from the ambient water and adjacent biofilms and is dominated by Sediminibacterium, Comamonas, and unclassified Rhodospirillales. We also observed phylotype-level differences in sponge microbiome taxonomic composition among different rivers. These differences were not reflected in the ambient water, suggesting that other environmental or host-specific factors may drive the observed geographic variation. Shotgun metagenomes and metagenome-assembled genomes further revealed that freshwater sponge-associated bacteria share many genomic similarities with marine sponge microbiota, including an abundance of defense-related proteins (CRISPR, restriction-modification systems, and transposases) and genes for vitamin B12 production. Overall, our results provide foundational information on the composition and function of freshwater sponge-associated microbes, which represent an important yet underappreciated component of the global sponge microbiome.
Spatial evaluation of animal health care accessibility and veterinary shortage in France
Authors: Berrada Mehdi , Ndiaye Youba , Raboisson Didier , Lhermie Guillaume 
Published: July 2022

AbstractThe decrease in the supply of veterinary healthcare in France adversely affects health of food-producing animals. In a One Health perspective, the health of people, animals and their shared environment are interconnected, and adequate supply of veterinary healthcare is required to ensure public health. Prevention of outbreaks and zoonotic diseases that may impact public health mobilizes a set of public policies, including strengthening veterinary workforce. These policies should be informed by quantification of animal health care accessibility, yet this has not been well characterized. The objective was to quantify the accessibility to veterinary healthcare for cattle, swine, and poultry sectors in France. A Two-Step Floating Catchment Area (2SFCA) approach was used to measure the level of accessibility to veterinary clinics. In the cattle sector, the 2SFCA score indicated relatively high accessibility in the north and south of France, but insufficient accessibility elsewhere. In the swine sector, there was high accessibility in the north east and in north of France, medium accessibility in the south west, and insufficient accessibility elsewhere. Finally, in the poultry sector, all regions had insufficient accessibility. Sensitivity analysis examining the effects of a change in spatial accessibility according to various travel time showed that the optimal threshold to compute 2SFCA score in cattle, swine and poultry sectors were respectively, 45, 60 and 60 min. According to a definition of “underserved area” derived from an official decree and the optimal thresholds to compute 2SFCA, the cattle, swine and poultry sector have on average 75.3, 89.9 and 98.3% underserved area, respectively. We provided evidence that the supply of animal health care was not sufficient and we proposed recommendations on how to assess animal health care accessibility, enabling modelling and visualization of the effects of potential public policies aimed at reducing veterinary shortages.
Genomic analysis of a novel Neanderthal from Mezmaiskaya Cave provides insights into the genetic relationships of Middle Palaeolithic populations
Authors: Andreeva Tatiana V. , Manakhov Andrey D. , Gusev Fedor E. , Patrikeev Anton D. , Golovanova Lyubov V. , Doronichev Vladimir B. , Shirobokov Ivan G. , Rogaev Evgeny I. 
Published: July 2022

AbstractThe Mezmaiskaya cave is located on the North Caucasus near the border that divides Europe and Asia. Previously, fossil remains for two Neanderthals were reported from Mezmaiskaya Cave. A tooth from the third archaic hominin specimen (Mezmaiskaya 3) was retrieved from layer 3 in Mezmaiskaya Cave. We performed genome sequencing of Mezmaiskaya 3. Analysis of partial nuclear genome sequence revealed that it belongs to a Homo sapiens neanderthalensis female. Based on a high-coverage mitochondrial genome sequence, we demonstrated that the relationships of Mezmaiskaya 3 to Mezmaiskaya 1 and Stajnia S5000 individuals were closer than those to other Neanderthals. Our data demonstrate the close genetic connections between the early Middle Palaeolithic Neanderthals that were replaced by genetically distant later group in the same geographic areas. Based on mitochondrial DNA (mtDNA) data, we suggest that Mezmaiskaya 3 was the latest Neanderthal individual from the early Neanderthal’s branches. We proposed a hierarchical nomenclature for the mtDNA haplogroups of Neanderthals. In addition, we retrieved ancestral mtDNA mutations in presumably functional sites fixed in the Neanderthal clades, and also provided the first data showing mtDNA heteroplasmy in Neanderthal specimen.
Automated sleep stage scoring employing a reasoning mechanism and evaluation of its explainability
Authors: Horie Kazumasa , Ota Leo , Miyamoto Ryusuke , Abe Takashi , Suzuki Yoko , Kawana Fusae , Kokubo Toshio , Yanagisawa Masashi , Kitagawa Hiroyuki 
Published: July 2022

AbstractScoring sleep stages from biological signals is an essential but labor-intensive inspection for sleep diagnosis. The existing automated scoring methods have achieved high accuracy but are not widely applied in clinical practice. In our understanding, the existing methods have failed to establish the trust of sleep experts (e.g., physicians and clinical technologists) due to a lack of ability to explain the evidences/clues for scoring. In this study, we developed a deep-learning-based scoring model with a reasoning mechanism called class activation mapping (CAM) to solve this problem. This mechanism explicitly shows which portions of the signals support our model’s sleep stage decision, and we verified that these portions overlap with the “characteristic waves,” which are evidences/clues used in the manual scoring process. In exchange for the acquisition of explainability, employing CAM makes it difficult to follow some scoring rules. Although we concerned the negative effect of CAM on the scoring accuracy, we have found that the impact is limited. The evaluation experiment shows that the proposed model achieved a scoring accuracy of $$86.9\%$$

86.9
%

. It is superior to those of some existing methods and the inter-rater reliability among the sleep experts. These results suggest that Sleep-CAM achieved both explainability and required scoring accuracy for practical usage.
KOPI: Kinase inhibitOr Proteome Impact analysis
Authors: Li Ginny Xiaohe , Zhao Tianyun , Wang Loo Chien , Choi Hyungwon , Lim Yan Ting , Sobota Radoslaw M. 
Published: July 2022

AbstractKinase inhibitors often exert on/off-target effects, and efficient data analysis is essential for assessing these effects on the proteome. We developed a workflow for rapidly performing such a proteomic assessment, termed as kinase inhibitor proteome impact analysis (KOPI). We demonstrate KOPI’s utility with staurosporine (STS) on the leukemic K562 cell proteome. We identified systematically staurosporine’s non-kinome interactors, and showed for the first time that it caused paradoxical hyper- and biphasic phosphorylation.
Childhood deprivations predict late-life cognitive impairment among older adults in India
Authors: Muhammad T. , Debnath Paramita , Srivastava Shobhit , Sekher T. V. 
Published: July 2022

AbstractLarge population-based studies on the associations of childhood factors with late-life cognition are lacking in many low and middle income countries including India. In this study, we assessed the prevalence of late-life cognitive impairment and examined the associations of childhood socioeconomic status (SES) and health conditions with cognitive impairment among older adults in India. Data for this study were derived from the Longitudinal Ageing Study in India conducted in 2017–18. The effective sample size was 31,464 older adults aged 60 years and above. Cognitive functioning was measured through five global domains (memory, orientation, arithmetic function, executive function, and object naming). The overall score ranged between 0 and 43, and the score was reversed indicating cognitive impairment. Descriptive statistics along with mean scores of cognitive impairment were presented. Additionally, moderated multivariable linear regression models were employed to examine the association between explanatory variables, including childhood SES and health conditions and late-life cognitive impairment. The mean score of cognitive functioning among the study participants was 21.72 (CI 2.64–21.80). About 15% of older adults had poor health conditions, and 44% had lower financial status during their childhood. Older adults who had a fair health during their childhood were more likely to suffer from cognitive impairment in comparison to older adults who had good health during their childhood (Coef: 0.60; CI 0.39, 0.81). In comparison to older adults who had good childhood financial status, those who had poor childhood financial status were more likely to suffer from cognitive impairment (Coef: 0.81; CI 0.56, 1.07). Older adults who had fair childhood health status and poor childhood financial status were more likely to suffer from cognitive impairment in comparison to older adults who had good childhood health and good financial status (Coef: 1.26; CI 0.86, 1.66). Social policies such as improving educational and financial resources in disadvantaged communities and socioeconomically poor children and their families, would help to enhance a better cognitive ageing and a healthy and dignified life in old age.
Genome-wide association study of Senegalese sorghum seedlings responding to a Texas isolate of Colletotrichum sublineola
Authors: Ahn Ezekiel , Fall Coumba , Prom Louis K. , Magill Clint 
Published: July 2022

AbstractColletotrichum sublineola is a destructive fungal pathogen that causes anthracnose in sorghum. Senegalese sorghum germplasm is currently being considered as an option of sources for genetic resistance. In a recent study, Senegalese sorghum accessions were evaluated for response to a mixture of Texas isolates of C. sublineola at the 8-leaf stage in the greenhouse. As a comparison, 159 Senegalese sorghum accessions at the 1-leaf developmental stage were evaluated against a single Texas isolate of C. sublineola (FSP53) using an excised-leaf assay. A genome-wide association study (GWAS) was conducted based on the phenotypic data acquired to discover genetic variation associated with response to C. sublineola using 193,727 single nucleotide polymorphisms (SNPs) throughout the genome. Sorghum seedlings tended to be more resistant when compared with sorghum plants inoculated at the 8-leaf stage in the greenhouse in previous experiments. Based on the highest score evaluated in the 1-leaf developmental stage excised leaf assay for each accession, 16 accessions were labeled as susceptible. GWAS identified the SNP locus S01_72868925 that is associated with protein kinase domain // Leucine rich repeat N-terminal domain at a level of confidence that surpassed Bonferroni correction. Along with the SNP locus S01_72868925, other top SNP loci were also associated with genes that are known to play critical roles in plant defense or plant stress responses.
Automated histological classification for digital pathology images of colonoscopy specimen via deep learning
Authors: Byeon Sun-ju , Park Jungkap , Cho Yoon Ah , Cho Bum-Joo 
Published: July 2022

AbstractColonoscopy is an effective tool to detect colorectal lesions and needs the support of pathological diagnosis. This study aimed to develop and validate deep learning models that automatically classify digital pathology images of colon lesions obtained from colonoscopy-related specimen. Histopathological slides of colonoscopic biopsy or resection specimens were collected and grouped into six classes by disease category: adenocarcinoma, tubular adenoma (TA), traditional serrated adenoma (TSA), sessile serrated adenoma (SSA), hyperplastic polyp (HP), and non-specific lesions. Digital photographs were taken of each pathological slide to fine-tune two pre-trained convolutional neural networks, and the model performances were evaluated. A total of 1865 images were included from 703 patients, of which 10% were used as a test dataset. For six-class classification, the mean diagnostic accuracy was 97.3% (95% confidence interval [CI], 96.0–98.6%) by DenseNet-161 and 95.9% (95% CI 94.1–97.7%) by EfficientNet-B7. The per-class area under the receiver operating characteristic curve (AUC) was highest for adenocarcinoma (1.000; 95% CI 0.999–1.000) by DenseNet-161 and TSA (1.000; 95% CI 1.000–1.000) by EfficientNet-B7. The lowest per-class AUCs were still excellent: 0.991 (95% CI 0.983–0.999) for HP by DenseNet-161 and 0.995 for SSA (95% CI 0.992–0.998) by EfficientNet-B7. Deep learning models achieved excellent performances for discriminating adenocarcinoma from non-adenocarcinoma lesions with an AUC of 0.995 or 0.998. The pathognomonic area for each class was appropriately highlighted in digital images by saliency map, particularly focusing epithelial lesions. Deep learning models might be a useful tool to help the diagnosis for pathologic slides of colonoscopy-related specimens.
Systemic long-term metabolic effects of acute non-severe paediatric burn injury
Authors: Begum Sofina , Johnson Blair Z. , Morillon Aude-Claire , Yang Rongchang , Bong Sze How , Whiley Luke , Gray Nicola , Fear Vanessa S. , Cuttle Leila , Holland Andrew J. A. , Nicholson Jeremy K. , Wood Fiona M. , Fear Mark W. , Holmes Elaine 
Published: July 2022

AbstractA growing body of evidence supports the concept of a systemic response to non-severe thermal trauma. This provokes an immunosuppressed state that predisposes paediatric patients to poor recovery and increased risk of secondary morbidity. In this study, to understand the long-term systemic effects of non-severe burns in children, targeted mass spectrometry assays for biogenic amines and tryptophan metabolites were performed on plasma collected from child burn patients at least three years post injury and compared to age and sex matched non-burn (healthy) controls. A panel of 12 metabolites, including urea cycle intermediates, aromatic amino acids and quinolinic acid were present in significantly higher concentrations in children with previous burn injury. Correlation analysis of metabolite levels to previously measured cytokine levels indicated the presence of multiple cytokine-metabolite associations in the burn injury participants that were absent from the healthy controls. These data suggest that there is a sustained immunometabolic imprint of non-severe burn trauma, potentially linked to long-term immune changes that may contribute to the poor long-term health outcomes observed in children after burn injury.
CombPDX: a unified statistical framework for evaluating drug synergism in patient-derived xenografts
Authors: Huang Licai , Wang Jing , Fang Bingliang , Meric-Bernstam Funda , Roth Jack A. , Ha Min Jin 
Published: July 2022

AbstractAnticancer combination therapy has been developed to increase efficacy by enhancing synergy. Patient-derived xenografts (PDXs) have emerged as reliable preclinical models to develop effective treatments in translational cancer research. However, most PDX combination study designs focus on single dose levels, and dose–response surface models are not appropriate for testing synergism. We propose a comprehensive statistical framework to assess joint action of drug combinations from PDX tumor growth curve data. We provide various metrics and robust statistical inference procedures that locally (at a fixed time) and globally (across time) access combination effects under classical drug interaction models. Integrating genomic and pharmacological profiles in non-small-cell lung cancer (NSCLC), we have shown the utilities of combPDX in discovering effective therapeutic combinations and relevant biological mechanisms. We provide an interactive web server, combPDX (https://licaih.shinyapps.io/CombPDX/), to analyze PDX tumor growth curve data and perform power analyses.
Two-step movement of tsunami boulders unveiled by modified viscous remanent magnetization and radiocarbon dating
Authors: Sato Tetsuro , Sato Masahiko , Yamada Masaki , Saito Hirotake , Satake Kenji , Nakamura Norihiro , Goto Kazuhisa , Miyairi Yosuke , Yokoyama Yusuke 
Published: July 2022

AbstractMassive boulders in landslide and tsunami deposits are prominent geomorphic features in various landscapes. Tracking their movement history is important for reconstructing past geologic dynamics; however, the reworking movements of massive boulders remain unresolved. The boulder field on the Ishigaki Island was formed by repeated tsunamis. Although the individual movement histories of boulders contribute to retrodict the history of different magnitude tsunamis, their radiocarbon ages only correspond to the tsunamis that detached boulders from the reef. Viscous remanent magnetization dating methods have been applied in reworking movements. These methods reveal signals associated with remanent magnetization that gradually grew since the reworking event, which helps to determine the passage of time. The methods were verified by comparison to the radiocarbon ages of un-reworked boulders detached by the recent Meiwa tsunami, while the estimated ages of such two boulders based on the classical relaxation theory contradicted the radiocarbon ages. Here, we show that a method based on the stretched exponential function addressed this contradiction. The reworking movement was estimated using an additional boulder, whose, using our method, radiocarbon age indicated that an older tsunami moved it, whereas the remanent magnetization age unveiled a reworking of the boulder attributed to the Meiwa tsunami.