bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of proton therapy on the DNA damage induction and repair in hematopoietic stem and progenitor cells
Authors: Sioen Simon , Vanhove Oniecha , Vanderstraeten Barbara , De Wagter Carlos , Engelbrecht Monique , Vandevoorde Charlot , De Kock Evan , Van Goethem Marc-Jan , Vral Anne , Baeyens Ans 
Published: October 2023

AbstractProton therapy is of great interest to pediatric cancer patients because of its optimal depth dose distribution. In view of healthy tissue damage and the increased risk of secondary cancers, we investigated DNA damage induction and repair of radiosensitive hematopoietic stem and progenitor cells (HSPCs) exposed to therapeutic proton and photon irradiation due to their role in radiation-induced leukemia. Human CD34+ HSPCs were exposed to 6 MV X-rays, mid- and distal spread-out Bragg peak (SOBP) protons at doses ranging from 0.5 to 2 Gy. Persistent chromosomal damage was assessed with the micronucleus assay, while DNA damage induction and repair were analyzed with the γ-H2AX foci assay. No differences were found in induction and disappearance of γ-H2AX foci between 6 MV X-rays, mid- and distal SOBP protons at 1 Gy. A significantly higher number of micronuclei was found for distal SOBP protons compared to 6 MV X-rays and mid- SOBP protons at 0.5 and 1 Gy, while no significant differences in micronuclei were found at 2 Gy. In HSPCs, mid-SOBP protons are as damaging as conventional X-rays. Distal SOBP protons showed a higher number of micronuclei in HSPCs depending on the radiation dose, indicating possible changes of the in vivo biological response.
Volcanic glass from the 1.8 ka Taupō eruption (New Zealand) detected in Antarctic ice at ~ 230 CE
Authors: Piva Stephen B. , Barker Simon J. , Iverson Nels A. , Winton V. Holly L. , Bertler Nancy A. N. , Sigl Michael , Wilson Colin J. N. , Dunbar Nelia W. , Kurbatov Andrei V. , Carter Lionel , Charlier Bruce L. A. , Newnham Rewi M. 
Published: October 2023

AbstractChemical anomalies in polar ice core records are frequently linked to volcanism; however, without the presence of (crypto)tephra particles, links to specific eruptions remain speculative. Correlating tephras yields estimates of eruption timing and potential source volcano, offers refinement of ice core chronologies, and provides insights into volcanic impacts. Here, we report on sparse rhyolitic glass shards detected in the Roosevelt Island Climate Evolution (RICE) ice core (West Antarctica), attributed to the 1.8 ka Taupō eruption (New Zealand)—one of the largest and most energetic Holocene eruptions globally. Six shards of a distinctive geochemical composition, identical within analytical uncertainties to proximal Taupō glass, are accompanied by a single shard indistinguishable from glass of the ~25.5 ka Ōruanui supereruption, also from Taupō volcano. This double fingerprint uniquely identifies the source volcano and helps link the shards to the climactic phase of the Taupō eruption. The englacial Taupō-derived glass shards coincide with a particle spike and conductivity anomaly at 278.84 m core depth, along with trachytic glass from a local Antarctic eruption of Mt. Melbourne. The assessed age of the sampled ice is 230 ± 19 CE (95% confidence), confirming that the published radiocarbon wiggle-match date of 232 ± 10 CE (2 SD) for the Taupō eruption is robust.
Revision of the Schistura cincticauda species group (Teleostei, Nemacheilidae) using molecular and morphological markers
Authors: Dvořák Tomáš , Bohlen Jörg , Kottelat Maurice , Šlechtová Vendula 
Published: October 2023

AbstractTo approach the taxonomy of large and complex animal groups it is of advantage to focus on species groups with shared derived character state. We investigate the composition, morphological characteristics and relationships of and within the Schistura cincticauda species group, whose members are small freshwater fishes that inhabit streams and rivers in eastern Myanmar and western and southern Thailand. A phylogenetic analysis using molecular genetic markers demonstrated the monophyly of this group; a combined genetic and morphological analysis revealed the inclusion of at least twelve species. They share the presence of a pair of black marks on the lower lip, one on each side of the median interruption (these marks may be reduced to few melanophores or even missing in some individuals). Additionally, all species share a small body size (max. 60 mm SL), an incomplete lateral line reaching at most to vertical through anal-fin base, and the absence of sexual dimorphism. Each of the 12 species is diagnosed by a unique combination of character states in fin ray numbers, anus position, presence/absence of an axillary pelvic lobe, and colour pattern. The distribution areas of several species overlap and five cases of syntopic occurrence are known. Five unnamed species are described herein.
Fully automated sequential immunofluorescence (seqIF) for hyperplex spatial proteomics
Authors: Rivest François , Eroglu Deniz , Pelz Benjamin , Kowal Joanna , Kehren Alexandre , Navikas Vytautas , Procopio Maria Giuseppina , Bordignon Pino , Pérès Emilie , Ammann Marco , Dorel Emmanuel , Scalmazzi Sylvain , Bruno Lorenzo , Ruegg Matthieu , Campargue Gabriel , Casqueiro Gilles , Arn Lionel , Fischer Jérôme , Brajkovic Saska , Joris Pierre , Cassano Marco , Dupouy Diego 
Published: October 2023

AbstractTissues are complex environments where different cell types are in constant interaction with each other and with non-cellular components. Preserving the spatial context during proteomics analyses of tissue samples has become an important objective for different applications, one of the most important being the investigation of the tumor microenvironment. Here, we describe a multiplexed protein biomarker detection method on the COMET instrument, coined sequential ImmunoFluorescence (seqIF). The fully automated method uses successive applications of antibody incubation and elution, and in-situ imaging enabled by an integrated microscope and a microfluidic chip that provides optimized optical access to the sample. We show seqIF data on different sample types such as tumor and healthy tissue, including 40-plex on a single tissue section that is obtained in less than 24 h, using off-the-shelf antibodies. We also present extensive characterization of the developed method, including elution efficiency, epitope stability, repeatability and reproducibility, signal uniformity, and dynamic range, in addition to marker and panel optimization strategies. The streamlined workflow using off-the-shelf antibodies, data quality enabling downstream analysis, and ease of reaching hyperplex levels make seqIF suitable for immune-oncology research and other disciplines requiring spatial analysis, paving the way for its adoption in clinical settings.
A personalized classification of behavioral severity of autism spectrum disorder using a comprehensive machine learning framework
Authors: Ali Mohamed T. , Gebreil Ahmad , ElNakieb Yaser , Elnakib Ahmed , Shalaby Ahmed , Mahmoud Ali , Sleman Ahmed , Giridharan Guruprasad A. , Barnes Gregory , Elbaz Ayman S. 
Published: October 2023

AbstractAutism Spectrum Disorder (ASD) is characterized as a neurodevelopmental disorder with a heterogeneous nature, influenced by genetics and exhibiting diverse clinical presentations. In this study, we dissect Autism Spectrum Disorder (ASD) into its behavioral components, mirroring the diagnostic process used in clinical settings. Morphological features are extracted from magnetic resonance imaging (MRI) scans, found in the publicly available dataset ABIDE II, identifying the most discriminative features that differentiate ASD within various behavioral domains. Then, each subject is categorized as having severe, moderate, or mild ASD, or typical neurodevelopment (TD), based on the behavioral domains of the Social Responsiveness Scale (SRS). Through this study, multiple artificial intelligence (AI) models are utilized for feature selection and classifying each ASD severity and behavioural group. A multivariate feature selection algorithm, investigating four different classifiers with linear and non-linear hypotheses, is applied iteratively while shuffling the training-validation subjects to find the set of cortical regions with statistically significant association with ASD. A set of six classifiers are optimized and trained on the selected set of features using 5-fold cross-validation for the purpose of severity classification for each behavioural group. Our AI-based model achieved an average accuracy of 96%, computed as the mean accuracy across the top-performing AI models for feature selection and severity classification across the different behavioral groups. The proposed AI model has the ability to accurately differentiate between the functionalities of specific brain regions, such as the left and right caudal middle frontal regions. We propose an AI-based model that dissects ASD into behavioral components. For each behavioral component, the AI-based model is capable of identifying the brain regions which are associated with ASD as well as utilizing those regions for diagnosis. The proposed system can increase the speed and accuracy of the diagnostic process and result in improved outcomes for individuals with ASD, highlighting the potential of AI in this area.
Genetic diversity of hepatitis B virus quasispecies in different biological compartments reveals distinct genotypes
Authors: do Lago Bárbara Vieira , Bezerra Cristianne Sousa , Moreira Daniel Andrade , Parente Thiago Estevam , Portilho Moyra Machado , Pessôa Rodrigo , Sanabani Sabri Saeed , Villar Livia Melo 
Published: October 2023

AbstractThe selection pressure imposed by the host immune system impacts hepatitis B virus (HBV) quasispecies variability. This study evaluates HBV genetic diversity in different biological fluids. Twenty paired serum, oral fluid, and DBS samples from chronic HBV carriers were analyzed using both Sanger and next generation sequencing (NGS). The mean HBV viral load in serum was 5.19 ± 4.3 log IU/mL (median 5.29, IQR 3.01–7.93). Genotype distribution was: HBV/A1 55% (11/20), A2 15% (3/20), D3 10% (2/20), F2 15% (3/20), and F4 5% (1/20). Genotype agreement between serum and oral fluid was 100% (genetic distances 0.0–0.006), while that between serum and DBS was 80% (genetic distances 0.0–0.115). Two individuals presented discordant genotypes in serum and DBS. Minor population analysis revealed a mixed population. All samples displayed mutations in polymerase and/or surface genes. Major population analysis of the polymerase pointed to positions H122 and M129 as the most polymorphic (≥ 75% variability), followed by V163 (55%) and I253 (50%). Neither Sanger nor NGS detected any antiviral primary resistance mutations in the major populations. Minor population analysis, however, demonstrated the rtM204I resistance mutation in all individuals, ranging from 2.8 to 7.5% in serum, 2.5 to 6.3% in oral fluid, and 3.6 to 7.2% in DBS. This study demonstrated that different fluids can be used to assess HBV diversity, nonetheless, genotypic differences according to biological compartments can be observed.
RETRACTED ARTICLE: Sign language recognition using the fusion of image and hand landmarks through multi-headed convolutional neural network
Authors: Pathan Refat Khan , Biswas Munmun , Yasmin Suraiya , Khandaker Mayeen Uddin , Salman Mohammad , Youssef Ahmed A. F. 
Published: October 2023

AbstractSign Language Recognition is a breakthrough for communication among deaf-mute society and has been a critical research topic for years. Although some of the previous studies have successfully recognized sign language, it requires many costly instruments including sensors, devices, and high-end processing power. However, such drawbacks can be easily overcome by employing artificial intelligence-based techniques. Since, in this modern era of advanced mobile technology, using a camera to take video or images is much easier, this study demonstrates a cost-effective technique to detect American Sign Language (ASL) using an image dataset. Here, “Finger Spelling, A” dataset has been used, with 24 letters (except j and z as they contain motion). The main reason for using this dataset is that these images have a complex background with different environments and scene colors. Two layers of image processing have been used: in the first layer, images are processed as a whole for training, and in the second layer, the hand landmarks are extracted. A multi-headed convolutional neural network (CNN) model has been proposed and tested with 30% of the dataset to train these two layers. To avoid the overfitting problem, data augmentation and dynamic learning rate reduction have been used. With the proposed model, 98.981% test accuracy has been achieved. It is expected that this study may help to develop an efficient human–machine communication system for a deaf-mute society.
Male sex and pretreatment weight loss are associated with poor outcome in patients with advanced non-small cell lung cancer treated with immunotherapy: a retrospective study
Authors: Jin Jingxiao , Visina Jacqueline , Burns Timothy F. , Diergaarde Brenda , Stabile Laura P. 
Published: October 2023

AbstractThe influence of sex and body mass index (BMI) on the efficacy of immune checkpoint inhibitors (ICIs) in advanced non-small cell lung cancer (NSCLC) patients remains unclear. We conducted a retrospective study to evaluate the relationship between sex, BMI, pretreatment weight loss (PWL), and clinical outcomes in 399 stage IV NSCLC patients treated with ICIs using data abstracted from medical records. Multivariable Cox proportional hazards models were used to assess the impact on overall survival and progression-free survival. Females were significantly more likely to experience immune-related adverse events and had a significantly lower risk of death compared to males in our patient cohort. In stratified analyses, the latter was limited to those receiving first-line monotherapy. BMI was overall not significantly associated with outcome. However, underweight patients had a significantly higher risk of both progression and death compared to normal weight patients in the first-line monotherapy group. When stratified by sex, underweight males had a significantly higher risk of progression and death compared to normal weight males. This was not observed among females. Those with PWL had overall significantly worse outcomes compared to those without. In stratified analyses, PWL was associated with significantly worse OS in both females and males. Stratified by treatment, the worse outcome was limited to those receiving ICI monotherapy. In summary, utilizing real-world data, this study suggests that male sex, being underweight, and PWL negatively impact ICI efficacy in NSCLC patients. Therapeutic approaches to improve ICI outcomes in underweight patients and those with PWL should be investigated.
Study on the effect of excavation sequence of three-hole shield tunnel on surface settlement and segment deformation
Authors: Wang You , Dai Fang , Ding Bosong , Zhong Ming , Zhang Heng 
Published: October 2023

AbstractIn order to study the influence of excavation sequence of three-hole parallel shield tunnel on surface settlement and segment convergence, an improved “three-stage analysis method” was proposed to calculate the surface settlement of three-hole parallel shield tunnel. Based on Peck's existing theory, this method deduced the ground settlement formula under the three-hole parallel condition, and can calculate the ground settlement more accurately. Based on the engineering background of a shield tunnel section in Jiangsu Province, a three-dimensional model of a three-hole parallel shield tunnel was established by using Flac3d software, and the three-hole parallel shield tunnel was simulated under four working conditions: right–center–left, right–left–center, right–left–right and right–center (reverse)–left. This paper analyzed the influence of tunnel excavation sequence on surface settlement, soil displacement and deformation of tunnel segments. The construction sequence was optimized based on the above influencing factors. It was found that Case 4, S-type sequential excavation, produced the least ground settlement. The surface settlement value caused by S-type excavation sequence was only 11.41 mm, and the convergence value of the segments generated by S-type excavation sequence was relatively small. Considering the economic factors such as construction efficiency and benefit, the S-shaped excavation sequence was better. The new calculation method of tunnel surface settlement and the optimal sequence of tunnel construction proposed in this paper can provide reference for actual construction.
Influence of the strain effect on magnetocrystalline anisotropy in Co2Fe0.4Mn0.6Si Heusler alloys
Authors: Nabiałek A. , Chumak O. M. , Aleshkevych P. , Domagala J. Z. , Pacewicz A. , Salski B. , Krupka J. , Seki T. , Takanashi K. , Baczewski L. T. , Szymczak H. 
Published: October 2023

AbstractThe perpendicular magnetocrystalline anisotropy, magnetoelastic properties as well as the Gilbert damping factor in Co2Fe0.4Mn0.6Si thin films were found to depend on a magnetic layer thickness, and they can be also tuned by the application of additional Ag buffer layer. The tetragonal distortion of a magnetic layer was found to increase with decreasing thickness, and after the application of an additional Ag buffer layer, the character of this distortion was changed from tensile to compressive in the plane of a film. A correlation between the tetragonal distortion and perpendicular magnetocrystalline anisotropy was found. However, the magnitude of the observed tetragonal distortion for most samples seems to be too small to explain alone the experimentally found large magnitude of the perpendicular magnetocrystalline anisotropy. For these samples, other mechanisms including both surface and volume effects must be taken into account.
Joint analysis of the metabolomics and transcriptomics uncovers the dysregulated network and develops the diagnostic model of high-risk neuroblastoma
Authors: Du Bang , Zhang Fei , Zhou Qiumei , Cheng Weyland , Yu Zhidan , Li Lifeng , Yang Jianwei , Zhang Xianwei , Zhou Chongchen , Zhang Wancun 
Published: October 2023

AbstractHigh-risk neuroblastoma (HR-NB) has a significantly lower survival rate compared to low- and intermediate-risk NB (LIR-NB) due to the lack of risk classification diagnostic models and effective therapeutic targets. The present study aims to characterize the differences between neuroblastomas with different risks through transcriptomic and metabolomic, and establish an early diagnostic model for risk classification of neuroblastoma.Plasma samples from 58 HR-NB and 38 LIR-NB patients were used for metabolomics analysis. Meanwhile, NB tissue samples from 32 HR-NB and 23 LIR-NB patients were used for transcriptomics analysis. In particular, integrative metabolomics and transcriptomic analysis was performed between HR-NB and LIR-NB. A total of 44 metabolites (P < 0.05 and fold change > 1.5) were altered, including 12 that increased and 32 that decreased in HR-NB. A total of 1,408 mRNAs (P < 0.05 and |log2(fold change)|> 1) showed significantly altered in HR-NB, of which 1,116 were upregulated and 292 were downregulated. Joint analysis of both omic data identified 4 aberrant pathways (P < 0.05 and impact ≥ 0.5) consisting of glycerolipid metabolism, retinol metabolism, arginine biosynthesis and linoleic acid metabolism. Importantly, a HR-NB risk classification diagnostic model was developed using plasma circulating-free S100A9, CDK2, and UNC5D, with an area under receiver operating characteristic curve of 0.837 where the sensitivity and specificity in the validation set were both 80.0%. This study presents a novel pioneering study demonstrating the metabolomics and transcriptomics profiles of HR-NB. The glycerolipid metabolism, retinol metabolism, arginine biosynthesis and linoleic acid metabolism were altered in HR-NB. The risk classification diagnostic model based on S100A9, CDK2, and UNC5D can be clinically used for HR-NB risk classification.
Safety assessment of slope on in-service dump under severe dry–wet cycles at high-altitude
Authors: Dong Jianjun , Jiang Hao , Yang Di , Gao Ke 
Published: October 2023

AbstractThis study aimed to evaluate the safety of dump slopes in high-altitude areas subjected to severe dry–wet cycles. The slope of No. 1 and No. 2 in-service dumps in limestone mining areas for cement in high-altitude mining areas is taken as the research object. The unsaturated soil shear strength and matrix suction distribution equations were imported based on the unsaturated–saturated seepage theory. Therefore, the evolution characteristics of the unsaturated–saturated seepage field in the dump are analyzed by numerical calculation, and the safety state of the dump slope is evaluated. The results indicated the following rules: under the action of four dry–wet cycles, the surface soil of the dump slope changes from an unsaturated state to a saturated state. Furthermore, with the increase in the times of the dry–wet cycle, the maximum vertical displacement of the No. 1 and No. 2 dump slopes increased. The numerical calculations of the maximum cumulative vertical displacement of the slope were consistent with the actual monitoring data. The factor of safety of the dump slope decreased continuously with the increase in the times of dry–wet cycles. Nevertheless, it still met the safety and stability standards. It was concluded that the slope of the in-service dump remains stable after enduring four severe cycles of dry–wet.
AutoGIS processing for site selection for solar pond development as efficient water treatment plants in Egypt
Authors: Altahan Mahmoud Fatehy , Nower Mohamed 
Published: October 2023

AbstractThe increasing demand for renewable and environmentally friendly energy sources is a top priority for many countries around the world. It is obvious that renewable solar energy will help to meet most of the energy demand in the coming years. A solar pond is a huge Salt artificial Lake that serves as a solar energy collection system. However, site selection is a critical factor that affects the effectiveness and lifetime of a solar pond. Here, we present an innovative methodology for site selection based on three environmental factors, including direct solar irradiance (DNI), temperature, and wind speed. Our approach uses Python programming and clustering analysis with several libraries, including Pandas, Geopandas, Rasterio, Osgeo, and Sklearn, to analyse and process data collected over a 30-year period from NASA power. This method was applied to the geographic boundaries of Egypt, but the methods can be applied to any spatial context if the same dataset is available. The results show that Egypt has a potential land area of 500 km2 suitable for solar ponds construction along the border with Sudan throughout the year, including 2000 km2 in winter (between January and March), 800 km2 in spring (between April and June), 900 km2 in summer (between July and September), and the largest area of 3700 km2 (between October and December), most of which is located in the south of the Eastern Desert and around the Nile River. Notably, the northwestern region, close to the Mediterranean Sea on the border with Libya, exhibits suitability for solar pond development, with consistent performance throughout the year. Our results provide an efficient way for GIS and data processing and could be useful for implementing new software to find the best location for solar ponds development. This could be beneficial for those interested in investing in renewable energy and using solar ponds as an efficient water treatment plant.