bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 infection analysis framework using novel boosted CNNs and radiological images
Authors: Khan Saddam Hussain , Alahmadi Tahani Jaser , Alsahfi Tariq , Alsadhan Abeer Abdullah , Mazroa Alanoud Al , Alkahtani Hend Khalid , Albanyan Abdullah , Sakr Hesham A. 
Published: December 2023

AbstractCOVID-19, a novel pathogen that emerged in late 2019, has the potential to cause pneumonia with unique variants upon infection. Hence, the development of efficient diagnostic systems is crucial in accurately identifying infected patients and effectively mitigating the spread of the disease. However, the system poses several challenges because of the limited availability of labeled data, distortion, and complexity in image representation, as well as variations in contrast and texture. Therefore, a novel two-phase analysis framework has been developed to scrutinize the subtle irregularities associated with COVID-19 contamination. A new Convolutional Neural Network-based STM-BRNet is developed, which integrates the Split-Transform-Merge (STM) block and Feature map enrichment (FME) techniques in the first phase. The STM block captures boundary and regional-specific features essential for detecting COVID-19 infectious CT slices. Additionally, by incorporating the FME and Transfer Learning (TL) concept into the STM blocks, multiple enhanced channels are generated to effectively capture minute variations in illumination and texture specific to COVID-19-infected images. Additionally, residual multipath learning is used to improve the learning capacity of STM-BRNet and progressively increase the feature representation by boosting at a high level through TL. In the second phase of the analysis, the COVID-19 CT scans are processed using the newly developed SA-CB-BRSeg segmentation CNN to accurately delineate infection in the images. The SA-CB-BRSeg method utilizes a unique approach that combines smooth and heterogeneous processes in both the encoder and decoder. These operations are structured to effectively capture COVID-19 patterns, including region-homogenous, texture variation, and border. By incorporating these techniques, the SA-CB-BRSeg method demonstrates its ability to accurately analyze and segment COVID-19 related data. Furthermore, the SA-CB-BRSeg model incorporates the novel concept of CB in the decoder, where additional channels are combined using TL to enhance the learning of low contrast regions. The developed STM-BRNet and SA-CB-BRSeg models achieve impressive results, with an accuracy of 98.01%, recall of 98.12%, F-score of 98.11%, Dice Similarity of 96.396%, and IOU of 98.85%. The proposed framework will alleviate the workload and enhance the radiologist's decision-making capacity in identifying the infected region of COVID-19 and evaluating the severity stages of the disease.
Insights from the 2-year-long human confinement experiment in Grand Cayman reveal the resilience of coral reef fish communities
Authors: Johnson Jack V. , Chequer Alex D. , Goodbody-Gringley Gretchen 
Published: December 2023

AbstractIn March 2020, the world went into lockdown to curb the spread of the novel coronavirus (SARS-CoV-2), with immediate impacts on wildlife across ecosystems. The strict 2-year long lockdown in Grand Cayman provided an unprecedented opportunity to assess how the ‘human confinement experiment’ influenced the community composition of reef fish. Using a suite of multivariate statistics, our findings revealed a stark increase in reef fish biomass during the 2 years of lockdown, especially among herbivores, including parrotfish, with drastic increases in juvenile parrotfishes identified. Additionally, when comparing baseline data of the community from 2018 to the 2 years during lockdown, over a three-fold significant increase in mean reef fish biomass was observed, with a clear shift in community composition. Our findings provide unique insights into the resilience of reef fish communities when local anthropogenic stressors are removed for an unprecedented length of time. Given the functional role of herbivores including parrotfish, our results suggest that reductions in human water-based activities have positive implications for coral reef ecosystems and should be considered in future management strategies.
Comprehensive modeling of cell culture profile using Raman spectroscopy and machine learning
Authors: Tanemura Hiroki , Kitamura Ryunosuke , Yamada Yasuko , Hoshino Masato , Kakihara Hirofumi , Nonaka Koichi 
Published: December 2023

AbstractChinese hamster ovary (CHO) cells are widely utilized in the production of antibody drugs. To ensure the production of large quantities of antibodies that meet the required specifications, it is crucial to monitor and control the levels of metabolites comprehensively during CHO cell culture. In recent years, continuous analysis methods employing on-line/in-line techniques using Raman spectroscopy have attracted attention. While these analytical methods can nondestructively monitor culture data, constructing a highly accurate measurement model for numerous components is time-consuming, making it challenging to implement in the rapid research and development of pharmaceutical manufacturing processes. In this study, we developed a comprehensive, simple, and automated method for constructing a Raman model of various components measured by LC–MS and other techniques using machine learning with Python. Preprocessing and spectral-range optimization of data for model construction (partial least square (PLS) regression) were automated and accelerated using Bayes optimization. Subsequently, models were constructed for each component using various model construction techniques, including linear regression, ridge regression, XGBoost, and neural network. This enabled the model accuracy to be improved compared with PLS regression. This automated approach allows continuous monitoring of various parameters for over 100 components, facilitating process optimization and process monitoring of CHO cells.
Appraising the role of circulating concentrations of micronutrients in attention deficit hyperactivity disorder: a Mendelian randomization study
Authors: Sui Xiaohui , Liu Tingting , Zou Zhiyun , Zhang Baoqing 
Published: December 2023

AbstractPrevious observational researches have discovered a connection between circulating concentrations of micronutrients and attention deficit hyperactivity disorder (ADHD). However, the results may be influenced by confounding factors and reverse causation. This study aims to explore the causal relationship between circulating concentrations of micronutrients and ADHD using Mendelian randomization (MR). In a two-sample MR context, we used summary data from the major European genome-wide association studies (GWAS) for these illnesses to assess the genetically anticipated effects of circulating concentrations of micronutrients on ADHD risk. In order to achieve this, we took single nucleotide polymorphisms (SNPs) from the GWAS that were highly related with concentrations of nine micronutrients. The corresponding data for ADHD were extracted from the Psychiatric Genomics Consortium. Inverse-variance weighted (IVW) method was used as the main MR analysis, and the reliability of the study’s conclusions was assessed using sensitivity analyses. Our MR analyses showed that the copper level may be associated with a reduced risk of ADHD. However, the significance of the research results is weak. There were no clear relationships between other micronutrients and ADHD. Our sensitivity studies confirmed the findings of the primary IVW MR analyses. According to this study, there may be some association between copper level and ADHD, but the significance of the research results is weak, and it is recommended that copper level should be used as a long-term monitoring indicator for further research. The results provide a new idea for the further study of ADHD, and provide guidance for the prevention and treatment of ADHD.
Altered cortical thickness of the superior frontal gyrus and fusiform gyrus in individuals with subthreshold social anxiety
Authors: Kim Byoung-Ho , Park So-Young , Park Chun Il , Bang Minji , Kim Hyun-Ju , Lee Sang-Hyuk 
Published: December 2023

AbstractSubthreshold social anxiety (SSA) is a condition in which individuals experience social anxiety that does not reach the threshold required for a clinical diagnosis of a social anxiety disorder (SAD). Although SSA may not impair lives as severely as SAD, it can affect social functioning. However, only a few studies focused on structural neural correlates of SSA. We recruited 65 individuals with SSA and used the Leibowitz Social Anxiety Scale to assess their social and performance anxiety levels and other relevant measures of social anxiety. Voxel-wise whole-brain correlational analyses showed a positive association between the cortical thickness (CT) of the superior frontal gyrus (SFG) and social anxiety levels and a negative correlation between the CT of the fusiform gyrus (FG) and performance anxiety levels in individuals with SSA. Exploratory Pearson’s correlation analyses showed significant positive correlations between the CT of the SFG and Generalized Anxiety Disorder-7 total scores and negative associations between the CT of the FG and Beck Anxiety Inventory total scores. Our study provides insight into the neural basis of SSA, particularly performance anxiety, by highlighting the association between CT in specific brain regions and SSA characteristics.
PNO1 promotes the progression of osteosarcoma via TGF-β and YAP/TAZ pathway
Authors: Fang Long , Wang Baolong , Yang Zengkun , Zhao Tingbao , Hao Wei 
Published: December 2023

AbstractThis study aimed to explore the potential role and mechanisms of the partner of NOB1 homolog (PNO1) in osteosarcoma. The expression of PNO1 in tumor and adjacent tissue samples was examined using western blotting. Lentiviral transfection was used to establish sh-Ctrl and sh-PNO1 osteosarcoma cell lines. MTT assay, Celigo cell cytometer count, and cell colony formation assay were used to investigate the proliferation of osteosarcoma cells in vitro, whereas xenotransplantation assay was performed for in vivo experiments. Wound-healing and Transwell assays were chosen to verify the migration and invasion of osteosarcoma cells. Flow cytometry assay and caspase-3/7 activity analysis were adopted for the analysis of cell apoptosis and cell cycle. Finally, transcriptome sequencing and bioinformatics analysis were adopted to explore the acting mechanisms. The expression of PNO1 was higher in osteosarcoma tissues than that in adjacent tissues. Down-regulation of PNO1 inhibited the proliferation, migration, and invasion, and induced cell apoptosis and cell cycle arrest of osteosarcoma cells. Furthermore, according to transcriptome sequencing and Kyoto Encyclopedia of Genes and Genomes pathway analysis, we found that PNO1 might affect the progression of osteosarcoma via TGF-β and YAP/TAZ signaling pathways. PNO1 could be a potential target for osteosarcoma treatment.
Large spread in interannual variance of atmospheric CO2 concentration across CMIP6 Earth System Models
Authors: Martín-Gómez Verónica , Ruprich-Robert Yohan , Tourigny Etienne , Bernardello Raffaele , Ortega Pablo , Donat Markus G. , Cabré Margarida Samsó 
Published: December 2023

AbstractNumerical Earth System Models (ESMs) are our best tool to predict the evolution of atmospheric CO2 concentration and its effect on Global temperature. However, large uncertainties exist among ESMs in the variance of the year-to-year changes of atmospheric CO2 concentration. This prevents us from precisely understanding its past evolution and from accurately estimating its future evolution. Here we analyze various ESMs simulations from the 6th Coupled Model Intercomparison Projects (CMIP6) to understand the origins of the inter-model uncertainty in the interannual variability of the atmospheric CO2 concentration. Considering the observed period 1986-2013, we show that most of this uncertainty is coming from the simulation of the land CO2 flux internal variability. Although models agree that those variations are driven by El Niño Southern Oscillation (ENSO), similar ENSO-related surface temperature and precipitation teleconnections across models drive different land CO2 fluxes, pointing to the land vegetation models as the dominant source of the inter-model uncertainty.
Activation of the glutamatergic cingulate cortical-cortical connection facilitates pain in adult mice
Authors: Li Xu-Hui , Shi Wantong , Chen Qi-Yu , Hao Shun , Miao Hui-Hui , Miao Zhuang , Xu Fang , Bi Guo-Qiang , Zhuo Min 
Published: December 2023

AbstractThe brain consists of the left and right cerebral hemispheres and both are connected by callosal projections. Less is known about the basic mechanism of this cortical-cortical connection and its functional importance. Here we investigate the cortical-cortical connection between the bilateral anterior cingulate cortex (ACC) by using the classic electrophysiological and optogenetic approach. We find that there is a direct synaptic projection from one side ACC to the contralateral ACC. Glutamate is the major excitatory transmitter for bilateral ACC connection, including projections to pyramidal cells in superficial (II/III) and deep (V/VI) layers of the ACC. Both AMPA and kainate receptors contribute to synaptic transmission. Repetitive stimulation of the projection also evoked postsynaptic Ca2+ influx in contralateral ACC pyramidal neurons. Behaviorally, light activation of the ACC-ACC connection facilitated behavioral withdrawal responses to mechanical stimuli and noxious heat. In an animal model of neuropathic pain, light inhibitory of ACC-ACC connection reduces both primary and secondary hyperalgesia. Our findings provide strong direct evidence for the excitatory or facilitatory contribution of ACC-ACC connection to pain perception, and this mechanism may provide therapeutic targets for future treatment of chronic pain and related emotional disorders.
Substitution of arginine 219 by glycine compromises stability, dimerization, and catalytic activity in a G6PD mutant
Authors: Zgheib Omar , Chamchoy Kamonwan , Nouspikel Thierry , Blouin Jean-Louis , Cimasoni Laurent , Quteineh Lina , Boonyuen Usa 
Published: December 2023

AbstractGlucose-6-phosphate dehydrogenase (G6PD) deficiency is one of the most common enzymopathies in humans, present in approximately half a billion people worldwide. More than 230 clinically relevant G6PD mutations of different classes have been reported to date. We hereby describe a patient with chronic hemolysis who presents a substitution of arginine by glycine at position 219 in G6PD protein. The variant was never described in an original publication or characterized on a molecular level. In the present study, we provide structural and biochemical evidence for the molecular basis of its pathogenicity. When compared to the wild-type enzyme, the Arg219Gly mutation markedly reduces the catalytic activity by 50-fold while having a negligible effect on substrate binding affinity. The mutation preserves secondary protein structure, but greatly decreases stability at higher temperatures and to trypsin digestion. Size exclusion chromatography elution profiles show monomeric and dimeric forms for the mutant, but only the latter for the wild-type form, suggesting a critical role of arginine 219 in G6PD dimer formation. Our findings have implications in the development of small molecule activators, with the goal of rescuing the phenotype observed in this and possibly other related mutants.
Single-cell map of dynamic cellular microenvironment of radiation-induced intestinal injury
Authors: Lu Hao , Yan Hua , Li Xiaoyu , Xing Yuan , Ye Yumeng , Jiang Siao , Ma Luyu , Ping Jie , Zuo Hongyan , Hao Yanhui , Yu Chao , Li Yang , Zhou Gangqiao , Lu Yiming 
Published: December 2023

AbstractIntestine is a highly radiation-sensitive organ that could be injured during the radiotherapy for pelvic, abdominal, and retroperitoneal tumors. However, the dynamic change of the intestinal microenvironment related to radiation-induced intestine injury (RIII) is still unclear. Using single-cell RNA sequencing, we pictured a dynamic landscape of the intestinal microenvironment during RIII and regeneration. We showed that the various cell types of intestine exhibited heterogeneous radiosensitivities. We revealed the distinct dynamic patterns of three subtypes of intestinal stem cells (ISCs), and the cellular trajectory analysis suggested a complex interconversion pattern among them. For the immune cells, we found that Ly6c+ monocytes can give rise to both pro-inflammatory macrophages and resident macrophages after RIII. Through cellular communication analysis, we identified a positive feedback loop between the macrophages and endothelial cells, which could amplify the inflammatory response induced by radiation. Besides, we identified different T cell subtypes and revealed their role in immunomodulation during the early stage of RIII through inflammation and defense response relevant signaling pathways. Overall, our study provides a valuable single-cell map of the multicellular dynamics during RIII and regeneration, which may facilitate the understanding of the mechanism of RIII.
Siliceous zeolite-derived topology of amorphous silica
Authors: Masai Hirokazu , Kohara Shinji , Wakihara Toru , Shibazaki Yuki , Onodera Yohei , Masuno Atsunobu , Sukenaga Sohei , Ohara Koji , Sakai Yuki , Haines Julien , Levelut Claire , Hébert Philippe , Isambert Aude , Keen David A. , Azuma Masaki 
Published: December 2023

Abstract
The topology of amorphous materials can be affected by mechanical forces during compression or milling, which can induce material densification. Here, we show that densified amorphous silica (SiO2) fabricated by cold compression of siliceous zeolite (SZ) is permanently densified, unlike densified glassy SiO2 (GS) fabricated by cold compression although the X-ray diffraction data and density of the former are identical to those of the latter. Moreover, the topology of the densified amorphous SiO2 fabricated from SZ retains that of crystalline SZ, whereas the densified GS relaxes to pristine GS after thermal annealing. These results indicate that it is possible to design new functional amorphous materials by tuning the topology of the initial zeolitic crystalline phases.
Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic
Authors: Priest Taylor , Vidal-Melgosa Silvia , Hehemann Jan-Hendrik , Amann Rudolf , Fuchs Bernhard M 
Published: December 2023

Abstract
Carbohydrates are chemically and structurally diverse, represent a substantial fraction of marine organic matter and are key substrates for heterotrophic microbes. Studies on carbohydrate utilisation by marine microbes have been centred on phytoplankton blooms in temperate regions, while far less is known from high-latitude waters and during later seasonal stages. Here, we combine glycan microarrays and analytical chromatography with metagenomics and metatranscriptomics to show the spatial heterogeneity in glycan distribution and potential carbohydrate utilisation by microbes in Atlantic waters of the Arctic. The composition and abundance of monomers and glycan structures in POM varied with location and depth. Complex fucose-containing sulfated polysaccharides, known to accumulate in the ocean, were consistently detected, while the more labile β-1,3-glucan exhibited a patchy distribution. Through ‘omics analysis, we identify variations in the abundance and transcription of carbohydrate degradation-related genes across samples at the community and population level. The populations contributing the most to transcription were taxonomically related to those known as primary responders and key carbohydrate degraders in temperate ecosystems, such as NS4 Marine Group and Formosa. The unique transcription profiles for these populations suggest distinct substrate utilisation potentials, with predicted glycan targets corresponding to those structurally identified in POM from the same sampling sites. By combining cutting-edge technologies and protocols, we provide insights into the carbohydrate component of the carbon cycle in the Arctic during late summer and present a high-quality dataset that will be of great value for future comparative analyses.
First-in-human diagnostic study of hepatic steatosis with computed ultrasound tomography in echo mode
Authors: Stähli Patrick , Becchetti Chiara , Korta Martiartu Naiara , Berzigotti Annalisa , Frenz Martin , Jaeger Michael 
Published: December 2023

Abstract
Background
Non-alcoholic fatty liver disease is rapidly emerging as the leading global cause of chronic liver disease. Efficient disease management requires low-cost, non-invasive techniques for diagnosing hepatic steatosis accurately. Here, we propose quantifying liver speed of sound (SoS) with computed ultrasound tomography in echo mode (CUTE), a recently developed ultrasound imaging modality adapted to clinical pulse-echo systems. CUTE reconstructs the spatial distribution of SoS by measuring local echo phase shifts when probing tissue at varying steering angles in transmission and reception.

Methods
In this first-in-human phase II diagnostic study, we evaluated the liver of 22 healthy volunteers and 22 steatotic patients. We used conventional B-mode ultrasound images and controlled attenuation parameter (CAP) to diagnose the presence (CAP≥ 280 dB/m) or absence (CAP < 248 dB/m) of steatosis in the liver. A fully integrated convex-probe CUTE implementation was developed on the ultrasound system to estimate liver SoS. We investigated its diagnostic value via the receiver operating characteristic (ROC) analysis and correlation to CAP measurements.

Results
We show that liver CUTE-SoS estimates correlate strongly (r = −0.84, p = 8.27 × 10−13) with CAP values and have 90.9% (95% confidence interval: 84–100%) sensitivity and 95.5% (81–100%) specificity for differentiating between normal and steatotic livers (area under the ROC curve: 0.93–1.0).

Conclusions
Our results demonstrate that liver CUTE-SoS is a promising quantitative biomarker for diagnosing liver steatosis. This is a necessary first step towards establishing CUTE as a new quantitative add-on to diagnostic ultrasound that can potentially be as versatile as conventional ultrasound imaging.
Deep network with double reuses and convolutional shortcuts
Authors: Liu Qian , Wang Cunbao 
Published: December 2023

AbstractThe authors design a novel convolutional network architecture, that is, deep network with double reuses and convolutional shortcuts, in which new compressed reuse units are presented. Compressed reuse units combine the reused features from the first 3 × 3 convolutional layer and the features from the last 3 × 3 convolutional layer to produce new feature maps in the current compressed reuse unit, simultaneously reuse the feature maps from all previous compressed reuse units to generate a shortcut by an 1 × 1 convolution, and then concatenate these new maps and this shortcut as the input to next compressed reuse unit. Deep network with double reuses and convolutional shortcuts uses the feature reuse concatenation from all compressed reuse units as the final features for classification. In deep network with double reuses and convolutional shortcuts, the inner‐ and outer‐unit feature reuses and the convolutional shortcut compressed from the previous outer‐unit feature reuses can alleviate the vanishing‐gradient problem by strengthening the forward feature propagation inside and outside the units, improve the effectiveness of features and reduce calculation cost. Experimental results on CIFAR‐10, CIFAR‐100, ImageNet ILSVRC 2012, Pascal VOC2007 and MS COCO benchmark databases demonstrate the effectiveness of authors’ architecture for object recognition and detection, as compared with the state‐of‐the‐art.