bluuebunny/crossref_metadata_2025 huggingface dataset:
Research on road surface temperature characteristics and road ice warning model of ordinary highways in winter in Hunan province, central China
Authors: Xie Ruiheng , Liao Chunhua , Luo Xiao , Guo Haifeng , Huang Zequn , Peng Weiying
Published: September 2023

The study of road surface temperature (Ts) characteristics in winter and the early warning method of road icing is of great significance to reduce traffic accidents and improve transportation efficiency. Using the hourly observation data of Hunan traffic meteorological stations from December 2020 to February 2022, this study analyzes the winter Ts characteristics of ordinary roads in Hunan Province, and uses the Logistic regression model to establish the temperature threshold for icing of ordinary roads in the province. So as to build a road icing early warning model hierarchically. The results show that the Ts in southern Hunan is relatively high, the Ts at most stations is above 10 °C, and the low Ts area is in western Hunan, and the stations below 8 °C are mostly distributed in this area. This may be due to the higher altitude in western Hunan. In terms of diurnal variation, the lowest value of average Ts and air temperature (Ta) in Hunan Province in winter both appeared at 7:00 Beijing Time (BT), while the highest value appeared at 15:00 BT, and the average Ta is always lower than the Ts. The temperature variation on the bridge surface is more pronounced. When the Ta is lower than −2.5 °C, more than 70% of the sites have a rapid increase in the risk of icing; and when the Ta is lower than −5°C, nearly 87% of the sites have a risk level of 4, which means icing risk is extremely high. Furthermore, combining the warning model with thermal spectrum mapping can improve the spatial resolution of the warning model and also solve the problem of lack of observations in some areas.
Molecular simulation of adsorption behaviors of methane and carbon dioxide on typical clay minerals
Authors: Hui Dong , Li Longxin , Zhang Yan , Peng Xian , Li Tao , Jia Changqing , Pan Yi
Published: September 2023

Knowledge of the interaction mechanisms between shale and CH4/CO2 is crucial for the implementation of CO2 sequestration with enhanced CH4 recovery (CS-EGR) in shale reservoir. As one of the main constituents of shale, clay minerals can profoundly affect the storage capacity of gases in nanopores. In this paper, the adsorption behaviors of both CO2 and CH4 on montmorillonite, illite as well as kaolinite under dry condition are investigated by Grand Canonical Monte Carlo (GCMC) simulation. The results exhibit that the maximum adsorption capacity of single-component CH4 and CO2 is associated with the types of clay crystals. Specifically, the montmorillonite has the strongest adsorption capacity for CO2, followed by illite and kaolinite, while the sequence in maximum adsorption capacity of CH4 is predicted in the order of kaolinite > montmorillonite > illite. These discrepancies are closely related to the characteristics of adsorbate molecules as well as the different structures of clay crystals. Meanwhile, the maximum adsorption capacity of CH4 in studied clay minerals gradually decreases as pore size increases, while nanopores with 2-nm basal spacing demonstrate the highest adsorption capacity for CO2. In addition, it is observed that the studied clay minerals tend to preferentially adsorb CO2 rather than CH4 during binary gas mixtures simulation. The selectivity of CH4/CO2 mixtures in montmorillonite and kaolinite exhibits various performances as the adsorption pressure increases, with the selectivity in montmorillonite being the largest, especially at low pressure. The cation exchange significantly enhances the electrostatic interaction with CO2 molecules, leading to a higher loading of CO2 as well as larger value of selectivity. These findings can provide basis and guidance for the CS-EGR project in shale reservoirs.
Research on the identification of high-resistance ground faults in the flexible DC distribution network based on VMD–inception–CNN
Authors: Zheng Feng , Peng Yaling , Jiang Changxu , Lin Yanzhen , Liang Ning
Published: September 2023

With the rapid development of flexible DC distribution networks, fault detection and identification have also attracted people’s attention. High-resistance grounding fault poses a great challenge to the distribution network. The fault current is very small and random, which makes its detection and identification difficult. The traditional overcurrent protection device cannot identify and act on the fault current. Therefore, this paper proposes a fault detection method based on variational mode decomposition (VMD) combined with the convolutional neural network (CNN) of the inception module. This method first uses VMD to decompose the positive transient voltage. Second, it inputs the decomposed signal into CNN for training to obtain the optimal parameters of the model. Finally, the model performance is tested based on the PSCAD/EMTDC simulation platform. Experiments show that the detection method is accurate and effective. It can realize the accurate identification of seven different fault types.
Ecological vulnerability assessment of coral islands and reefs in the South China Sea based on remote sensing and reanalysis data
Authors: Ma Yuan , Jiang Changbo , Li Shanshan , Liu Yizhuang , Wen Xiaofeng , Long Yuannan , Yuan Shuai , Kang Yuantai , Wang Yongjie , Wu Ruixuan
Published: September 2023

Coral reefs are ecosystems that are highly vulnerable to external environmental impacts, including changes associated with ocean acidification and global warming. Assessing the vulnerability of coral reef growth environments over large areas of the sea is a difficult and complex process, as it is influenced by many variables. There are few studies on environmental vulnerability assessment of coral islands and reefs in the South China Sea. It is therefore particularly important to understand the environmental sensitivity of corals and how coral communities respond to changes in climate-related environmental variables. In this study, indicators were selected mainly from natural environmental factors that hinder the development of coral reefs. The sea surface temperature (SST), sea surface salinity (SSS), wind velocity (WV) and direction, sea level height (SL), ocean currents (OC), and chlorophyll concentration (Chl) of coral reefs in South China Sea Island were integrated to calculate the coral reef environmental vulnerability region. In a GIS environment, Spatial Principal Component Analysis (SPCA) was used to develop sensitivity models and evaluate the ecological vulnerability of coral reefs. Based on the Environmental vulnerability indicator (EVI) values, the study area was classified as 5 grades of ecological vulnerability: Potential (0.000–0.577), Light (0.577–0.780), Medium (0.780–0.886), Heavy (0.886–0.993) and Very Heavy (0.993–1.131). Sensitivity models identified regional gradients of environmental stress and found that some coral reefs in western Malaysia and southwestern Philippines have higher vulnerability. Meanwhile, the study found that the reefs of Paracel Islands and Macclesfield Bank areas of medium vulnerability. Future use of high-precision data from long time series will allow better estimates of site-specific vulnerability and allow for the precise establishment of marine protected areas so that the ecological diversity of coral reefs can be sustained.
Recalcitrance to transformation, a hindrance for genome editing of legumes
Authors: Nivya V. M. , Shah Jasmine M.
Published: September 2023

Plant genome editing, a recently discovered method for targeted mutagenesis, has emerged as a promising tool for crop improvement and gene function research. Many genome-edited plants, such as rice, wheat, and tomato, have emerged over the last decade. As the preliminary steps in the procedure for genome editing involve genetic transformation, amenability to genome editing depends on the efficiency of genetic engineering. Hence, there are numerous reports on the aforementioned crops because they are transformed with relative ease. Legume crops are rich in protein and, thus, are a favored source of plant proteins for the human diet in most countries. However, legume cultivation often succumbs to various biotic/abiotic threats, thereby leading to high yield loss. Furthermore, certain legumes like peanuts possess allergens, and these need to be eliminated as these deprive many people from gaining the benefits of such crops. Further genetic variations are limited in certain legumes. Genome editing has the potential to offer solutions to not only combat biotic/abiotic stress but also generate desirable knock-outs and genetic variants. However, excluding soybean, alfalfa, and Lotus japonicus, reports obtained on genome editing of other legume crops are less. This is because, excluding the aforementioned three legume crops, the transformation efficiency of most legumes is found to be very low. Obtaining a higher number of genome-edited events is desirable as it offers the option to genotypically/phenotypically select the best candidate, without the baggage of off-target mutations. Eliminating the barriers to genetic engineering would directly help in increasing genome-editing rates. Thus, this review aims to compare various legumes for their transformation, editing, and regeneration efficiencies and discusses various solutions available for increasing transformation and genome-editing rates in legumes.
Case Report: Decrypting an interchromosomal insertion associated with Marfan’s syndrome: how optical genome mapping emphasizes the morbid burden of copy-neutral variants
Authors: Bonaglia Maria Clara , Salvo Eliana , Sironi Manuela , Bertuzzo Sara , Errichiello Edoardo , Mattina Teresa , Zuffardi Orsetta
Published: September 2023

Optical genome mapping (OGM), which allows analysis of ultra-high molecular weight (UHMW) DNA molecules, represents a response to the restriction created by short-read next-generation-sequencing, even in cases where the causative variant is a neutral copy-number-variant insensitive to quantitative investigations. This study aimed to provide a molecular diagnosis to a boy with Marfan syndrome (MFS) and intellectual disability (ID) carrying a de novo translocation involving chromosomes 3, 4, and 13 and a 1.7 Mb deletion at the breakpoint of chromosome 3. No FBN1 alteration explaining his Marfan phenotype was highlighted. UHMW gDNA was isolated from both the patient and his parents and processed using OGM. Genome assembly was followed by variant calling and annotation. Multiple strategies confirmed the results. The 3p deletion, which disrupted ROBO2, (MIM*602431) included three copy-neutral insertions. Two came from chromosome 13; the third contained 15q21.1, including the FBN1 from intron-45 onwards, thus explaining the MFS phenotype. We could not attribute the ID to a specific gene variant nor to the reshuffling of topologically associating domains (TADs). Our patient did not have vesicular reflux-2, as reported by missense alterations of ROBO2 (VUR2, MIM#610878), implying that reduced expression of all or some isoforms has a different effect than some of the point mutations. Indeed, the ROBO2 expression pattern and its role as an axon-guide suggests that its partial deletion is responsible for the patient’s neurological phenotype. Conclusion: OGM testing 1) highlights copy-neutral variants that could remain invisible if no loss of heterozygosity is observed and 2) is mandatory before other molecular studies in the presence of any chromosomal rearrangement for an accurate genotype-phenotype relationship.
Utilizing proficiency testing survey data to create advanced educational content: the virtual crossmatch challenge model
Authors: Hod-Dvorai Reut , Philogene Mary Carmelle , Timofeeva Olga , Gimferrer Idoia , Dunckley Heather , Greenshields Anna , Jindra Peter
Published: September 2023

Proficiency testing (PT) surveys include data from laboratories across the world and are ideal for creating advanced educational content, beyond just consensus grading. Educational challenges provide a unique opportunity to probe common laboratory practices and risk assessment, especially in cases where there is no “analyte” tested. Human leukocyte antigen (HLA) compatibility evaluation between donor and recipient pairs has been traditionally assessed using T-cell and B-cell physical crossmatches. However, advancements in our ability to identify and characterize HLA antibodies using solid phase assays, in combination with changing deceased donor allocation schemes and improved HLA typing, have shifted the paradigm from performing physical crossmatches to the use of the virtual crossmatch (VXM). VXM is a compatibility assessment relying on the interpretation of pre-transplant HLA laboratory data and as such, it is not an “analyte”. However, VXM results are used in clinical decision-making. The VXM assessment depends on patient characteristics as well as laboratory and transplant center practices but must ensure safe transplantation outcomes while maintaining equity in access to transplantation. In this manuscript, we describe the American Society for Histocompatibility and Immunogenetics (ASHI) PT Educational VXM Challenge, as a model for creating educational content using PT survey data. We discuss the different components of the VXM Challenge and highlight major findings and learning points acquired from ASHI VXM Challenges performed between 2018–2022, such as the lack of correlation between the VXM and the physical crossmatch in the presence of low level donor-specific antibodies (DSA), or when the DSA were aimed against donor alleles that are not present on the antibody panel, and in the presence of an antibody to a shared eplet. Finally, we show that the VXM Educational Challenge serves as a valuable tool to highlight the strengths and pitfalls of the VXM assessment and reveals differences in testing and result interpretation among participating HLA laboratories.
PheWAS and cross-disorder analysis reveal genetic architecture, pleiotropic loci and phenotypic correlations across 11 autoimmune disorders
Authors: Topaloudi Apostolia , Jain Pritesh , Martinez Melanie B. , Bryant Josephine K. , Reynolds Grace , Zagoriti Zoi , Lagoumintzis George , Zamba-Papanicolaou Eleni , Tzartos John , Poulas Konstantinos , Kleopa Kleopas A. , Tzartos Socrates , Georgitsi Marianthi , Drineas Petros , Paschou Peristera
Published: September 2023

Introduction

Autoimmune disorders (ADs) are a group of about 80 disorders that occur when self-attacking autoantibodies are produced due to failure in the self-tolerance mechanisms. ADs are polygenic disorders and associations with genes both in the human leukocyte antigen (HLA) region and outside of it have been described. Previous studies have shown that they are highly comorbid with shared genetic risk factors, while epidemiological studies revealed associations between various lifestyle and health-related phenotypes and ADs.

Methods

Here, for the first time, we performed a comparative polygenic risk score (PRS) - Phenome Wide Association Study (PheWAS) for 11 different ADs (Juvenile Idiopathic Arthritis, Primary Sclerosing Cholangitis, Celiac Disease, Multiple Sclerosis, Rheumatoid Arthritis, Psoriasis, Myasthenia Gravis, Type 1 Diabetes, Systemic Lupus Erythematosus, Vitiligo Late Onset, Vitiligo Early Onset) and 3,254 phenotypes available in the UK Biobank that include a wide range of socio-demographic, lifestyle and health-related outcomes. Additionally, we investigated the genetic relationships of the studied ADs, calculating their genetic correlation and conducting cross-disorder GWAS meta-analyses for the observed AD clusters.

Results

In total, we identified 508 phenotypes significantly associated with at least one AD PRS. 272 phenotypes were significantly associated after excluding variants in the HLA region from the PRS estimation. Through genetic correlation and genetic factor analyses, we identified four genetic factors that run across studied ADs. Cross-trait meta-analyses within each factor revealed pleiotropic genome-wide significant loci.

Discussion

Overall, our study confirms the association of different factors with genetic susceptibility for ADs and reveals novel observations that need to be further explored.
A quantitative systems pharmacology model for certolizumab pegol treatment in moderate-to-severe psoriasis
Authors: Coto-Segura Pablo , Segú-Vergés Cristina , Martorell Antonio , Moreno-Ramírez David , Jorba Guillem , Junet Valentin , Guerri Filippo , Daura Xavier , Oliva Baldomero , Cara Carlos , Suárez-Magdalena Olaya , Abraham Sonya , Mas José Manuel
Published: September 2023

Background

Psoriasis is a chronic immune-mediated inflammatory systemic disease with skin manifestations characterized by erythematous, scaly, itchy and/or painful plaques resulting from hyperproliferation of keratinocytes. Certolizumab pegol [CZP], a PEGylated antigen binding fragment of a humanized monoclonal antibody against TNF-alpha, is approved for the treatment of moderate-to-severe plaque psoriasis. Patients with psoriasis present clinical and molecular variability, affecting response to treatment. Herein, we utilized anin silicoapproach to model the effects of CZP in a virtual population (vPop) with moderate-to-severe psoriasis. Our proof-of-concept study aims to assess the performance of our model in generating a vPop and defining CZP response variability based on patient profiles.

Methods

We built a quantitative systems pharmacology (QSP) model of a clinical trial-like vPop with moderate-to-severe psoriasis treated with two dosing schemes of CZP (200 mg and 400 mg, both every two weeks for 16 weeks, starting with a loading dose of CZP 400 mg at weeks 0, 2, and 4). We applied different modelling approaches: (i) an algorithm to generate vPop according to reference population values and comorbidity frequencies in real-world populations; (ii) physiologically based pharmacokinetic (PBPK) models of CZP dosing schemes in each virtual patient; and (iii) systems biology-based models of the mechanism of action (MoA) of the drug.

Results

The combination of our different modelling approaches yielded a vPop distribution and a PBPK model that aligned with existing literature. Our systems biology and QSP models reproduced known biological and clinical activity, presenting outcomes correlating with clinical efficacy measures. We identified distinct clusters of virtual patients based on their psoriasis-related protein predicted activity when treated with CZP, which could help unravel differences in drug efficacy in diverse subpopulations. Moreover, our models revealed clusters of MoA solutions irrespective of the dosing regimen employed.

Conclusion

Our study provided patient specific QSP models that reproduced clinical and molecular efficacy features, supporting the use of computational methods as modelling strategy to explore drug response variability. This might shed light on the differences in drug efficacy in diverse subpopulations, especially useful in complex diseases such as psoriasis, through the generation of mechanistically based hypotheses.
Interleukin-17 producing cells in swine induced by microbiota during the early postnatal period - a brief research report
Authors: Stepanova Hana , Scheirichova Marketa , Matiasovic Jan , Hlavova Karolina , Sinkora Marek , Stepanova Katerina , Faldyna Martin
Published: September 2023

Interleukin-17A (IL-17) is a pro-inflammatory cytokine involved in the immune response to many pathogens playing also a role in certain chronic and autoimmune diseases. The presented study focused on the early postnatal development of IL-17 producing cells in swine. In agreement with previous studies, αβ T-helper (CD3+CD4+) and γδ T (CD3+TCRγδ+) cells were found to be the major producers of IL-17. In newborn conventional piglets, αβ T-helper cells positive for IL-17 were almost undetectable, but their frequency increased markedly with age in all issues examined, i.e., blood, spleen, and mesenteric lymph nodes (MLN). Additional analyses of CD8 and CD27 expression showed that the main αβ T-helper producers of IL-17 has CD8+CD27- phenotype in all tissues. IL-17 positive CD8+CD27+ αβ T-helper subpopulation was found only in blood and spleen. The production of IL17 in CD8-CD27+ αβ T-helper cells was always minor. In contrast, γδ T cells positive for IL-17 did not show a similar age-dependent increase in blood and spleen, whereas they increased in MLN. Because of the age-dependent increase in conventional animals, we included a comparison with germ-free piglets to show that the increase in IL-17 positive cells was clearly depended on the presence of the microbiota as the production in germ-free animals was negligible without any age-dependent increase.
Reconstruction of subsurface ocean state variables using Convolutional Neural Networks with combined satellite and in situ data
Authors: Smith Philip A. H. , Sørensen Kristian Aa. , Buongiorno Nardelli Bruno , Chauhan Anshul , Christensen Asbjørn , St. John Michael , Rodrigues Filipe , Mariani Patrizio
Published: September 2023

Subsurface ocean measurements are extremely sparse and irregularly distributed, narrowing our ability to describe deep ocean processes and thus also limiting our understanding of the role of ocean and marine ecosystems in the Earth system. To overcome these observational limitations, neural networks combining remotely-sensed surface measurements and in situ vertical profiles are increasingly being used to retrieve high-quality three-dimensional estimates of the ocean state. This study proposes a convolutional neural network (CNN) architecture for the reconstruction of vertical profiles of temperature and salinity starting from surface observation-based data. The model is trained on satellite and in situ data collected between 2005 and 2020 in the Atlantic Ocean. Rather than using spatially gridded in situ observations, we use directly measured vertical profiles. Different combinations of surface variables are analyzed and compared in order to determine the most effective inputs for the CNN. Furthermore, the relative importance of each of these variables in the vertical reconstruction is assessed using Shapley values, originally developed in the framework of cooperative game theory. The model performance is shown to be superior to current state-of-the-art methods and the same approach can easily be extended to other basins or to the global ocean.
Climate change with increasing seawater temperature will challenge the health of farmed Atlantic Cod (Gadus morhua L.)
Authors: Ytteborg Elisabeth , Falconer Lynne , Krasnov Aleksei , Johansen Lill-Heidi , Timmerhaus Gerrit , Johansson Gunhild Seljehaug , Afanasyev Sergey , Høst Vibeke , Hjøllo Solfrid Sætre , Hansen Øyvind J. , Lazado Carlo C.
Published: September 2023

Aquaculture is one of the fastest growing food production sectors in the world and further expansion is expected throughout the 21st century. However, climate change is threatening the development of the sector and action is needed to prepare the industry for the coming challenges. Using downscaled temperature projections based on the Intergovernmental Panel on Climate Change (IPCC) climate projection (Shared Socioeconomic Pathway, SSP2-4.5), we analysed potential future temperatures at a selected Atlantic cod (Gadus morhua L.) farm site in Northern Norway. Results showed that the farming area may experience increased temperatures the next 10–15 years, including more days with temperatures above 17°C. Based on the predicted future conditions, we designed a study with Atlantic cod (Gadus morhua L.) to evaluate effects from high temperature alone and in combination with Fransicella noatunensis infection. Fish were kept at 12°C and 17°C for eight weeks and samples of skin and spleen collected at different timepoints were analysed with transcriptomics, histology, scanning electron microscopy and immunohistochemistry. Results showed that high temperature had a stronger effect on the barrier functions of skin than the infection. Increased temperature induced gene expression changes in skin and spleen, heat shock protein 47 and cold inducible RNA binding protein were identified as potential gene markers for thermal stress. The effect of bacterial challenge was small at 12°C. At high temperature, the development of severe pathology in spleen coincided with a significant decrease of immunoglobulins transcripts, which contrasted with the activation of multiple immune genes. In addition, we used an in vitro model of skin biopsies and scale explants exposed to hydrogen peroxide (H2O2) to assess the effects of thermal and oxidative stress. High temperature and H2O2 reduced proliferation and migration of keratocytes, and increased expression of stress markers, and compounding effects were observed with combined stressors. Results suggest that the projected increased seawater temperature will pose a significant threat to Norwegian cod farming, affecting various biological processes and making fish more vulnerable to stressors and pathogens. Cod farming needs high attention to temperature changes, and special precautions should be taken if the temperature increases beyond cods’ thermal optimum.
Global research of artificial intelligence in strabismus: a bibliometric analysis
Authors: Zhou Ziying , Zhang Xuan , Tang Xiajing , Grzybowski Andrzej , Ye Juan , Lou Lixia
Published: September 2023

Purpose

To analyze the global publications on artificial intelligence (AI) in strabismus using a bibliometric approach.

Methods

The Web of Science Core Collection (WoSCC) database was used to retrieve all of the publications on AI in strabismus from 2002 to 2023. We analyzed the publication and citation trend and identified highly-cited articles, prolific countries, institutions, authors and journals, relevant research domains and keywords. VOSviewer (software) and Bibliometrix (package) were used for data analysis and visualization.

Results

By analyzing a total of 146 relevant publications, this study found an overall increasing trend in the number of annual publications and citations in the last decade. USA was the most productive country with the closest international cooperation. The top 3 research domains were Ophthalmology, Engineering Biomedical and Optics. Journal of AAPOS was the most productive journal in this field. The keywords analysis showed that “deep learning” and “machine learning” may be the hotspots in the future.

Conclusion

In recent years, research on the application of AI in strabismus has made remarkable progress. The future trends will be toward optimized technology and algorithms. Our findings help researchers better understand the development of this field and provide valuable clues for future research directions.
Molecular typing and characterization of Staphylococcus aureus isolates from burn wound infections in Fujian, China
Authors: Hong Xiaolan , Zhou Shaobo , Dai Xubo , Xie Dandan , Cai Yuanyuan , Zhao Guimei , Li Bin
Published: September 2023

Background

Staphylococcus aureus (S. aureus) is the most common causative agent of burn wound infection, that often leads to high morbidity and mortality. However, there is not enough knowledge about the molecular epidemiology and antimicrobial susceptibility of S. aureus isolates from burn wound infections in Fujian, China.

Methods

Between 2016 and 2021, 90 S. aureus isolates were collected from burn wound infections in Fujian, China, including 59 methicillin-resistant (MRSA) strains and 31 methicillin-susceptible (MSSA) strains. These were investigated for molecular characteristics, virulence genes, biofilms, and antimicrobial susceptibility. All the isolates were genotyped by multilocus sequence typing (MLST), spa typing, agr typing, and SCCmec typing. Conventional PCR was performed for the detection of virulence genes. Biofilm formation capacity was assessed by tissue culture plate assay (TCP). The antimicrobial susceptibility of the isolates was evaluated using the dilution method.

Results

In total, 37 sequence types (ST) and 34 Staphylococcal protein A (spa) types (including a new type named spa-t20720) were identified based on multilocus sequence typing (MLST) and spa typing, respectively. CC8-ST239-t030-agrI-SCCmecIII (57.6%,34/59) and CC7-ST7-t091-agrI (16.1%, 5/31) represented the main clone of MRSA and MSSA isolates, respectively. Antibiotic susceptibility testing identified a significant difference in resistance rates between ST239 and non-ST239 isolates (p < 0.05). Twelve virulence genes were detected, of which the most common were icaA and icaD (both 100%), followed by icaB and icaC (both 96.7%), icaR (95.6%), lukED (81.1%), lukAB (62.2%), pvl (50%), hlgBC (26.7%), and eta (4.4%). Moreover, lukAB, hlgBC, agrI, and agrIII were significantly correlated with burn severity (p < 0.05). MRSA isolates were less likely, compared with MSSA isolates, to carry pvl, lukAB, and hlgBC (p < 0.05). A new spa type, t20720, was identified that contains pvl, lukED, lukAB, hlgBC, icaA, icaB, icaC, icaD, and icaR genes and has strong biofilm formation ability.

Conclusion

CC8-ST239-t030-agrI-SCCmecIII and CC7-ST-7-t091-agrI were the prevalent molecular signatures of MRSA and MSSA isolates from burn wound infections in Fujian, China, respectively. The newly identified spa-t20720 isolate, which carries a wide range of virulence genes and has strong biofilm formation ability, requires special clinical attention.
Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action
Authors: D’Elia Domenica , Truu Jaak , Lahti Leo , Berland Magali , Papoutsoglou Georgios , Ceci Michelangelo , Zomer Aldert , Lopes Marta B. , Ibrahimi Eliana , Gruca Aleksandra , Nechyporenko Alina , Frohme Marcus , Klammsteiner Thomas , Pau Enrique Carrillo-de Santa , Marcos-Zambrano Laura Judith , Hron Karel , Pio Gianvito , Simeon Andrea , Suharoschi Ramona , Moreno-Indias Isabel , Temko Andriy , Nedyalkova Miroslava , Apostol Elena-Simona , Truică Ciprian-Octavian , Shigdel Rajesh , Telalović Jasminka Hasić , Bongcam-Rudloff Erik , Przymus Piotr , Jordamović Naida Babić , Falquet Laurent , Tarazona Sonia , Sampri Alexia , Isola Gaetano , Pérez-Serrano David , Trajkovik Vladimir , Klucar Lubos , Loncar-Turukalo Tatjana , Havulinna Aki S. , Jansen Christian , Bertelsen Randi J. , Claesson Marcus Joakim
Published: September 2023

The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices.
The cultivation regimes of Morchella sextelata trigger shifts in the community assemblage and ecological traits of soil bacteria
Authors: Zhang Yan , Zhao Qi , Uroz Stéphane , Gao Tianpeng , Li Jing , He Fengqin , Rosazlina Rusly , Martin Francis , Xu Lingling
Published: September 2023

The successful large-scale cultivation of morel mushrooms (Morchella sextelata) requires a comprehensive understanding of the soil bacterial communities associated with morel-farming beds, as the interactions between fungi and bacteria play a crucial role in shaping the soil microbiome. In this study, we investigated the temporal distribution and ecological characteristics of soil bacteria associated with morel fruiting bodies at different stages, specifically the conidial and primordial stages, under two cropping regimes, non-continuous cropping (NCC) and continuous cropping (CC). Our findings revealed a significant reduction in the yield of morel primordia during the third year following 2 years of CC (0.29 ± 0.25 primordia/grid), in comparison to the NCC regime (12.39 ± 6.09 primordia/grid). Furthermore, inoculation with morel mycelia had a notable impact on soil bacterial diversity, decreasing it in the NCC regime and increasing the number of generalist bacterial members in the CC regime. The latter regime also led to the accumulation of nutrients in the soil beds, resulting in a shift from a stochastic to a deterministic process in the composition of the bacterial community, which differed from the NCC regime. Additionally, mycelial inoculation had a positive effect on the abundance of potential copiotrophic/denitrifying and N-fixing bacteria while decreasing the abundance of oligotrophic/nitrifying bacteria. Interestingly, this effect was more pronounced in the NCC regime than in the CC regime. These results suggest that the increase in potential copiotrophic/denitrifying and N-fixing bacteria facilitated the decomposition of nutrients in exogenous nutrient bags by morel mushrooms, thereby maintaining nitrogen balance in the soil. Overall, our study provides valuable insights into the interactions between morel mycelia and the associated soil bacteriome as well as the influence of different cultivation regimes on these interactions. These findings contribute to our understanding of the complex dynamics of the soil microbiome and can inform strategies for optimizing morel mushroom cultivation.
Anti-nucleolin aptamer AS1411: an advancing therapeutic
Authors: Van den Avont Alexander , Sharma-Walia Neelam
Published: September 2023

Targeted therapy is highly desirable, as it allows for selective cytotoxicity on diseased cells without off-target side effects. Nucleolin is a remarkable target for cancer therapy given its high abundance, selective presence on the plasma membrane, and multifaceted influence on the initiation and progression of cancer. Nucleolin is a protein overexpressed on the cell membrane in many tumors and serves as a binding protein for several ligands implicated in angiogenesis and tumorigenesis. Nucleolin is present in the cytoplasm, nucleoplasm, and nucleolus and is used by selected pathogens for cell entry. AS1411 is a guanosine-rich oligonucleotide aptamer that binds nucleolin and is internalized in the tumor cells. AS1411 is well tolerated at therapeutic doses and localizes to tumor cells overexpressing nucleolin. AS1411 has a good safety profile with efficacy in relapsed acute myeloid leukemia and renal cell carcinoma producing mild or moderate side effects. The promising potential of AS1411 is its ability to be conjugated to drugs and nanoparticles. When a drug is bound to AS1411, the drug will localize to tumor cells leading to targeted therapy with fewer systemic side effects than traditional practices. AS1411 can also be bound to nanoparticles capable of detecting nucleolin at concentrations far lower than lab techniques used today for cancer diagnosis. AS1411 has a promising potential to change cancer diagnoses and treatment.
Cell-type expression and activation by light of neuropsins in the developing and mature Xenopus retina
Authors: Man Lawrence L. H. , Storey Samuel S. , Bertolesi Gabriel E. , McFarlane Sarah
Published: September 2023

Photosensitive opsins detect light and perform image- or nonimage-forming tasks. Opsins such as the “classical” visual opsins and melanopsin are well studied. However, the retinal expression and functions of a novel family of neuropsins are poorly understood. We explored the developmental time-course and cell-type specificity of neuropsin (opn5, 6a, 6b, and 8) expression in Xenopus laevis by in situ hybridization and immunohistochemistry. We compared the Xenopus results with publicly available single cell RNA sequencing (scRNA-seq) data from zebrafish, chicken, and mouse. Additionally, we analyzed light-activation of neuropsin-expressing cells through induction of c-fos mRNA. opn5 and opn8 expression begins at stage 37/38 when the retinal circuits begin to be activated. Once retinal circuits connect to the brain, opn5 mRNA is distributed across multiple retinal cell types, including bipolar (~70%–75%), amacrine (~10%), and retinal ganglion (~20%) cells, with opn8 present in amacrine (~70%) and retinal ganglion (~30%) cells. opn6a and opn6b mRNAs emerge in newborn-photoreceptors (stage 35), and are colocalized in rods and cones by stage 37/38. Interestingly, in the mature larval retina (stage 43/44), opn6a and opn6b mRNAs become preferentially localized to rods and cones, respectively, while newborn photoreceptors bordering the proliferative ciliary marginal zone express both genes. In zebrafish, opn6a and opn6b are also expressed in photoreceptors, while Müller glia and amacrine cells express opn8c. Most neuropsin-expressing retinal ganglion cells display c-fos expression in response to light, as do over half of the neuropsin-expressing interneurons. This study gave a better understanding of retinal neuropsin-expressing cells, their developmental onset, and light activation.
Knowledge and awareness of stroke and associated factors in the Saudi general population: a cross-sectional study
Authors: Alzayer Reem , Barakat Muna , Jirjees Feras , Alhamdan Aqeelah , Aloraifej Shatha , Cherri Sara , Mansour Sara , El Khatib Sami , Kharaba Zelal , Rahal Mohamad , Hallit Souheil , Malaeb Diana , Hosseini Hassan
Published: September 2023

Introduction

Stroke is a major cause of death and disability globally and in Saudi Arabia as well. Prevention and management of stroke depend highly on raising knowledge and awareness about the disease.

Purpose

The purpose of this study was to evaluate Saudi adult's knowledge and awareness about stroke and determine the associated factors.

Materials and methods

A cross-sectional online survey was conducted in May–July 2022 among Saudi citizens. Assessments of stroke knowledge about risk factors, symptoms, and response to stroke symptoms were evaluated. Logistic regression was conducted to assess the association between the socio-demographic characteristics and knowledge.

Results

A total of 389 participants were enrolled with the majority (81.7%) being male participants. Less than half of the study subjects (43.3%) identified four out of five correct answers related to general knowledge about stroke. Almost all the participants were able to identify at least one risk factor associated with stroke. The majority of the participants (81.2%) believed that physical inactivity was the most common risk factor associated with stroke. Approximately three-quarters of participants considered difficulty speaking and understanding speech, followed by the sudden loss of consciousness as the most common stroke manifestation. Participants with a history of hypertension, dyslipidemia, and obesity had significantly higher odds of identifying at least one early stroke symptom (OR 2.271 [95% CI 1.402 3.677], 2.059 [95% CI 1.273 3.328], and 2.665 [95% CI 1.431 4.963], respectively).

Conclusion

Our study revealed that participants have good knowledge about stroke. Nonetheless, further efforts are required to raise awareness and educate the public to optimize and ensure better treatment outcomes.
Case report: Clinical and neuroradiological longitudinal follow-up in Leukoencephalopathy with Calcifications and Cysts during treatment with bevacizumab
Authors: Scaffei Elena , Buchignani Bianca , Pasquariello Rosa , Cristofani Paola , Canapicchi Raffaello , Biagi Laura , Giordano Flavio , De Marco Emanuela , Crow Yanick J. , Battini Roberta
Published: September 2023

Leukoencephalopathy with Calcifications and Cysts (LCC) is a rare genetic microangiopathy exclusively affecting the central nervous system caused by biallelic mutations in SNORD118. Brain magnetic resonance imaging (MRI) is often diagnostic due to the highly characteristic triad of leukoencephalopathy, intracranial calcifications, and brain cysts. Age at onset, presentation and disease evolution can all vary, ranging from pauci-symptomatic disease to rapid evolution of signs with loss of motor and cognitive abilities. No specific therapies for LCC are currently licensed. According to the literature, bevacizumab might represent an effective modality to improve the clinical and MRI features of the disease. However, uncertainty remains as to the true efficacy of this approach, when to begin therapy, appropriate dosing, and the consequences of drug withdrawal. According to CARE guidelines, we describe the long-term clinical and neuro-radiological follow-up of a 10-year-old child with LCC. We report disease evolution following repeated cycles of treatment with bevacizumab. Our case report suggests that repeated cycles of bevacizumab might effectively modify disease progression, possibly indicating a time-dependent effect.
CNS-LAND score: predicting early neurological deterioration after intravenous thrombolysis based on systemic responses and injury
Authors: Jin Huijuan , Bi Rentang , Zhou Yifan , Xiao Qinghui , Li Min , Sun Shuai , Zhou Jinghua , Hu Jichuan , Huang Ming , Li Yanan , Hong Candong , Chen Shengcai , Chang Jiang , Wan Yan , Hu Bo
Published: September 2023

Importance

Early neurological deterioration (END) is a critical complication in acute ischemic stroke (AIS) patients receiving intravenous thrombolysis (IVT), with a need for reliable prediction tools to guide clinical interventions.

Objective

This study aimed to develop and validate a rating scale, utilizing clinical variables and multisystem laboratory evaluation, to predict END after IVT.

Design, setting, and participants

The Clinical Trial of Revascularization Treatment for Acute Ischemic Stroke (TRAIS) cohort enrolled consecutive AIS patients from 14 stroke centers in China (Jan 2018 to Jun 2022).

Outcomes

END defined as NIHSS score increase >4 points or death within 24 h of stroke onset.

Results

1,213 patients (751 in the derivation cohort, 462 in the validation cohort) were included. The CNS-LAND score, a 9-point scale comprising seven variables (CK-MB, NIHSS score, systolic blood pressure, LDH, ALT, neutrophil, and D-dimer), demonstrated excellent differentiation of END (derivation cohort C statistic: 0.862; 95% CI: 0.796–0.928) and successful external validation (validation cohort C statistic: 0.851; 95% CI: 0.814–0.882). Risk stratification showed END risks of 2.1% vs. 29.5% (derivation cohort) and 2.6% vs. 31.2% (validation cohort) for scores 0–3 and 4–9, respectively.

Conclusion

CNS-LAND score is a reliable predictor of END risk in AIS patients receiving IVT.
Neural fingerprinting on MEG time series using MiniRocket
Authors: Kampel Nikolas , Kiefer Christian M. , Shah N. Jon , Neuner Irene , Dammers Jürgen
Published: September 2023

Neural fingerprinting is the identification of individuals in a cohort based on neuroimaging recordings of brain activity. In magneto- and electroencephalography (M/EEG), it is common practice to use second-order statistical measures, such as correlation or connectivity matrices, when neural fingerprinting is performed. These measures or features typically require coupling between signal channels and often ignore the individual temporal dynamics. In this study, we show that, following recent advances in multivariate time series classification, such as the development of the RandOm Convolutional KErnel Transformation (ROCKET) classifier, it is possible to perform classification directly on short time segments from MEG resting-state recordings with remarkably high classification accuracies. In a cohort of 124 subjects, it was possible to assign windows of time series of 1 s in duration to the correct subject with above 99% accuracy. The achieved accuracies are vastly superior to those of previous methods while simultaneously requiring considerably shorter time segments.
Assigning channel weights using an attention mechanism: an EEG interpolation algorithm
Authors: Liu Renjie , Wang Zaijun , Qiu Jiang , Wang Xue
Published: September 2023

During the acquisition of electroencephalographic (EEG) signals, various factors can influence the data and lead to the presence of one or multiple bad channels. Bad channel interpolation is the use of good channels data to reconstruct bad channel, thereby maintaining the original dimensions of the data for subsequent analysis tasks. The mainstream interpolation algorithm assigns weights to channels based on the physical distance of the electrodes and does not take into account the effect of physiological factors on the EEG signal. The algorithm proposed in this study utilizes an attention mechanism to allocate channel weights (AMACW). The model gets the correlation among channels by learning from good channel data. Interpolation assigns weights based on learned correlations without the need for electrode location information, solving the difficulty that traditional methods cannot interpolate bad channels at unknown locations. To avoid an overly concentrated weight distribution of the model when generating data, we designed the channel masking (CM). This method spreads attention and allows the model to utilize data from multiple channels. We evaluate the reconstruction performance of the model using EEG data with 1 to 5 bad channels. With EEGLAB’s interpolation method as a performance reference, tests have shown that the AMACW models can effectively reconstruct bad channels.
Nutritional intervention is promising in alleviating liver injury during tuberculosis treatment: a review
Authors: Fu Yujin , Du Xianfa , Cui Yingchun , Xiong Ke , Wang Jinyu
Published: September 2023

Liver injury is a main adverse effect of first-line tuberculosis drugs. Current management of tuberculosis-drug-induced liver injury (TBLI) mainly relies on withdrawing tuberculosis drugs when necessary. No effective treatment exists. Various nutrients and functional food ingredients may play a protective role in TBLI. However, a comprehensive review has not been conducted to compare the effects of these nutrients and functional food ingredients. We searched Pubmed and Web of Science databases from the earliest date of the database to March 2023. All available in-vitro, animal and clinical studies that examined the effects of nutritional intervention on TBLI were included. The underlying mechanism was briefly reviewed. Folic acid, quercetin, curcumin, Lactobacillus casei, spirulina and Moringa oleifera possessed moderate evidence to have a beneficial effect on alleviating TBLI mostly based on animal studies. The evidence of other nutritional interventions on TBLI was weak. Alleviating oxidative stress and apoptosis were the leading mechanisms for the beneficial effects of nutritional intervention on TBLI. In conclusion, a few nutritional interventions are promising for alleviating TBLI including folic acid, quercetin, curcumin, L. casei, spirulina and M. oleifera, the effectiveness and safety of which need further confirmation by well-designed randomized controlled trials. The mechanisms for the protective role of these nutritional interventions on TBLI warrant further study, particularly by establishing the animal model of TBLI using the tuberculosis drugs separately.